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Mead DJT, Lunagomez S, Gatherer D. Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling. J Mol Graph Model 2019; 92:180-191. [PMID: 31377535 PMCID: PMC7110651 DOI: 10.1016/j.jmgm.2019.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/15/2022]
Abstract
The protein sequence-structure gap results from the contrast between rapid, low-cost deep sequencing, and slow, expensive experimental structure determination techniques. Comparative homology modelling may have the potential to close this gap by predicting protein structure in target sequences using existing experimentally solved structures as templates. This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. Homology modelling was then carried out for target-template pairs in different species, different genera and different families, and model quality assessed using several metrics. Reconstructed ancestral RdRP sequences for individual genera were also used as templates for the production of ancestral RdRP homology models. High quality ancestral RdRP models were consistently produced, as were good quality models for target-template pairs in the same genus. Homology modelling between genera in the same family produced mixed results and inter-family modelling was unreliable. We present a protocol for the production of optimal RdRP homology models for use in further experiments, e.g. docking to discover novel anti-viral compounds. (219 words) The first use of force-directed graphs for the visualization of multidimensional protein sequence space in two dimensions. Measures of centrality in protein sequence space to identify sequences for production of homology models. Homology modelling for RNA-dependent RNA polymerase (RdRP) target-template pairs in different species, genera and families. A protocol for the production of optimal RdRP homology models for use in further experiments.
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Affiliation(s)
- Dylan J T Mead
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, LA1 4YT, UK.
| | - Simón Lunagomez
- Department of Mathematics & Statistics, Lancaster University, Lancaster, LA1 4YF, UK.
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, LA1 4YT, UK.
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2
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An Y, Wang Y, Zhan J, Tang X, Shen K, Shen F, Wang C, Luan W, Wang X, Wang X, Liu M, Zheng Q, Yu L. Fosfomycin Protects Mice From Staphylococcus aureus Pneumonia Caused by α-Hemolysin in Extracellular Vesicles by Inhibiting MAPK-Regulated NLRP3 Inflammasomes. Front Cell Infect Microbiol 2019; 9:253. [PMID: 31380296 PMCID: PMC6644418 DOI: 10.3389/fcimb.2019.00253] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/28/2019] [Indexed: 01/22/2023] Open
Abstract
α-Hemolysin (Hla) is a significant virulence factor in Staphylococcus aureus (S. aureus)-caused infectious diseases such as pneumonia. Thus, to prevent the production of Hla when treating S. aureus infection, it is necessary to choose an antibiotic with good antibacterial activity and effect. In our study, we observed that Fosfomycin (FOM) at a sub-inhibitory concentration inhibited expression of Hla. Molecular dynamics demonstrated that FOM bound to the binding sites LYS 154 and ASP 108 of Hla, potentially inhibiting Hla. Furthermore, we verified that staphylococcal membrane-derived vesicles (SMVs) contain Hla and that FOM treatment significantly reduced the production of SMVs and Hla. Based on our pharmacological inhibition analysis, ERK and p38 activated NLRP3 inflammasomes. Moreover, FOM inhibited expression of MAPKs and NLRP3 inflammasome-related proteins in S. aureus as well as SMV-infected human macrophages (MΦ) and alveolar epithelial cells. In vivo, SMVs isolated from S. aureus DU1090 (an isogenic Hla deletion mutant) or the strain itself caused weaker inflammation than that of its parent strain 8325-4. FOM also significantly reduced the phosphorylation levels of ERK and P38 and expression of NLRP3 inflammasome-related proteins. In addition, FOM decreased MPO activity, pulmonary vascular permeability and edema formation in the lungs of mice with S. aureus-caused pneumonia. Taken together, these data indicate that FOM exerts protective effects against S. aureus infection in vitro and in vivo by inhibiting Hla in SMVs and blocking ERK/P38-mediated NLRP3 inflammasome activation by Hla.
