[{"oa":1,"ddc":["580","576"],"date_created":"2019-05-19T21:59:15Z","issue":"7","quality_controlled":"1","oa_version":"Published Version","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Breaking down barriers in morning glories","article_processing_charge":"No","file":[{"relation":"main_file","access_level":"open_access","file_size":367711,"creator":"dernst","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","date_updated":"2020-07-14T12:47:31Z","file_id":"6472","content_type":"application/pdf","date_created":"2019-05-20T11:49:06Z","file_name":"2019_MolecularEcology_Field.pdf"}],"page":"1579-1581","abstract":[{"text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.","lang":"eng"}],"has_accepted_license":"1","external_id":{"isi":["000474808300001"]},"scopus_import":"1","publication_identifier":{"eissn":["1365294X"]},"intvolume":" 28","language":[{"iso":"eng"}],"doi":"10.1111/mec.15048","publication":"Molecular ecology","author":[{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"}],"file_date_updated":"2020-07-14T12:47:31Z","citation":{"apa":"Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581."},"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)"},"publication_status":"published","status":"public","type":"journal_article","volume":28,"_id":"6466","isi":1,"department":[{"_id":"NiBa"}],"month":"04","date_published":"2019-04-01T00:00:00Z","date_updated":"2023-08-25T10:37:30Z","year":"2019","day":"01"},{"isi":1,"department":[{"_id":"CaGu"}],"_id":"6465","article_number":"2013","date_published":"2019-05-01T00:00:00Z","month":"05","date_updated":"2023-08-25T10:33:51Z","year":"2019","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-023-36111-0","relation":"erratum"}]},"day":"01","language":[{"iso":"eng"}],"intvolume":" 10","publication_identifier":{"eissn":["20411723"]},"publication":"Nature Communications","doi":"10.1038/s41467-019-09974-5","file_date_updated":"2020-07-14T12:47:31Z","author":[{"last_name":"Chassin","first_name":"Hélène","full_name":"Chassin, Hélène"},{"full_name":"Müller, Marius","last_name":"Müller","first_name":"Marius"},{"first_name":"Marcel","last_name":"Tigges","full_name":"Tigges, Marcel"},{"last_name":"Scheller","first_name":"Leo","full_name":"Scheller, Leo"},{"last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","full_name":"Lang, Moritz"},{"full_name":"Fussenegger, Martin","last_name":"Fussenegger","first_name":"Martin"}],"citation":{"ieee":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","short":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019).","apa":"Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., & Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09974-5","ama":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09974-5","ista":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 10(1), 2013.","chicago":"Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5.","mla":"Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications, vol. 10, no. 1, 2013, Springer Nature, 2019, doi:10.1038/s41467-019-09974-5."},"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)"},"publication_status":"published","type":"journal_article","volume":10,"status":"public","article_processing_charge":"No","file":[{"creator":"dernst","checksum":"e214d3e4f8c81e35981583c4569b51b8","date_updated":"2020-07-14T12:47:31Z","access_level":"open_access","relation":"main_file","file_size":1191827,"date_created":"2019-05-20T07:33:54Z","file_name":"2019_NatureComm_Chassin.pdf","file_id":"6471","content_type":"application/pdf"}],"abstract":[{"text":"Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells.","lang":"eng"}],"has_accepted_license":"1","external_id":{"isi":["000466338600006"]},"scopus_import":"1","ddc":["570"],"oa":1,"date_created":"2019-05-19T21:59:14Z","issue":"1","quality_controlled":"1","oa_version":"Published Version","title":"A modular degron library for synthetic circuits in mammalian cells","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature"},{"related_material":{"record":[{"id":"9798","relation":"research_data","status":"public"},{"id":"9799","relation":"research_data","status":"public"}],"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008","relation":"supplementary_material"}]},"day":"03","date_updated":"2023-08-25T10:34:41Z","year":"2019","article_number":"0881","month":"04","date_published":"2019-04-03T00:00:00Z","_id":"6467","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"isi":1,"publication_status":"published","status":"public","volume":15,"type":"journal_article","citation":{"ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881."