[{"publisher":"ACM","publication_status":"published","_id":"1393","oa_version":"Published Version","type":"conference","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"year":"2014","month":"05","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:50:22Z","scopus_import":1,"main_file_link":[{"url":"https://doi.org/10.1145/2593882.2593900","open_access":"1"}],"abstract":[{"lang":"eng","text":"Probabilistic programs are usual functional or imperative programs with two added constructs: (1) the ability to draw values at random from distributions, and (2) the ability to condition values of variables in a program via observations. Models from diverse application areas such as computer vision, coding theory, cryptographic protocols, biology and reliability analysis can be written as probabilistic programs. Probabilistic inference is the problem of computing an explicit representation of the probability distribution implicitly specified by a probabilistic program. Depending on the application, the desired output from inference may vary-we may want to estimate the expected value of some function f with respect to the distribution, or the mode of the distribution, or simply a set of samples drawn from the distribution. In this paper, we describe connections this research area called \\Probabilistic Programming&quot; has with programming languages and software engineering, and this includes language design, and the static and dynamic analysis of programs. We survey current state of the art and speculate on promising directions for future research."}],"status":"public","author":[{"full_name":"Gordon, Andrew","last_name":"Gordon","first_name":"Andrew"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Aditya","full_name":"Nori, Aditya","last_name":"Nori"},{"first_name":"Sriram","last_name":"Rajamani","full_name":"Rajamani, Sriram"}],"oa":1,"quality_controlled":"1","conference":{"name":"FOSE: Future of Software Engineering","start_date":"2014-05-31","end_date":"2014-06-07","location":"Hyderabad, India"},"date_created":"2018-12-11T11:51:45Z","citation":{"ista":"Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming. Proceedings of the on Future of Software Engineering. FOSE: Future of Software Engineering, 167–181.","short":"A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181.","ieee":"A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in <i>Proceedings of the on Future of Software Engineering</i>, Hyderabad, India, 2014, pp. 167–181.","ama":"Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: <i>Proceedings of the on Future of Software Engineering</i>. ACM; 2014:167-181. doi:<a href=\"https://doi.org/10.1145/2593882.2593900\">10.1145/2593882.2593900</a>","chicago":"Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In <i>Proceedings of the on Future of Software Engineering</i>, 167–81. ACM, 2014. <a href=\"https://doi.org/10.1145/2593882.2593900\">https://doi.org/10.1145/2593882.2593900</a>.","apa":"Gordon, A., Henzinger, T. A., Nori, A., &#38; Rajamani, S. (2014). Probabilistic programming. In <i>Proceedings of the on Future of Software Engineering</i> (pp. 167–181). Hyderabad, India: ACM. <a href=\"https://doi.org/10.1145/2593882.2593900\">https://doi.org/10.1145/2593882.2593900</a>","mla":"Gordon, Andrew, et al. “Probabilistic Programming.” <i>Proceedings of the on Future of Software Engineering</i>, ACM, 2014, pp. 167–81, doi:<a href=\"https://doi.org/10.1145/2593882.2593900\">10.1145/2593882.2593900</a>."},"page":"167 - 181","publist_id":"5816","title":"Probabilistic programming","day":"31","publication":"Proceedings of the on Future of Software Engineering","date_published":"2014-05-31T00:00:00Z","doi":"10.1145/2593882.2593900","article_processing_charge":"No","ec_funded":1},{"title":"Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus","department":[{"_id":"SyCr"}],"year":"2014","month":"02","page":"131","publist_id":"5814","publication_identifier":{"issn":["2663-337X"]},"_id":"1395","publication_status":"published","alternative_title":["ISTA Thesis"],"citation":{"ama":"Konrad M. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. 2014.","ieee":"M. Konrad, “Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology Austria, 2014.","ista":"Konrad M. 2014. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","short":"M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology Austria, 2014.","apa":"Konrad, M. (2014). <i>Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus</i>. Institute of Science and Technology Austria.","chicago":"Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and Technology Austria, 2014.","mla":"Konrad, Matthias. <i>Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus</i>. Institute of Science and Technology Austria, 2014."},"date_created":"2018-12-11T11:51:46Z","oa_version":"None","type":"dissertation","supervisor":[{"full_name":"Cremer, Sylvia M","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M"}],"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Konrad","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"}],"article_processing_charge":"No","status":"public","date_published":"2014-02-01T00:00:00Z","abstract":[{"text":"In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi.  