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Affiliation(s)
- Yanan An
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
| | - Yang Wang
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
| | - Jiuyu Zhan
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
| | - Xudong Tang
- Key Lab for New Drugs Research of TCM in Shenzhen, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China
| | - Keshu Shen
- Jilin Hepatobiliary Hospital, Changchun, China
| | - Fengge Shen
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
| | - Chao Wang
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
| | - Wenjing Luan
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
| | - Xuefei Wang
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
| | - Xueyan Wang
- Key Lab for New Drugs Research of TCM in Shenzhen, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China
| | - Mingyuan Liu
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China.,Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
| | - Lu Yu
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory Nano-Micro Architecture Chemistry, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Theoretical Chemistry, Institute of Zoonosis, College of Veterinary Medicine, Department of Infectious Diseases, First Hospital of Jilin University, Jilin University, Changchun, China
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3
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Peng L, Xing R, Liu D, Bao L, Cheng W, Wang H, Yu Y, Liu X, Jiang L, Wu Y, An Z, Liang Q, Kim RN, Shin YK, Yang H, Wang J, Yu J, Zhang X, Xu X, Yang J, Wu K, Zhu S, Lu Y. Characterization and validation of somatic mutation spectrum to reveal heterogeneity in gastric cancer by single cell sequencing. Sci Bull (Beijing) 2019; 64:236-244. [PMID: 36659713 DOI: 10.1016/j.scib.2018.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/12/2018] [Accepted: 11/02/2018] [Indexed: 01/21/2023]
Abstract
Gastric cancer (GC) is a highly heterogeneous disease with multiple cellular types and poor prognosis. However, the cellular evolution and molecular basis of GC at the individual intra-tumor level has not been well demonstrated. We performed single-cell whole exome sequencing to detect somatic single-nucleotide variants (SNVs) and significantly mutated genes (SMGs) among 34 tumor cells and 9 normal cells from a patient with GC. The Complete Prediction for Protein Conformation (CPPC) approach directly predicting the folding conformation of the protein 3D structure with Protein Folding Shape Code, combined with functional experiments were used to confirm the characterization of mutated SMGs in GC cells. We identified 201 somatic SNVs, including 117 non-synonymous mutations in GC cells. Further analysis identified 24 significant mutated genes (SMGs) in single cells, for which a single amino acid change might affect protein conformation. Among them, two genes (CDC27 and FLG) that were mutated only in single cells but not in the corresponding tumor tissue, were recurrently present in another GC tissue cohort, and may play a potential role to promote carcinogenesis, as confirmed by functional characterization. Our findings showed a mutational landscape of GC at intra-tumor level for the first time and provided opportunities for understanding the heterogeneity and individualized target therapy for this disease.
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Affiliation(s)
- Lihua Peng
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Rui Xing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Dongbing Liu
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Li Bao
- BGI-Shenzhen, Shenzhen 518083, China; Department of Drug Design and Pharmacology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Wenxiang Cheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hongyi Wang
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yuan Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaofeng Liu
- Department of Histology and Embryology, Inner Mongolia Medical University, Huhhot 010110, China
| | - Lu Jiang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yan Wu
- Department of Histology and Embryology, Inner Mongolia Medical University, Huhhot 010110, China
| | | | - Qiaoyi Liang
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ryong Nam Kim
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - Young Kee Shin
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jun Yu
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Xiuqing Zhang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiaan Yang
- Micro Pharmatech, Ltd, Wuhan 430075, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark.
| | - Youyong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China.
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4
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Liu C, Niu C, Zhao Y, Tian Y, Wang J, Li Q. Genome Analysis of the Yeast M14, an Industrial Brewing Yeast Strain Widely Used in China. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1080/03610470.2018.1496633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
- Lab of Brewing Science and Engineering, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
- Lab of Brewing Science and Engineering, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
| | - Yun Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
- Lab of Brewing Science and Engineering, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
| | - Yaping Tian
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
- Lab of Brewing Science and Engineering, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
- Lab of Brewing Science and Engineering, Jiangnan University, Wuxi, JiangSu Province, P. R. of China
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5
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Jung SW, Gessner RV, Keudell KC, Romano MA. Systematics of Morchella Esculenta Complex Using Enzyme-Linked Immunosorbent Assay. Mycologia 2018. [DOI: 10.1080/00275514.1993.12026320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- S. W. Jung
