[{"file_date_updated":"2022-08-05T06:29:18Z","publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Elsevier","acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","year":"2022","pmid":1,"date_created":"2022-05-04T06:22:06Z","date_updated":"2023-08-03T07:05:36Z","volume":32,"author":[{"full_name":"Nicolas, William J.","first_name":"William J.","last_name":"Nicolas"},{"full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler"},{"last_name":"Dutka","first_name":"Przemysław","full_name":"Dutka, Przemysław"},{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"},{"full_name":"Jensen, Grant","first_name":"Grant","last_name":"Jensen"},{"first_name":"Elliot","last_name":"Meyerowitz","full_name":"Meyerowitz, Elliot"}],"month":"06","publication_identifier":{"issn":["0960-9822"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000822399200019"],"pmid":["35508170"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2022.04.024","type":"journal_article","abstract":[{"text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.","lang":"eng"}],"issue":"11","title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","ddc":["570"],"status":"public","intvolume":" 32","_id":"11351","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_size":12827717,"content_type":"application/pdf","file_name":"2022_CurrentBiology_Nicolas.pdf","access_level":"open_access","date_created":"2022-08-05T06:29:18Z","date_updated":"2022-08-05T06:29:18Z","success":1,"checksum":"af3f24d97c016d844df237abef987639","file_id":"11730","relation":"main_file"}],"oa_version":"Published Version","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","day":"06","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"P2375-2389","publication":"Current Biology","citation":{"mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” Current Biology, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:10.1016/j.cub.2022.04.024.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” Current Biology. Elsevier, 2022. https://doi.org/10.1016/j.cub.2022.04.024.","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 2022;32(11):P2375-2389. doi:10.1016/j.cub.2022.04.024","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., & Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2022.04.024","ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” Current Biology, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022."},"date_published":"2022-06-06T00:00:00Z"},{"type":"journal_article","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"issue":"8","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","ddc":["510","570"],"status":"public","intvolume":" 84","_id":"11447","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"11455","date_updated":"2022-06-20T07:51:32Z","date_created":"2022-06-20T07:51:32Z","checksum":"05a1fe7d10914a00c2bca9b447993a65","success":1,"file_name":"2022_BulletinMathBiology_Saona.pdf","access_level":"open_access","file_size":463025,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"scopus_import":"1","day":"17","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","publication":"Bulletin of Mathematical Biology","citation":{"ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.","apa":"Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022. https://doi.org/10.1007/s11538-022-01029-z.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022)."},"date_published":"2022-06-17T00:00:00Z","article_number":"74","file_date_updated":"2022-06-20T07:51:32Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"year":"2022","acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","date_updated":"2023-08-03T07:20:53Z","date_created":"2022-06-17T16:16:15Z","volume":84,"author":[{"last_name":"Saona Urmeneta","first_name":"Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","first_name":"Kseniia","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia"}],"related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"month":"06","publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"},{"name":"Evolutionary analysis of gene regulation","grant_number":"I05127","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000812509800001"]},"language":[{"iso":"eng"}],"doi":"10.1007/s11538-022-01029-z"},{"file_date_updated":"2023-02-02T08:20:29Z","article_number":"20210203","volume":377,"date_created":"2022-07-08T11:41:56Z","date_updated":"2023-08-03T11:55:42Z","author":[{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Royal Society of London","publication_status":"published","year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2021.0203","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000812317300005"]},"issue":"1856","abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","access_level":"open_access","file_size":920304,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12479","date_created":"2023-02-02T08:20:29Z","date_updated":"2023-02-02T08:20:29Z","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","success":1}],"intvolume":" 377","ddc":["570"],"title":"Inversions and parallel evolution","status":"public","_id":"11546","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","date_published":"2022-08-01T00:00:00Z","article_type":"original","citation":{"short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1856). doi:10.1098/rstb.2021.0203","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H. (2022). Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203."},"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences"},{"volume":5,"date_created":"2023-01-16T09:48:19Z","date_updated":"2023-08-04T09:25:59Z","author":[{"full_name":"Muhia, Mary W","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","last_name":"Muhia","first_name":"Mary W"},{"first_name":"PingAn","last_name":"YuanXiang","full_name":"YuanXiang, PingAn"},{"full_name":"Sedlacik, Jan","last_name":"Sedlacik","first_name":"Jan"},{"last_name":"Schwarz","first_name":"Jürgen R.","full_name":"Schwarz, Jürgen R."},{"last_name":"Heisler","first_name":"Frank F.","full_name":"Heisler, Frank F."},{"full_name":"Gromova, Kira V.","first_name":"Kira V.","last_name":"Gromova"},{"full_name":"Thies, Edda","first_name":"Edda","last_name":"Thies"},{"last_name":"Breiden","first_name":"Petra","full_name":"Breiden, Petra"},{"full_name":"Pechmann, Yvonne","last_name":"Pechmann","first_name":"Yvonne"},{"first_name":"Michael R.","last_name":"Kreutz","full_name":"Kreutz, Michael R."},{"full_name":"Kneussel, Matthias","last_name":"Kneussel","first_name":"Matthias"}],"publisher":"Springer Nature","department":[{"_id":"PreCl"}],"publication_status":"published","year":"2022","acknowledgement":"The authors are grateful to the UKE Animal Facilities (Hamburg) for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision of animal care. We thank Dr. Franco Lombino for critically reading the manuscript and for helpful discussion. This work was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1) and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding enabled and organized by Projekt DEAL.","file_date_updated":"2023-01-27T08:23:46Z","article_number":"589","language":[{"iso":"eng"}],"doi":"10.1038/s42003-022-03446-1","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000811777900003"]},"publication_identifier":{"issn":["2399-3642"]},"month":"06","file":[{"relation":"main_file","file_id":"12417","date_created":"2023-01-27T08:23:46Z","date_updated":"2023-01-27T08:23:46Z","checksum":"bd95be1e77090208b79bc45ea8785d0b","success":1,"file_name":"2022_CommBiology_Muhia.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3968356,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 5","ddc":["570"],"status":"public","title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12224","abstract":[{"text":"Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane receptor trafficking. However, its influence on intrinsic brain activity and corresponding behavioral processes remains unclear. Here we show that murine Mkln1 knockout causes non-habituating locomotor activity, increased exploratory drive, and decreased locomotor response to amphetamine. Muskelin deficiency impairs social novelty detection while promoting the retention of spatial reference memory and fear extinction recall. This is strongly mirrored in either weaker or stronger resting-state functional connectivity between critical circuits mediating locomotor exploration and cognition. We show that Mkln1 deletion alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated synaptic transmission but selective impairment in synaptic potentiation maintenance. We identify muskelin at excitatory synapses and highlight its role in regulating dendritic spine actin stability. Our findings point to aberrant spine actin modulation and changes in glutamatergic synaptic function as critical mechanisms that contribute to the neurobehavioral phenotype arising from Mkln1 ablation.","lang":"eng"}],"type":"journal_article","date_published":"2022-06-15T00:00:00Z","article_type":"original","citation":{"ama":"Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 2022;5. doi:10.1038/s42003-022-03446-1","ista":"Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 5, 589.","ieee":"M. W. Muhia et al., “Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes,” Communications Biology, vol. 5. Springer Nature, 2022.","apa":"Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F., Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03446-1","mla":"Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” Communications Biology, vol. 5, 589, Springer Nature, 2022, doi:10.1038/s42003-022-03446-1.","short":"M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova, E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology 5 (2022).","chicago":"Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03446-1."