[{"abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"da3993c5f90f59a8e8623cc31ad501dd","file_id":"6210","creator":"dernst","file_size":6331071,"date_updated":"2020-07-14T12:48:09Z","file_name":"Thesis_KarinMitosch.docx","date_created":"2019-04-05T08:48:51Z"},{"file_name":"Thesis_KarinMitosch.pdf","date_created":"2019-04-05T08:48:51Z","file_size":9289852,"date_updated":"2020-07-14T12:48:09Z","creator":"dernst","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","file_id":"6211","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"2001","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"666"}]},"_id":"818","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"862","supervisor":[{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"date_updated":"2023-09-07T12:00:26Z","ddc":["571","579"],"department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:48:09Z","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","oa":1,"has_accepted_license":"1","year":"2017","day":"27","page":"113","date_published":"2017-09-27T00:00:00Z","doi":"10.15479/AT:ISTA:th_862","date_created":"2018-12-11T11:48:40Z","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.","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.","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","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","full_name":"Mitosch, Karin"}],"publist_id":"6831","article_processing_charge":"No","title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics"},{"day":"26","publication":"Cell Systems","has_accepted_license":"1","year":"2017","date_published":"2017-04-26T00:00:00Z","doi":"10.1016/j.cels.2017.03.001","date_created":"2018-12-11T11:47:48Z","page":"393 - 403","quality_controlled":"1","publisher":"Cell Press","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.","apa":"Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403."},"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","publist_id":"7061","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","full_name":"Mitosch, Karin","last_name":"Mitosch"},{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","last_name":"Rieckh","full_name":"Rieckh, Georg"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X"}],"article_processing_charge":"Yes (in subscription journal)","project":[{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"file":[{"date_created":"2018-12-12T10:13:54Z","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","creator":"system","date_updated":"2020-07-14T12:47:35Z","file_size":2438660,"checksum":"04ff20011c3d9a601c514aa999a5fe1a","file_id":"5041","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["24054712"]},"publication_status":"published","issue":"4","volume":4,"related_material":{"record":[{"status":"public","id":"818","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"month":"04","intvolume":" 4","scopus_import":1,"ddc":["576","610"],"date_updated":"2023-09-07T12:00:25Z","department":[{"_id":"ToBo"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:35Z","_id":"666","status":"public","pubrep_id":"901","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"ddc":["000"],"date_updated":"2023-09-07T12:01:59Z","supervisor":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"file_date_updated":"2020-07-14T12:48:10Z","department":[{"_id":"KrCh"}],"_id":"821","pubrep_id":"854","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:10Z","file_size":4103115,"creator":"system","date_created":"2018-12-12T10:11:44Z","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","file_id":"4900"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","file_id":"6201","date_updated":"2020-07-14T12:48:10Z","file_size":14744374,"creator":"dernst","date_created":"2019-04-05T07:59:31Z","file_name":"2017_thesis_Pavlogiannis.zip"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"1071","status":"public"},{"status":"public","id":"1437","relation":"part_of_dissertation"},{"status":"public","id":"1602","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1604"},{"relation":"part_of_dissertation","status":"public","id":"1607"},{"relation":"part_of_dissertation","id":"1714","status":"public"}]},"oa_version":"Published Version","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."}],"month":"08","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","short":"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","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.","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria."},"title":"Algorithmic advances in program analysis and their applications","article_processing_charge":"No","author":[{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"publist_id":"6828","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"09","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:48:41Z","date_published":"2017-08-09T00:00:00Z","doi":"10.15479/AT:ISTA:th_854","page":"418","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.","oa":1,"publisher":"Institute of Science and Technology Austria"},{"alternative_title":["ISTA Thesis"],"month":"08","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."}],"oa_version":"Published Version","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","file_id":"5252","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","date_created":"2018-12-12T10:17:00Z","file_size":3417773,"date_updated":"2020-07-14T12:48:10Z","creator":"system"},{"file_name":"2017_thesis_Jesse_source.tex","date_created":"2019-04-05T08:51:59Z","creator":"dernst","file_size":215899,"date_updated":"2020-07-14T12:48:10Z","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_id":"6212","relation":"source_file","access_level":"closed","content_type":"application/x-tex"}],"language":[{"iso":"eng"}],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"857","_id":"820","department":[{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:48:10Z","supervisor":[{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"date_updated":"2023-09-07T12:01:21Z","ddc":["576","577","579"],"publisher":"Institute of Science and Technology Austria","oa":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. ","page":"87","date_published":"2017-08-25T00:00:00Z","doi":"10.15479/AT:ISTA:th_857","date_created":"2018-12-11T11:48:41Z","has_accepted_license":"1","year":"2017","day":"25","project":[{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440"}],"publist_id":"6829","author":[{"first_name":"Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","last_name":"Jesse","full_name":"Jesse, Fabienne"}],"article_processing_charge":"No","title":"The lac operon in the wild","citation":{"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.","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.","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"abstract":[{"lang":"eng","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. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","date_created":"2018-12-12T10:10:13Z","file_size":847400,"date_updated":"2020-07-14T12:48:12Z","creator":"system","checksum":"ff8639ec4bded6186f44c7bd3ee26804","file_id":"4799","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"content_type":"application/zip","relation":"source_file","access_level":"closed","checksum":"3462101745ce8ad199c2d0f75dae4a7e","file_id":"6202","file_size":26054879,"date_updated":"2020-07-14T12:48:12Z","creator":"dernst","file_name":"2017_Thesis_Rybar_source.zip","date_created":"2019-04-05T08:24:11Z"}],"related_material":{"record":[{"id":"2082","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6196","status":"public"}]},"_id":"838","type":"dissertation","pubrep_id":"828","status":"public","date_updated":"2023-09-07T12:02:28Z","ddc":["000"],"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:48:12Z","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2017","has_accepted_license":"1","day":"26","page":"86","date_created":"2018-12-11T11:48:46Z","doi":"10.15479/AT:ISTA:th_828","date_published":"2017-06-26T00:00:00Z","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.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","mla":"Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.","ama":"Rybar M. (The exact security of) Message authentication codes. 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.","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar","full_name":"Rybar, Michal"}],"publist_id":"6810","title":"(The exact security of) Message authentication codes"}]