- Department of Biological Sciences, Western Illinois University, Macomb, Illinois 61455
| | - R. V. Gessner
- Department of Biological Sciences, Western Illinois University, Macomb, Illinois 61455
| | - K. C. Keudell
- Department of Biological Sciences, Western Illinois University, Macomb, Illinois 61455
| | - M. A. Romano
- Department of Biological Sciences, Western Illinois University, Macomb, Illinois 61455
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6
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Shaffer HB. EVOLUTION IN A PAEDOMORPHIC LINEAGE. I. AN ELECTROPHORETIC ANALYSIS OF THE MEXICAN AMBYSTOMATID SALAMANDERS. Evolution 2017; 38:1194-1206. [DOI: 10.1111/j.1558-5646.1984.tb05643.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/1983] [Revised: 03/16/1984] [Indexed: 11/28/2022]
Affiliation(s)
- H. Bradley Shaffer
- Committee on Evolutionary Biology; University of Chicago; Chicago Illinois 60637
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7
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Lansman RA, Avise JC, Aquadro CF, Shapira JF, Daniel SW. EXTENSIVE GENETIC VARIATION IN MITOCHONDRIAL DNA'S AMONG GEOGRAPHIC POPULATIONS OF THE DEER MOUSE, PEROMYSCUS MANICULATUS. Evolution 2017; 37:1-16. [DOI: 10.1111/j.1558-5646.1983.tb05509.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/1982] [Revised: 09/15/1982] [Indexed: 11/29/2022]
Affiliation(s)
- Robert A. Lansman
- Department of Molecular and Population Genetics; University of Georgia; Athens Georgia 30602
| | - John C. Avise
- Department of Molecular and Population Genetics; University of Georgia; Athens Georgia 30602
| | - Charles F. Aquadro
- Department of Molecular and Population Genetics; University of Georgia; Athens Georgia 30602
| | - John F. Shapira
- Department of Molecular and Population Genetics; University of Georgia; Athens Georgia 30602
| | - Susan W. Daniel
- Department of Molecular and Population Genetics; University of Georgia; Athens Georgia 30602
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8
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Larson A, Wake DB, Maxson LR, Highton R. A MOLECULAR PHYLOGENETIC PERSPECTIVE ON THE ORIGINS OF MORPHOLOGICAL NOVELTIES IN THE SALAMANDERS OF THE TRIBE PLETHODONTINI (AMPHIBIA, PLETHODONTIDAE). Evolution 2017; 35:405-422. [PMID: 28563578 DOI: 10.1111/j.1558-5646.1981.tb04902.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/1980] [Revised: 09/26/1980] [Indexed: 11/30/2022]
Affiliation(s)
- Allan Larson
- Department of Genetics and Museum of Vertebrate Zoology, University of California, Berkeley, California, 94720
| | - David B Wake
- Museum of Vertebrate Zoology and Department of Zoology, University of California, Berkeley, California, 94720
| | - Linda R Maxson
- Departments of Genetics and Development, and of Ecology, Ethology,and Evolution, University of Illinois, Urbana, Illinois, 61801
| | - Richard Highton
- Department of Zoology, University of Maryland, College Park, Maryland, 20742
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9
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Baker RJ, Bickham JW, Arnold ML. CHROMOSOMAL EVOLUTION IN
RHOGEESSA
(CHIROPTERA: VESPERTILIONIDAE): POSSIBLE SPECIATION BY CENTRIC FUSIONS. Evolution 2017; 39:233-243. [DOI: 10.1111/j.1558-5646.1985.tb05663.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/1984] [Accepted: 09/28/1984] [Indexed: 11/30/2022]
Affiliation(s)
- Robert J. Baker
- The Museum and Department of Biological Sciences Texas Tech University Lubbock TX 79409
| | - John W. Bickham
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station TX 77843
| | - Michael L. Arnold
- The Museum and Department of Biological Sciences Texas Tech University Lubbock TX 79409
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10
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Larson A. PAEDOMORPHOSIS IN RELATION TO RATES OF MORPHOLOGICAL AND MOLECULAR EVOLUTION IN THE SALAMANDER
ANEIDES FLAVIPUNCTATUS
(AMPHIBIA, PLETHODONTIDAE). Evolution 2017; 34:1-17. [DOI: 10.1111/j.1558-5646.1980.tb04785.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/1979] [Revised: 08/14/1979] [Indexed: 11/28/2022]
Affiliation(s)
- Allan Larson
- Department of Genetics and Museum of Vertebrate Zoology University of California Berkeley California 94720
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11
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Zhan JY, Zhang JL, Wang Y, Li Y, Zhang HX, Zheng QC. Exploring the interaction between human focal adhesion kinase and inhibitors: a molecular dynamic simulation and free energy calculations. J Biomol Struct Dyn 2016; 34:2351-66. [PMID: 26549408 DOI: 10.1080/07391102.2015.1115780] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Focal adhesion kinase is an important target for the treatment of many kinds of cancers. Inhibitors of FAK are proposed to be the anticancer agents for multiple tumors. The interaction characteristic between FAK and its inhibitors is crucial to develop new inhibitors. In the present article, we used Molecular Dynamic (MD) simulation method to explore the characteristic of interaction between FAK and three inhibitors (PHM16, TAE226, and ligand3). The MD simulation results together with MM-GB/SA calculations show that the combinations are enthalpy-driven process. Cys502 and Asp564 are both essential residues due to the hydrogen bond interactions with inhibitors, which was in good agreement with experimental data. Glu500 can form a non-classical hydrogen bond with each inhibitor. Arg426 can form electrostatic interactions with PHM16 and ligand3, while weaker with TAE226. The electronic static potential was employed, and we found that the ortho-position methoxy of TAE226 has a weaker negative charge than the meta-position one in PHM16 or ligand3. Ile428, Val436, Ala452, Val484, Leu501, Glu505, Glu506, Leu553, Gly563 Leu567, Ser568 are all crucial residues in hydrophobic interactions. The key residues in this work will be available for further inhibitor design of FAK and also give assistance to further research of cancer.