The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants.","lang":"eng"}],"degree_awarded":"PhD","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-07T11:38:56Z","day":"01"},{"status":"public","article_processing_charge":"No","author":[{"last_name":"Marhavá","full_name":"Marhavá, Petra","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2014-12-01T00:00:00Z","degree_awarded":"PhD","abstract":[{"text":"Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"day":"01","date_updated":"2023-09-07T11:39:38Z","department":[{"_id":"JiFr"}],"title":"Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana","page":"90","publist_id":"5805","month":"12","year":"2014","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","alternative_title":["ISTA Thesis"],"_id":"1402","type":"dissertation","oa_version":"None","date_created":"2018-12-11T11:51:49Z","citation":{"mla":"Marhavá, Petra. <i>Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2014.","chicago":"Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.","apa":"Marhavá, P. (2014). <i>Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana</i>. Institute of Science and Technology Austria.","short":"P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.","ista":"Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ieee":"P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.","ama":"Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014."},"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}]},{"status":"public","author":[{"last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2014-08-01T00:00:00Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2282"},{"status":"public","relation":"part_of_dissertation","id":"2950"},{"relation":"part_of_dissertation","status":"public","id":"3373"}]},"abstract":[{"text":"A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models  the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"01","date_updated":"2023-10-17T12:16:58Z","department":[{"_id":"CaHe"}],"title":"Forces driving epithelial spreading in zebrafish epiboly","page":"91","publist_id":"5804","month":"08","year":"2014","publication_status":"published","alternative_title":["IST Austria Thesis"],"_id":"1403","oa_version":"None","type":"dissertation","date_created":"2018-12-11T11:51:49Z","acknowledged_ssus":[{"_id":"SSU"}],"citation":{"apa":"Behrndt, M. (2014). <i>Forces driving epithelial spreading in zebrafish epiboly</i>. IST Austria.","chicago":"Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.” IST Austria, 2014.","mla":"Behrndt, Martin. <i>Forces Driving Epithelial Spreading in Zebrafish Epiboly</i>. IST Austria, 2014.","ama":"Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014.","ieee":"M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST Austria, 2014.","ista":"Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly. IST Austria.","short":"M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST Austria, 2014."},"publisher":"IST Austria","supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}]},{"publisher":"IST Austria","supervisor":[{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M","last_name":"Cremer","first_name":"Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","type":"dissertation","date_created":"2018-12-11T11:51:49Z","citation":{"mla":"Stock, Miriam. <i>Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants</i>. IST Austria, 2014.","chicago":"Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants.” IST Austria, 2014.","apa":"Stock, M. (2014). <i>Evolution of a fungal pathogen towards individual versus social immunity in ants</i>. IST Austria.","short":"M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants, IST Austria, 2014.","ista":"Stock M. 2014. Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria.","ieee":"M. Stock, “Evolution of a fungal pathogen towards individual versus social immunity in ants,” IST Austria, 2014.","ama":"Stock M. Evolution of a fungal pathogen towards individual versus social immunity in ants. 2014."},"alternative_title":["IST Austria Thesis"],"publication_status":"published","_id":"1404","publist_id":"5803","page":"101","year":"2014","month":"04","department":[{"_id":"SyCr"}],"title":"Evolution of a fungal pathogen towards individual versus social immunity in ants","acknowledgement":"This work was funded by the DFG and the ERC.","day":"01","date_updated":"2021-01-12T06:50:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The co-evolution of hosts and pathogens is characterized by continuous adaptations of both parties. Pathogens of social insects need to adapt towards disease defences at two levels: 1) individual immunity of each colony member consisting of behavioural defence strategies as well as humoral and cellular immune responses and 2) social immunity that is collectively performed by all group members comprising behavioural, physiological and organisational defence strategies.