--- _id: '9864' abstract: - lang: eng text: Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima. article_processing_charge: No author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Tomasz full_name: Włodarski, Tomasz last_name: Włodarski - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1 apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1 chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1. ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016. ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1. mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family. The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1. short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016). date_created: 2021-08-10T08:29:47Z date_published: 2016-12-14T00:00:00Z date_updated: 2023-09-20T11:56:33Z day: '14' department: - _id: NiBa - _id: JoBo doi: 10.6084/m9.figshare.4315652.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.4315652.v1 month: '12' oa: 1 oa_version: Published Version publisher: The Royal Society related_material: record: - id: '1077' relation: used_in_publication status: public status: public title: Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '5554' abstract: - lang: eng text: "The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution." article_processing_charge: No author: - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 citation: ama: Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43 apa: Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43 chicago: Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43. ieee: M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. ista: Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43. mla: Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43. short: M. Tugrul, (2016). contributor: - contributor_type: researcher first_name: Magdalena id: 2C023F40-F248-11E8-B48F-1D18A9856A87 last_name: Steinrück - contributor_type: researcher first_name: Fabienne id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87 last_name: Jesse datarep_id: '43' date_created: 2018-12-12T12:31:30Z date_published: 2016-05-12T00:00:00Z date_updated: 2024-02-21T13:50:34Z day: '12' department: - _id: NiBa - _id: JoBo doi: 10.15479/AT:ISTA:43 file: - access_level: open_access checksum: 1fc0a10bb7ce110fcb5e1fbe3cf0c4e2 content_type: application/zip creator: system date_created: 2018-12-12T13:03:08Z date_updated: 2020-07-14T12:47:01Z file_id: '5626' file_name: IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip file_size: 1123495 relation: main_file file_date_updated: 2020-07-14T12:47:01Z has_accepted_license: '1' keyword: - RNAP binding - de novo promoter evolution - lac promoter license: https://creativecommons.org/publicdomain/zero/1.0/ month: '05' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '1131' relation: used_in_publication status: public status: public title: Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1902' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Barry full_name: Hall, Barry last_name: Hall - first_name: Hande full_name: Acar, Hande id: 2DDF136A-F248-11E8-B48F-1D18A9856A87 last_name: Acar orcid: 0000-0003-1986-9753 - first_name: Anna full_name: Nandipati, Anna last_name: Nandipati - first_name: Miriam full_name: Barlow, Miriam last_name: Barlow citation: ama: Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187 apa: Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187 chicago: Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187. ieee: B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014. 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.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187. short: B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238. date_created: 2018-12-11T11:54:37Z date_published: 2014-01-01T00:00:00Z date_updated: 2022-06-07T11:08:13Z day: '01' department: - _id: JoBo doi: 10.1093/molbev/mst187 external_id: pmid: - '24170494' intvolume: ' 31' issue: '1' language: - iso: eng month: '01' oa_version: None page: 232 - 238 pmid: 1 publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press publist_id: '5193' quality_controlled: '1' scopus_import: '1' status: public title: Growth rates made easy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2014' ... --- _id: '2042' abstract: - lang: eng text: 'Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here.' article_number: '663' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663 apa: Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-15-663 chicago: Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics. BioMed Central, 2014. https://doi.org/10.1186/1471-2164-15-663. ieee: A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central, 2014. ista: Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663. mla: Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663. short: A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014). date_created: 2018-12-11T11:55:23Z date_published: 2014-08-08T00:00:00Z date_updated: 2021-01-12T06:54:56Z day: '08' ddc: - '570' department: - _id: JoBo doi: 10.1186/1471-2164-15-663 file: - access_level: open_access checksum: 3f6d2776b90a842a28359cc957d3d04b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:24Z date_updated: 2020-07-14T12:45:26Z file_id: '4878' file_name: IST-2015-396-v1+1_1471-2164-15-663.pdf file_size: 1489769 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 15' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: BMC Genomics publication_status: published publisher: BioMed Central publist_id: '5009' pubrep_id: '396' quality_controlled: '1' scopus_import: 1 status: public title: Motif depletion in bacteriophages infecting hosts with CRISPR systems tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2014' ... --- _id: '2412' abstract: - lang: eng text: 'Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54 apa: Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54 chicago: Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-54. ieee: A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013. ista: Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54. mla: Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:10.1186/1471-2148-13-54. short: A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54. date_created: 2018-12-11T11:57:31Z date_published: 2013-02-26T00:00:00Z date_updated: 2021-01-12T06:57:20Z day: '26' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-13-54 file: - access_level: open_access checksum: 029c7e0b198c19312b66ecce3cabb22f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:15Z date_updated: 2020-07-14T12:45:40Z file_id: '5268' file_name: IST-2015-397-v1+1_1471-2148-13-54.pdf file_size: 518729 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '02' oa: 1 oa_version: Published Version page: 54 - 54 publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '4514' pubrep_id: '397' quality_controlled: '1' scopus_import: 1 status: public title: 'Probabilistic models for CRISPR spacer content evolution ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '2410' abstract: - lang: eng text: 'Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. ' author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Gertraud full_name: Stift, Gertraud id: 2DB195CA-F248-11E8-B48F-1D18A9856A87 last_name: Stift - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 2013;1(3). doi:10.1128/genomeA.00216-13 apa: Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13 chicago: Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements. American Society for Microbiology, 2013. https://doi.org/10.1128/genomeA.00216-13. ieee: R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” Genome Announcements, vol. 1, no. 3. American Society for Microbiology, 2013. ista: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3). mla: Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements, vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13. short: R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013). date_created: 2018-12-11T11:57:30Z date_published: 2013-06-13T00:00:00Z date_updated: 2021-01-12T06:57:19Z day: '13' ddc: - '576' department: - _id: JoBo - _id: LifeSc doi: 10.1128/genomeA.00216-13 file: - access_level: open_access checksum: 0751ec74b695567e0cdf02aaf9c26829 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:36Z date_updated: 2020-07-14T12:45:40Z file_id: '5291' file_name: IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf file_size: 130026 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 1' issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Genome Announcements publication_status: published publisher: American Society for Microbiology publist_id: '4516' pubrep_id: '398' quality_controlled: '1' scopus_import: 1 status: public title: Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '500' abstract: - lang: eng text: 'Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.' acknowledgement: "This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n" article_number: '222' author: - first_name: Melissa full_name: Ward, Melissa last_name: Ward - first_name: Samantha full_name: Lycett, Samantha last_name: Lycett - first_name: Dorita full_name: Avila, Dorita last_name: Avila - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Andrew full_name: Leigh Brown, Andrew last_name: Leigh Brown citation: ama: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-222 apa: Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222 chicago: Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222. ieee: M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013. ista: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222. mla: Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no. 1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222. short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013). date_created: 2018-12-11T11:46:49Z date_published: 2013-10-09T00:00:00Z date_updated: 2021-01-12T08:01:08Z day: '09' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-13-222 file: - access_level: open_access checksum: 52cf48a7c1794676ae8b0029573a84a9 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:59Z date_updated: 2020-07-14T12:46:36Z file_id: '4722' file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf file_size: 1150052 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '7320' pubrep_id: '941' quality_controlled: '1' scopus_import: 1 status: public title: Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '501' abstract: - lang: eng text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.' author: - first_name: Mario full_name: Cozzuol, Mario last_name: Cozzuol - first_name: Camila full_name: Clozato, Camila last_name: Clozato - first_name: Elizete full_name: Holanda, Elizete last_name: Holanda - first_name: Flávio full_name: Rodrigues, Flávio last_name: Rodrigues - first_name: Samuel full_name: Nienow, Samuel last_name: Nienow - first_name: Benoit full_name: De Thoisy, Benoit last_name: De Thoisy - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Fabrício full_name: Santos, Fabrício last_name: Santos citation: ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1 apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1 chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1. ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013. ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345. mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:10.1644/12-MAMM-A-169.1. short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345. date_created: 2018-12-11T11:46:49Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T08:01:09Z day: '01' ddc: - '570' department: - _id: JoBo doi: 10.1644/12-MAMM-A-169.1 file: - access_level: open_access checksum: 8007815078dccac21ecd1cf73a269dc6 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:59Z date_updated: 2020-07-14T12:46:36Z file_id: '4980' file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf file_size: 1040765 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 94' issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '12' oa: 1 oa_version: Published Version page: 1331 - 1345 publication: Journal of Mammalogy publication_status: published publisher: Oxford University Press publist_id: '7319' pubrep_id: '940' quality_controlled: '1' scopus_import: 1 status: public title: A new species of tapir from the Amazon tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 94 year: '2013' ... --- _id: '508' abstract: - lang: eng text: The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases. author: - first_name: Eduardo full_name: Tarazona Santos, Eduardo last_name: Tarazona Santos - first_name: Moara full_name: Machado, Moara last_name: Machado - first_name: Wagner full_name: Magalhães, Wagner last_name: Magalhães - first_name: Renee full_name: Chen, Renee last_name: Chen - first_name: Fernanda full_name: Lyon, Fernanda last_name: Lyon - first_name: Laurie full_name: Burdett, Laurie last_name: Burdett - first_name: Andrew full_name: Crenshaw, Andrew last_name: Crenshaw - first_name: Cristina full_name: Fabbri, Cristina last_name: Fabbri - first_name: Latife full_name: Pereira, Latife last_name: Pereira - first_name: Laelia full_name: Pinto, Laelia last_name: Pinto - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Ben full_name: Sestanovich, Ben last_name: Sestanovich - first_name: Meredith full_name: Yeager, Meredith last_name: Yeager - first_name: Stephen full_name: Chanock, Stephen last_name: Chanock citation: ama: 'Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119' apa: 'Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119' chicago: 'Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.' ieee: 'E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013.' ista: 'Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.' mla: 'Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:10.1093/molbev/mst119.' short: E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167. date_created: 2018-12-11T11:46:52Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:01:12Z day: '01' department: - _id: JoBo doi: 10.1093/molbev/mst119 external_id: pmid: - '23821607' intvolume: ' 30' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/ month: '09' oa: 1 oa_version: Submitted Version page: 2157 - 2167 pmid: 1 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '7310' quality_controlled: '1' scopus_import: 1 status: public title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2013' ... --- _id: '2411' abstract: - lang: eng text: The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. author: - first_name: Ingo full_name: Ebersberger, Ingo last_name: Ebersberger - first_name: Ricardo full_name: De Matos Simoes, Ricardo last_name: De Matos Simoes - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Matthias full_name: Gube, Matthias last_name: Gube - first_name: Erika full_name: Kothe, Erika last_name: Kothe - first_name: Kerstin full_name: Voigt, Kerstin last_name: Voigt - first_name: Arndt full_name: Von Haeseler, Arndt last_name: Von Haeseler citation: ama: Ebersberger I, De Matos Simoes R, Kupczok A, et al. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. 2012;29(5):1319-1334. doi:10.1093/molbev/msr285 apa: Ebersberger, I., De Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt, K., & Von Haeseler, A. (2012). A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msr285 chicago: Ebersberger, Ingo, Ricardo De Matos Simoes, Anne Kupczok, Matthias Gube, Erika Kothe, Kerstin Voigt, and Arndt Von Haeseler. “A Consistent Phylogenetic Backbone for the Fungi.” Molecular Biology and Evolution. Oxford University Press, 2012. https://doi.org/10.1093/molbev/msr285. ieee: I. Ebersberger et al., “A consistent phylogenetic backbone for the fungi,” Molecular Biology and Evolution, vol. 29, no. 5. Oxford University Press, pp. 1319–1334, 2012. ista: Ebersberger I, De Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, Von Haeseler A. 2012. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. 29(5), 1319–1334. mla: Ebersberger, Ingo, et al. “A Consistent Phylogenetic Backbone for the Fungi.” Molecular Biology and Evolution, vol. 29, no. 5, Oxford University Press, 2012, pp. 1319–34, doi:10.1093/molbev/msr285. short: I. Ebersberger, R. De Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, A. Von Haeseler, Molecular Biology and Evolution 29 (2012) 1319–1334. date_created: 2018-12-11T11:57:30Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T06:57:19Z day: '01' ddc: - '570' - '576' department: - _id: JoBo doi: 10.1093/molbev/msr285 file: - access_level: open_access checksum: d565dcac27d1736c0c378ea6fcf22d69 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:30Z date_updated: 2020-07-14T12:45:40Z file_id: '5013' file_name: IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf file_size: 754922 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 29' issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '05' oa: 1 oa_version: Published Version page: 1319 - 1334 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '4515' pubrep_id: '384' quality_controlled: '1' scopus_import: 1 status: public title: A consistent phylogenetic backbone for the fungi tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2012' ...