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Affiliation(s)
- Jiu-Yu Zhan
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , P.R. China
| | - Ji-Long Zhang
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , P.R. China
| | - Yan Wang
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , P.R. China
| | - Ye Li
- c Changchun Institute of Biological Products Co. Ltd , Changchun 130012 , P.R. China
| | - Hong-Xing Zhang
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , P.R. China
| | - Qing-Chuan Zheng
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , P.R. China.,b Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , Jilin University , Changchun 130023 , P.R. China
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12
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Henze R, Huwald J, Mostajo N, Dittrich P, Ibrahim B. Structural analysis of in silico mutant experiments of human inner-kinetochore structure. Biosystems 2014; 127:47-59. [PMID: 25451768 DOI: 10.1016/j.biosystems.2014.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 08/20/2014] [Accepted: 11/04/2014] [Indexed: 12/31/2022]
Abstract
Large multi-molecular complexes like the kinetochore are lacking of suitable methods to determine their spatial structure. Here, we use and evaluate a novel modeling approach that combines rule-bases reaction network models with spatial molecular geometries. In particular, we introduce a method that allows to study in silico the influence of single interactions (e.g. bonds) on the spatial organization of large multi-molecular complexes and apply this method to an extended model of the human inner-kinetochore. Our computational analysis method encompasses determination of bond frequency, geometrical distances, statistical moments, and inter-dependencies between bonds using mutual information. For the analysis we have extend our previously reported human inner-kinetochore model by adding 13 new protein interactions and three protein geometry details. The model is validated by comparing the results of in silico with reported in vitro single protein deletion experiments. Our studies revealed that most simulations mimic the in vitro behavior of the kinetochore complex as expected. To identify the most important bonds in this model, we have created 39 mutants in silico by selectively disabling single protein interactions. In a total of 11,800 simulation runs we have compared the resulting structures to the wild-type. In particular, this allowed us to identify the interaction Cenp-W-H3 and Cenp-S-Cenp-X as having the strongest influence on the inner-kinetochore's structure. We conclude that our approach can become a useful tool for the in silico dynamical study of large, multi-molecular complexes.
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Affiliation(s)
- Richard Henze
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Jan Huwald
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Nelly Mostajo
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Peter Dittrich
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Bashar Ibrahim
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany; Umm Al-Qura University, 1109 Makkah Al-Mukarramah, Saudi Arabia; Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Saudi Arabia.
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13
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Yu C, Yu J, Yao X, Wu WKK, Lu Y, Tang S, Li X, Bao L, Li X, Hou Y, Wu R, Jian M, Chen R, Zhang F, Xu L, Fan F, He J, Liang Q, Wang H, Hu X, He M, Zhang X, Zheng H, Li Q, Wu H, Chen Y, Yang X, Zhu S, Xu X, Yang H, Wang J, Zhang X, Sung JJY, Li Y, Wang J. Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. Cell Res 2014; 24:701-12. [PMID: 24699064 PMCID: PMC4042168 DOI: 10.1038/cr.2014.43] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/22/2014] [Accepted: 02/26/2014] [Indexed: 12/19/2022] Open
Abstract
Single-cell sequencing is a powerful tool for delineating clonal relationship and identifying key driver genes for personalized cancer management. Here we performed single-cell sequencing analysis of a case of colon cancer. Population genetics analyses identified two independent clones in tumor cell population. The major tumor clone harbored APC and TP53 mutations as early oncogenic events, whereas the minor clone contained preponderant CDC27 and PABPC1 mutations. The absence of APC and TP53 mutations in the minor clone supports that these two clones were derived from two cellular origins. Examination of somatic mutation allele frequency spectra of additional 21 whole-tissue exome-sequenced cases revealed the heterogeneity of clonal origins in colon cancer. Next, we identified a mutated gene SLC12A5 that showed a high frequency of mutation at the single-cell level but exhibited low prevalence at the population level. Functional characterization of mutant SLC12A5 revealed its potential oncogenic effect in colon cancer. Our study provides the first exome-wide evidence at single-cell level supporting that colon cancer could be of a biclonal origin, and suggests that low-prevalence mutations in a cohort may also play important protumorigenic roles at the individual level.
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Affiliation(s)
- Chang Yu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jun Yu
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - William KK Wu
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Youyong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University School of Oncology, Beijing Cancer Hospital/Institute, Beijing 100142, China
| | - Senwei Tang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Li Bao
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xiaoxing Li
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu 210096, China
| | - Renhua Wu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Min Jian
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Ruoyan Chen
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Department of Peadiatrics & Adolescent medicine, The University of Hong Kong, Hong Kong, China
| | - Fan Zhang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, USA
| | - Lixia Xu
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Fan Fan
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jun He
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiaoyi Liang
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hongyi Wang
- Department of Surgery, Peking University School of Oncology, Beijing Cancer Hospital/Institute, Beijing 100142, China
| | - Xueda Hu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Minghui He
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xiang Zhang
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Qibin Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Hanjie Wu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yan Chen
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xu Yang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Joseph JY Sung
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yingrui Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China
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14
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Ball RM, Freeman S, James FC, Bermingham E, Avise JC. Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA. Proc Natl Acad Sci U S A 2010; 85:1558-62. [PMID: 16593914 PMCID: PMC279812 DOI: 10.1073/pnas.85.5.1558] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P approximately 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow.
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Affiliation(s)
- R M Ball
- Department of Genetics, University of Georgia, Athens, GA 30602
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15
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Thomas PD. GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics 2010; 11:312. [PMID: 20534164 PMCID: PMC2905364 DOI: 10.1186/1471-2105-11-312] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 06/09/2010] [Indexed: 11/10/2022] Open
Abstract
Background Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. Results We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. Conclusions GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events.
