[{"month":"05","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"doi":"10.15479/AT:ISTA:6392","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"supervisor":[{"last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2021-02-11T11:17:16Z","extern":"1","author":[{"full_name":"Lukacisin, Martin","last_name":"Lukacisin","first_name":"Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1029"}]},"date_created":"2019-05-09T19:53:00Z","date_updated":"2023-09-22T09:19:41Z","year":"2019","publication_status":"published","publisher":"IST Austria","department":[{"_id":"ToBo"}],"day":"09","has_accepted_license":"1","date_published":"2019-05-09T00:00:00Z","citation":{"ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","apa":"Lukacisin, M. (2019). Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria. https://doi.org/10.15479/AT:ISTA:6392","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6392.","mla":"Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019."},"page":"103","abstract":[{"lang":"eng","text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes. \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. "}],"type":"dissertation","alternative_title":["IST Austria Thesis"],"file":[{"access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Draft_v3.4Final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":43740796,"creator":"mlukacisin","relation":"hidden","file_id":"6409","checksum":"829bda074444857c7935171237bb7c0c","date_created":"2019-05-10T13:51:49Z","date_updated":"2020-07-14T12:47:29Z"},{"access_level":"open_access","file_name":"Thesis_Draft_v3.4FinalA.pdf","content_type":"application/pdf","file_size":35228388,"creator":"mlukacisin","relation":"main_file","embargo":"2020-04-17","file_id":"6410","checksum":"56cb5e97f5f8fc41692401b53832d8e0","date_created":"2019-05-10T14:13:42Z","date_updated":"2021-02-11T11:17:16Z"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6392","ddc":["570"],"status":"public","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory"},{"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Cremer, Sylvia M","first_name":"Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6435","publication_identifier":{"issn":["2663-337X"]},"month":"05","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SyCr"}],"publication_status":"published","year":"2019","date_updated":"2023-09-07T12:57:04Z","date_created":"2019-05-13T08:58:35Z","related_material":{"record":[{"id":"1999","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"file_date_updated":"2021-02-11T11:17:15Z","page":"183","citation":{"ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","apa":"Casillas Perez, B. E. (2019). Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:10.15479/AT:ISTA:6435","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","mla":"Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435."},"date_published":"2019-05-07T00:00:00Z","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"has_accepted_license":"1","article_processing_charge":"No","day":"07","ddc":["570","006","578","592"],"status":"public","title":"Collective defenses of garden ants against a fungal pathogen","_id":"6435","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":3895187,"content_type":"application/pdf","creator":"casillas","file_name":"tesisDoctoradoBC.pdf","access_level":"open_access","date_created":"2019-05-13T09:16:20Z","date_updated":"2021-02-11T11:17:15Z","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","relation":"main_file","embargo":"2020-05-08","file_id":"6438"},{"file_id":"6439","relation":"source_file","date_created":"2019-05-13T09:16:20Z","date_updated":"2020-07-14T12:47:30Z","checksum":"3d221aaff7559a7060230a1ff610594f","file_name":"tesisDoctoradoBC.zip","embargo_to":"open_access","access_level":"closed","creator":"casillas","content_type":"application/zip","file_size":7365118}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour."}]},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. ","lang":"eng"}],"title":"Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants 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Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","apa":"Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th1075","mla":"Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants . Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th1075.","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075."},"date_published":"2019-02-04T00:00:00Z","file_date_updated":"2021-02-11T23:30:15Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"year":"2019","date_updated":"2023-09-08T11:43:03Z","date_created":"2019-04-09T14:37:06Z","author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"412"}]},"month":"02","publication_identifier":{"issn":["2663-337X"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:th1075"},{"month":"10","publication_identifier":{"issn":["2663-337X"]},"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6947","file_date_updated":"2020-11-07T23:30:03Z","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","year":"2019","date_created":"2019-10-14T16:54:52Z","date_updated":"2023-09-13T08:50:57Z","author":[{"full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","last_name":"Assen","first_name":"Frank P"}],"related_material":{"record":[{"id":"664","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"402"}]},"day":"9","article_processing_charge":"No","has_accepted_license":"1","page":"142","citation":{"chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","mla":"Assen, Frank P. Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947.","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","apa":"Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947"},"date_published":"2019-10-09T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Lymph nodes are es s ential organs of the immune s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells and form a sponge-like extracellular matrix network, called conduits , which they thems elves enwrap and contract. Lymph, containing s oluble antigens , arrive in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps ular s inus and conduit network. According to the current paradigm, the conduit network dis tributes afferent lymph through lymph nodes and thus provides acces s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s ize remains remarkedly s table under homeostatic conditions. It is only partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is able to swell in inflammation. The role of the FRC network in lymph node s welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal metastases.We examined the role of a mechanical feedback in regulation of lymph node swelling. Using parallel plate compression and UV-las er cutting experiments we dis s ected the mechanical force dynamics of the whole lymph node, and individually for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells ∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps ule, and how are lymphocytes able to enter in conditions that resist swelling remain open ques tions . We s how that tens ion on the FRC network is important to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates and a dis organized FRC network in the inflamed lymph node. Growth of the FRC network in turn is expected to releas e tens ion on thes e s tructures and lowers the res is tance to swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of swelling coincides with a thickening of the caps ule, which forms a thick res is tant band around the organ and lowers tens ion on the FRC network to form a new force equilibrium.The FRC and conduit network are further believed to be a privileged s ite of s oluble information within the lymph node, although many details remain uns olved. We s how by 3D ultra-recons truction that FRCs and antigen pres enting cells cover the s urface of conduit s ys tem for more than 99% and we dis cus s the implications for s oluble information exchangeat the conduit level.Finally, there is an ongoing debate in the cancer field whether and how cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels. Once in the blood circulation, these cells are able to form metastases in distal tissues.","lang":"eng"}],"ddc":["570"],"title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","status":"public","_id":"6947","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_name":"PhDthesis_FrankAssen_revised2.docx","embargo_to":"open_access","access_level":"closed","creator":"fassen","file_size":214172667,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6990","relation":"source_file","date_updated":"2020-11-07T23:30:03Z","date_created":"2019-11-06T12:30:02Z","checksum":"53a739752a500f84d0f8ec953cbbd0b6"},{"date_created":"2019-11-06T12:30:57Z","date_updated":"2020-11-07T23:30:03Z","checksum":"8c156b65d9347bb599623a4b09f15d15","relation":"main_file","file_id":"6991","embargo":"2020-11-06","content_type":"application/pdf","file_size":83637532,"creator":"fassen","file_name":"PhDthesis_FrankAssen_revised2.pdf","access_level":"open_access"}]},{"file_date_updated":"2021-02-10T23:30:09Z","author":[{"full_name":"Rangel Guerrero, Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374","first_name":"Dámaris K","last_name":"Rangel Guerrero"}],"related_material":{"record":[{"id":"5914","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-09-19T10:01:12Z","date_created":"2019-09-06T06:54:16Z","year":"2019","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","month":"09","publication_identifier":{"isbn":["9783990780039"],"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6849","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"language":[{"iso":"eng"}],"oa":1,"abstract":[{"text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_id":"6865","relation":"source_file","checksum":"244dc4f74dbfc94f414156092298831f","date_updated":"2021-02-10T23:30:09Z","date_created":"2019-09-09T13:09:45Z","access_level":"closed","file_name":"Thesis_Damaris_Rangel_source.docx","embargo_to":"open_access","creator":"drangel","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":18253100},{"access_level":"open_access","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","file_size":2160109,"content_type":"application/pdf","request_a_copy":0,"creator":"drangel","relation":"main_file","file_id":"6866","embargo":"2020-09-10","checksum":"59c73be40eeaa1c4db24067270151555","date_created":"2019-09-09T13:09:52Z","date_updated":"2020-09-11T22:30:04Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6849","title":"The role of CCK-interneurons in regulating hippocampal network dynamics","status":"public","ddc":["570"],"day":"09","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-09-09T00:00:00Z","citation":{"short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","mla":"Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.","chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6849.","ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:10.15479/AT:ISTA:6849","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","apa":"Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6849","ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria."},"page":"97"},{"abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":5054633,"file_id":"7133","relation":"source_file","date_created":"2019-11-27T09:06:10Z","date_updated":"2020-07-14T12:47:50Z","checksum":"34d0fe0f6e0af97b5937205a3e350423"},{"creator":"dernst","content_type":"application/pdf","file_size":3231837,"file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","access_level":"open_access","date_created":"2019-11-27T09:06:10Z","date_updated":"2020-07-14T12:47:50Z","checksum":"140dfb5e3df7edca34f4b6fcc55d876f","file_id":"7134","relation":"main_file"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7132","ddc":["571","573"],"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"27","date_published":"2019-06-27T00:00:00Z","citation":{"ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","apa":"Mckenzie, C. (2019). Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:7132","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:10.15479/at:ista:7132","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:7132.","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:7132.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019."},"page":"95","file_date_updated":"2020-07-14T12:47:50Z","related_material":{"record":[{"id":"6266","relation":"old_edition","status":"public"}]},"author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","first_name":"Catherine","full_name":"Mckenzie, Catherine"}],"date_created":"2019-11-27T09:07:14Z","date_updated":"2024-03-28T23:30:21Z","year":"2019","department":[{"_id":"HaJa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"06","doi":"10.15479/at:ista:7132","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"oa":1},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. "}],"_id":"6825","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The hippocampus and medial prefrontal cortex during flexible behavior","status":"public","ddc":["570"],"file":[{"file_name":"Thesis_Kaefer_PDFA.pdf","access_level":"open_access","creator":"kkaefer","content_type":"application/pdf","request_a_copy":0,"file_size":3205202,"file_id":"6846","embargo":"2020-09-05","relation":"main_file","date_created":"2019-09-03T08:07:13Z","date_updated":"2020-09-06T22:30:03Z","checksum":"2664420e332a33338568f4f3bfc59287"},{"file_size":2506835,"content_type":"application/zip","creator":"kkaefer","embargo_to":"open_access","file_name":"Thesis_Kaefer.zip","access_level":"closed","date_created":"2019-09-03T08:07:17Z","date_updated":"2020-09-15T22:30:05Z","checksum":"9a154eab6f07aa590a3d2651dc0d926a","relation":"main_file","file_id":"6847"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"24","citation":{"short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","mla":"Käfer, Karola. The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6825.","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6825.","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:10.15479/AT:ISTA:6825","apa":"Käfer, K. (2019). The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6825","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019.","ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria."},"page":"89","date_published":"2019-08-24T00:00:00Z","file_date_updated":"2020-09-15T22:30:05Z","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5949"}]},"author":[{"full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","first_name":"Karola"}],"date_updated":"2023-09-07T13:01:42Z","date_created":"2019-08-21T15:00:57Z","publication_identifier":{"issn":["2663-337X"]},"month":"08","oa":1,"doi":"10.15479/AT:ISTA:6825","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"degree_awarded":"PhD"},{"citation":{"mla":"Valosková, Katarina. The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6546.","short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019.","chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6546.","ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:10.15479/AT:ISTA:6546","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria.","apa":"Valosková, K. (2019). The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6546","ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019."},"page":"141","date_published":"2019-06-07T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"07","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6546","title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","status":"public","ddc":["570"],"file":[{"file_id":"6549","relation":"source_file","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-07T13:00:04Z","checksum":"68949c2d96210b45b981a23e9c9cd93c","file_name":"Katarina Valoskova_PhD thesis_final version.docx","embargo_to":"open_access","access_level":"closed","creator":"khribikova","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":14110626},{"creator":"khribikova","content_type":"application/pdf","file_size":10054156,"access_level":"open_access","file_name":"Katarina Valoskova_PhD thesis_final version.pdf","checksum":"555329cd76e196c96f5278c480ee2e6e","date_created":"2019-06-07T13:00:08Z","date_updated":"2021-02-11T11:17:14Z","file_id":"6550","embargo":"2020-06-07","relation":"main_file"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n","lang":"eng"}],"oa":1,"project":[{"grant_number":"24283","_id":"253CDE40-B435-11E9-9278-68D0E5697425","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells"}],"doi":"10.15479/AT:ISTA:6546","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"06","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"DaSi"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6187"},{"status":"public","relation":"part_of_dissertation","id":"544"}]},"author":[{"id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková","first_name":"Katarina","full_name":"Valosková, Katarina"}],"date_created":"2019-06-07T12:49:19Z","date_updated":"2023-09-19T10:15:54Z","file_date_updated":"2021-02-11T11:17:14Z"},{"year":"2019","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","first_name":"Claudia ","last_name":"Espinoza Martinez"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"21"}]},"date_created":"2019-04-30T11:56:10Z","date_updated":"2023-09-15T12:03:48Z","file_date_updated":"2021-02-11T11:17:15Z","oa":1,"doi":"10.15479/AT:ISTA:6363","degree_awarded":"PhD","supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"}],"language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-000-8"]},"_id":"6363","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","ddc":["570"],"status":"public","file":[{"file_id":"6389","embargo":"2020-05-09","relation":"main_file","date_updated":"2021-02-11T11:17:15Z","date_created":"2019-05-07T16:00:39Z","checksum":"77c6c05cfe8b58c8abcf1b854375d084","file_name":"Espinozathesis_all2.pdf","access_level":"open_access","creator":"cespinoza","content_type":"application/pdf","file_size":13966891},{"file_id":"6390","relation":"source_file","checksum":"f6aa819f127691a2b0fc21c76eb09746","date_created":"2019-05-07T16:00:48Z","date_updated":"2020-07-14T12:47:28Z","access_level":"closed","file_name":"Espinoza_Thesis.docx","embargo_to":"open_access","creator":"cespinoza","file_size":11159900,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Distinguishing between similar experiences is achieved by the brain in a process called pattern separation. In the hippocampus, pattern separation reduces the interference of memories and increases the storage capacity by decorrelating similar inputs patterns of neuronal activity into non-overlapping output firing patterns. Winners-take-all (WTA) mechanism is a theoretical model for pattern separation in which a \"winner\" cell suppresses the activity of the neighboring neurons through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of feedback inhibition in which a GC inhibits other GCs but not itself through the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron connectivity was more spatially confined but less abundant than PV+interneurons–GC connectivity, leading to an asymmetrical distribution of excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the primary mechanism. This process relied on lateral inhibition, fast-signaling properties of PV+interneurons and the asymmetrical distribution of excitatory and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in vivoleads to acute deficits in discrimination between similar environments, suggesting that PV+interneuron networks are necessary for behavioral relevant computations. Our results demonstrate that PV+interneurons possess unique connectivity and fast signaling properties that confer to the dentate gyrus network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n"}],"citation":{"ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363","apa":"Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6363","ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","mla":"Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6363.","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363."},"page":"140","date_published":"2019-04-30T00:00:00Z","day":"30","has_accepted_license":"1","article_processing_charge":"No"},{"keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"has_accepted_license":"1","article_processing_charge":"No","day":"24","citation":{"ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","apa":"Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:10.15479/AT:ISTA:6891","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","mla":"Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891."},"page":"171","date_published":"2019-07-24T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"_id":"6891","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The implication of cytoskeletal dynamics on leukocyte migration","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"checksum":"00d100d6468e31e583051e0a006b640c","date_updated":"2020-10-17T22:30:03Z","date_created":"2019-10-15T05:28:42Z","file_id":"6950","relation":"source_file","creator":"akopf","file_size":74735267,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"Kopf_PhD_Thesis.docx","embargo_to":"open_access"},{"embargo":"2020-10-16","file_id":"6951","relation":"main_file","checksum":"5d1baa899993ae6ca81aebebe1797000","date_updated":"2020-10-17T22:30:03Z","date_created":"2019-10-15T05:28:47Z","access_level":"open_access","file_name":"Kopf_PhD_Thesis1.pdf","creator":"akopf","content_type":"application/pdf","file_size":52787224}],"publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"month":"07","oa":1,"project":[{"call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"}],"doi":"10.15479/AT:ISTA:6891","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"file_date_updated":"2020-10-17T22:30:03Z","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiSi"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6328"},{"status":"public","relation":"part_of_dissertation","id":"15"},{"status":"public","relation":"part_of_dissertation","id":"6877"}],"link":[{"url":"https://ist.ac.at/en/news/feeling-like-a-cell/","relation":"press_release"}]},"author":[{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","first_name":"Aglaja","last_name":"Kopf","full_name":"Kopf, Aglaja"}],"date_created":"2019-09-19T08:19:44Z","date_updated":"2023-10-18T08:49:17Z"},{"related_material":{"record":[{"id":"67","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"popular_science","id":"5585"}]},"author":[{"first_name":"Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"}],"date_created":"2019-05-03T11:55:51Z","date_updated":"2024-02-21T13:45:52Z","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"publication_status":"published","file_date_updated":"2021-02-11T11:17:13Z","doi":"10.15479/AT:ISTA:6371","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"degree_awarded":"PhD","oa":1,"project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573"}],"publication_identifier":{"issn":["2663-337X"]},"month":"05","file":[{"access_level":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","creator":"cigler","file_size":12597663,"content_type":"application/pdf","file_id":"6373","embargo":"2020-05-02","relation":"main_file","checksum":"c0085d47c58c9cbcab1b0a783480f6da","date_created":"2019-05-03T11:54:52Z","date_updated":"2021-02-11T11:17:13Z"},{"relation":"source_file","file_id":"6374","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-05-03T11:54:54Z","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","embargo_to":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":34644426,"creator":"cigler"}],"oa_version":"Published Version","_id":"6371","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["576","579"],"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2019-05-03T00:00:00Z","citation":{"ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371."},"page":"152","article_processing_charge":"No","has_accepted_license":"1","day":"03","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"]},{"author":[{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","first_name":"Hannes"}],"date_updated":"2023-09-07T12:27:43Z","date_created":"2018-12-11T11:44:21Z","year":"2018","publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:46:35Z","publist_id":"8005","doi":"10.15479/AT:ISTA:th_1033","degree_awarded":"PhD","supervisor":[{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"07","publication_identifier":{"issn":["2663-337X"]},"pubrep_id":"1033","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6249","checksum":"b653b5216251f938ddbeafd1de88667c","date_created":"2019-04-09T07:13:28Z","date_updated":"2020-07-14T12:46:35Z","access_level":"open_access","file_name":"2018_Thesis_Watzinger.pdf","content_type":"application/pdf","file_size":85539748,"creator":"dernst"},{"file_id":"6250","relation":"source_file","checksum":"39bcf8de7ac5b1bb516b11ce2f966785","date_created":"2019-04-09T07:13:27Z","date_updated":"2020-07-14T12:46:35Z","access_level":"closed","file_name":"2018_Thesis_Watzinger_source.zip","creator":"dernst","file_size":21830697,"content_type":"application/zip"}],"_id":"49","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["530"],"title":"Ge hut wires - from growth to hole spin resonance","abstract":[{"text":"Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2018-07-30T00:00:00Z","citation":{"short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","mla":"Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033.","chicago":"Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033.","ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033","ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","apa":"Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033","ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria."},"page":"77","day":"30","has_accepted_license":"1","article_processing_charge":"No"},{"month":"06","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_1026","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2020-07-14T12:45:24Z","publist_id":"7712","author":[{"full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:45:10Z","date_updated":"2023-09-07T12:25:32Z","year":"2018","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","day":"11","article_processing_charge":"No","has_accepted_license":"1","date_published":"2018-06-11T00:00:00Z","citation":{"chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria.","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026"},"page":"171","abstract":[{"lang":"eng","text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1026","file":[{"file_size":11827713,"content_type":"application/zip","creator":"kschuh","access_level":"closed","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","checksum":"dd699303623e96d1478a6ae07210dd05","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-02-05T07:43:31Z","relation":"source_file","file_id":"5918"},{"date_created":"2019-02-05T07:43:45Z","date_updated":"2020-07-14T12:45:24Z","checksum":"ba163849a190d2b41d66fef0e4983294","relation":"main_file","file_id":"5919","content_type":"application/pdf","file_size":4783846,"creator":"kschuh","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"201","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["514","516"],"title":"Multiple covers with balls"},{"abstract":[{"lang":"eng","text":"The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1048","file":[{"file_id":"6253","relation":"main_file","date_created":"2019-04-09T07:32:47Z","date_updated":"2020-07-14T12:47:40Z","checksum":"e849dd40a915e4d6c5572b51b517f098","file_name":"2018_Thesis_Zimin.pdf","access_level":"open_access","creator":"dernst","file_size":1036137,"content_type":"application/pdf"},{"file_id":"6254","relation":"source_file","checksum":"da092153cec55c97461bd53c45c5d139","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-04-09T07:32:47Z","access_level":"closed","file_name":"2018_Thesis_Zimin_Source.zip","creator":"dernst","file_size":637490,"content_type":"application/zip"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"68","title":"Learning from dependent data","status":"public","ddc":["004","519"],"day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-09-01T00:00:00Z","citation":{"chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048.","mla":"Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","apa":"Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048"},"page":"92","file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"publist_id":"7986","author":[{"first_name":"Alexander","last_name":"Zimin","id":"37099E9C-F248-11E8-B48F-1D18A9856A87","full_name":"Zimin, Alexander"}],"date_created":"2018-12-11T11:44:27Z","date_updated":"2023-09-07T12:29:07Z","year":"2018","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","month":"09","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:TH1048","degree_awarded":"PhD","supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}]},{"related_material":{"record":[{"id":"1229","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1235"},{"status":"public","relation":"part_of_dissertation","id":"1236"},{"id":"559","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Hamza M","last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"}],"date_created":"2018-12-11T11:44:32Z","date_updated":"2023-09-07T12:30:23Z","year":"2018","department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publist_id":"7971","ec_funded":1,"file_date_updated":"2020-07-14T12:48:11Z","doi":"10.15479/AT:ISTA:TH_1046","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"degree_awarded":"PhD","oa":1,"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","pubrep_id":"1046","file":[{"file_id":"6245","relation":"main_file","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-04-09T06:43:41Z","checksum":"c4b5f7d111755d1396787f41886fc674","file_name":"2018_Thesis_Abusalah.