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A Pluralistic Account of Homology: Adapting the Models to the Data

Leanne S. Haggerty, Pierre-Alain Jachiet, William P. Hanage, David A. Fitzpatrick, Philippe Lopez, Mary J. O'Connell, Davide Pisani, Mark Wilkinson, Eric Bapteste, James O. McInerney
2013 Molecular biology and evolution  
some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information.  ...  In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent  ...  separately, we aligned the three fusion proteins with the seven members of COG0842.  ... 
doi:10.1093/molbev/mst228 pmid:24273322 pmcid:PMC3935183 fatcat:wjzrt5hlmvhwjloho53p726e2y

MultiSeq: unifying sequence and structure data for evolutionary analysis

Elijah Roberts, John Eargle, Dan Wright, Zaida Luthey-Schulten
2006 BMC Bioinformatics  
Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5.  ...  This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate  ...  Acknowledgements The authors would like to thank John Stone and Michael Bach for discussions and development assistance and both the Luthey-Schulten group and the Theoretical and Computational Biophysics  ... 
doi:10.1186/1471-2105-7-382 pmid:16914055 pmcid:PMC1586216 fatcat:qdppsxqqazf2vkxe2s2x3kudbm

Cloning and characterization of α-pinene synthase from Chamaecyparis formosensis Matsum

Fang-Hua Chu, Pei-Min Kuo, Yu-Rong Chen, Sheng-Yang Wang
2009 Holzforschung  
To understand the biosynthesis mechanism of terpenes in this tree, a full length of putative mono-TPS, named as Cf-Pin (GeneBank accession no.  ...  To identify the function of Cf-Pin, the recombinant protein from Escherichia coli was incubated with geranyl diphosphate, produced one major product, the structure of which was elucidated.  ...  The authors also thank the reviewers and the Editorial Office of Holzforschung for their constructive and valuable comments.  ... 
doi:10.1515/hf.2009.019 fatcat:eoqzohz5bngmxggkvhmttccqu4

Formation of chimeric genes with essential functions at the origin of eukaryotes

Raphaël Méheust, Debashish Bhattacharya, Jananan S. Pathmanathan, James O. McInerney, Philippe Lopez, Eric Bapteste
2018 BMC Biology  
with important functions.  ...  Conclusion: This study demonstrates the extent and process through which prokaryotic fragments from bacterial and archaeal genes inherited during eukaryogenesis underly the creation of novel chimeric genes  ...  For those trees, the origin of the components is clear, in agreement with the BLAST assignation.  ... 
doi:10.1186/s12915-018-0500-0 pmid:29534719 pmcid:PMC5851275 fatcat:hfhe3hs5cbasvg6f6dzyd3yx6m

SMBE Satellite Meeting on Reticulated Microbial Evolution 2014--Meeting Report

T. Dagan, E. Bapteste, J. O. McInerney, W. F. Martin
2014 Genome Biology and Evolution  
Acknowledgments The meeting was supported by the Society for Molecular Biology and Evolution (SMBE), Christian-Albrechts University of Kiel, and the Kiel Cluster of Excellence "The Future Ocean."  ...  (1967) showed how one can study evolution using sequences with their method for phylogenetic tree reconstruction from protein sequences.  ...  His presentation included examples of gene fusions and domain reshuffling which constitute cases of multiple ancestral origins that could not be reconstructed using trees but require a new type of network  ... 
doi:10.1093/gbe/evu173 pmid:25115940 pmcid:PMC4202314 fatcat:4fjqzakxpjc2tdlqsb3pgugrh4

The polybasic insert of the SARS CoV-2 spike protein, the RBD and the feline SARS – Evolved or yet to evolve