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Affiliation(s)
- Paul D Thomas
- Evolutionary Systems Biology Group, SRI International, Menlo Park, CA, USA.
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16
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Cadle JE, Sarich VM. An immunological assessment of the phylogenetic position of New World coral snakes. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.1981.tb03456.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Burch SJ, Lawson R, Davies DH. The relationships of cartilaginous fishes: an immunological study of serum transferrins of holocephalans and elasmobranchs. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.1984.tb02334.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- S. J. Burch
- Department of Biology, University ofSalford, Salford M5 4WT, U.K
| | - R. Lawson
- Department of Biology, University ofSalford, Salford M5 4WT, U.K
| | - D. H. Davies
- Department of Biology, University ofSalford, Salford M5 4WT, U.K
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18
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Sage RD, Prager EM, Wake DB. A Cretaceous divergence time between pelobatid frogs(Pelobates and Scaphiopus): immunological studies of serum albumin. J Zool (1987) 2009. [DOI: 10.1111/jzo.1982.198.4.481] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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20
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Schlegel M. Comparative study of allozyme variation in eight species of hypotrichous ciliates (Polyhymenophora, Ciliophora)1. J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.1985.tb00580.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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22
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McANDREW BJ, MAJUMDAR KC. Evolutionary relationships within three Tilapiine genera (Pisces: Cichlidae). Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.1984.tb02553.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Abstract
Organisms have acquired plastids by convoluted paths that have provided multiple opportunities for gene transfer into a host nucleus from intracellular organisms, including the cyanobacterial ancestor of plastids, the proteobacterial ancestor of mitochondria, and both green and red algae whose engulfment has led to secondary acquisition of plastids. These gene movements are most accurately demonstrated by building phylogenetic trees that identify the evolutionary origin of each gene, and one effective tool for this is "PhIGs" (Phylogenetically Inferred Groups; http://PhIGs.org), a set of databases and computer tools with a Web interface for whole-genome evolutionary analysis. PhIGs takes as input gene sets of completely sequenced genomes, builds clusters of genes using a novel, graph-based approach, and reconstructs the evolutionary relationships among all gene families. The user can view and download the sequence alignments, compare intron-exon structures, and follow links to functional genomic databases. Currently, PhIGs contains 652,756 genes from 45 genomes grouped into 61,059 gene families. Graphical displays show the relative positions of these genes among genomes. PhIGs has been used to detect the evolutionary transfer of hundreds of genes from cyanobacteria and red algae into oömycete nuclear genomes, revealing that even though they have no plastids, their ancestors did, having secondarily acquired them from an intracellular red alga. A great number of genomes are soon to become available that are relevant to our broader understanding of the movement of genes among intracellular compartments after engulfing other organisms, and PhIGs will be an effective tool to interpret these gene movements.
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Affiliation(s)
- Jeffrey L Boore
- Genome Project Solutions, Hercules, California 94547, USA DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA University of California Berkeley, California 94720, USA
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24
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WALLIS GP, BEARDMORE JA. An electrophoretic study of the systematic relationships of some closely related goby species (Pisces, Gobiidae). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.1984.tb01673.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Koike M, Takahashi K, Mishiro S, Matsui A, Inao M, Nagoshi S, Ohno A, Mochida S, Fujiwara K. Full-Length Sequences of Two Hepatitis E Virus Isolates Representing an Eastern China-Indigenous Subgroup of Genotype 4. Intervirology 2007; 50:181-9. [PMID: 17259737 DOI: 10.1159/000098961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Accepted: 09/27/2006] [Indexed: 11/19/2022] Open
Abstract
Although the majority of hepatitis E virus (HEV) infections in Japan are 'domestic' due to the presence of indigenous strains, there are still 'imported' cases as well. Among 83 patients with non-A, non-B and non-C acute liver diseases admitted to Saitama Medical University Hospital, 7 (8.4%) were positive for serum HEV-RNA, of whom 2 had a recent history of traveling to China, one to Xian and another to Shanghai. We determined the full-genome sequences of HEV from these 2 patients (isolate names are JKO-ChiSai98c and JYI-ChiSai01c, genotype 4 in both) for phylogenetic analyses. Initially, when compared only to the 13 full-genome sequences of genotype 4 so far reported, our 2 isolates were thought to be novel strains because they showed a significant genetic difference from the sequences known to date. However, when we included a set of short sequences (150 nt) recently reported from China in the comparison, we found that our 2 isolates represent a subgroup of genotype 4, which seems to be restricted to eastern China. In conclusion, the 2 HEV isolates reported here could serve as full-genome prototypes for an eastern China-indigenous subgroup of the genotype 4 HEV.