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":876241},{"creator":"dernst","file_size":2029190,"content_type":"application/x-gzip","access_level":"closed","file_name":"2018_Thesis_Abusalah_source.tar.gz","checksum":"0f382ac56b471c48fd907d63eb87dafe","date_created":"2019-04-09T06:43:41Z","date_updated":"2020-07-14T12:48:11Z","file_id":"6246","relation":"source_file"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"83","ddc":["004"],"title":"Proof systems for sustainable decentralized cryptocurrencies","status":"public","abstract":[{"lang":"eng","text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2018-09-05T00:00:00Z","citation":{"chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","mla":"Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046.","apa":"Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046"},"page":"59","article_processing_charge":"No","has_accepted_license":"1","day":"05"},{"publication_identifier":{"issn":["2663-337X"]},"month":"05","project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_1021","publist_id":"7718","ec_funded":1,"file_date_updated":"2020-07-14T12:45:22Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"}],"publication_status":"published","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","year":"2018","date_created":"2018-12-11T11:45:09Z","date_updated":"2023-09-07T12:51:46Z","author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander","full_name":"Kolesnikov, Alexander"}],"article_processing_charge":"No","has_accepted_license":"1","day":"25","page":"113","citation":{"chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1021.","short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","mla":"Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021.","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018.","apa":"Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:10.15479/AT:ISTA:th_1021"},"date_published":"2018-05-25T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task.","lang":"eng"}],"status":"public","title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","ddc":["004"],"_id":"197","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2018-12-12T10:14:57Z","date_updated":"2020-07-14T12:45:22Z","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","file_id":"5113","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":12918758,"file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","access_level":"open_access"},{"checksum":"bc66973b086da5a043f1162dcfb1fde4","date_created":"2019-04-05T09:34:49Z","date_updated":"2020-07-14T12:45:22Z","relation":"source_file","file_id":"6225","file_size":55973760,"content_type":"application/zip","creator":"dernst","access_level":"closed","file_name":"2018_Thesis_Kolesnikov_source.zip"}],"oa_version":"Published Version","pubrep_id":"1021"},{"abstract":[{"lang":"eng","text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"main_file","file_id":"5111","checksum":"8cc534d2b528ae017acf80874cce48c9","date_created":"2018-12-12T10:14:55Z","date_updated":"2020-07-14T12:45:23Z","access_level":"open_access","file_name":"IST-2018-963-v1+1_thesis.pdf","content_type":"application/pdf","file_size":5792935,"creator":"system"},{"file_size":113365,"content_type":"application/zip","creator":"dernst","file_name":"2018_thesis_ringbauer_source.zip","access_level":"closed","date_updated":"2020-07-14T12:45:23Z","date_created":"2019-04-05T09:30:12Z","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","relation":"source_file","file_id":"6224"}],"oa_version":"Published Version","pubrep_id":"963","ddc":["576"],"status":"public","title":"Inferring recent demography from spatial genetic structure","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"200","day":"21","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-02-21T00:00:00Z","page":"146","citation":{"chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963"},"file_date_updated":"2020-07-14T12:45:23Z","publist_id":"7713","date_updated":"2023-09-20T12:00:56Z","date_created":"2018-12-11T11:45:10Z","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"563"},{"status":"public","relation":"part_of_dissertation","id":"1074"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2018","month":"02","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_963","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1},{"citation":{"chicago":"Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation and Survival .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_913.","short":"E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation and Survival , Institute of Science and Technology Austria, 2018.","mla":"Gschaider-Reichhart, Eva. Optical and Optogenetic Control of Proliferation and Survival . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_913.","apa":"Gschaider-Reichhart, E. (2018). Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_913","ieee":"E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation and survival ,” Institute of Science and Technology Austria, 2018.","ista":"Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria.","ama":"Gschaider-Reichhart E. Optical and optogenetic control of proliferation and survival . 2018. doi:10.15479/AT:ISTA:th_913"},"page":"107","date_published":"2018-01-08T00:00:00Z","day":"08","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"418","title":"Optical and optogenetic control of proliferation and survival ","status":"public","ddc":["571","570"],"pubrep_id":"913","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"6222","checksum":"697fa72ca36fb1b8ceabc133d58a73e5","date_created":"2019-04-05T09:28:03Z","date_updated":"2020-07-14T12:46:24Z","access_level":"closed","file_name":"2018_THESIS_Gschaider-Reichhart_source.docx","file_size":7012495,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst"},{"checksum":"58d7d1e9e58aeb7f061ab686b1d8a48c","date_updated":"2020-07-14T12:46:24Z","date_created":"2019-04-05T09:28:03Z","file_id":"6223","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":6355280,"access_level":"open_access","file_name":"2018_THESIS_Gschaider-Reichhart.pdf"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown.\r\nSummarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion."}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:th_913","supervisor":[{"full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["2663-337X"]},"year":"2018","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HaJa"}],"author":[{"last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva"}],"related_material":{"record":[{"id":"1441","relation":"part_of_dissertation","status":"public"},{"id":"1678","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"2084"},{"relation":"part_of_dissertation","status":"public","id":"1028"}]},"date_updated":"2023-09-22T09:20:10Z","date_created":"2018-12-11T11:46:22Z","file_date_updated":"2020-07-14T12:46:24Z","publist_id":"7405"},{"has_accepted_license":"1","article_processing_charge":"No","day":"04","date_published":"2018-09-04T00:00:00Z","citation":{"ista":"Moser T. 2018. Point interactions in systems of fermions. Institute of Science and Technology Austria.","apa":"Moser, T. (2018). Point interactions in systems of fermions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1043","ieee":"T. Moser, “Point interactions in systems of fermions,” Institute of Science and Technology Austria, 2018.","ama":"Moser T. Point interactions in systems of fermions. 2018. doi:10.15479/AT:ISTA:th_1043","chicago":"Moser, Thomas. “Point Interactions in Systems of Fermions.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1043.","mla":"Moser, Thomas. Point Interactions in Systems of Fermions. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1043.","short":"T. Moser, Point Interactions in Systems of Fermions, Institute of Science and Technology Austria, 2018."},"page":"115","abstract":[{"text":"In this thesis we will discuss systems of point interacting fermions, their stability and other spectral properties. Whereas for bosons a point interacting system is always unstable this ques- tion is more subtle for a gas of two species of fermions. In particular the answer depends on the mass ratio between these two species. Most of this work will be focused on the N + M model which consists of two species of fermions with N, M particles respectively which interact via point interactions. We will introduce this model using a formal limit and discuss the N + 1 system in more detail. In particular, we will show that for mass ratios above a critical one, which does not depend on the particle number, the N + 1 system is stable. In the context of this model we will prove rigorous versions of Tan relations which relate various quantities of the point-interacting model. By restricting the N + 1 system to a box we define a finite density model with point in- teractions. In the context of this system we will discuss the energy change when introducing a point-interacting impurity into a system of non-interacting fermions. We will see that this change in energy is bounded independently of the particle number and in particular the bound only depends on the density and the scattering length. As another special case of the N + M model we will show stability of the 2 + 2 model for mass ratios in an interval around one. Further we will investigate a different model of point interactions which was discussed before in the literature and which is, contrary to the N + M model, not given by a limiting procedure but is based on a Dirichlet form. We will show that this system behaves trivially in the thermodynamic limit, i.e. the free energy per particle is the same as the one of the non-interacting system.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1043","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_Thesis_Moser.pdf","creator":"dernst","file_size":851164,"content_type":"application/pdf","file_id":"6256","relation":"main_file","checksum":"fbd8c747d148b468a21213b7cf175225","date_created":"2019-04-09T07:45:38Z","date_updated":"2020-07-14T12:46:37Z"},{"file_name":"2018_Thesis_Moser_Source.zip","access_level":"closed","file_size":1531516,"content_type":"application/zip","creator":"dernst","relation":"source_file","file_id":"6257","date_updated":"2020-07-14T12:46:37Z","date_created":"2019-04-09T07:45:38Z","checksum":"c28e16ecfc1126d3ce324ec96493c01e"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"52","ddc":["515","530","519"],"status":"public","title":"Point interactions in systems of fermions","publication_identifier":{"issn":["2663-337X"]},"month":"09","doi":"10.15479/AT:ISTA:th_1043","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","oa":1,"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"}],"publist_id":"8002","file_date_updated":"2020-07-14T12:46:37Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5856"},{"id":"154","status":"public","relation":"part_of_dissertation"},{"id":"1198","relation":"part_of_dissertation","status":"public"},{"id":"741","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Moser, Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Moser"}],"date_created":"2018-12-11T11:44:22Z","date_updated":"2023-09-27T12:34:14Z","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"RoSe"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"doi":"10.15479/AT:ISTA:TH_1047","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["2663-337X"]},"month":"09","date_updated":"2023-09-26T15:50:22Z","date_created":"2018-12-11T11:44:28Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"23"},{"status":"public","relation":"part_of_dissertation","id":"840"}]},"author":[{"last_name":"Vukušić","first_name":"Lada","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","full_name":"Vukušić, Lada"}],"department":[{"_id":"GeKa"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","publist_id":"7985","file_date_updated":"2020-07-14T12:47:44Z","date_published":"2018-09-01T00:00:00Z","page":"103","citation":{"mla":"Vukušić, Lada. Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1047.","short":"L. Vukušić, Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires, Institute of Science and Technology Austria, 2018.","chicago":"Vukušić, Lada. “Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1047.","ama":"Vukušić L. Charge sensing and spin relaxation times of holes in Ge hut wires. 2018. doi:10.15479/AT:ISTA:TH_1047","ista":"Vukušić L. 2018. Charge sensing and spin relaxation times of holes in Ge hut wires. Institute of Science and Technology Austria.","apa":"Vukušić, L. (2018). Charge sensing and spin relaxation times of holes in Ge hut wires. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1047","ieee":"L. Vukušić, “Charge sensing and spin relaxation times of holes in Ge hut wires,” Institute of Science and Technology Austria, 2018."