\r\n\r\nTo disentangle the selection pressure on pathogens by the collective versus individual level of disease defence in social insects, we performed an evolution experiment using the Argentine Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution over 10 serial host passages to two different evolution host treatments: (1) only individual host immunity in a single host treatment, and (2) simultaneously acting individual and social immunity in a social host treatment, in which an exposed ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen evolution experiment, the 6 Metarhizium spp. strains were characterised concerning conidiospore size killing rates in singly and socially reared ants, their competitiveness under coinfecting conditions and their influence on ant behaviour. We analysed how the ancestral atrain mixture changed in conidiospere size, killing rate and strain composition dependent on host treatment (single or social hosts) during 10 passages and found that killing rate and conidiospere size of the pathogen increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting the evolved strain mixtures that evolved under either the single or social host treatment under both single and social current rearing conditions in a full factorial design experiment revealed that the additional collective defences in insect societies add new selection pressure for their coevolving pathogens that compromise their ability to adapt to its host at the group level. To our knowledge, this is the first study directly measuring the influence of social immunity on pathogen evolution."}],"date_published":"2014-04-01T00:00:00Z","status":"public","author":[{"last_name":"Stock","full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"}]},{"doi":"10.1016/j.cell.2014.01.029","article_processing_charge":"No","pmid":1,"day":"13","publication":"Cell","volume":156,"date_published":"2014-03-13T00:00:00Z","intvolume":"       156","page":"1286-1297","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","oa":1,"quality_controlled":"1","citation":{"mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014."},"date_created":"2021-06-04T12:00:16Z","status":"public","author":[{"first_name":"Jason T.","last_name":"Huff","full_name":"Huff, Jason T."},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:22:36Z","extern":"1","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"abstract":[{"lang":"eng","text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints."}],"year":"2014","month":"03","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"article_type":"original","department":[{"_id":"DaZi"}],"publisher":"Elsevier","publication_status":"published","external_id":{"pmid":["24630728"]},"_id":"9458","issue":"6","oa_version":"Published Version","type":"journal_article"},{"month":"11","year":"2014","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_type":"original","department":[{"_id":"DaZi"}],"publisher":"National Academy of Sciences","_id":"9479","issue":"45","external_id":{"pmid":["25344531"]},"publication_status":"published","oa_version":"Published Version","type":"journal_article","author":[{"full_name":"Mérai, Zsuzsanna","last_name":"Mérai","first_name":"Zsuzsanna"},{"full_name":"Chumak, Nina","last_name":"Chumak","first_name":"Nina"},{"full_name":"García-Aguilar, Marcelina","last_name":"García-Aguilar","first_name":"Marcelina"},{"first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh"},{"last_name":"Nishimura","full_name":"Nishimura, Toshiro","first_name":"Toshiro"},{"first_name":"Vera K.","full_name":"Schoft, Vera K.","last_name":"Schoft"},{"first_name":"János","last_name":"Bindics","full_name":"Bindics, János"},{"first_name":"Lucyna","last_name":"Ślusarz","full_name":"Ślusarz, Lucyna"},{"first_name":"Stéphanie","full_name":"Arnoux, Stéphanie","last_name":"Arnoux"},{"first_name":"Susanne","last_name":"Opravil","full_name":"Opravil, Susanne"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"last_name":"Tamaru","full_name":"Tamaru, Hisashi","first_name":"Hisashi"}],"status":"public","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:23:26Z","extern":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1418564111"}],"page":"16166-16171","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","oa":1,"quality_controlled":"1","citation":{"apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014."},"date_created":"2021-06-07T07:23:43Z","doi":"10.1073/pnas.1418564111","article_processing_charge":"No","pmid":1,"volume":111,"publication":"Proceedings of the National Academy of Sciences","day":"11","date_published":"2014-11-11T00:00:00Z","intvolume":"       111"},{"date_published":"2014-05-04T00:00:00Z","intvolume":"        19","pmid":1,"day":"04","publication":"Trends in Plant Science","volume":19,"article_processing_charge":"No","doi":"10.1016/j.tplants.2014.01.014","quality_controlled":"1","citation":{"ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>."