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Affiliation(s)
- Masami Koike
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saitama Medical University, Saitama, Japan
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Abstract
Multilocus sequence typing (MLST) was proposed in 1998 as a portable, universal, and definitive method for characterizing bacteria, using the human pathogen Neisseria meningitidis as an example. In addition to providing a standardized approach to data collection, by examining the nucleotide sequences of multiple loci encoding housekeeping genes, or fragments of them, MLST data are made freely available over the Internet to ensure that a uniform nomenclature is readily available to all those interested in categorizing bacteria. At the time of writing, over thirty MLST schemes have been published and made available on the Internet, mostly for pathogenic bacteria, although there are schemes for pathogenic fungi and some nonpathogenic bacteria. MLST data have been employed in epidemiological investigations of various scales and in studies of the population biology, pathogenicity, and evolution of bacteria. The increasing speed and reduced cost of nucleotide sequence determination, together with improved web-based databases and analysis tools, present the prospect of increasingly wide application of MLST.
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Affiliation(s)
- Martin C J Maiden
- Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, OX1 3SY, United Kingdom.
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27
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Sato JJ, Wolsan M, Suzuki H, Hosoda T, Yamaguchi Y, Hiyama K, Kobayashi M, Minami S. Evidence from nuclear DNA sequences sheds light on the phylogenetic relationships of Pinnipedia: single origin with affinity to Musteloidea. Zoolog Sci 2006; 23:125-46. [PMID: 16603806 DOI: 10.2108/zsj.23.125] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Considerable long-standing controversy and confusion surround the phylogenetic affinities of pinnipeds, the largely marine group of "fin-footed" members of the placental mammalian order Carnivora. Until most recently, the two major competing hypotheses were that the pinnipeds have a single (monophyletic) origin from a bear-like ancestor, or that they have a dual (diphyletic) origin, with sea lions (Otariidae) derived from a bear-like ancestor, and seals (Phocidae) derived from an otter-, mustelid-, or musteloid-like ancestor. We examined phylogenetic relationships among 29 species of arctoid carnivorans using a concatenated sequence of 3228 bp from three nuclear loci (apolipoprotein B, APOB; interphotoreceptor retinoid-binding protein, IRBP; recombination-activating gene 1, RAG1). The species represented Pinnipedia (Otariidae: Callorhinus, Eumetopias; Phocidae: Phoca), bears (Ursidae: Ursus, Melursus), and Musteloidea (Mustelidae: Mustela, Enhydra, Melogale, Martes, Gulo, Meles; Procyonidae: Procyon; Ailuridae: Ailurus; Mephitidae: Mephitis). Maximum parsimony, maximum likelihood, and Bayesian inference phylogenetic analyses of separate and combined datasets produced trees with largely congruent topologies. The analyses of the combined dataset resulted in well-resolved and well-supported phylogeny reconstructions. Evidence from nuclear DNA evolution presented here contradicts the two major hypotheses of pinniped relationships and strongly suggests a single origin of the pinnipeds from an arctoid ancestor shared with Musteloidea to the exclusion of Ursidae.
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Affiliation(s)
- Jun J Sato
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Japan.
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28
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Truong K, Ikura M. Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach. BMC Bioinformatics 2002; 3:1. [PMID: 11818024 PMCID: PMC65048 DOI: 10.1186/1471-2105-3-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2001] [Accepted: 01/10/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include the development of classification systems capable of distinguishing between subfamilies within a structurally and functionally diverse superfamily. This would be helpful in elucidating sequence-structure-function relationships of proteins. RESULTS Here, we present a method to diagnose sequences into subfamilies by employing hidden Markov models (HMMs) to find windows of residues that are distinct among subfamilies (called signatures). The method starts with a multiple sequence alignment (MSA) of the subfamily. Then, we build a HMM database representing all sliding windows of the MSA of a fixed size. Finally, we construct a HMM histogram of the matches of each sliding window in the entire superfamily. To illustrate the efficacy of the method, we have applied the analysis to find subfamily signatures in two well-studied superfamilies: the cadherin and the EF-hand protein superfamilies. As a corollary, the HMM histograms of the analyzed subfamilies revealed information about their Ca2+ binding sites and loops. CONCLUSIONS The method is used to create HMM databases to diagnose subfamilies of protein superfamilies that complement broad profile and motif databases such as BLOCKS, PROSITE, Pfam, SMART, PRINTS and InterPro.
