[{"date_published":"2023-12-01T00:00:00Z","ddc":["570"],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"publication_status":"published","has_accepted_license":"1","intvolume":"        40","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage"}],"record":[{"status":"public","id":"14614","relation":"research_data"}]},"citation":{"mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>."},"external_id":{"pmid":["37988296"]},"status":"public","volume":40,"file_date_updated":"2024-01-02T11:39:38Z","date_created":"2023-11-27T16:14:37Z","month":"12","oa_version":"Published Version","type":"journal_article","date_updated":"2024-02-21T12:18:35Z","abstract":[{"text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"_id":"14613","acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","year":"2023","doi":"10.1093/molbev/msad245","quality_controlled":"1","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"issue":"12","language":[{"iso":"eng"}],"project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"},{"_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","name":"Mechanisms and Evolution of Reproductive Plasticity","grant_number":"ESP39 49461"}],"article_number":"msad245","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","author":[{"first_name":"Clementine","last_name":"Lasne","full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","orcid":"0000-0002-1197-8616"},{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Layana Franco, Lorena Alexandra","orcid":"0000-0002-1253-6297","id":"02814589-eb8f-11eb-b029-a70074f3f18f","first_name":"Lorena Alexandra","last_name":"Layana Franco"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","first_name":"Ariana","last_name":"Macon"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"day":"01","file":[{"file_name":"2023_MolecularBioEvo_Lasne.pdf","success":1,"file_size":8623505,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"14727","date_updated":"2024-01-02T11:39:38Z","checksum":"47c1c72fb499f26ea52d216b242208c8","date_created":"2024-01-02T11:39:38Z","access_level":"open_access"}],"publication":"Molecular Biology and Evolution","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"}],"pmid":1},{"has_accepted_license":"1","publication_status":"published","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2021-06-19T00:00:00Z","ddc":["610"],"external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"status":"public","citation":{"ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, Oxford University Press , 2021, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021)."},"date_updated":"2023-08-14T08:03:06Z","abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}],"month":"06","oa_version":"Published Version","type":"journal_article","date_created":"2021-10-21T07:49:12Z","file_date_updated":"2022-05-06T09:47:18Z","year":"2021","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","_id":"10167","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"quality_controlled":"1","doi":"10.1093/molbev/msab178","project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"language":[{"iso":"eng"}],"isi":1,"keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"file":[{"date_updated":"2022-05-06T09:47:18Z","file_id":"11352","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","date_created":"2022-05-06T09:47:18Z","access_level":"open_access","success":1,"file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","content_type":"application/pdf","relation":"main_file","file_size":1008594,"creator":"dernst"}],"day":"19","author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi"},{"last_name":"Moldovan","first_name":"Mikhail A.","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","orcid":"0000-0002-8876-6494","full_name":"Moldovan, Mikhail A."},{"last_name":"Picard","first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","pmid":1,"department":[{"_id":"BeVi"}],"publisher":"Oxford University Press ","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","scopus_import":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Molecular Biology and Evolution"},{"pmid":1,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Oxford University Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","scopus_import":"1","publication":"Molecular biology and evolution","day":"01","author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","first_name":"Gemma"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"issue":"3","isi":1,"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"quality_controlled":"1","doi":"10.1093/molbev/msy246","year":"2019","_id":"6089","abstract":[{"lang":"eng","text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general."}],"date_updated":"2024-02-21T13:59:17Z","type":"journal_article","oa_version":"Submitted Version","month":"03","page":"500-515","date_created":"2019-03-10T22:59:19Z","volume":36,"status":"public","external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"citation":{"ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular biology and evolution</i>. 2019;36(3):500-515. doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>.","apa":"Fraisse, C., Puixeu Sala, G., &#38; Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” <i>Molecular biology and evolution</i>, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515."},"related_material":{"record":[{"status":"public","id":"5757","relation":"popular_science"}]},"intvolume":"        36","oa":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"date_published":"2019-03-01T00:00:00Z"},{"oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2016-03-01T00:00:00Z","ddc":["576"],"status":"public","external_id":{"pmid":["26609077"]},"intvolume":"        33","related_material":{"record":[{"relation":"research_data","status":"public","id":"9719"}]},"citation":{"ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782."},"page":"770-782","type":"journal_article","month":"03","oa_version":"Published Version","date_updated":"2023-09-05T13:46:05Z","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"volume":33,"file_date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-18T13:18:10Z","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","year":"2016","_id":"5749","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"pubrep_id":"587","doi":"10.1093/molbev/msv270","quality_controlled":"1","issue":"3","language":[{"iso":"eng"}],"author":[{"full_name":"Wielgoss, Sébastien","last_name":"Wielgoss","first_name":"Sébastien"},{"last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Bischofberger","first_name":"Anna M.","full_name":"Bischofberger, Anna M."},{"first_name":"Alex R.","last_name":"Hall","full_name":"Hall, Alex R."