},"article_processing_charge":"No","has_accepted_license":"1","day":"01","file":[{"checksum":"c570b656e30749cd65b1c7e13a9ce0a8","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-04-09T07:00:40Z","file_id":"6247","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":28452385,"access_level":"open_access","file_name":"2018_Thesis_Vukusic.pdf"},{"file_id":"6248","relation":"source_file","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-04-09T07:00:40Z","checksum":"7856771d9cd401fe0b311191076db6e1","file_name":"2018_Thesis_Vukusic_source.zip","access_level":"closed","creator":"dernst","content_type":"application/zip","file_size":53058704}],"oa_version":"Published Version","pubrep_id":"1047","ddc":["530","600"],"title":"Charge sensing and spin relaxation times of holes in Ge hut wires","status":"public","_id":"69","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"A qubit, a unit of quantum information, is essentially any quantum mechanical two-level system which can be coherently controlled. Still, to be used for computation, it has to fulfill criteria. Qubits, regardless of the system in which they are realized, suffer from decoherence. This leads to loss of the information stored in the qubit. The upper bound of the time scale on which decoherence happens is set by the spin relaxation time. In this thesis I studied a two-level system consisting of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire. Such Ge hut wires have emerged as a promising material system for the realization of spin qubits, due to the combination of two significant properties: long spin coherence time as expected for group IV semiconductors due to the low hyperfine interaction and a strong valence band spin-orbit coupling. Here, I present how to fabricate quantum dot devices suitable for electrical transport measurements. Coupled quantum dot devices allowed the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot. By integrating the charge sensor into a radio-frequency reflectometry setup, I performed for the first time single-shot readout measurements of hole spins and extracted the hole spin relaxation times in Ge hut wires.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"abstract":[{"lang":"eng","text":"Neuronal networks in the brain consist of two main types of neuron, glutamatergic principal neurons and GABAergic interneurons. Although these interneurons only represent 10–20% of the whole population, they mediate feedback and feedforward inhibition and are involved in the generation of high-frequency network oscillations. A hallmark functional property of GABAergic interneurons, especially of the parvalbumin‑expressing (PV+) subtypes, is the speed of signaling at their output synapse across species and brain regions. Several molecular and subcellular factors may underlie the submillisecond signaling at GABAergic synapses. Such as the selective use of P/Q type Ca2+ channels and the tight coupling between Ca2+ channels and Ca2+ sensors of exocytosis. However, whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Besides, these interneurons are mainly show depression in response to train of stimuli. How could they keep sufficient release to control the activity of postsynaptic principal neurons during high network activity, is largely elusive. For my Ph.D. work, we firstly examined the Ca2+ sensor of exocytosis at the GABAergic basket cell (BC) to Purkinje cell (PC) synapse in the cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ~10% compared to the wild-type control, identifying Syt2 as the major Ca2+ sensor at BC‑PC synapses. Differential adenovirus-mediated rescue revealed Syt2 triggered release with shorter latency and higher temporal precision, and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as the release sensor at BC–PC synapse ensures fast feedforward inhibition in cerebellar microcircuits. Additionally, we tested the function of another synaptotagmin member, Syt7, for inhibitory synaptic transmission at the BC–PC synapse. Syt7 is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, it is strongly expressed in fast-spiking, PV+ GABAergic interneurons and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. How could Syt7, a facilitation sensor, contribute to the depressed inhibitory synaptic transmission needs to be further investigated and understood. Our results indicated that at the BC–PC synapse, Syt7 contributes to asynchronous release, pool replenishment and facilitation. In combination, these three effects ensure efficient transmitter release during high‑frequency activity and guarantee frequency independence of inhibition. Taken together, our results confirmed that Syt2, which has the fastest kinetic properties among all synaptotagmin members, is mainly used by the inhibitory BC‑PC synapse for synaptic transmission, contributing to the speed and temporal precision of transmitter release. Furthermore, we showed that Syt7, another highly expressed synaptotagmin member in the output synapses of cerebellar BCs, is used for ensuring efficient inhibitor synaptic transmission during high activity."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"997","oa_version":"Published Version","file":[{"file_id":"5046","relation":"main_file","date_created":"2018-12-12T10:13:58Z","date_updated":"2020-07-14T12:46:04Z","checksum":"8e163ae9e927401b9fa7c1b3e6a3631a","file_name":"IST-2018-997-v1+1_Thesis_chong_a.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":8719458},{"date_updated":"2020-07-14T12:46:04Z","date_created":"2019-04-05T09:25:26Z","checksum":"f7d7260029a5fbb5c982db61328ade52","relation":"source_file","file_id":"6221","file_size":47841940,"content_type":"application/octet-stream","creator":"dernst","file_name":"2018_Thesis_chong_source.pages","access_level":"closed"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"324","title":"Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release","status":"public","ddc":["571"],"day":"01","article_processing_charge":"No","has_accepted_license":"1","date_published":"2018-03-01T00:00:00Z","citation":{"ieee":"C. Chen, “Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release,” Institute of Science and Technology Austria, 2018.","apa":"Chen, C. (2018). Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_997","ista":"Chen C. 2018. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. Institute of Science and Technology Austria.","ama":"Chen C. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. 2018. doi:10.15479/AT:ISTA:th_997","chicago":"Chen, Chong. “Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_997.","short":"C. Chen, Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release, Institute of Science and Technology Austria, 2018.","mla":"Chen, Chong. Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_997."},"page":"110","file_date_updated":"2020-07-14T12:46:04Z","publist_id":"7541","author":[{"full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chong"}],"related_material":{"record":[{"id":"1117","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"749"}]},"date_created":"2018-12-11T11:45:49Z","date_updated":"2023-09-27T12:26:03Z","year":"2018","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"PeJo"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_997","supervisor":[{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"author":[{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius","full_name":"Praetorius, Florian M"}],"date_created":"2023-09-06T13:11:22Z","date_updated":"2023-11-07T11:43:38Z","oa_version":"Published Version","_id":"14306","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures","status":"public","publication_status":"published","publisher":"Technische Universität München","abstract":[{"lang":"eng","text":"Function and activity of biomolecules often depend on their spatial arrangement. The method introduced here allows genetically encoding the spatial arrangement of proteins and DNA. The approach relies on staple proteins that fold double-stranded DNA into user-defined shapes. This thesis describes the development of staple proteins based on the DNA recognition of TAL effectors and presents experimentally derived rules for designing a variety of self-assembling nanoscale shapes featuring structural motifs such as curvature, vertices, corners, and multilayer helix packing. "}],"extern":"1","type":"dissertation","date_published":"2018-01-16T00:00:00Z","supervisor":[{"full_name":"Dietz, Hendrik","last_name":"Dietz","first_name":"Hendrik"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"citation":{"mla":"Praetorius, Florian M. Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures. Technische Universität München, 2018.","short":"F.M. Praetorius, Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures, Technische Universität München, 2018.","chicago":"Praetorius, Florian M. “Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures.” Technische Universität München, 2018.","ama":"Praetorius FM. Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures. 2018.","ista":"Praetorius FM. 2018. Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures. Technische Universität München.","apa":"Praetorius, F. M. (2018). Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures. Technische Universität München.","ieee":"F. M. Praetorius, “Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures,” Technische Universität München, 2018."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://mediatum.ub.tum.de/1398662"}],"day":"16","month":"01","article_processing_charge":"No"},{"type":"dissertation","abstract":[{"lang":"eng","text":"Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. The finding of this study shall provide guidance."}],"publist_id":"7624","status":"public","publication_status":"published","title":"Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken","department":[{"_id":"E-Lib"}],"publisher":"Universität Wien","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"278","year":"2018","date_created":"2018-12-11T11:45:34Z","date_updated":"2024-02-21T13:44:07Z","oa_version":"Published Version","author":[{"first_name":"Márton","last_name":"Villányi","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8126-0426","full_name":"Villányi, Márton"}],"related_material":{"record":[{"id":"5577","status":"public","relation":"dissertation_contains"},{"id":"5574","status":"public","relation":"dissertation_contains"},{"id":"5578","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"5579"},{"status":"public","relation":"dissertation_contains","id":"5576"},{"id":"5575","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"5582"},{"relation":"dissertation_contains","status":"public","id":"5581"},{"id":"5580","status":"public","relation":"dissertation_contains"}]},"day":"06","month":"04","page":"94","citation":{"chicago":"Villányi, Márton. “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken.” Universität Wien, 2018.","short":"M. Villányi, Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken, Universität Wien, 2018.","mla":"Villányi, Márton. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien, 2018.","ieee":"M. Villányi, “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken,” Universität Wien, 2018.","apa":"Villányi, M. (2018). Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien.","ista":"Villányi M. 2018. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien.","ama":"Villányi M. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. 2018."},"oa":1,"main_file_link":[{"url":"http://othes.univie.ac.at/51113/","open_access":"1"}],"supervisor":[{"full_name":"Kromp, Brigitte","last_name":"Kromp","first_name":"Brigitte"}],"language":[{"iso":"ger"}],"date_published":"2018-04-06T00:00:00Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"149","status":"public","title":"Dyson equation and eigenvalue statistics of random matrices","ddc":["515","519"],"pubrep_id":"1040","oa_version":"Published Version","file":[{"file_name":"2018_thesis_Alt.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5801709,"creator":"dernst","relation":"main_file","file_id":"6241","date_created":"2019-04-08T13:55:20Z","date_updated":"2020-07-14T12:44:57Z","checksum":"d4dad55a7513f345706aaaba90cb1bb8"},{"file_size":3802059,"content_type":"application/zip","creator":"dernst","file_name":"2018_thesis_Alt_source.zip","access_level":"closed","date_created":"2019-04-08T13:55:20Z","date_updated":"2020-07-14T12:44:57Z","checksum":"d73fcf46300dce74c403f2b491148ab4","relation":"source_file","file_id":"6242"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations."}],"citation":{"mla":"Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040.","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","apa":"Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040"},"page":"456","date_published":"2018-07-12T00:00:00Z","day":"12","has_accepted_license":"1","article_processing_charge":"No","year":"2018","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LaEr"}],"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","first_name":"Johannes","full_name":"Alt, Johannes"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1677"},{"id":"550","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6183"},{"id":"566","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1010"},{"id":"6240","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6184"}]},"date_updated":"2024-02-22T14:34:33Z","date_created":"2018-12-11T11:44:53Z","file_date_updated":"2020-07-14T12:44:57Z","ec_funded":1,"publist_id":"7772","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"doi":"10.15479/AT:ISTA:TH_1040","degree_awarded":"PhD","supervisor":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"}],"language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["2663-337X"]}},{"ddc":["570","616"],"title":"The branched chain amino acids in autism spectrum disorders ","status":"public","_id":"395","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-05T09:19:17Z","checksum":"9f5231c96e0ad945040841a8630232da","file_id":"6217","relation":"source_file","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":43684035,"file_name":"2018_Thesis_Tarlungeanu_source.docx","embargo_to":"open_access","access_level":"closed"},{"file_id":"6218","embargo":"2018-03-15","relation":"main_file","checksum":"0c33c370aa2010df5c552db57a6d01e9","date_created":"2019-04-05T09:19:17Z","date_updated":"2021-02-11T11:17:16Z","access_level":"open_access","file_name":"2018_Thesis_Tarlungeanu.pdf","creator":"dernst","file_size":30511532,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"992","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. ","lang":"eng"}],"page":"88","citation":{"chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992.","mla":"Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992.","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","apa":"Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:10.15479/AT:ISTA:th_992"},"date_published":"2018-03-01T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"01","department":[{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","date_updated":"2023-09-07T12:38:59Z","date_created":"2018-12-11T11:46:14Z","related_material":{"record":[{"id":"1183","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","last_name":"Tarlungeanu","first_name":"Dora-Clara","full_name":"Tarlungeanu, Dora-Clara"}],"publist_id":"7434","file_date_updated":"2021-02-11T23:30:15Z","project":[{"_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523","name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"doi":"10.15479/AT:ISTA:th_992","publication_identifier":{"issn":["2663-337X"]},"month":"03"},{"author":[{"full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","last_name":"Case"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"682"}]},"date_updated":"2023-09-07T12:39:22Z","date_created":"2018-12-11T11:44:22Z","year":"2018","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-11T23:30:13Z","publist_id":"8003","doi":"10.15479/AT:ISTA:th_1032","supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"month":"06","publication_identifier":{"issn":["2663-337X"]},"pubrep_id":"1032","file":[{"creator":"dernst","file_size":141270528,"content_type":"application/msword","file_name":"2018_Thesis_Case_Source.doc","embargo_to":"open_access","access_level":"closed","date_updated":"2021-02-11T23:30:13Z","date_created":"2019-04-09T07:16:26Z","checksum":"dcc7b55619d8509dd62b8e99d6cdee44","file_id":"6251","relation":"source_file"},{"access_level":"open_access","file_name":"2018_Thesis_Case.pdf","creator":"dernst","content_type":"application/pdf","file_size":15193621,"file_id":"6252","embargo":"2019-07-05","relation":"main_file","checksum":"f69fdd5c8709c4e618aa8c1a1221153d","date_created":"2019-04-09T07:16:23Z","date_updated":"2021-02-11T11:17:14Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"51","ddc":["571","576"],"status":"public","title":"From