},"publication":"Communications Biology","article_processing_charge":"No","has_accepted_license":"1","day":"15","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"scopus_import":"1"},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"date_published":"2022-11-01T00:00:00Z","citation":{"apa":"Stankowski, S. (2022). Digest: On the origin of a possible hybrid species. Evolution. Wiley. https://doi.org/10.1111/evo.14632","ieee":"S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution, vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.","ista":"Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution. 76(11), 2784–2785.","ama":"Stankowski S. Digest: On the origin of a possible hybrid species. Evolution. 2022;76(11):2784-2785. doi:10.1111/evo.14632","chicago":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.","short":"S. Stankowski, Evolution 76 (2022) 2784–2785.","mla":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution, vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632."},"publication":"Evolution","page":"2784-2785","article_type":"original","issue":"11","abstract":[{"lang":"eng","text":"Hybrid speciation—the origin of new species resulting from the hybridization of genetically divergent lineages—was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego found genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a broader range of host plants than either of its putative parents."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2022_Evolution_Stankowski.pdf","creator":"dernst","file_size":287282,"content_type":"application/pdf","file_id":"12425","relation":"main_file","success":1,"checksum":"4c0f05083b414ac0323a1b9ee1abc275","date_created":"2023-01-27T11:28:38Z","date_updated":"2023-01-27T11:28:38Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12234","intvolume":" 76","status":"public","title":"Digest: On the origin of a possible hybrid species","ddc":["570"],"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"11","doi":"10.1111/evo.14632","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000855751600001"]},"quality_controlled":"1","isi":1,"file_date_updated":"2023-01-27T11:28:38Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"volume":76,"date_updated":"2023-08-04T09:35:48Z","date_created":"2023-01-16T09:50:48Z","year":"2022","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published"},{"file":[{"checksum":"defd8a4bea61cf00a3c88d4a30e2728c","success":1,"date_created":"2023-01-30T08:45:35Z","date_updated":"2023-01-30T08:45:35Z","relation":"main_file","file_id":"12439","file_size":2990581,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2022_Evolution_Koch.pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12247","title":"Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution","status":"public","ddc":["570"],"intvolume":" 76","abstract":[{"lang":"eng","text":"Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence."}],"issue":"10","type":"journal_article","date_published":"2022-10-01T00:00:00Z","publication":"Evolution","citation":{"chicago":"Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.","short":"E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 76 (2022) 2332–2346.","mla":"Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022, pp. 2332–46, doi:10.1111/evo.14602.","apa":"Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602","ieee":"E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution,” Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.","ista":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 76(10), 2332–2346.","ama":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 2022;76(10):2332-2346. doi:10.1111/evo.14602"},"article_type":"original","page":"2332-2346","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"author":[{"full_name":"Koch, Eva L.","first_name":"Eva L.","last_name":"Koch"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13066"}]},"date_created":"2023-01-16T09:54:15Z","date_updated":"2023-08-04T09:42:11Z","volume":76,"acknowledgement":"We thank everyone who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson for their contributions, with inversions and shell shape respectively. KJ was funded by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B. and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS). R.K.B. was also funded by the Natural Environment Research Council and the Swedish Research Council Vetenskapsrådet.","year":"2022","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","file_date_updated":"2023-01-30T08:45:35Z","doi":"10.1111/evo.14602","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["35994296"],"isi":["000848449100001"]},"oa":1,"isi":1,"quality_controlled":"1","month":"10","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]}},{"date_published":"2022-09-01T00:00:00Z","publication":"Molecular Systems