}],"file":[{"access_level":"open_access","date_created":"2018-12-18T13:21:45Z","checksum":"47d9010690b6c5c17f2ac830cc63ac5c","date_updated":"2020-07-14T12:47:10Z","file_id":"5750","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":634037,"file_name":"2016_MolBiolEvol_Wielgoss.pdf"}],"day":"01","title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","publisher":"Oxford University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"CaGu"}],"pmid":1,"publication":"Molecular Biology and Evolution","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"scopus_import":"1","article_processing_charge":"No"},{"author":[{"first_name":"Barry","last_name":"Hall","full_name":"Hall, Barry"},{"full_name":"Acar, Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","first_name":"Hande","last_name":"Acar"},{"last_name":"Nandipati","first_name":"Anna","full_name":"Nandipati, Anna"},{"full_name":"Barlow, Miriam","first_name":"Miriam","last_name":"Barlow"}],"day":"01","title":"Growth rates made easy","publist_id":"5193","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoBo"}],"pmid":1,"publication":"Molecular Biology and Evolution","article_type":"original","article_processing_charge":"No","scopus_import":"1","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"doi":"10.1093/molbev/mst187","quality_controlled":"1","issue":"1","language":[{"iso":"eng"}],"page":"232 - 238","type":"journal_article","month":"01","oa_version":"None","abstract":[{"text":"In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates.","lang":"eng"}],"date_updated":"2022-06-07T11:08:13Z","volume":31,"date_created":"2018-12-11T11:54:37Z","year":"2014","_id":"1902","publication_status":"published","date_published":"2014-01-01T00:00:00Z","status":"public","external_id":{"pmid":["24170494"]},"intvolume":"        31","citation":{"short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/molbev/mst187\">https://doi.org/10.1093/molbev/mst187</a>.","ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” <i>Molecular Biology and Evolution</i>, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014.","apa":"Hall, B., Acar, H., Nandipati, A., &#38; Barlow, M. (2014). Growth rates made easy. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst187\">https://doi.org/10.1093/molbev/mst187</a>","ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238.","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:<a href=\"https://doi.org/10.1093/molbev/mst187\">10.1093/molbev/mst187</a>.","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. <i>Molecular Biology and Evolution</i>. 2014;31(1):232-238. doi:<a href=\"https://doi.org/10.1093/molbev/mst187\">10.1093/molbev/mst187</a>"}},{"title":"Interracial rDNA variation in the grasshopper Podisma Pedestris","publist_id":"2728","author":[{"last_name":"Dallas","first_name":"John","full_name":"Dallas, John"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Dover","first_name":"Gabriel","full_name":"Dover, Gabriel"}],"day":"01","publication":"Molecular Biology and Evolution","article_processing_charge":"No","article_type":"original","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publisher":"Oxford University Press","doi":"10.1093/oxfordjournals.molbev.a040528","quality_controlled":"1","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"language":[{"iso":"eng"}],"issue":"6","volume":5,"date_created":"2018-12-11T12:04:28Z","page":"660 - 674","abstract":[{"text":"The structural basis and distribution of variation in the ribosomal RNA multigene family ( rDNA) was studied in the X0 and neo-XY races of the Alpine grasshopper Podisma pedestris. Restriction-enzyme sites in the gene region of the rDNA repeat were identical in both races and homogeneous in the rDNA family. In contrast, sites for Hind111 and PvuII in the intergenic spacer (IGS) region showed racial divergence and variation within the rDNA family and within populations. A short insertion in the 28s gene region was present in a minority of repeats in both races. The distributions of four polymorphic IGS Hind111 fragments were surveyed at 43 locations in and around the hybrid zone. Two of these fragments appear to be distributed as clines, one of which is strongly associated with the neo-X chromosome. The other two fragments show considerable variation in both races and show negative association. It is proposed that the clinally distributed variants arise from processes of amplification and divergence of IGS sequence variants and that such \r\ndivergence may contribute to hybrid inviability. ","lang":"eng"}],"date_updated":"2022-02-08T13:20:51Z","oa_version":"None","month":"07","type":"journal_article","_id":"3655","acknowledgement":"We thank Dr. W. Kunz for providing the clones pLm6F4 and pLm4Bll and Dr. D. Glover for the clone pDm238. We thank Brian Curtis for his photographic assistance. ","year":"1988","date_published":"1988-07-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://academic.oup.com/mbe/article/5/6/660/1044340"}],"oa":1,"publication_status":"published","extern":"1","intvolume":"         5","citation":{"ieee":"J. Dallas, N. H. Barton, and G. Dover, “Interracial rDNA variation in the grasshopper Podisma Pedestris,” <i>Molecular Biology and Evolution</i>, vol. 5, no. 6. Oxford University Press, pp. 660–674, 1988.","chicago":"Dallas, John, Nicholas H Barton, and Gabriel Dover. “Interracial RDNA Variation in the Grasshopper Podisma Pedestris.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 1988. <a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a040528\">https://doi.org/10.1093/oxfordjournals.molbev.a040528</a>.","short":"J. Dallas, N.H. Barton, G. Dover, Molecular Biology and Evolution 5 (1988) 660–674.","ama":"Dallas J, Barton NH, Dover G. Interracial rDNA variation in the grasshopper Podisma Pedestris. <i>Molecular Biology and Evolution</i>. 1988;5(6):660-674. doi:<a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a040528\">10.1093/oxfordjournals.molbev.a040528</a>","mla":"Dallas, John, et al. “Interracial RDNA Variation in the Grasshopper Podisma Pedestris.” <i>Molecular Biology and Evolution</i>, vol. 5, no. 6, Oxford University Press, 1988, pp. 660–74, doi:<a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a040528\">10.1093/oxfordjournals.molbev.a040528</a>.","ista":"Dallas J, Barton NH, Dover G. 1988. Interracial rDNA variation in the grasshopper Podisma Pedestris. Molecular Biology and Evolution. 5(6), 660–674.","apa":"Dallas, J., Barton, N. H., &#38; Dover, G. (1988). Interracial rDNA variation in the grasshopper Podisma Pedestris. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a040528\">https://doi.org/10.1093/oxfordjournals.molbev.a040528</a>"},"status":"public"}]