Anshul Budhraja, Sakshi Pandey, Srinivasaraghavan Kannan, Chandra S. Verma, Prasanna Venkatraman
2021 Biochemistry and Biophysics Reports  
with peptides, PRRAR↓S binds less well and with distinct differences as compared to the all basic RRKRR↓S; c) these differences may be exploited for the design of virus-specific inhibitors; d) the novel  ...  through the domestic cat whose very human-like ACE2 receptor and furin may have played some role in optimizing the traits required for zoonotic transfer.  ...  Acknowledgement We thank Mahalakshmi Harish for careful reading of the manuscript and input. We thank all authors who would have contributed to the field but could not be cited here.  ... 
doi:10.1016/j.bbrep.2021.100907 pmid:33521335 pmcid:PMC7833556 fatcat:66gt4n6f5ffxzac4u45wymjc3y

Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor

Vasilina Zayats, Agata P. Perlinska, Aleksandra I. Jarmolinska, Borys Jastrzebski, Stanislaw Dunin-Horkawicz, Joanna I. Sulkowska, Patrícia F. N. Faísca
2021 PLoS Computational Biology  
This allows us to directly investigate the evolution of the slipknot motif.  ...  The tools we have developed in the process can now be used to investigate the evolution of other repeated-domain proteins.  ...  from PF00999). 4) Reverse-order fusion-gene duplication and fusion in a reverse order. 5) Fusion of the domains from different lineages (shown with blue and green). 6) Fast fusion-gene duplication followed  ... 
doi:10.1371/journal.pcbi.1009502 pmid:34648493 pmcid:PMC8562792 fatcat:n5rukqnewzca7anio5e3lifyee

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Hiran A. Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde (+15 others)
2020 IMA Fungus  
Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species.  ...  number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery.  ...  Authors' contributions All co-authoring members of the ICTF participated in the discussion leading up to the first manuscript draft. The manuscript was initially drafted from Lücking et al.  ... 
doi:10.1186/s43008-020-00033-z pmid:32714773 pmcid:PMC7353689 fatcat:shpddgh3zze6fcdakwgl5znpou

Molecular Identification and Expression Analysis of Filaggrin-2, a Member of the S100 Fused-Type Protein Family

Zhihong Wu, Britta Hansmann, Ulf Meyer-Hoffert, Regine Gläser, Jens-Michael Schröder, Christophe Egles
2009 PLoS ONE  
Thus, FLG2 and filaggrin may have overlapping and perhaps synergistic roles in the formation of the epidermal barrier, protecting the skin from environmental insults and the escape of moisture by offering  ...  The FLG2 gene encodes a histidine-and glutamine-rich protein of approximately 248 kDa, which shares common structural features with other SFTP members, in particular filaggrin.  ...  We thank the Central Microscopy Unit, CAU Kiel, for help with Immuno-EM.  ... 
doi:10.1371/journal.pone.0005227 pmid:19384417 pmcid:PMC2668185 fatcat:nfcby4jsqfawvfmwrj2w453coa

Rotavirus VP8*: Phylogeny, Host Range, and Interaction with Histo-Blood Group Antigens

Yang Liu, Pengwei Huang, Ming Tan, Yiliu Liu, Jacek Biesiada, Jarek Meller, Alejandro A. Castello, Baoming Jiang, Xi Jiang
2012 Journal of Virology  
Homology modeling and mutagenesis study showed that the locations of the carbohydrate binding interfaces are shared with the sialic acid-dependent RVs, although different amino acids are involved.  ...  In this study, we performed a phylogenetic analysis of RVs and showed further variations of RV interaction with HBGAs.  ...  ACKNOWLEDGMENTS This study was supported by grants from the National Institutes of Health through the National Institute of Allergy and Infectious Diseases (R01 AI37093 and R01 AI055649) and National Institute  ... 
doi:10.1128/jvi.00979-12 pmid:22761376 pmcid:PMC3446626 fatcat:55uxdtq3ufgrfkn3eb52a2nof4

Molecular evolution of the ATP-binding cassette subfamily G member 2 gene subfamily and its paralogs in birds