the left to the right: A tale of asymmetries, environments, and hippocampal development","abstract":[{"lang":"eng","text":"Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2018-06-27T00:00:00Z","citation":{"ista":"Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria.","apa":"Case, M. J. (2018). From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1032","ieee":"M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018.","ama":"Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:10.15479/AT:ISTA:th_1032","chicago":"Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1032.","mla":"Case, Matthew J. From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1032.","short":"M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018."},"page":"186","day":"27","article_processing_charge":"No","has_accepted_license":"1"},{"author":[{"orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","first_name":"Susanne","full_name":"Laukoter, Susanne"}],"date_updated":"2023-09-07T12:40:44Z","date_created":"2018-12-11T11:44:08Z","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SiHi"}],"publication_status":"published","publist_id":"8046","file_date_updated":"2021-02-11T11:17:16Z","doi":"10.15479/AT:ISTA:th1057","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"degree_awarded":"PhD","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"11","pubrep_id":"1057","oa_version":"Published Version","file":[{"file_name":"Thesis_LaukoterSusanne_FINAL.docx","embargo_to":"open_access","access_level":"closed","creator":"dernst","file_size":17949175,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6396","relation":"source_file","date_created":"2019-05-10T07:47:04Z","date_updated":"2019-11-23T23:30:03Z","checksum":"41fdbf5fdce312802935d88a8ad9932c"},{"content_type":"application/pdf","file_size":21187245,"creator":"dernst","access_level":"open_access","file_name":"Thesis_LaukoterSusanne_FINAL.pdf","checksum":"53001a9a0c9e570e598d861bb0af28aa","date_created":"2019-05-10T07:47:04Z","date_updated":"2021-02-11T11:17:16Z","relation":"main_file","file_id":"6397","embargo":"2019-11-21"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10","title":"Role of genomic imprinting in cerebral cortex development","ddc":["570"],"status":"public","abstract":[{"text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2018-11-21T00:00:00Z","citation":{"ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","apa":"Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057","ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria.","ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:10.15479/AT:ISTA:th1057","chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018.","mla":"Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057."},"page":"1 - 139","article_processing_charge":"No","has_accepted_license":"1","day":"21"},{"file_date_updated":"2021-02-11T23:30:17Z","publist_id":"7542","author":[{"full_name":"Leithner, Alexander F","first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X"}],"related_material":{"record":[{"id":"1321","status":"public","relation":"part_of_dissertation"}]},"date_created":"2018-12-11T11:45:49Z","date_updated":"2023-09-07T12:39:44Z","year":"2018","acknowledgement":"First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe best boss one can imagine. I would also like to thank all current and past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m proud that I could be part of it. Furthermore, I would like to say ‘thank you’ to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to Federica Benvenuti for being part of my committee. I am also grateful to Jack \r\nMerrin in the nanofabrication facility and all the people working in the bioimaging-\r\n, the electron microscopy- and the preclinical facilities.","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","month":"04","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_998","degree_awarded":"PhD","supervisor":[{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"998","oa_version":"Published Version","file":[{"file_size":29027671,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","embargo_to":"open_access","file_name":"PhD_thesis_AlexLeithner_final_version.docx","access_level":"closed","date_created":"2019-04-05T09:23:11Z","date_updated":"2021-02-11T23:30:17Z","checksum":"d5e3edbac548c26c1fa43a4b37a54a4c","relation":"source_file","file_id":"6219"},{"access_level":"open_access","file_name":"PhD_thesis_AlexLeithner.pdf","creator":"dernst","content_type":"application/pdf","file_size":66045341,"file_id":"6220","embargo":"2019-04-15","relation":"main_file","checksum":"071f7476db29e41146824ebd0697cb10","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-05T09:23:11Z"}],"_id":"323","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["571","599","610"],"title":"Branched actin networks in dendritic cell biology","day":"12","article_processing_charge":"No","has_accepted_license":"1","date_published":"2018-04-12T00:00:00Z","citation":{"chicago":"Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_998.","short":"A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018.","mla":"Leithner, Alexander F. Branched Actin Networks in Dendritic Cell Biology. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_998.","apa":"Leithner, A. F. (2018). Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_998","ieee":"A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018.","ista":"Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria.","ama":"Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:10.15479/AT:ISTA:th_998"},"page":"99"},{"publication_identifier":{"issn":["2663-337X"]},"month":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_930","publist_id":"7277","file_date_updated":"2020-12-02T23:30:08Z","department":[{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","date_updated":"2023-09-07T12:41:06Z","date_created":"2018-12-11T11:47:03Z","related_material":{"record":[{"id":"1024","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Hurny, Andrej","last_name":"Hurny","first_name":"Andrej","orcid":"0000-0003-3638-1426","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"147","citation":{"ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018.","apa":"Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930","ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria.","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:10.15479/AT:ISTA:th_930","chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930.","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","mla":"Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_930."},"date_published":"2018-01-01T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth."}],"title":"Identification and characterization of novel auxin-cytokinin cross-talk components","status":"public","ddc":["570"],"_id":"539","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"embargo_to":"open_access","file_name":"2018_Hurny_thesis_source.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":28112114,"creator":"dernst","relation":"source_file","file_id":"6226","date_updated":"2020-12-02T23:30:08Z","date_created":"2019-04-05T09:37:56Z","checksum":"0c9d6d1c80d9857e6e545213467bbcb2"},{"access_level":"open_access","file_name":"2018_Hurny_thesis.pdf","creator":"dernst","content_type":"application/pdf","file_size":12524427,"file_id":"6227","embargo":"2019-07-10","relation":"main_file","checksum":"ecbe481a1413d270bd501b872c7ed54f","date_updated":"2020-12-02T09:52:16Z","date_created":"2019-04-05T09:37:55Z"}],"oa_version":"Published Version","pubrep_id":"930"},{"publist_id":"8006","file_date_updated":"2021-02-11T23:30:22Z","author":[{"full_name":"Gridchyn, Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","first_name":"Igor","last_name":"Gridchyn"}],"date_created":"2018-12-11T11:44:21Z","date_updated":"2023-09-07T12:42:44Z","year":"2018","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"08","doi":"10.15479/AT:ISTA:th_1042","language":[{"iso":"eng"}],"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"degree_awarded":"PhD","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1042","oa_version":"Published Version","file":[{"checksum":"7db4415e435590fa33542c7b0a0321d7","date_created":"2019-04-08T13:36:01Z","date_updated":"2021-02-11T23:30:22Z","relation":"source_file","file_id":"6236","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":7666687,"creator":"dernst","access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Gridchyn_source.docx"},{"content_type":"application/pdf","file_size":6034153,"creator":"dernst","access_level":"open_access","file_name":"2018_Thesis_Gridchyn.pdf","checksum":"f96f3fe8979f7b1e6db6acaca962b10c","date_updated":"2021-02-11T11:17:18Z","date_created":"2019-04-08T13:36:01Z","relation":"main_file","embargo":"2019-08-29","file_id":"6237"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"48","title":"Reactivation content is important for consolidation of spatial memory","status":"public","ddc":["573"],"has_accepted_license":"1","article_processing_charge":"No","day":"27","date_published":"2018-08-27T00:00:00Z","citation":{"apa":"Gridchyn, I. (2018). Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1042","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018.","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria.","ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:10.15479/AT:ISTA:th_1042","chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1042.","short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","mla":"Gridchyn, Igor. Reactivation Content Is Important for Consolidation of Spatial Memory. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1042."},"page":"104"},{"abstract":[{"text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"date_created":"2019-04-08T14:13:12Z","date_updated":"2020-07-14T12:48:14Z","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","file_id":"6243","relation":"source_file","creator":"dernst","file_size":102737483,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2018_Thesis_Belyaeva_source.docx","embargo_to":"open_access","access_level":"closed"},{"relation":"main_file","file_id":"6244","embargo":"2019-11-19","date_created":"2019-04-08T14:14:08Z","date_updated":"2021-02-11T11:17:16Z","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","file_name":"2018_Thesis_Belyaeva.pdf","access_level":"open_access","content_type":"application/pdf","file_size":88077843,"creator":"dernst"}],"oa_version":"Published Version","pubrep_id":"1064","ddc":["570"],"title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","status":"public","_id":"9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"01","date_published":"2018-07-01T00:00:00Z","page":"96","citation":{"chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1064.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018.","mla":"Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1064.","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","apa":"Belyaeva, V. (2018). Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1064","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064"},"publist_id":"8047","file_date_updated":"2021-02-11T11:17:16Z","date_updated":"2023-09-07T12:43:10Z","date_created":"2018-12-11T11:44:08Z","author":[{"last_name":"Belyaeva","first_name":"Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","full_name":"Belyaeva, Vera"}],"department":[{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","publication_identifier":{"issn":["2663-337X"]},"month":"07","language":[{"iso":"eng"}],"supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th1064","oa":1},{"citation":{"chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055.","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission . Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:th_1055.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018.","ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","apa":"Mckenzie, C. (2018). Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th_1055","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055"},"page":"95","date_published":"2018-10-31T00:00:00Z","day":"31","has_accepted_license":"1","article_processing_charge":"No","_id":"6266","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["571","573"],"status":"public","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","pubrep_id":"1055","file":[{"content_type":"application/pdf","file_size":4906420,"creator":"dernst","file_name":"2018_Thesis_McKenzie.pdf","access_level":"open_access","date_created":"2019-04-09T14:12:40Z","date_updated":"2021-02-11T11:17:16Z","checksum":"9d2c2dca04b00e485470c28b262af59a","relation":"main_file","embargo":"2019-11-24","file_id":"6267"},{"access_level":"closed","file_name":"2018_Thesis_McKenzie_source.docx","embargo_to":"open_access","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":5053545,"file_id":"6268","relation":"source_file","checksum":"50b58c272899601bc6fd9642c4dc97f1","date_updated":"2020-07-14T12:47:25Z","date_created":"2019-04-09T14:12:40Z"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. ","lang":"eng"}],"oa":1,"doi":"10.15479/at:ista:th_1055","degree_awarded":"PhD","supervisor":[{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2663-337X"]},"year":"2018","publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Mckenzie","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine"}],"related_material":{"record":[{"id":"7132","status":"public","relation":"new_edition"}]},"date_updated":"2023-09-07T13:02:37Z","date_created":"2019-04-09T14:13:39Z","file_date_updated":"2021-02-11T11:17:16Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"22","date_published":"2018-06-22T00:00:00Z","citation":{"ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:10.15479/AT:ISTA:TH_1031","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","apa":"Capek, D. (2018). Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1031","ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria.","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","mla":"Capek, Daniel. Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1031.","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1031."},"page":"95","abstract":[{"text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1031","file":[{"file_size":31576521,"content_type":"application/pdf","creator":"dernst","file_name":"2018_Thesis_Capek.pdf","access_level":"open_access","date_created":"2019-04-08T13:42:26Z","date_updated":"2021-02-11T11:17:17Z","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","relation":"main_file","embargo":"2019-06-25","file_id":"6238"},{"relation":"source_file","file_id":"6239","date_created":"2019-04-08T13:42:27Z","date_updated":"2021-02-11T23:30:21Z","checksum":"876deb14067e638aba65d209668bd821","embargo_to":"open_access","file_name":"2018_Thesis_Capek_source.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":38992956,"creator":"dernst"}],"oa_version":"Published Version","_id":"50","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","status":"public","ddc":["570","591","596"],"publication_identifier":{"issn":["2663-337X"]},"month":"06","doi":"10.15479/AT:ISTA:TH_1031","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"oa":1,"publist_id":"8004","file_date_updated":"2021-02-11T23:30:21Z","related_material":{"record":[{"id":"1100","relation":"part_of_dissertation","status":"public"},{"id":"661","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"676"}]},"author":[{"full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","first_name":"Daniel","last_name":"Capek"}],"date_created":"2018-12-11T11:44:21Z","date_updated":"2023-09-07T12:48:16Z","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaHe"}],"publication_status":"published"},{"pubrep_id":"1059","file":[{"creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":9190845,"access_level":"closed","file_name":"Thesis_Steinrueck_final.docx","embargo_to":"open_access","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","date_created":"2019-02-08T10:51:22Z","date_updated":"2020-07-14T12:45:43Z","file_id":"5941","relation":"source_file"},{"file_size":7521973,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"Thesis_Steinrueck_final.pdf","checksum":"3def8b7854c8b42d643597ce0215efac","date_created":"2019-02-08T10:51:22Z","date_updated":"2021-02-11T11:17:14Z","relation":"main_file","file_id":"5942","embargo":"2019-11-02"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"26","ddc":["576","579"],"title":"The influence of sequence context on the evolution of bacterial gene expression","status":"public","abstract":[{"text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2018-10-30T00:00:00Z","citation":{"ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:10.15479/AT:ISTA:th1059","apa":"Steinrück, M. (2018). The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1059","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","mla":"Steinrück, Magdalena. The Influence of Sequence Context on the Evolution of Bacterial Gene Expression. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1059.","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1059."},"page":"109","article_processing_charge":"No","has_accepted_license":"1","day":"30","related_material":{"record":[{"id":"704","status":"public","relation":"part_of_dissertation"}]},"author":[{"orcid":"0000-0003-1229-9719","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","first_name":"Magdalena","full_name":"Steinrück, Magdalena"}],"date_updated":"2023-09-07T12:48:43Z","date_created":"2018-12-11T11:44:14Z","year":"2018","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publist_id":"8029","file_date_updated":"2021-02-11T11:17:14Z","doi":"10.15479/AT:ISTA:th1059","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"10"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Antibiotic resistance can emerge spontaneously through genomic mutation and render treatment ineffective. To counteract this process, in addition to the discovery and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its determinantsis needed. To address this challenge, this thesisuncoversnew genetic determinants of resistance evolvability using a customized robotic setup, exploressystematic ways in which resistance evolution is perturbed due to dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order to identify them, we first developedan automated high-throughput feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic concentration. We implementedthis protocol on a customized liquid handling robot and propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100 generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more compared to less sensitive ones. Our data uncover that deletions of certain genes which do not affect mutation rate,including efflux pump components, a chaperone and severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution. Sequencing analysis of evolved populations indicates that epistasis with resistance mutations is the most likelyexplanation. This work could inspire treatment strategies in which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model, toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations. We show that in silicothis also leads to slower resistance evolution. We see and confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier –a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under periodic selectionakin to clinical treatment. We set up a deterministic infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and evaluate various treatment schemes in how well they maintain a stress-induced mutator allele. In particular,a high diversity of stresses is crucial for the persistence of the mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. "}],"ddc":["570","576","579"],"title":"Genetic determinants of antibiotic resistance evolution","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6263","oa_version":"Published Version","file":[{"embargo":"2020-01-25","file_id":"6264","relation":"main_file","checksum":"fc60585c9eaad868ac007004ef130908","date_created":"2019-04-09T13:49:24Z","date_updated":"2021-02-11T11:17:17Z","access_level":"open_access","file_name":"2018_Thesis_Lukacisinova.pdf","creator":"dernst","content_type":"application/pdf","file_size":5656866},{"relation":"source_file","file_id":"6265","checksum":"264057ec0a92ab348cc83b41f021ba92","date_created":"2019-04-09T13:49:23Z","date_updated":"2020-07-14T12:47:25Z","access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Lukacisinova_source.docx","file_size":5168054,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst"}],"day":"28","has_accepted_license":"1","article_processing_charge":"No","page":"91","citation":{"chicago":"Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072.","mla":"Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072.","short":"M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018.","ista":"Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria.","apa":"Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072","ieee":"M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018.","ama":"Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:10.15479/AT:ISTA:th1072"},"date_published":"2018-12-28T00:00:00Z","file_date_updated":"2021-02-11T11:17:17Z","publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"Institute of Science and Technology Austria","year":"2018","date_updated":"2023-09-22T09:20:37Z","date_created":"2019-04-09T13:57:15Z","author":[{"last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1619"},{"relation":"part_of_dissertation","status":"public","id":"696"},{"status":"public","relation":"part_of_dissertation","id":"1027"}]},"month":"12","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"full_name":"Bollenbach, Tobias","first_name":"Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th1072"},{"date_created":"2022-01-25T14:54:14Z","date_updated":"2022-01-25T15:00:26Z","oa_version":"Published Version","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy"}],"publication_status":"published","status":"public","title":"Magnetic force microscopy studies of mesoscopic superconducting structures","publisher":"University of Illinois at Urbana-Champaign","_id":"10663","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2017","extern":"1","abstract":[{"text":"The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures.","lang":"eng"}],"alternative_title":["Graduate Dissertations and Theses at Illinois"],"type":"dissertation","degree_awarded":"PhD","supervisor":[{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"language":[{"iso":"eng"}],"date_published":"2017-09-18T00:00:00Z","page":"103","citation":{"ama":"Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017.","ista":"Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","apa":"Polshyn, H. (2017). Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","ieee":"H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting structures,” University of Illinois at Urbana-Champaign, 2017.","mla":"Polshyn, Hryhoriy. Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures. University of Illinois at Urbana-Champaign, 2017.","short":"H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures, University of Illinois at Urbana-Champaign, 2017.","chicago":"Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/2142/99178"}],"month":"09","day":"18","article_processing_charge":"No","keyword":["physics","superconductivity","magnetic force microscopy","phase slips"]},{"publist_id":"6203","ec_funded":1,"file_date_updated":"2020-07-14T12:44:34Z","acknowledgement":" First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ","year":"2017","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"id":"1093","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1230"},{"id":"1234","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1391"},{"id":"1501","status":"public","relation":"part_of_dissertation"},{"id":"1502","status":"public","relation":"part_of_dissertation"},{"id":"2063","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2167"}]},"author":[{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","last_name":"Daca"}],"date_created":"2018-12-11T11:50:27Z","date_updated":"2023-09-07T11:58:34Z","publication_identifier":{"issn":["2663-337X"]},"month":"01","oa":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"doi":"10.15479/AT:ISTA:TH_730","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1155","status":"public","ddc":["004","005"],"title":"Statistical and logical methods for property checking","pubrep_id":"730","file":[{"access_level":"open_access","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","file_size":1028586,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4880","checksum":"1406a681cb737508234fde34766be2c2","date_created":"2018-12-12T10:11:26Z","date_updated":"2020-07-14T12:44:34Z"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"02","citation":{"chicago":"Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:TH_730.","short":"P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017.","mla":"Daca, Przemyslaw. Statistical and Logical Methods for Property Checking. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730.","apa":"Daca, P. (2017). Statistical and logical methods for property checking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_730","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730"},"page":"163","date_published":"2017-01-02T00:00:00Z"},{"month":"02","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","supervisor":[{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"date_published":"2017-02-01T00:00:00Z","page":"83","citation":{"ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","apa":"Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017.","mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017."},"oa":1,"file_date_updated":"2021-02-22T13:45:59Z","abstract":[{"lang":"eng","text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_created":"2019-04-09T15:16:45Z","date_updated":"2023-09-07T12:00:00Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6292","date_created":"2019-04-09T15:15:32Z","date_updated":"2020-07-14T12:47:27Z","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","access_level":"closed","content_type":"application/pdf","file_size":3025175,"creator":"dernst"},{"date_created":"2021-02-22T13:45:59Z","date_updated":"2021-02-22T13:45:59Z","success":1,"checksum":"af531e921a7f64a9e0af4cd8783b2226","file_id":"9187","relation":"main_file","creator":"dernst","file_size":3111536,"content_type":"application/pdf","file_name":"2017_Payne_Thesis.pdf","access_level":"open_access"}],"author":[{"orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","first_name":"Pavel","full_name":"Payne, Pavel"}],"publication_status":"published","title":"Bacterial herd and social immunity to phages","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"year":"2017","_id":"6291","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"related_material":{"record":[{"id":"2001","status":"public","relation":"part_of_dissertation"},{"id":"666","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","first_name":"Karin","full_name":"Mitosch, Karin"}],"date_updated":"2023-09-07T12:00:26Z","date_created":"2018-12-11T11:48:40Z","year":"2017","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToBo"}],"publication_status":"published","publist_id":"6831","file_date_updated":"2020-07-14T12:48:09Z","doi":"10.15479/AT:ISTA:th_862","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach"}],"degree_awarded":"PhD","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["2663-337X"]},"month":"09","pubrep_id":"862","oa_version":"Published Version","file":[{"creator":"dernst","file_size":6331071,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_KarinMitosch.docx","access_level":"closed","date_created":"2019-04-05T08:48:51Z","date_updated":"2020-07-14T12:48:09Z","checksum":"da3993c5f90f59a8e8623cc31ad501dd","file_id":"6210","relation":"source_file"},{"relation":"main_file","file_id":"6211","date_created":"2019-04-05T08:48:51Z","date_updated":"2020-07-14T12:48:09Z","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","file_name":"Thesis_KarinMitosch.pdf","access_level":"open_access","file_size":9289852,"content_type":"application/pdf","creator":"dernst"}],"_id":"818","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["571","579"],"status":"public","title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","abstract":[{"lang":"eng","text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2017-09-27T00:00:00Z","citation":{"ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017.","apa":"Mitosch, K. (2017). Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862","ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862.","mla":"Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017."},"page":"113","article_processing_charge":"No","has_accepted_license":"1","day":"27"},{"abstract":[{"lang":"eng","text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"854","file":[{"relation":"main_file","file_id":"4900","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-12T10:11:44Z","access_level":"open_access","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","content_type":"application/pdf","file_size":4103115,"creator":"system"},{"access_level":"closed","file_name":"2017_thesis_Pavlogiannis.zip","content_type":"application/zip","file_size":14744374,"creator":"dernst","relation":"source_file","file_id":"6201","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T07:59:31Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"821","status":"public","title":"Algorithmic advances in program analysis and their applications","ddc":["000"],"has_accepted_license":"1","article_processing_charge":"No","day":"09","date_published":"2017-08-09T00:00:00Z","citation":{"ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","apa":"Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854","chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","mla":"Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854."},"page":"418","ec_funded":1,"publist_id":"6828","file_date_updated":"2020-07-14T12:48:10Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1071"},{"relation":"part_of_dissertation","status":"public","id":"1437"},{"id":"1602","status":"public","relation":"part_of_dissertation"},{"id":"1604","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1607"},{"status":"public","relation":"part_of_dissertation","id":"1714"}]},"author":[{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"date_created":"2018-12-11T11:48:41Z","date_updated":"2023-09-07T12:01:59Z","year":"2017","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","department":[{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"08","doi":"10.15479/AT:ISTA:th_854","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}]},{"month":"08","publication_identifier":{"issn":["2663-337X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:th_857","degree_awarded":"PhD","supervisor":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:10Z","publist_id":"6829","ec_funded":1,"acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","year":"2017","publication_status":"published","department":[{"_id":"JoBo"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Jesse, Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","last_name":"Jesse","first_name":"Fabienne"}],"date_updated":"2023-09-07T12:01:21Z","date_created":"2018-12-11T11:48:41Z","day":"25","article_processing_charge":"No","has_accepted_license":"1","citation":{"ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","apa":"Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857","ama":"Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857","chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857.","mla":"Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017."},"page":"87","date_published":"2017-08-25T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"820","title":"The lac operon in the wild","status":"public","ddc":["576","577","579"],"pubrep_id":"857","file":[{"access_level":"open_access","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","content_type":"application/pdf","file_size":3417773,"creator":"system","relation":"main_file","file_id":"5252","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-12T10:17:00Z"},{"file_size":215899,"content_type":"application/x-tex","creator":"dernst","access_level":"closed","file_name":"2017_thesis_Jesse_source.tex","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T08:51:59Z","relation":"source_file","file_id":"6212"}],"oa_version":"Published Version"},{"publist_id":"6810","file_date_updated":"2020-07-14T12:48:12Z","year":"2017","department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"2082","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6196"}]},"author":[{"full_name":"Rybar, Michal","last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:48:46Z","date_updated":"2023-09-07T12:02:28Z","publication_identifier":{"issn":["2663-337X"]},"month":"06","oa":1,"doi":"10.15479/AT:ISTA:th_828","language":[{"iso":"eng"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. ","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"838","ddc":["000"],"status":"public","title":"(The exact security of) Message authentication codes","pubrep_id":"828","oa_version":"Published Version","file":[{"file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":847400,"file_id":"4799","relation":"main_file","date_updated":"2020-07-14T12:48:12Z","date_created":"2018-12-12T10:10:13Z","checksum":"ff8639ec4bded6186f44c7bd3ee26804"},{"file_id":"6202","relation":"source_file","date_created":"2019-04-05T08:24:11Z","date_updated":"2020-07-14T12:48:12Z","checksum":"3462101745ce8ad199c2d0f75dae4a7e","file_name":"2017_Thesis_Rybar_source.zip","access_level":"closed","creator":"dernst","content_type":"application/zip","file_size":26054879}],"article_processing_charge":"No","has_accepted_license":"1","day":"26","citation":{"chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","mla":"Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.","apa":"Rybar, M. (2017). (The exact security of) Message authentication codes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828"},"page":"86","date_published":"2017-06-26T00:00:00Z"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ","lang":"eng"}],"title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","ddc":["571"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"837","file":[{"relation":"source_file","file_id":"6213","checksum":"f11925fbbce31e495124b6bc4f10573c","date_created":"2019-04-05T08:59:51Z","date_updated":"2020-07-14T12:48:12Z","access_level":"closed","file_name":"2017_Xu_Haibing_Thesis_Source.docx","file_size":3589490,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst"},{"file_name":"2017_Xu_Thesis_IST.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":11668613,"file_id":"6214","relation":"main_file","date_created":"2019-04-05T08:59:51Z","date_updated":"2020-07-14T12:48:12Z","checksum":"ffb10749a537d615fab1ef0937ccb157"}],"oa_version":"Published Version","pubrep_id":"858","day":"23","article_processing_charge":"No","has_accepted_license":"1","page":"93","citation":{"chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.","mla":"Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","apa":"Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858"},"date_published":"2017-08-23T00:00:00Z","file_date_updated":"2020-07-14T12:48:12Z","publist_id":"6811","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"year":"2017","acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","date_updated":"2023-09-07T12:06:38Z","date_created":"2018-12-11T11:48:46Z","author":[{"full_name":"Xu, Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing","last_name":"Xu"}],"related_material":{"record":[{"id":"5828","status":"public","relation":"part_of_dissertation"}]},"month":"08","publication_identifier":{"issn":["2663-337X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"degree_awarded":"PhD","supervisor":[{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_858"},{"abstract":[{"lang":"eng","text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"842","oa_version":"Published Version","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":46903863,"creator":"dernst","access_level":"closed","file_name":"2017_Adamowski-Thesis_Source.docx","checksum":"193425764d9aaaed3ac57062a867b315","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:20Z","relation":"source_file","file_id":"6215"},{"file_id":"6216","relation":"main_file","checksum":"df5ab01be81f821e1b958596a1ec8d21","date_created":"2019-04-05T09:03:19Z","date_updated":"2020-07-14T12:48:15Z","access_level":"open_access","file_name":"2017_Adamowski-Thesis.pdf","creator":"dernst","file_size":8698888,"content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"938","title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","ddc":["581","583","580"],"status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"02","date_published":"2017-06-02T00:00:00Z","citation":{"short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","mla":"Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842.","chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","apa":"Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria."},"page":"117","publist_id":"6483","file_date_updated":"2020-07-14T12:48:15Z","related_material":{"record":[{"id":"1591","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek"}],"date_created":"2018-12-11T11:49:18Z","date_updated":"2023-09-07T12:06:09Z","year":"2017","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"06","doi":"10.15479/AT:ISTA:th_842","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"oa":1},{"oa":1,"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"doi":"10.15479/AT:ISTA:th_815","degree_awarded":"PhD","supervisor":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"}],"language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"FP7/2007-2013/ERC grant agreement no 616160","year":"2017","publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal"}],"date_updated":"2023-09-07T12:05:41Z","date_created":"2018-12-11T11:49:35Z","file_date_updated":"2020-07-14T12:48:18Z","ec_funded":1,"publist_id":"6407","citation":{"mla":"Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815.","short":"M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017.","chicago":"Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815.","ama":"Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815","ista":"Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria.","apa":"Rolinek, M. (2017). Complexity of constraint satisfaction. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815","ieee":"M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017."},"page":"97","date_published":"2017-05-01T00:00:00Z","day":"01","has_accepted_license":"1","article_processing_charge":"No","_id":"992","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["004"],"status":"public","title":"Complexity of constraint satisfaction","pubrep_id":"815","file":[{"access_level":"open_access","file_name":"IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf","creator":"system","file_size":786145,"content_type":"application/pdf","file_id":"4654","relation":"main_file","checksum":"81761fb939acb7585c36629f765b4373","date_updated":"2020-07-14T12:48:18Z","date_created":"2018-12-12T10:07:55Z"},{"relation":"source_file","file_id":"6208","date_created":"2019-04-05T08:43:24Z","date_updated":"2020-07-14T12:48:18Z","checksum":"2b2d7e1d6c1c79a9795a7aa0f860baf3","file_name":"2017_Thesis_Rolinek_source.zip","access_level":"closed","content_type":"application/zip","file_size":5936337,"creator":"dernst"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of\r\nvariables, a finite domain of labels, and a set of constraints, each constraint acting on\r\na subset of the variables. The goal is to find an assignment of labels to its variables\r\nthat satisfies all constraints (or decide whether one exists). If we allow more general\r\n“soft” constraints, which come with (possibly infinite) costs of particular assignments,\r\nwe obtain instances from a richer class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal is to find an assignment with minimum total cost.\r\nIn this thesis, we focus (assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage, that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe complexity classification modulo (missing pieces of) complexity classification for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’ perfect\r\nmatching algorithm. This generalization contributes to complexity classfications in two\r\nways. First, it gives a new (largest known) polynomial-time solvable class of Boolean\r\nCSPs in which every variable may appear in at most two constraints and second, it\r\nsettles full classification of Boolean CSPs with planar drawing (again parametrized by a\r\nconstraint language).","lang":"eng"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","date_published":"2017-10-01T00:00:00Z","citation":{"ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","apa":"Pleska, M. (2017). Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:10.15479/AT:ISTA:th_916","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.","mla":"Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017."