},"author":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"publication_identifier":{"issn":["17449561"],"eissn":["1744957X"]},"intvolume":" 15","language":[{"iso":"eng"}],"doi":"10.1098/rsbl.2018.0881","publication":"Biology Letters","scopus_import":"1","external_id":{"pmid":["31014191"],"isi":["000465405300010"]},"pmid":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"article_processing_charge":"No","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"oa_version":"Published Version","quality_controlled":"1","publisher":"Royal Society of London","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The distribution of epistasis on simple fitness landscapes","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2018.0881"}],"issue":"4","ec_funded":1,"date_created":"2019-05-19T21:59:15Z","oa":1,"article_type":"original"},{"scopus_import":"1","pmid":1,"external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"page":"2925–2947","abstract":[{"text":"Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. ","lang":"eng"}],"article_processing_charge":"No","title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","oa_version":"Published Version","quality_controlled":"1","issue":"11","main_file_link":[{"url":"https://doi.org/10.1113/JP277681","open_access":"1"}],"date_created":"2019-05-19T21:59:17Z","article_type":"original","oa":1,"day":"01","year":"2019","date_updated":"2023-08-25T10:34:15Z","date_published":"2019-06-01T00:00:00Z","month":"06","department":[{"_id":"GaNo"}],"isi":1,"_id":"6470","volume":597,"type":"journal_article","status":"public","publication_status":"published","citation":{"short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947.","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. Wiley. https://doi.org/10.1113/JP277681","ieee":"T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","chicago":"Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.","mla":"Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681.","ista":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947.","ama":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681"},"author":[{"first_name":"Tímea","last_name":"Éltes","full_name":"Éltes, Tímea"},{"full_name":"Szoboszlay, Miklos","last_name":"Szoboszlay","first_name":"Miklos"},{"first_name":"Margit Katalin","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","last_name":"Szigeti","full_name":"Szigeti, Margit Katalin","orcid":"0000-0001-9500-8758"},{"full_name":"Nusser, Zoltan","first_name":"Zoltan","last_name":"Nusser"}],"publication":"Journal of Physiology","doi":"10.1113/JP277681","intvolume":" 597","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00223751"],"eissn":["14697793"]}},{"publisher":"Springer","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Membership-based synthesis of linear hybrid automata","quality_controlled":"1","oa_version":"Published Version","ec_funded":1,"date_created":"2019-05-27T07:09:53Z","oa":1,"ddc":["000"],"scopus_import":"1","external_id":{"isi":["000491468000016"]},"file":[{"content_type":"application/pdf","file_id":"6817","file_name":"2019_CAV_GarciaSoto.pdf","date_created":"2019-08-14T11:05:30Z","file_size":674795,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:32Z","creator":"dernst","checksum":"1f1d61b83a151031745ef70a501da3d6"}],"abstract":[{"text":"We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements.","lang":"eng"}],"page":"297-314","has_accepted_license":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"article_processing_charge":"No","status":"public","volume":11561,"type":"conference","publication_status":"published","conference":{"location":"New York City, NY, USA","start_date":"2019-07-15","name":"CAV: Computer-Aided Verification","end_date":"2019-07-18"},"citation":{"ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.","apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16","ista":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314.","mla":"Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16."},"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)"},"keyword":["Synthesis","Linear hybrid automaton","Membership"],"author":[{"last_name":"Garcia Soto","first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","full_name":"Garcia Soto, Miriam"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"},{"id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","first_name":"Luka","last_name":"Zeleznik","full_name":"Zeleznik, Luka"}],"file_date_updated":"2020-07-14T12:47:32Z","doi":"10.1007/978-3-030-25540-4_16","publication":"31st International Conference on Computer-Aided Verification","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]},"intvolume":" 11561","language":[{"iso":"eng"}],"day":"12","year":"2019","date_updated":"2023-08-25T10:40:41Z","month":"07","date_published":"2019-07-12T00:00:00Z","alternative_title":["LNCS"],"_id":"6493","department":[{"_id":"ToHe"}],"isi":1},{"date_created":"2019-05-24T10:09:12Z","author":[{"full_name":"Koval, Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"},{"full_name":"Elizarov, Roman","last_name":"Elizarov","first_name":"Roman"}],"doi":"10.1145/3293883.3297000","publication":"Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming","publication_identifier":{"isbn":["9781450362252"]},"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"ACM Press","status":"public","title":"Lock-free channels for programming via communicating sequential processes","type":"conference_poster","quality_controlled":"1","conference":{"location":"Washington, NY, United States","start_date":"2019-02-16","name":"PPoPP: Principles and Practice of Parallel Programming","end_date":"2019-02-20"},"publication_status":"published","oa_version":"None","citation":{"ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming via communicating sequential processes. ACM Press, 2019, pp. 417–418.