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Affiliation(s)
- Kevin Truong
- Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mitsuhiko Ikura
- Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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29
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Tomiyama H, Ohshima M, Ishii S, Satoh K, Takahashi R, Isobe K, Iwano H, Tokuyama T. Characteristics of Newly Isolated Nitrifying Bacteria from Rhizoplane of Paddy Rice. Microbes Environ 2001. [DOI: 10.1264/jsme2.2001.101] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Satoko Ishii
- College of Bioresource Sciences, Nihon University
| | - Kazuo Satoh
- College of Bioresource Sciences, Nihon University
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30
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Kluge AG. Total Evidence Or Taxonomic Congruence: Cladistics Or Consensus Classification. Cladistics 1998; 14:151-158. [DOI: 10.1111/j.1096-0031.1998.tb00328.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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31
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Van Der Bank F. Molecular systematics of fifteen old world cichlid species using allozyme data. BIOCHEM SYST ECOL 1994. [DOI: 10.1016/0305-1978(94)90082-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Nikoletopoulos NP, Chondropoulos BP, Fraguedakis-Tsolis SE. Albumin evolution and phylogenetic relationships among Greek rodents of the families Arvicolidae and Muridae. J Zool (1987) 1992. [DOI: 10.1111/j.1469-7998.1992.tb04447.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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10 Statistical methods for phylogenetic tree reconstruction. ACTA ACUST UNITED AC 1991. [DOI: 10.1016/s0169-7161(05)80166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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34
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Abstract
We have determined the sequence of the human mdr3 gene using cDNA derived from liver RNA. The mdr3 gene codes for a member of a family of membrane proteins, the P-glycoproteins, overproduced in many multi-drug-resistant (MDR) cell lines. Like its relatives, the protein encoded by mdr3 has a deduced Mr of 140,000, which is presumably increased by glycosylation after synthesis. The sequence consists of two similar halves, each with a series of six hydrophobic segments that may form a membrane channel. The halves also possess nucleotide-binding consensus sequences, which presumably act as ATPases and drive drug transport. The presumed ATPase domains are all but identical to those of the human mdr1 gene product [Chen et al., Cell 47 (1986) 381-389]. We attribute this high level of sequence conservation to the repeated gene conversion that is evident from segments in which mdr1 and mdr3 differ only in a few silent mutations. Divergence between P-glycoprotein family members is greatest at the N terminus and in the 60 amino acid linker connecting the two halves. In the putative trans-membrane domains approx. 80% of the amino acids are conserved between the products of mdr1 and mdr3. Although the function of mdr3 is not yet known, its high homology with mdr1 suggests that it also encodes an efflux pump with broad specificity.
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Affiliation(s)
- A M van der Bliek
- The Netherlands Cancer Institute, Department of Molecular Biology, Amsterdam
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35
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36
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de Jong WW, Leunissen JA, Leenen PJ, Zweers A, Versteeg M. Dogfish alpha-crystallin sequences. Comparison with small heat shock proteins and Schistosoma egg antigen. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)60691-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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37
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38
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Lake JA. Determining evolutionary distances from highly diverged nucleic acid sequences: operator metrics. J Mol Evol 1987; 26:59-73. [PMID: 3125338 DOI: 10.1007/bf02111282] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Operator metrics are explicitly designed to measure evolutionary distances from nucleic acid sequences when substitution rates differ greatly among the organisms being compared, or when substitutions have been extensive. Unlike lengths calculated by the distance matrix and parsimony methods, in which substitutions in one branch of a tree can alter the measured length of another branch, lengths determined by operator metrics are not affected by substitutions outside the branch. In the method, lengths (operator metrics) corresponding to each of the branches of an unrooted tree are calculated. The metric length of a branch reconstructs the number of (transversion) differences between sequences at a tip and a node (or between nodes) of a tree. The theory is general and is fundamentally independent of differences in substitution rates among the organisms being compared. Mathematically, the independence has been obtained because the metrics are eigenvectors of fundamental equations which describe the evolution of all unrooted trees. Even under conditions when both the distance matrix method or a simple parismony length method are shown to indicate lengths that are an order of magnitude too large or too small, the operator metrics are accurate. Examples, using data calculated with evolutionary rates and branchings designed to confuse the measurement of branch lengths and to camouflage the topology of the true tree, demonstrate the validity of operator metrics. The method is robust. Operator metric distances are easy to calculate, can be extended to any number of taxa, and provide a statistical estimate of their variances. The utility of the method is demonstrated by using it to analyze the origins and evolution of chloroplasts, mitochondria, and eubacteria.
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Affiliation(s)
- J A Lake
- Molecular Biology Institute, University of California, Los Angeles 90024
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39
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Menéndez-Arias L, Gavilanes JG, Rodriguez R. A structural comparison of type c lysozymes based on their hydropathic profiles. J Theor Biol 1987; 127:221-8. [PMID: 3695547 DOI: 10.1016/s0022-5193(87)80132-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hydropathic profiles can be considered as an approach to the three-dimensional structure of a protein and so their use for comparison of homologous proteins is proposed, as they provide information on relative structural conservativeness. A simple approach was developed for comparison of hydropathic profiles and applied to 19 lysozymes c of known primary structure. Trees were constructed in order to discover which method yielded the best estimation of the phenotypic differences between the proteins considered, by means of the goodness-of-fit criterion. Iterative methods, such as the Fitch-and-Margoliash and the unweighted-pair-group methods, gave a better fit than did a non-iterative method. When the hydropathic approach is used for comparison of lysozymes c, the enzyme obtained from chachalaca egg-white is placed closer to those from pheasant-like birds than to those of ducks; this result agrees with the morphological resemblance of the chachalaca to pheasant-like birds. Pigeon egg-white and equine milk lysozymes differ greatly in sequence from other lysozymes c and their hydropathic analysis shows important differences with respect to the other homologous enzymes.