},"date_created":"2021-06-07T14:38:09Z","title":"DNA methylation as a system of plant genomic immunity","page":"320-326","extern":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"date_updated":"2021-12-14T08:24:48Z","status":"public","author":[{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"publication_status":"published","external_id":{"pmid":["24618094 "]},"issue":"5","_id":"9519","type":"journal_article","oa_version":"None","publisher":"Elsevier","article_type":"review","department":[{"_id":"DaZi"}],"year":"2014","month":"05","publication_identifier":{"issn":["1360-1385"],"eissn":["1878-4372"]}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"14","date_updated":"2023-02-23T10:24:07Z","date_published":"2014-11-14T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2004"}]},"doi":"10.1371/journal.pone.0111430.s006","status":"public","article_processing_charge":"No","author":[{"full_name":"Lovrics, Anna","last_name":"Lovrics","first_name":"Anna"},{"last_name":"Gao","full_name":"Gao, Yu","first_name":"Yu"},{"first_name":"Bianka","last_name":"Juhász","full_name":"Juhász, Bianka"},{"first_name":"István","last_name":"Bock","full_name":"Bock, István"},{"first_name":"Helen M.","full_name":"Byrne, Helen M.","last_name":"Byrne"},{"last_name":"Dinnyés","full_name":"Dinnyés, András","first_name":"András"},{"first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","full_name":"Kovács, Krisztián","last_name":"Kovács"}],"publisher":"Public Library of Science","_id":"9722","type":"research_data_reference","oa_version":"Published Version","date_created":"2021-07-26T14:35:00Z","citation":{"ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>.","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>."},"month":"11","year":"2014","department":[{"_id":"JoCs"}],"title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2"},{"oa_version":"Published Version","type":"research_data_reference","citation":{"apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Detailed Proofs for “The Time Scale of Evolutionary Innovation.”</i> Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014)."},"date_created":"2021-07-28T08:13:57Z","_id":"9739","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"title":"Detailed proofs for “The time scale of evolutionary innovation”","year":"2014","month":"09","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2039"}]},"date_published":"2014-09-11T00:00:00Z","day":"11","date_updated":"2023-02-23T10:25:37Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"first_name":"Ben","last_name":"Adlam","full_name":"Adlam, Ben"},{"last_name":"Novak","full_name":"Novak, Martin","first_name":"Martin"}],"article_processing_charge":"No","doi":"10.1371/journal.pcbi.1003818.s001"},{"publisher":"Dryad","oa":1,"citation":{"ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>"},"date_created":"2021-07-28T08:38:40Z","oa_version":"Published Version","type":"research_data_reference","_id":"9740","month":"11","year":"2014","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","department":[{"_id":"SyCr"}],"date_updated":"2023-02-23T10:23:32Z","day":"13","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1993"}]},"date_published":"2014-11-13T00:00:00Z","doi":"10.5061/dryad.vm0vc","author":[{"full_name":"Konrad, Matthias","last_name":"Konrad","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","full_name":"Tragust, Simon","last_name":"Tragust"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","status":"public"},{"day":"21","date_updated":"2023-02-23T10:25:31Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"id":"2036","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.85dn7","open_access":"1"}],"abstract":[{"lang":"eng","text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments."}],"date_published":"2014-08-21T00:00:00Z","doi":"10.5061/dryad.85dn7","status":"public","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator"},{"full_name":"Colegrave, Nick","last_name":"Colegrave","first_name":"Nick"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"article_processing_charge":"No","publisher":"Dryad","oa":1,"type":"research_data_reference","oa_version":"Published Version","citation":{"mla":"Lagator, Mato, et al. <i>Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>.","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","short":"M. Lagator, N. Colegrave, P. Neve, (2014).","ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, <a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>."},"date_created":"2021-07-28T08:48:06Z","_id":"9741","month":"08","year":"2014","department":[{"_id":"CaGu"}],"title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses"},{"doi":"10.5061/dryad.s42n1","status":"public","article_processing_charge":"No","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato"},{"last_name":"Morgan","full_name":"Morgan, Andrew","first_name":"Andrew"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"17","date_updated":"2023-02-23T10:27:31Z","date_published":"2014-04-17T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.s42n1","open_access":"1"}],"related_material":{"record":[{"id":"2083","status":"public","relation":"used_in_publication"}]},"abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"year":"2014","month":"04","department":[{"_id":"CaGu"}],"title":"Data from: Role of sex and migration in adaptation to sink environments","oa":1,"publisher":"Dryad","_id":"9747","oa_version":"Published Version","type":"research_data_reference","date_created":"2021-07-28T15:32:55Z","citation":{"mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>."