Shengchao Ma, Hehe Liu, Wenqiang Sun, Ahsan Mustafa, Yang Xi, Fajun Pu, Yanying Li, Chunchun Han, Lili Bai, He Hua
2020 BMC Evolutionary Biology  
Over the long course of evolution, only the ABCG2 gene was retained on chromosome 4 in birds. The ABCG2-like gene on chromosome 6 might have originated from chromosome replication or fusion.  ...  A detailed comparative study of the ABCG2 and ABCG2-like genes aid our understanding of their evolutionary history at the molecular level and provide a theoretical reference for studying the specific functions  ...  The ML search was started with the tree generated using BIONJ [46] , and the optimal tree was determined through a heuristic search using the nearest-neighbor interchange (NNI) algorithm [43] .  ... 
doi:10.1186/s12862-020-01654-z pmid:32664916 fatcat:2kovmypcmrdpvabyw7gf4jjjvm

The OsSPK1–OsRac1–RAI1 defense signaling pathway is shared by two distantly related NLR proteins in rice blast resistance

Minxiang Yu, Zhuangzhi Zhou, Xue Liu, Dedong Yin, Dayong Li, Xianfeng Zhao, Xiaobing Li, Shengping Li, Renjie Chen, Ling Lu, Dewei Yang, Dingzhong Tang (+1 others)
2021 Plant Physiology  
We found that in blast resistance mediated by the NLR PIRICULARIA ORYZAE RESISTANCE IN DIGU 3 (PID3), the guanine nucleotide exchange factor OsSPK1 works downstream of PID3.  ...  In addition, we observed changes in RAI1 levels during blast infection, which led to identification of OsRPT2a, a subunit of the 19S regulatory particle of the 26S proteasome.  ...  Acknowledgments We thank Professor Guo-Liang Wang for providing the above-mentioned experimental materials.  ... 
doi:10.1093/plphys/kiab445 pmid:34597396 pmcid:PMC8644225 fatcat:ji56kzuhhbdh3aurcy5ns5vqz4

Infant leukaemia – faithful models, cell of origin and the niche

Alasdair Duguid, Domenico Mattiucci, Katrin Ottersbach
2021 Disease Models & Mechanisms  
This disease has not seen the improvements in outcomes experienced with other paediatric leukaemias and it is becoming ever more apparent that infant leukaemia is a distinct biological entity.  ...  Insights into some of the distinguishing features of infant leukaemia, such as a single mutation – the MLL-gene rearrangement, the biology of disease aggressiveness and lineage plasticity, and the high  ...  originating in the HSPC compartment. 2006; Malouf et al., 2021; the haematopoietic tree.  ... 
doi:10.1242/dmm.049189 pmid:34713888 pmcid:PMC8560498 fatcat:odabcemjezehhm3lnaio37yenm

Identification of CkSNAP33, a gene encoding synaptosomal-associated protein from Cynanchum komarovii, that enhances Arabidopsis resistance to Verticillium dahliae

Ping Wang, Xueyan Zhang, Xiaowen Ma, Yun Sun, Nana Liu, Fuguang Li, Yuxia Hou, Zhengguang Zhang
2017 PLoS ONE  
The leaves of transgenic plants infected with V. dahliae showed strong callose deposition and cell death that hindered the penetration and spread of the fungus at the infection site.  ...  SNARE proteins are essential to vesicle trafficking and membrane fusion in eukaryotic cells.  ...  However, further research is necessary to define the role of CkSNAP33 in transport of defense signal molecules or products via membrane fusion. Supporting information Fig).  ... 
doi:10.1371/journal.pone.0178101 pmid:28575006 pmcid:PMC5456056 fatcat:j463inaje5h2pfwfwpchgulkve

PROJECT ICARUS: Son of Daedalus, Flying Closer to Another Star [article]

K. F. Long, R. K. Obousy, A. C. Tziolas, A. Mann, R. Osborne, A. Presby, M. Fogg
2010 arXiv   pre-print
During the 1970s members of the British Interplanetary Society embarked on a landmark theoretical engineering design study to send a probe to Barnard's star.  ...  This paper sets out the proposal for a successor interstellar design study called Project Icarus. This is an attempt to redesign the Daedalus vehicle with similar terms of reference.  ...  The staff of the British Interplanetary Society is thanked for hosting the successful symposium.  ... 
arXiv:1005.3833v1 fatcat:3cul2hn6s5fflnuj27pbn5sxiu
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