[{"publication_identifier":{"issn":["2058-5276"]},"month":"07","doi":"10.1038/s41564-019-0412-y","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000480348200017"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/340828v2"}],"isi":1,"quality_controlled":"1","author":[{"first_name":"Lianet","last_name":"Noda-García","full_name":"Noda-García, Lianet"},{"full_name":"Davidi, Dan","last_name":"Davidi","first_name":"Dan"},{"first_name":"Elisa","last_name":"Korenblum","full_name":"Korenblum, Elisa"},{"first_name":"Assaf","last_name":"Elazar","full_name":"Elazar, Assaf"},{"full_name":"Putintseva, Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","last_name":"Putintseva","first_name":"Ekaterina"},{"full_name":"Aharoni, Asaph","first_name":"Asaph","last_name":"Aharoni"},{"full_name":"Tawfik, Dan S.","first_name":"Dan S.","last_name":"Tawfik"}],"volume":4,"date_updated":"2023-08-28T08:39:47Z","date_created":"2019-05-29T13:03:30Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","citation":{"ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230.","ieee":"L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y","mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y."},"publication":"Nature Microbiology","page":"1221–1230","article_type":"original","issue":"7","abstract":[{"lang":"eng","text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele."}],"type":"journal_article","oa_version":"Preprint","_id":"6506","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 4","status":"public","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments"},{"article_number":"134310","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SaSi"}],"author":[{"orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E","full_name":"Maes, Margaret E"},{"first_name":"Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria"},{"id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X","first_name":"Rouven","last_name":"Schulz","full_name":"Schulz, Rouven"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"}],"date_created":"2019-06-05T13:16:24Z","date_updated":"2023-08-28T09:30:57Z","volume":707,"month":"08","publication_identifier":{"issn":["0304-3940"]},"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":["000486094600037"],"pmid":["31158432"]},"quality_controlled":"1","isi":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020","grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425"},{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"doi":"10.1016/j.neulet.2019.134310","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies.","lang":"eng"}],"_id":"6521","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges","ddc":["570"],"intvolume":" 707","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-08T11:44:20Z","checksum":"553c9dbd39727fbed55ee991c51ca4d1","relation":"main_file","file_id":"6551","content_type":"application/pdf","file_size":1779287,"creator":"dernst","file_name":"2019_Neuroscience_Maes.pdf","access_level":"open_access"}],"scopus_import":"1","day":"10","article_processing_charge":"No","has_accepted_license":"1","publication":"Neuroscience Letters","citation":{"chicago":"Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.","short":"M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019).","mla":"Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310, Elsevier, 2019, doi:10.1016/j.neulet.2019.134310.","apa":"Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310","ieee":"M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience Letters, vol. 707. Elsevier, 2019.","ista":"Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310.","ama":"Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 2019;707. doi:10.1016/j.neulet.2019.134310"},"article_type":"original","date_published":"2019-08-10T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41586-019-1212-5","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928"}],"external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"month":"06","volume":570,"date_created":"2019-06-02T21:59:14Z","date_updated":"2023-08-28T09:30:23Z","author":[{"full_name":"Guiu, Jordi","first_name":"Jordi","last_name":"Guiu"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"last_name":"Yui","first_name":"Shiro","full_name":"Yui, Shiro"},{"first_name":"Samuel","last_name":"Demharter","full_name":"Demharter, Samuel"},{"full_name":"Ulyanchenko, Svetlana","last_name":"Ulyanchenko","first_name":"Svetlana"},{"full_name":"Maimets, Martti","first_name":"Martti","last_name":"Maimets"},{"last_name":"Jørgensen","first_name":"Anne","full_name":"Jørgensen, Anne"},{"full_name":"Perlman, Signe","first_name":"Signe","last_name":"Perlman"},{"last_name":"Lundvall","first_name":"Lene","full_name":"Lundvall, Lene"},{"full_name":"Mamsen, Linn Salto","first_name":"Linn Salto","last_name":"Mamsen"},{"first_name":"Agnete","last_name":"Larsen","full_name":"Larsen, Agnete"},{"last_name":"Olesen","first_name":"Rasmus H.","full_name":"Olesen, Rasmus H."