}},{"abstract":[{"lang":"eng","text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2277"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.246qg"}],"date_published":"2014-11-07T00:00:00Z","date_updated":"2023-02-23T10:35:57Z","day":"07","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Kristina","full_name":"Simmons, Kristina","last_name":"Simmons"},{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Homann, Jan","last_name":"Homann"},{"first_name":"Heather","full_name":"Yee, Heather","last_name":"Yee"},{"first_name":"Stephanie","full_name":"Palmer, Stephanie","last_name":"Palmer"},{"full_name":"Nelson, Philip","last_name":"Nelson","first_name":"Philip"},{"last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay","first_name":"Vijay"}],"status":"public","doi":"10.5061/dryad.246qg","date_created":"2021-07-30T08:13:52Z","citation":{"mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>"},"oa_version":"Published Version","type":"research_data_reference","_id":"9752","publisher":"Dryad","oa":1,"title":"Data from: Transformation of stimulus correlations by the retina","department":[{"_id":"GaTk"}],"year":"2014","month":"11"},{"publisher":"Dryad","oa":1,"date_created":"2021-07-30T08:24:11Z","citation":{"mla":"Tragust, Simon, et al. <i>Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2014). Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.” Dryad, 2014.","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>."},"type":"research_data_reference","oa_version":"Published Version","_id":"9753","year":"2014","month":"10","title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","department":[{"_id":"SyCr"}],"date_updated":"2023-02-23T10:36:17Z","day":"08","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.nc0gc"}],"related_material":{"record":[{"id":"2284","status":"public","relation":"used_in_publication"}]},"date_published":"2014-10-08T00:00:00Z","doi":"10.5061/dryad.nc0gc","author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","last_name":"Ugelvig"},{"full_name":"Chapuisat, Michel","last_name":"Chapuisat","first_name":"Michel"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"article_processing_charge":"No","status":"public"},{"_id":"9888","citation":{"ama":"Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>","ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting information, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>.","ieee":"S. Wolf <i>et al.</i>, “Supporting information.” Public Library of Science, 2014.","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014).","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., &#38; Osborne, J. (2014). Supporting information. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">https://doi.org/10.1371/journal.pone.0103989.s003</a>","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">https://doi.org/10.1371/journal.pone.0103989.s003</a>.","mla":"Wolf, Stephan, et al. <i>Supporting Information</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>."},"date_created":"2021-08-11T14:17:53Z","oa_version":"Published Version","type":"research_data_reference","publisher":"Public Library of Science","title":"Supporting information","department":[{"_id":"SyCr"}],"month":"08","year":"2014","abstract":[{"lang":"eng","text":"Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2086"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:27:38Z","day":"06","author":[{"full_name":"Wolf, Stephan","last_name":"Wolf","first_name":"Stephan"},{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"full_name":"Lim, Ka","last_name":"Lim","first_name":"Ka"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","full_name":"Pull, Christopher","last_name":"Pull","orcid":"0000-0003-1122-3982"},{"full_name":"Clark, Suzanne","last_name":"Clark","first_name":"Suzanne"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"},{"first_name":"Juliet","full_name":"Osborne, Juliet","last_name":"Osborne"}],"article_processing_charge":"No","status":"public","doi":"10.1371/journal.pone.0103989.s003"},{"page":"1775-1791","title":"Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","citation":{"mla":"Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” <i>Evolution</i>, vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:<a href=\"https://doi.org/10.1111/evo.12373\">10.1111/evo.12373</a>.","apa":"Dhar, R., Bergmiller, T., &#38; Wagner, A. (2014). Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12373\">https://doi.org/10.1111/evo.12373</a>","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” <i>Evolution</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/evo.12373\">https://doi.org/10.1111/evo.12373</a>.","ama":"Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. <i>Evolution</i>. 2014;68(6):1775-1791. doi:<a href=\"https://doi.org/10.1111/evo.12373\">10.1111/evo.12373</a>","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 68(6), 1775–1791.","short":"R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,” <i>Evolution</i>, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014."