Biology","citation":{"short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022).","mla":"Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” Molecular Systems Biology, vol. 18, no. 9, e10490, Embo Press, 2022, doi:10.15252/msb.202110490.","chicago":"Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” Molecular Systems Biology. Embo Press, 2022. https://doi.org/10.15252/msb.202110490.","ama":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 2022;18(9). doi:10.15252/msb.202110490","apa":"Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., & Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.202110490","ieee":"A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M. T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic response,” Molecular Systems Biology, vol. 18, no. 9. Embo Press, 2022.","ista":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 18(9), e10490."},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12446","checksum":"8b1d8f5ea20c8408acf466435fb6ae01","success":1,"date_updated":"2023-01-30T09:49:55Z","date_created":"2023-01-30T09:49:55Z","access_level":"open_access","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","file_size":1098812,"content_type":"application/pdf","creator":"dernst"}],"_id":"12261","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","intvolume":" 18","abstract":[{"text":"Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.","lang":"eng"}],"issue":"9","type":"journal_article","doi":"10.15252/msb.202110490","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000856482800001"]},"oa":1,"isi":1,"quality_controlled":"1","month":"09","publication_identifier":{"eissn":["1744-4292"]},"author":[{"full_name":"Angermayr, Andreas","orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","last_name":"Angermayr","first_name":"Andreas"},{"last_name":"Pang","first_name":"Tin Yau","full_name":"Pang, Tin Yau"},{"full_name":"Chevereau, Guillaume","last_name":"Chevereau","first_name":"Guillaume"},{"full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch"},{"last_name":"Lercher","first_name":"Martin J","full_name":"Lercher, Martin J"},{"first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"date_created":"2023-01-16T09:58:34Z","date_updated":"2023-08-04T09:51:49Z","volume":18,"acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","year":"2022","publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"Embo Press","file_date_updated":"2023-01-30T09:49:55Z","article_number":"e10490"},{"date_published":"2022-04-11T00:00:00Z","article_type":"original","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","citation":{"ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1848). doi:10.1098/rstb.2021.0009","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848. The Royal Society, 2022.","apa":"Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009."},"day":"11","article_processing_charge":"No","has_accepted_license":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11719","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","success":1,"date_created":"2022-08-02T06:14:32Z","date_updated":"2022-08-02T06:14:32Z","access_level":"open_access","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","file_size":1349672,"content_type":"application/pdf","creator":"dernst"}],"title":"The response of a metapopulation to a changing environment","ddc":["570"],"status":"public","intvolume":" 377","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10787","abstract":[{"lang":"eng","text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’."}],"issue":"1848","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2021.0009","isi":1,"quality_controlled":"1","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"oa":1,"month":"04","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"date_created":"2022-02-21T16:08:10Z","date_updated":"2024-01-26T12:00:53Z","volume":377,"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya","first_name":"Oluwafunmilola O"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14711"}]},"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"year":"2022","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","pmid":1,"file_date_updated":"2022-08-02T06:14:32Z"},{"_id":"9387","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Two linked loci under mutation-selection balance and Muller’s ratchet","status":"public","intvolume":" 524","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift."}],"publication":"Journal of Theoretical Biology","citation":{"chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729.","short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729, Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729.","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology, vol. 524. Elsevier , 2021.","apa":"Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729","ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524. doi:10.1016/j.jtbi.2021.110729"},"article_type":"original","date_published":"2021-04-24T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"day":"24","article_processing_charge":"No","acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","year":"2021","publication_status":"published","publisher":"Elsevier ","department":[{"_id":"GradSch"}],"author":[{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","first_name":"Kseniia","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia"},{"last_name":"Neretina","first_name":"Tatiana Yu.","full_name":"Neretina, Tatiana Yu."},{"last_name":"Kondrashov","first_name":"Alexey S.","full_name":"Kondrashov, Alexey S."}],"date_updated":"2023-08-08T13:32:40Z","date_created":"2021-05-12T05:58:42Z","volume":524,"article_number":"110729","oa":1,"external_id":{"isi":["000659161500002"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.jtbi.2021.110729","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["0022-5193"]}},{"keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"08","article_type":"original","citation":{"ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","ieee":"M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021.","apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9","ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9.","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021)."},"publication":"Communications Biology","date_published":"2021-03-08T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700."}],"intvolume":" 4","ddc":["570"],"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","status":"public","_id":"10310","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"10318","date_updated":"2021-11-19T15:09:18Z","date_created":"2021-11-19T15:09:18Z","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1,"file_name":"2021_CommBio_Çoruh.pdf","access_level":"open_access","file_size":6030261,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","publication_identifier":{"issn":["2399-3642"]},"month":"03","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000627440700001"],"pmid":["33686186"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42003-021-01808-9","article_number":"304","file_date_updated":"2021-11-19T15:09:18Z","department":[{"_id":"LeSa"}],"publisher":"Springer ","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","volume":4,"date_updated":"2023-08-14T11:51:19Z","date_created":"2021-11-19T11:37:29Z","author":[{"id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022","first_name":"Mehmet Orkun","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun"},{"full_name":"Frank, Anna","first_name":"Anna","last_name":"Frank"},{"last_name":"Tanaka","first_name":"Hideaki","full_name":"Tanaka, Hideaki"},{"last_name":"Kawamoto","first_name":"Akihiro","full_name":"Kawamoto, Akihiro"},{"first_name":"Eithar","last_name":"El-Mohsnawy","full_name":"El-Mohsnawy, Eithar"},{"full_name":"Kato, Takayuki","first_name":"Takayuki","last_name":"Kato"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"full_name":"Gerle, Christoph","last_name":"Gerle","first_name":"Christoph"},{"full_name":"Nowaczyk, Marc M.","first_name":"Marc M.","last_name":"Nowaczyk"},{"first_name":"Genji","last_name":"Kurisu","full_name":"Kurisu, Genji"}]},{"page":"2051-2064.e8","article_type":"original","citation":{"mla":"Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” Current Biology, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:10.1016/j.cub.2021.02.043.","short":"S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8.","chicago":"Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.043.","ama":"Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 2021;31(10):2051-2064.e8. doi:10.1016/j.cub.2021.02.043","ista":"Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8.","apa":"Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2021.02.043","ieee":"S. Stahnke et al., “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” Current Biology, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021."},"publication":"Current Biology","date_published":"2021-05-24T00:00:00Z","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","article_processing_charge":"No","day":"24","intvolume":" 31","title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10834","oa_version":"Preprint","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis."}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["33711252"],"isi":["000654652200002"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2020.03.24.005835","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2021.02.043","publication_identifier":{"issn":["0960-9822"]},"month":"05","publisher":"Elsevier","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).","volume":31,"date_created":"2022-03-08T07:51:04Z","date_updated":"2023-08-17T07:01:14Z","author":[{"full_name":"Stahnke, Stephanie","last_name":"Stahnke","first_name":"Stephanie"},{"full_name":"Döring, Hermann","first_name":"Hermann","last_name":"Döring"},{"first_name":"Charly","last_name":"Kusch","full_name":"Kusch, Charly"},{"full_name":"de Gorter, David J.J.","last_name":"de Gorter","first_name":"David J.J."