},{"last_name":"Andersen","first_name":"Claus Yding","full_name":"Andersen, Claus Yding"},{"last_name":"Thuesen","first_name":"Lea Langhoff","full_name":"Thuesen, Lea Langhoff"},{"full_name":"Hare, Kristine Juul","first_name":"Kristine Juul","last_name":"Hare"},{"full_name":"Pers, Tune H.","last_name":"Pers","first_name":"Tune H."},{"full_name":"Khodosevich, Konstantin","first_name":"Konstantin","last_name":"Khodosevich"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"first_name":"Kim B.","last_name":"Jensen","full_name":"Jensen, Kim B."}],"publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2019","date_published":"2019-06-06T00:00:00Z","page":"107-111","article_type":"original","citation":{"ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111.","ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5.","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5.","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111."},"publication":"Nature","article_processing_charge":"No","day":"06","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 570","status":"public","title":"Tracing the origin of adult intestinal stem cells","_id":"6513","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property.","lang":"eng"}],"type":"journal_article"},{"publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Elsevier","year":"2019","date_created":"2019-06-16T21:59:14Z","date_updated":"2023-08-28T09:39:22Z","volume":431,"author":[{"id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra-Madelaine","last_name":"Tichy","full_name":"Tichy, Alexandra-Madelaine"},{"first_name":"Elliot J.","last_name":"Gerrard","full_name":"Gerrard, Elliot J."},{"last_name":"Legrand","first_name":"Julien M.D.","full_name":"Legrand, Julien M.D."},{"full_name":"Hobbs, Robin M.","first_name":"Robin M.","last_name":"Hobbs"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"month":"08","publication_identifier":{"eissn":["10898638"],"issn":["00222836"]},"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/10.1101/583369v1"}],"external_id":{"isi":["000482872100002"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jmb.2019.05.033","type":"journal_article","abstract":[{"text":"Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology.","lang":"eng"}],"issue":"17","status":"public","title":"Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions","intvolume":" 431","_id":"6564","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","day":"09","article_processing_charge":"No","article_type":"original","page":"3046-3055","publication":"Journal of Molecular Biology","citation":{"chicago":"Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology. Elsevier, 2019. https://doi.org/10.1016/j.jmb.2019.05.033.","short":"A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055.","mla":"Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:10.1016/j.jmb.2019.05.033.","apa":"Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., & Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2019.05.033","ieee":"A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” Journal of Molecular Biology, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019.","ista":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.","ama":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 2019;431(17):3046-3055. doi:10.1016/j.jmb.2019.05.033"},"date_published":"2019-08-09T00:00:00Z"},{"publication":"Current Biology","citation":{"short":"S. Cremer, Current Biology 29 (2019) R458–R463.","mla":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology, vol. 29, no. 11, Elsevier, 2019, pp. R458–63, doi:10.1016/j.cub.2019.03.035.","chicago":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.03.035.","ama":"Cremer S. Social immunity in insects. Current Biology. 2019;29(11):R458-R463. doi:10.1016/j.cub.2019.03.035","apa":"Cremer, S. (2019). Social immunity in insects. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.03.035","ieee":"S. Cremer, “Social immunity in insects,” Current Biology, vol. 29, no. 11. Elsevier, pp. R458–R463, 2019.","ista":"Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463."},"article_type":"original","page":"R458-R463","date_published":"2019-06-03T00:00:00Z","scopus_import":"1","day":"03","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6552","title":"Social immunity in insects","status":"public","intvolume":" 29","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege). "}],"issue":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2019.03.035"}],"oa":1,"external_id":{"pmid":["31163158"],"isi":["000470902000023"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.cub.2019.03.035","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["09609822"]},"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Elsevier","author":[{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-06-09T21:59:10Z","date_updated":"2023-08-28T09:38:00Z","volume":29}]