},"date_created":"2021-08-17T09:03:09Z","quality_controlled":"1","doi":"10.1111/evo.12373","article_processing_charge":"No","volume":68,"day":"03","publication":"Evolution","acknowledgement":"We thank the Functional Genomics Center Zurich for its service in generating sequencing data, M. Ackermann and E. Hayden for helpful discussions, A. de Visser for comments on earlier versions of this manuscript, and M. Moser for help with quantitative PCR. This work was supported by Swiss National Science Foundation (grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in Systems Biology at the University of Zurich. RD acknowledges support from the Forschungskredit program of the University of Zurich. The authors declare no conflict of interest.","pmid":1,"intvolume":"        68","date_published":"2014-06-03T00:00:00Z","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"year":"2014","month":"06","department":[{"_id":"CaGu"}],"article_type":"original","publisher":"Wiley","oa_version":"None","type":"journal_article","issue":"6","_id":"9931","publication_status":"published","external_id":{"pmid":["24495000"]},"author":[{"full_name":"Dhar, Riddhiman","last_name":"Dhar","first_name":"Riddhiman"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","full_name":"Bergmiller, Tobias"},{"last_name":"Wagner","full_name":"Wagner, Andreas","first_name":"Andreas"}],"status":"public","date_updated":"2023-02-23T14:13:27Z","language":[{"iso":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region."}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9932"}]},"scopus_import":"1"},{"department":[{"_id":"CaGu"}],"title":"Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","year":"2014","month":"01","_id":"9932","type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-17T09:11:40Z","citation":{"ama":"Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes, Dryad, <a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>.","short":"R. Dhar, T. Bergmiller, A. Wagner, (2014).","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.” Dryad, 2014.","mla":"Dhar, Riddhiman, et al. <i>Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>.","apa":"Dhar, R., Bergmiller, T., &#38; Wagner, A. (2014). Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Dryad. <a href=\"https://doi.org/10.5061/dryad.jc402\">https://doi.org/10.5061/dryad.jc402</a>","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.jc402\">https://doi.org/10.5061/dryad.jc402</a>."},"oa":1,"publisher":"Dryad","status":"public","article_processing_charge":"No","author":[{"full_name":"Dhar, Riddhiman","last_name":"Dhar","first_name":"Riddhiman"},{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"last_name":"Wagner","full_name":"Wagner, Andreas","first_name":"Andreas"}],"doi":"10.5061/dryad.jc402","date_published":"2014-01-27T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.jc402","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9931"}]},"abstract":[{"text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","date_updated":"2023-02-23T14:13:24Z"},{"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"month":"12","year":"2013","article_type":"original","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"published","_id":"2443","issue":"4","type":"journal_article","oa_version":"Published Version","status":"public","author":[{"last_name":"Simon","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","full_name":"Kubeš, Martin","last_name":"Kubeš"},{"last_name":"Baster","full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Dobrev, Petre","last_name":"Dobrev","first_name":"Petre"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-07T11:12:32Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.12437"}],"abstract":[{"lang":"eng","text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery."}],"page":"1034 - 1048","publist_id":"4460","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:57:41Z","citation":{"mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>"},"doi":"10.1111/nph.12437","article_processing_charge":"No","ec_funded":1,"publication":"New Phytologist","acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","day":"01","volume":200,"date_published":"2013-12-01T00:00:00Z","intvolume":"       200"},{"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Jakub","last_name":"Ła̧Cki","full_name":"Ła̧Cki, Jakub"}],"status":"public","date_updated":"2020-08-11T10:09:47Z","series_title":"Lecture Notes in Computer Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.0084"}],"scopus_import":1,"year":"2013","month":"07","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","type":"conference","oa_version":"Preprint","_id":"2444","external_id":{"arxiv":["1304.0084"]},"alternative_title":["LNCS"],"publication_status":"published","doi":"10.1007/978-3-642-39799-8_36","ec_funded":1,"volume":8044,"day":"01","intvolume":"      8044","date_published":"2013-07-01T00:00:00Z","page":"543 - 558","publist_id":"4459","title":"Faster algorithms for Markov decision processes with low treewidth","oa":1,"date_created":"2018-12-11T11:57:42Z","citation":{"ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.","ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>","chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>.","apa":"Chatterjee, K., &#38; Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>","mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. <i>Faster Algorithms for Markov Decision Processes with Low Treewidth</i>. Vol. 8044, Springer, 2013, pp. 543–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>."},"conference":{"end_date":"2013-07-19","location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification","start_date":"2013-07-13"},"arxiv":1,"quality_controlled":"1"}]