},{"full_name":"Dütting, Sebastian","last_name":"Dütting","first_name":"Sebastian"},{"full_name":"Guledani, Aleks","last_name":"Guledani","first_name":"Aleks"},{"full_name":"Pleines, Irina","last_name":"Pleines","first_name":"Irina"},{"full_name":"Schnoor, Michael","last_name":"Schnoor","first_name":"Michael"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Geffers","first_name":"Robert","full_name":"Geffers, Robert"},{"full_name":"Rohde, Manfred","last_name":"Rohde","first_name":"Manfred"},{"first_name":"Mathias","last_name":"Müsken","full_name":"Müsken, Mathias"},{"full_name":"Kage, Frieda","last_name":"Kage","first_name":"Frieda"},{"full_name":"Steffen, Anika","first_name":"Anika","last_name":"Steffen"},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"},{"first_name":"Bernhard","last_name":"Nieswandt","full_name":"Nieswandt, Bernhard"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"},{"full_name":"Stradal, Theresia E.B.","last_name":"Stradal","first_name":"Theresia E.B."}]},{"status":"public","title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","ddc":["570"],"intvolume":" 75","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9252","file":[{"access_level":"open_access","file_name":"2021_Evolution_Szep.pdf","creator":"kschuh","file_size":734102,"content_type":"application/pdf","file_id":"9886","relation":"main_file","success":1,"checksum":"b90fb5767d623602046fed03725e16ca","date_created":"2021-08-11T13:39:19Z","date_updated":"2021-08-11T13:39:19Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments."}],"issue":"5","article_type":"original","page":"1030-1045","publication":"Evolution","citation":{"chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14210.","short":"E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045.","mla":"Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:10.1111/evo.14210.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley. https://doi.org/10.1111/evo.14210","ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","ama":"Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210"},"date_published":"2021-05-01T00:00:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2021","acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","date_created":"2021-03-20T08:22:10Z","date_updated":"2023-09-05T15:44:06Z","volume":75,"author":[{"last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"id":"13062","relation":"research_data","status":"public"}]},"file_date_updated":"2021-08-11T13:39:19Z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000636966300001"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.14210","month":"05","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]}},{"volume":75,"date_updated":"2023-09-05T15:44:33Z","date_created":"2021-05-06T04:34:47Z","author":[{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"first_name":"Maria R.","last_name":"Servedio","full_name":"Servedio, Maria R."},{"first_name":"Carole M.","last_name":"Smadja","full_name":"Smadja, Carole M."},{"first_name":"Claudia","last_name":"Bank","full_name":"Bank, Claudia"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Samuel M.","last_name":"Flaxman","full_name":"Flaxman, Samuel M."},{"first_name":"Tatiana","last_name":"Giraud","full_name":"Giraud, Tatiana"},{"first_name":"Robin","last_name":"Hopkins","full_name":"Hopkins, Robin"},{"first_name":"Erica L.","last_name":"Larson","full_name":"Larson, Erica L."},{"last_name":"Maan","first_name":"Martine E.","full_name":"Maan, Martine E."},{"last_name":"Meier","first_name":"Joana","full_name":"Meier, Joana"},{"full_name":"Merrill, Richard","first_name":"Richard","last_name":"Merrill"},{"full_name":"Noor, Mohamed A. F.","first_name":"Mohamed A. F.","last_name":"Noor"},{"full_name":"Ortiz‐Barrientos, Daniel","first_name":"Daniel","last_name":"Ortiz‐Barrientos"},{"full_name":"Qvarnström, Anna","last_name":"Qvarnström","first_name":"Anna"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","year":"2021","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1111/evo.14235","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235"}],"external_id":{"isi":["000647224000001"]},"issue":"5","abstract":[{"lang":"eng","text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 75","title":"Homage to Felsenstein 1981, or why are there so few/many species?","status":"public","_id":"9374","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"19","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"date_published":"2021-04-19T00:00:00Z","page":"978-988","article_type":"original","citation":{"chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235.","short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.","mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235.","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235","ieee":"R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988.","ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235"},"publication":"Evolution"},{"title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments","status":"public","intvolume":" 18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8402","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins."}],"article_type":"original","publication":"BMC Biology","citation":{"ama":"Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 2020;18. doi:10.1186/s12915-019-0733-6","ista":"Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 18, 2.","ieee":"H. Rampelt et al., “The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments,” BMC Biology, vol. 18. Springer Nature, 2020.","apa":"Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C., … Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0733-6","mla":"Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” BMC Biology, vol. 18, 2, Springer Nature, 2020, doi:10.1186/s12915-019-0733-6.","short":"H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou, M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).","chicago":"Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil, Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” BMC Biology. Springer Nature, 2020. https://doi.org/10.1186/s12915-019-0733-6."},"date_published":"2020-01-06T00:00:00Z","keyword":["Biotechnology","Plant Science","General Biochemistry","Genetics and Molecular Biology","Developmental Biology","Cell Biology","Physiology","Ecology","Evolution","Behavior and Systematics","Structural Biology","General Agricultural and Biological Sciences"],"day":"06","article_processing_charge":"No","publication_status":"published","publisher":"Springer Nature","year":"2020","pmid":1,"date_created":"2020-09-17T10:26:53Z","date_updated":"2021-01-12T08:19:02Z","volume":18,"author":[{"full_name":"Rampelt, Heike","first_name":"Heike","last_name":"Rampelt"},{"last_name":"Sucec","first_name":"Iva","full_name":"Sucec, Iva"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"last_name":"Horten","first_name":"Patrick","full_name":"Horten, Patrick"},{"first_name":"Inge","last_name":"Perschil","full_name":"Perschil, Inge"},{"first_name":"Jean-Claude","last_name":"Martinou","full_name":"Martinou, Jean-Claude"},{"full_name":"van der Laan, Martin","first_name":"Martin","last_name":"van der Laan"},{"full_name":"Wiedemann, Nils","last_name":"Wiedemann","first_name":"Nils"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"},{"full_name":"Pfanner, Nikolaus","first_name":"Nikolaus","last_name":"Pfanner"}],"article_number":"2","extern":"1","quality_controlled":"1","oa":1,"external_id":{"pmid":["31907035"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12915-019-0733-6"}],"language":[{"iso":"eng"}],"doi":"10.1186/s12915-019-0733-6","month":"01","publication_identifier":{"issn":["1741-7007"]}},{"page":"2676-2686.e3","article_type":"original","citation":{"ieee":"E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.","apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.","ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084.","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084."},"publication":"Current Biology","date_published":"2019-08-19T00:00:00Z","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","article_processing_charge":"No","day":"19","intvolume":" 29","status":"public","title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12190","oa_version":"None","type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor."}],"quality_controlled":"1","external_id":{"pmid":["31378616"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2019.06.084","publication_identifier":{"issn":["0960-9822"]},"month":"08","publisher":"Elsevier BV","department":[{"_id":"XiFe"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","year":"2019","volume":29,"date_updated":"2023-05-08T10:54:54Z","date_created":"2023-01-16T09:16:33Z","author":[{"first_name":"Emma J.","last_name":"Lawrence","full_name":"Lawrence, Emma J."},{"full_name":"Gao, Hongbo","first_name":"Hongbo","last_name":"Gao"},{"full_name":"Tock, Andrew J.","first_name":"Andrew J.","last_name":"Tock"},{"first_name":"Christophe","last_name":"Lambing","full_name":"Lambing, Christophe"},{"full_name":"Blackwell, Alexander R.","first_name":"Alexander R.","last_name":"Blackwell"},{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng"},{"last_name":"Henderson","first_name":"Ian R.","full_name":"Henderson, Ian R."}],"extern":"1"},{"_id":"11074","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","title":"Chromothripsis","status":"public","intvolume":" 25","oa_version":"Published Version","type":"journal_article","issue":"10","publication":"Current Biology","citation":{"ista":"Hatch EM, Hetzer M. 2015. Chromothripsis. Current Biology. 