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels for programming via communicating sequential processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming (pp. 417–418). Washington, NY, United States: ACM Press. https://doi.org/10.1145/3293883.3297000","short":"N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM Press, 2019.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM Press,p.","ama":"Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via Communicating Sequential Processes. ACM Press; 2019:417-418. doi:10.1145/3293883.3297000","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels for Programming via Communicating Sequential Processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming. ACM Press, 2019. https://doi.org/10.1145/3293883.3297000.","mla":"Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming, ACM Press, 2019, pp. 417–18, doi:10.1145/3293883.3297000."},"month":"02","date_published":"2019-02-01T00:00:00Z","abstract":[{"lang":"eng","text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous channelis the common abstraction for communication between several processes, where senders and receivers perform a rendezvous handshake as a part of their protocol (senders wait for receivers and vice versa). Additionally to this, channels support the select expression. In this work, we present the first efficient lock-free channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations."}],"page":"417-418","_id":"6485","article_processing_charge":"No","isi":1,"department":[{"_id":"DaAl"}],"day":"01","external_id":{"isi":["000587604600044"]},"year":"2019","date_updated":"2023-08-25T10:41:20Z"},{"publication_status":"published","status":"public","volume":224,"type":"journal_article","citation":{"ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774.","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932","chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932.","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.","ieee":"Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932","short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774."},"author":[{"last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"last_name":"He","first_name":"P","full_name":"He, P"},{"full_name":"Ma, X","last_name":"Ma","first_name":"X"},{"full_name":"Yang, Z","last_name":"Yang","first_name":"Z"},{"full_name":"Pang, C","last_name":"Pang","first_name":"C"},{"last_name":"Yu","first_name":"J","full_name":"Yu, J"},{"full_name":"Wang, G","last_name":"Wang","first_name":"G"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xiao, G","first_name":"G","last_name":"Xiao"}],"file_date_updated":"2020-10-14T08:59:33Z","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"intvolume":" 224","language":[{"iso":"eng"}],"doi":"10.1111/nph.15932","publication":"New Phytologist","day":"01","date_updated":"2023-08-28T08:40:13Z","year":"2019","month":"10","date_published":"2019-10-01T00:00:00Z","_id":"6504","isi":1,"department":[{"_id":"JiFr"}],"quality_controlled":"1","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","title":"Auxin-mediated statolith production for root gravitropism","issue":"2","date_created":"2019-05-28T14:33:26Z","oa":1,"article_type":"original","ddc":["580"],"scopus_import":"1","external_id":{"isi":["000487184200024"],"pmid":["31111487"]},"pmid":1,"article_processing_charge":"No","has_accepted_license":"1","page":"761-774","file":[{"content_type":"application/pdf","file_id":"8661","success":1,"file_name":"2019_NewPhytologist_Zhang_accepted.pdf","date_created":"2020-10-14T08:59:33Z","file_size":1099061,"relation":"main_file","access_level":"open_access","date_updated":"2020-10-14T08:59:33Z","checksum":"6488243334538f5c39099a701cbf76b9","creator":"dernst"}],"abstract":[{"lang":"eng","text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response."}]},{"intvolume":" 4","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2058-5276"]},"publication":"Nature Microbiology","doi":"10.1038/s41564-019-0412-y","author":[{"first_name":"Lianet","last_name":"Noda-García","full_name":"Noda-García, Lianet"},{"full_name":"Davidi, Dan","first_name":"Dan","last_name":"Davidi"},{"first_name":"Elisa","last_name":"Korenblum","full_name":"Korenblum, Elisa"},{"first_name":"Assaf","last_name":"Elazar","full_name":"Elazar, Assaf"},{"last_name":"Putintseva","first_name":"Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","full_name":"Putintseva, Ekaterina"},{"last_name":"Aharoni","first_name":"Asaph","full_name":"Aharoni, Asaph"},{"full_name":"Tawfik, Dan S.","first_name":"Dan S.","last_name":"Tawfik"}],"citation":{"ieee":"L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230.","ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y.","mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y."