},"page":"126","abstract":[{"lang":"eng","text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"916","oa_version":"Published Version","file":[{"checksum":"33cfb59674e91f82e3738396d3fb3776","date_created":"2018-12-12T10:08:48Z","date_updated":"2020-07-14T12:45:24Z","relation":"main_file","file_id":"4710","file_size":18569590,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf"},{"file_size":2801649,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","access_level":"closed","file_name":"2017_Pleska_Maros_Thesis.docx","checksum":"dcc239968decb233e7f98cf1083d8c26","date_created":"2019-04-05T08:33:14Z","date_updated":"2020-07-14T12:45:24Z","relation":"source_file","file_id":"6204"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"202","title":"Biology of restriction-modification systems at the single-cell and population level","status":"public","ddc":["576","579"],"publication_identifier":{"issn":["2663-337X"]},"month":"10","doi":"10.15479/AT:ISTA:th_916","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"degree_awarded":"PhD","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"publist_id":"7711","file_date_updated":"2020-07-14T12:45:24Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1243"},{"id":"561","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"457"}]},"author":[{"last_name":"Pleska","first_name":"Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros"}],"date_updated":"2023-09-15T12:04:56Z","date_created":"2018-12-11T11:45:10Z","acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","year":"2017","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"publication_status":"published"},{"publication_identifier":{"issn":["2663-337X"]},"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:th_873","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"file_date_updated":"2020-07-14T12:47:26Z","year":"2017","department":[{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"718","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"5678"},{"id":"87","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton"}],"date_created":"2019-04-09T15:04:32Z","date_updated":"2023-09-15T12:10:34Z","article_processing_charge":"No","has_accepted_license":"1","day":"27","citation":{"apa":"Nikitenko, A. (2017). Discrete Morse theory for random complexes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_873","ieee":"A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of Science and Technology Austria, 2017.","ista":"Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria.","ama":"Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:10.15479/AT:ISTA:th_873","chicago":"Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_873.","short":"A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science and Technology Austria, 2017.","mla":"Nikitenko, Anton. Discrete Morse Theory for Random Complexes . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_873."},"page":"86","date_published":"2017-10-27T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The main objects considered in the present work are simplicial and CW-complexes with vertices forming a random point cloud. In particular, we consider a Poisson point process in R^n and study Delaunay and Voronoi complexes of the first and higher orders and weighted Delaunay complexes obtained as sections of Delaunay complexes, as well as the Čech complex. Further, we examine theDelaunay complex of a Poisson point process on the sphere S^n, as well as of a uniform point cloud, which is equivalent to the convex hull, providing a connection to the theory of random polytopes. Each of the complexes in question can be endowed with a radius function, which maps its cells to the radii of appropriately chosen circumspheres, called the radius of the cell. Applying and developing discrete Morse theory for these functions, joining it together with probabilistic and sometimes analytic machinery, and developing several integral geometric tools, we aim at getting the distributions of circumradii of typical cells. For all considered complexes, we are able to generalize and obtain up to constants the distribution of radii of typical intervals of all types. In low dimensions the constants can be computed explicitly, thus providing the explicit expressions for the expected numbers of cells. In particular, it allows to find the expected density of simplices of every dimension for a Poisson point process in R^4, whereas the result for R^3 was known already in 1970's.","lang":"eng"}],"_id":"6287","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["514","516","519"],"status":"public","title":"Discrete Morse theory for random complexes ","pubrep_id":"873","file":[{"file_name":"2017_Thesis_Nikitenko.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2324870,"file_id":"6289","relation":"main_file","date_created":"2019-04-09T14:54:51Z","date_updated":"2020-07-14T12:47:26Z","checksum":"ece7e598a2f060b263c2febf7f3fe7f9"},{"file_id":"6290","relation":"source_file","date_updated":"2020-07-14T12:47:26Z","date_created":"2019-04-09T14:54:51Z","checksum":"99b7ad76e317efd447af60f91e29b49b","file_name":"2017_Thesis_Nikitenko_source.zip","access_level":"closed","creator":"dernst","file_size":2863219,"content_type":"application/zip"}],"oa_version":"Published Version"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms controlling plant development. Auxin itself could change localization of PINs and\r\nthereby control direction of its own flow. We performed an expression profiling experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity which are transcriptionally\r\nregulated by auxin signalling. We identified several novel regulators and performed a detailed\r\ncharacterization of the transcription factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin transport processes such as gravitropism and leaf vascular pattern\r\nformation were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct targets of WRKY23, we performed consequential expression\r\nprofiling experiments using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23 line that is defunct in PIN re-arrangement. Among several genes mostly related to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER 1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1; At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits transcriptional behaviour, subcellular localization. Based on global expression data, we\r\ntried to identify ligand responsible for mechanism of signalling and suggest signalling partner\r\nand interactors. Additionally, we described role of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement, that could be a fundament for future studies in this\r\nfield.\r\nOur results provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork and characterised its mediatory role in plant development. We identified direct\r\neffectors of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement and\r\nPIN-dependent auxin transport processes."}],"title":"Identification of novel regulators of PIN polarity and development of novel auxin sensor","ddc":["580"],"status":"public","_id":"1127","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"closed","file_name":"IST_Austria_Thesis_Tomáš_Prát.pdf","content_type":"application/pdf","file_size":10285946,"creator":"dernst","relation":"main_file","file_id":"6209","checksum":"d192c7c6c5ea32c8432437286dc4909e","date_updated":"2019-04-05T08:45:14Z","date_created":"2019-04-05T08:45:14Z"},{"content_type":"application/pdf","file_size":9802991,"creator":"dernst","access_level":"open_access","file_name":"2017_Thesis_Prat.pdf","checksum":"bab18b52cf98145926042d8ed99fdb3b","success":1,"date_created":"2021-02-22T11:52:56Z","date_updated":"2021-02-22T11:52:56Z","relation":"main_file","file_id":"9185"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"12","page":"131","citation":{"apa":"Prat, T. (2017). Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria.","ieee":"T. Prat, “Identification of novel regulators of PIN polarity and development of novel auxin sensor,” Institute of Science and Technology Austria, 2017.","ista":"Prat T. 2017. Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria.","ama":"Prat T. Identification of novel regulators of PIN polarity and development of novel auxin sensor. 2017.","chicago":"Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017.","short":"T. Prat, Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017.","mla":"Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017."},"date_published":"2017-01-12T00:00:00Z","publist_id":"6233","file_date_updated":"2021-02-22T11:52:56Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","acknowledgement":"I would like to first acknowledge my supervisor Jiří Friml for support, kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg forever. I would like to thank all past and present lab members for the friendship and friendly and scientific environment in the groups. It was so nice to cooperate with you, guys. There was always someone who helped me with experiments, troubleshoot issues coming from our work etc. At this place, I would like to thank especially to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became my tutor and guide through my PhD. From no one else during my entire professional career, I’ve learned that much.","year":"2017","date_created":"2018-12-11T11:50:17Z","date_updated":"2023-09-19T10:39:33Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"449"}]},"author":[{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","last_name":"Prat","first_name":"Tomas","full_name":"Prat, Tomas"}],"publication_identifier":{"issn":["2663-337X"]},"month":"01","oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}]},{"pubrep_id":"825","file":[{"file_id":"6205","relation":"source_file","checksum":"242f88c87f2cf267bf05049fa26a687b","date_created":"2019-04-05T08:36:52Z","date_updated":"2020-07-14T12:48:16Z","access_level":"closed","file_name":"2017_Barone_thesis_final.docx","creator":"dernst","file_size":14497822,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_name":"2017_Barone_thesis_.pdf","access_level":"open_access","file_size":14995941,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6206","date_created":"2019-04-05T08:36:52Z","date_updated":"2020-07-14T12:48:16Z","checksum":"ba5b0613ed8bade73a409acdd880fb8a"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"961","status":"public","ddc":["570","590"],"title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","abstract":[{"lang":"eng","text":"Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2017-03-01T00:00:00Z","citation":{"chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_825.","short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","mla":"Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_825.","apa":"Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_825","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:10.15479/AT:ISTA:th_825"},"page":"109","article_processing_charge":"No","has_accepted_license":"1","day":"01","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1100"},{"id":"1537","status":"public","relation":"part_of_dissertation"},{"id":"1912","relation":"part_of_dissertation","status":"public"},{"id":"2926","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"3246"},{"id":"676","status":"public","relation":"part_of_dissertation"},{"id":"735","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa"}],"date_created":"2018-12-11T11:49:25Z","date_updated":"2023-09-27T14:16:45Z","year":"2017","acknowledgement":"Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall the good science I witnessed and participated in. It has been a \r\nblast, an incredibly \r\nexciting one! Thanks to JLo, for teaching me how to master my pipettes and showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout zebrafish and being always there to advice, sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether for all the good laughs we\r\nhad. My start in Vienna would have been a lot more \r\ndifficult without you guys. Also it would not have been possible without Elena and Inês: \r\nthanks for helping setting up this lab and for the dinners in Gugging. Thanks to Martin, for \r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp, for the interest and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat. To Shayan, for being such a motivated student. To Matt, for helping out\r\nwith coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor setting up an amazing imaging facility and for building the best team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand to Patrick Lemaire f\r\nor the helpful insight and extremely interesting discussion we had \r\nabout the project. Also, this journey would not have been the same without all the friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William, e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaHe"}],"publication_status":"published","publist_id":"6444","file_date_updated":"2020-07-14T12:48:16Z","doi":"10.15479/AT:ISTA:th_825","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["2663-337X"]},"month":"03"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"819","ddc":["576","577","578","579","590","592"],"status":"public","title":"Disease defence in garden ants","pubrep_id":"861","file":[{"creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":18580400,"access_level":"closed","file_name":"2017_Thesis_Pull.docx","checksum":"4993cdd5382295758ecc3ecbd2a9aaff","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T07:53:04Z","file_id":"6199","relation":"source_file"},{"checksum":"ee2e3ebb5b53c154c866f5b052b25153","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T07:53:04Z","relation":"main_file","file_id":"6200","content_type":"application/pdf","file_size":14400681,"creator":"dernst","access_level":"open_access","file_name":"2017_Thesis_Pull.pdf"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. ","lang":"eng"}],"citation":{"ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","apa":"Pull, C. (2017). Disease defence in garden ants. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_861","ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017.","ama":"Pull C. Disease defence in garden ants. 2017. doi:10.15479/AT:ISTA:th_861","chicago":"Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_861.","mla":"Pull, Christopher. Disease Defence in Garden Ants. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_861.","short":"C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017."},"page":"122","date_published":"2017-09-26T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"26","year":"2017","acknowledgement":"ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. ","department":[{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"616"},{"id":"806","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"734"},{"id":"732","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull"}],"date_updated":"2023-09-28T11:31:32Z","date_created":"2018-12-11T11:48:40Z","publist_id":"6830","file_date_updated":"2020-07-14T12:48:09Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:th_861","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Cremer","first_name":"Sylvia M","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"09"}]