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Affiliation(s)
- L Menéndez-Arias
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad Complutense, Madrid, Spain
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40
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Davies DH, Lawson R, Burch SJ, Hanson JE. Evolutionary relationships of a "primitive" shark (Heterodontus) assessed by micro-complement fixation of serum transferrin. J Mol Evol 1987; 25:74-80. [PMID: 3114502 DOI: 10.1007/bf02100043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The evolutionary relationships of six sharks were investigated by comparing their transferrins using the micro-complement fixation method. The immunological distances observed were used to build a tree that confirms that the squaloid and galeoid species examined belong to two separate groups and that Heterodontus, a genus of hitherto uncertain position, belongs with the galeoids. The divergence time estimated from the transferrin comparisons is roughly 240 +/- 65 million years between Heterodontus and galeoids.
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Rodríguez R, Menéndez-Arias L, Gonzalez de Buitrago G, Gavilanes JG. Structure of the pigeon lysozyme and its relationship with other type c lysozymes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1987; 88:791-6. [PMID: 3427917 DOI: 10.1016/0305-0491(87)90245-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
1. The secondary structure of the pigeon egg-white lysozyme shows important differences when compared to other type c lysozymes. These differences are mainly located at the region comprising residues 77-84. This segment contains one alpha-helix in the lysozymes c studied by means of an X-ray analysis, while the residues at such positions in pigeon lysozyme would form two beta-bends. 2. Analysis of the tertiary structure of the pigeon lysozyme by means of hydropathy profiles reveals that the above segment seems to be more hydrophilic in the pigeon enzyme than in other type c lysozymes. 3. Though a certain similarity to the calcium-binding loop of alpha-lactalbumins is detected in pigeon lysozyme, the circular dichroism spectra of the protein at neutral pH do not change in the presence of Ca2+ ions. 4. The presented structural analysis is discussed in terms of function-structure and antigenicity relationships between the type c lysozymes.
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Affiliation(s)
- R Rodríguez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad Complutense, Madrid, Spain
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Blanc F, Cariou ML. Geographical variability of allozyme variation and genetic divergence between Tunisian lizards of the sand-dwelling lacertid genus Acanthodactylus. Genetica 1987. [DOI: 10.1007/bf00126974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Beverley SM, Ismach RB, Pratt DM. Evolution of the genus Leishmania as revealed by comparisons of nuclear DNA restriction fragment patterns. Proc Natl Acad Sci U S A 1987; 84:484-8. [PMID: 3025876 PMCID: PMC304233 DOI: 10.1073/pnas.84.2.484] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Restriction endonuclease DNA fragment patterns have been used to examine the relationships among 28 isolates of Leishmania as well as Crithidia, Endotrypanum, and Trypanosoma cruzi. Fragments of nuclear DNA were generated with six restriction enzymes, and blots were hybridized with probes from three loci. Among the major lineages the fragment patterns are essentially completely different, while within the major lineages various degrees of divergence are found. Molecular evolutionary trees were constructed using the method of Nei and Li to estimate the percent nucleotide sequence divergence among strains from the fraction of fragments shared. Defined groups, such as species or subspecies within the major lineages, are also grouped by nuclear DNA comparisons. Within the donovani complex, we find Leishmania donovani chagasi and Leishmania donovani infantum to be as similar as strains within Leishmania donovani donovani, consistent with the proposal by other workers that New World visceral leishmaniasis originated quite recently.
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Copper/Zinc superoxide dismutase: How likely is gene transfer from ponyfish toPhotobacterium leiognathi? J Mol Evol 1986. [DOI: 10.1007/bf02115581] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Functional-morphological and biochemical correlations of the keratinized structures in the African Grey Parrot, Psittacus erithacus (Aves). ZOOMORPHOLOGY 1986. [DOI: 10.1007/bf00312112] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Leunissen JA, de Jong WW. Phylogenetic trees constructed from hydrophobicity values of protein sequences. J Theor Biol 1986; 119:189-96. [PMID: 3016413 DOI: 10.1016/s0022-5193(86)80073-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Information about conformational properties of a protein is contained in the hydrophobicity values of the amino acids in its primary sequence. We have investigated the possibility of extracting meaningful evolutionary information from the comparison of the hydrophobicity values of the corresponding amino acids in the sequences of homologous proteins. Distance matrices for six families of homologous proteins were made on the basis of the differences in hydrophobicity values of the amino acids. The phylogenetic trees constructed from such matrices were at least as good (as judged from their faithful reflection of evolutionary relationships), as trees constructed from the usual minimum mutation distance matrix.
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LUCKOW MELISSA, PIMENTEL RICHARDA. AN EMPIRICAL COMPARISON OF NUMERICAL WAGNER COMPUTER PROGRAMS. Cladistics 1985; 1:47-66. [DOI: 10.1111/j.1096-0031.1985.tb00410.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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