},"publication_status":"published","volume":4,"type":"journal_article","status":"public","department":[{"_id":"FyKo"}],"isi":1,"_id":"6506","date_published":"2019-07-01T00:00:00Z","month":"07","date_updated":"2023-08-28T08:39:47Z","year":"2019","day":"01","article_type":"original","oa":1,"date_created":"2019-05-29T13:03:30Z","issue":"7","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/340828v2","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","abstract":[{"text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.","lang":"eng"}],"page":"1221–1230","external_id":{"isi":["000480348200017"]},"scopus_import":"1"},{"external_id":{"pmid":["31158432"],"isi":["000486094600037"]},"pmid":1,"scopus_import":"1","has_accepted_license":"1","abstract":[{"text":"Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies.","lang":"eng"}],"file":[{"file_name":"2019_Neuroscience_Maes.pdf","date_created":"2019-06-08T11:44:20Z","file_id":"6551","content_type":"application/pdf","date_updated":"2020-07-14T12:47:33Z","checksum":"553c9dbd39727fbed55ee991c51ca4d1","creator":"dernst","file_size":1779287,"access_level":"open_access","relation":"main_file"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020"},{"name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling","_id":"267F75D8-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges","oa_version":"Published Version","quality_controlled":"1","oa":1,"ddc":["570"],"article_type":"original","ec_funded":1,"date_created":"2019-06-05T13:16:24Z","year":"2019","date_updated":"2023-08-28T09:30:57Z","day":"10","_id":"6521","isi":1,"department":[{"_id":"SaSi"}],"month":"08","date_published":"2019-08-10T00:00:00Z","article_number":"134310","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)"},"citation":{"short":"M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019).","apa":"Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310","ieee":"M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience Letters, vol. 707. Elsevier, 2019.","chicago":"Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.","mla":"Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310, Elsevier, 2019, doi:10.1016/j.neulet.2019.134310.","ista":"Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310.","ama":"Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 2019;707. doi:10.1016/j.neulet.2019.134310"},"status":"public","type":"journal_article","volume":707,"publication_status":"published","doi":"10.1016/j.neulet.2019.134310","publication":"Neuroscience Letters","publication_identifier":{"issn":["0304-3940"]},"language":[{"iso":"eng"}],"intvolume":" 707","author":[{"orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E"},{"orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5297-733X","full_name":"Schulz, Rouven","last_name":"Schulz","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"file_date_updated":"2020-07-14T12:47:33Z"},{"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928"}],"title":"Tracing the origin of adult intestinal stem cells","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","oa_version":"Submitted Version","quality_controlled":"1","article_type":"original","oa":1,"date_created":"2019-06-02T21:59:14Z","pmid":1,"external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"scopus_import":"1","abstract":[{"text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property.","lang":"eng"}],"page":"107-111","article_processing_charge":"No","citation":{"apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111.","ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5.","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5.","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5","ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111."},"type":"journal_article","volume":570,"status":"public","publication_status":"published","publication":"Nature","doi":"10.1038/s41586-019-1212-5","intvolume":" 570","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"author":[{"last_name":"Guiu","first_name":"Jordi","full_name":"Guiu, Jordi"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"},{"first_name":"Shiro","last_name":"Yui","full_name":"Yui, Shiro"},{"full_name":"Demharter, Samuel","first_name":"Samuel","last_name":"Demharter"},{"full_name":"Ulyanchenko, Svetlana","first_name":"Svetlana","last_name":"Ulyanchenko"},{"last_name":"Maimets","first_name":"Martti","full_name":"Maimets, Martti"},{"full_name":"Jørgensen, Anne","first_name":"Anne","last_name":"Jørgensen"},{"full_name":"Perlman, Signe","last_name":"Perlman","first_name":"Signe"},{"full_name":"Lundvall, Lene","last_name":"Lundvall","first_name":"Lene"},{"full_name":"Mamsen, Linn Salto","first_name":"Linn Salto","last_name":"Mamsen"},{"last_name":"Larsen","first_name":"Agnete","full_name":"Larsen, Agnete"},{"full_name":"Olesen, Rasmus H.","first_name":"Rasmus H.","last_name":"Olesen"},{"first_name":"Claus Yding","last_name":"Andersen","full_name":"Andersen, Claus Yding"},{"full_name":"Thuesen, Lea Langhoff","last_name":"Thuesen","first_name":"Lea Langhoff"},{"last_name":"Hare","first_name":"Kristine Juul","full_name":"Hare, Kristine Juul"},{"last_name":"Pers","first_name":"Tune H.","full_name":"Pers, Tune H."},{"first_name":"Konstantin","last_name":"Khodosevich","full_name":"Khodosevich, Konstantin"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"last_name":"Jensen","first_name":"Kim B.","full_name":"Jensen, Kim B."}],"year":"2019","date_updated":"2023-08-28T09:30:23Z","day":"06","department":[{"_id":"EdHa"}],"isi":1,"_id":"6513","date_published":"2019-06-06T00:00:00Z","month":"06"}]