25(10), PR397-R399.","ieee":"E. M. Hatch and M. Hetzer, “Chromothripsis,” Current Biology, vol. 25, no. 10. Elsevier, pp. PR397-R399, 2015.","apa":"Hatch, E. M., & Hetzer, M. (2015). Chromothripsis. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2015.02.033","ama":"Hatch EM, Hetzer M. Chromothripsis. Current Biology. 2015;25(10):PR397-R399. doi:10.1016/j.cub.2015.02.033","chicago":"Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology. Elsevier, 2015. https://doi.org/10.1016/j.cub.2015.02.033.","mla":"Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology, vol. 25, no. 10, Elsevier, 2015, pp. PR397-R399, doi:10.1016/j.cub.2015.02.033.","short":"E.M. Hatch, M. Hetzer, Current Biology 25 (2015) PR397-R399."},"article_type":"original","page":"PR397-R399","date_published":"2015-05-18T00:00:00Z","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"day":"18","article_processing_charge":"No","year":"2015","pmid":1,"publication_status":"published","publisher":"Elsevier","author":[{"last_name":"Hatch","first_name":"Emily M.","full_name":"Hatch, Emily M."},{"full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"date_updated":"2022-07-18T08:34:34Z","date_created":"2022-04-07T07:49:00Z","volume":25,"extern":"1","external_id":{"pmid":["25989073"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2015.02.033"}],"quality_controlled":"1","doi":"10.1016/j.cub.2015.02.033","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["0960-9822"]}},{"publication_identifier":{"issn":["0960-9822"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1016/s0960-9822(02)00927-2","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/S0960-9822(02)00927-2","open_access":"1"}],"external_id":{"pmid":["12121625"]},"extern":"1","volume":12,"date_updated":"2022-07-18T08:58:05Z","date_created":"2022-04-07T07:57:31Z","author":[{"full_name":"Bilbao-Cortés, Daniel","last_name":"Bilbao-Cortés","first_name":"Daniel"},{"full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"HETZER"},{"full_name":"Längst, Gernot","last_name":"Längst","first_name":"Gernot"},{"first_name":"Peter B.","last_name":"Becker","full_name":"Becker, Peter B."},{"first_name":"Iain W.","last_name":"Mattaj","full_name":"Mattaj, Iain W."}],"publisher":"Elsevier BV","publication_status":"published","pmid":1,"year":"2002","article_processing_charge":"No","day":"09","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","date_published":"2002-07-09T00:00:00Z","page":"1151-1156","article_type":"letter_note","citation":{"ama":"Bilbao-Cortés D, Hetzer M, Längst G, Becker PB, Mattaj IW. Ran binds to chromatin by two distinct mechanisms. Current Biology. 2002;12(13):1151-1156. doi:10.1016/s0960-9822(02)00927-2","apa":"Bilbao-Cortés, D., Hetzer, M., Längst, G., Becker, P. B., & Mattaj, I. W. (2002). Ran binds to chromatin by two distinct mechanisms. Current Biology. Elsevier BV. https://doi.org/10.1016/s0960-9822(02)00927-2","ieee":"D. Bilbao-Cortés, M. Hetzer, G. Längst, P. B. Becker, and I. W. Mattaj, “Ran binds to chromatin by two distinct mechanisms,” Current Biology, vol. 12, no. 13. Elsevier BV, pp. 1151–1156, 2002.","ista":"Bilbao-Cortés D, Hetzer M, Längst G, Becker PB, Mattaj IW. 2002. Ran binds to chromatin by two distinct mechanisms. Current Biology. 12(13), 1151–1156.","short":"D. Bilbao-Cortés, M. Hetzer, G. Längst, P.B. Becker, I.W. Mattaj, Current Biology 12 (2002) 1151–1156.","mla":"Bilbao-Cortés, Daniel, et al. “Ran Binds to Chromatin by Two Distinct Mechanisms.” Current Biology, vol. 12, no. 13, Elsevier BV, 2002, pp. 1151–56, doi:10.1016/s0960-9822(02)00927-2.","chicago":"Bilbao-Cortés, Daniel, Martin Hetzer, Gernot Längst, Peter B. Becker, and Iain W. Mattaj. “Ran Binds to Chromatin by Two Distinct Mechanisms.” Current Biology. Elsevier BV, 2002. https://doi.org/10.1016/s0960-9822(02)00927-2."},"publication":"Current Biology","issue":"13","abstract":[{"text":"Ran GTPase plays important roles in nucleocytoplasmic transport in interphase [1, 2] and in both spindle formation and nuclear envelope (NE) assembly during mitosis [3, 4, 5]. The latter functions rely on the presence of high local concentrations of GTP-bound Ran near mitotic chromatin [3, 4, 5]. RanGTP localization has been proposed to result from the association of Ran's GDP/GTP exchange factor, RCC1, with chromatin [6, 7, 8, 9], but Ran is shown here to bind directly to chromatin in two modes, either dependent or independent of RCC1, and, where bound, to increase the affinity of chromatin for NE membranes. We propose that the Ran binding capacity of chromatin contributes to localized spindle and NE assembly.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 12","status":"public","title":"Ran binds to chromatin by two distinct mechanisms","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11124"}]