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Van Nguyen T, Kasantikul T, Piewbang C, Techangamsuwan S. Evolutionary dynamics of canine kobuvirus in Vietnam and Thailand reveal the evidence of viral ability to evade host immunity. Sci Rep 2024; 14:12037. [PMID: 38802579 PMCID: PMC11130191 DOI: 10.1038/s41598-024-62833-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
Canine kobuvirus (CaKoV) is a pathogen associated with canine gastrointestinal disease (GID). This study examined 327 rectal swabs (RS), including 113 from Vietnam (46 healthy, 67 with GID) and 214 from Thailand (107 healthy and 107 with GID). CaKoV was detected in both countries, with prevalences of 28.3% (33/113) in Vietnam and 7.9% (17/214) in Thailand. Additionally, CaKoV was found in both dogs with diarrhea and healthy dogs. CaKoV was mainly found in puppies under six months of age (30.8%). Co-detection with other canine viruses were also observed. The complete coding sequence (CDS) of nine Vietnamese and four Thai CaKoV strains were characterized. Phylogenetic analysis revealed a close genetic relationship between Vietnamese and Thai CaKoV strains, which were related to the Chinese strains. CDS analysis indicated a distinct lineage for two Vietnamese CaKoV strains. Selective pressure analysis on the viral capsid (VP1) region showed negative selection, with potential positive selection sites on B-cell epitopes. This study, the first of its kind in Vietnam, provides insights into CaKoV prevalence in dogs of different ages and healthy statuses, updates CaKoV occurrence in Thailand, and sheds light on its molecular characteristics and immune evasion strategies.
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Affiliation(s)
- Tin Van Nguyen
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City, Vietnam
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Tanit Kasantikul
- Veterinary Diagnostic Laboratory, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Chutchai Piewbang
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Somporn Techangamsuwan
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Dos Santos AT, Souza JPA, Jorge IR, Andrade SMM, Rosa BB, Moura MO, Zarbin PHG. Can Pheromones Contribute to Phylogenetic Hypotheses? A Case Study of Chrysomelidae. J Chem Ecol 2023; 49:611-641. [PMID: 37856061 DOI: 10.1007/s10886-023-01450-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 10/20/2023]
Abstract
Pheromones mediate species-level communication in the search for mates, nesting, and feeding sites. Although the role of pheromones has long been discussed by various authors, their existence was not proven until the mid-twentieth century when the first sex pheromone was identified. From this finding, much has been speculated about whether this communication mechanism has acted as a regulatory agent in the process of speciation, competition, and sexual selection since it acts as an intraspecific barrier. Chrysomelidae is one of the major Phytophaga lineages, with approximately 40,000 species. Due to this immense diversity the internal relationships remain unstable when analyzed only with morphological data, consequently recent efforts have been directed to molecular analyses to establish clarity for the relationships and found their respective monophyly. Therefore, our goals are twofold 1) to synthesize the current literature on Chrysomelidae sex pheromones and 2) to test whether Chrysomelidae sex pheromones and their chemical structures could be used in phylogenetic analysis for the group. The results show that, although this is the first analysis in Chrysomelidae to use pheromones as a phylogenetic character, much can be observed in agreement with previous analyses, thus confirming that pheromones, when known in their entirety within lineages, can be used as characters in phylogenetic analyses, bringing elucidation to the relationships and evolution of organisms.
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Affiliation(s)
- Aluska T Dos Santos
- Setor de Ciências Exatas, Departamento de Química, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
- Setor de Ciências Biológicas, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - João P A Souza
- Setor de Ciências Exatas, Departamento de Química, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Isaac R Jorge
- Setor de Ciências Biológicas, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Samara M M Andrade
- Natural Resources Canada - Great Lakes Forestry Centre, Sault Ste Marie, Ontario, P6A 2E5, Canada
- Graduate Department of Forestry, John H. Daniels Faculty of Architecture, Landscape and Design, University of Toronto, Toronto, Ontario, M5S 3B3, Canada
| | - Brunno B Rosa
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, 14040-901, Brazil
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, 10115, Berlin, Germany
| | - Maurício O Moura
- Setor de Ciências Biológicas, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Paulo H G Zarbin
- Setor de Ciências Exatas, Departamento de Química, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil.
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Tran THG, Dong VH, Le VT, Vu TN, Dang HA, Huynh TML. Detection and molecular characterization of virulent Newcastle disease virus (subgenotype VII.2) in broiler chickens in Northern Vietnam. Vet World 2023; 16:2086-2095. [PMID: 38023274 PMCID: PMC10668557 DOI: 10.14202/vetworld.2023.2086-2095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/08/2023] [Indexed: 12/01/2023] Open
Abstract
Background and Aim Newcastle disease (ND) is a major viral disease of poultry worldwide. However, data on the molecular characterization of Newcastle disease virus (NDV) in Vietnam are limited. This study aimed to identify the molecular characteristics of NDV strains from the vaccinated chickens farmed in Northern Vietnam. Materials and Methods We used reverse-transcription polymerase chain reaction (PCR), sequencing and phylogenetic analysis to characterize NDV strains from vaccinated chicken farms in Northern Vietnam. Results Seven out of 72 (9.7%) chicken tissue samples collected from seven chicken farms in the four cities/provinces in northern Vietnam were positive for the NDV genome by PCR method. The complete sequences of the fusion (F) and hemagglutinin-neuraminidase (HN) genes of NDVs isolated in the North of Vietnam from 2021 to 2022 were further evaluated. The results indicated that all seven Vietnamese isolates obtained were reported as virulent NDV strains with the amino acid (AA) sequence of the F0 protein proteolytic cleavage site motif (112RRRKRF117). Phylogenetic analysis revealed that they were grouped with other NDV class II from subgenotype VII.2, including the two previous Vietnamese NDV (2015), the Chinese (2017), and Southern African (2013) NDV strains. In addition, some AA substitutions were observed in the neutralizing epitopes of the F and HN proteins of the current Vietnamese NDV strains. Conclusion The present findings provide useful information for future studies of the evolution of NDVs and improve strategies for ND-controlling programs in Vietnam.
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Affiliation(s)
- Thi Huong Giang Tran
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Van Hieu Dong
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Van Truong Le
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Thi Ngoc Vu
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Huu Anh Dang
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Thi My Le Huynh
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
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Vázquez-Morón S, Iglesias-Caballero M, Lepe JA, Garcia F, Melón S, Marimon JM, García de Viedma D, Folgueira MD, Galán JC, López-Causapé C, Benito-Ruesca R, Alcoba-Florez J, Gonzalez Candelas F, Toro MD, Fajardo M, Ezpeleta C, Lázaro F, Pérez Castro S, Cuesta I, Zaballos A, Pozo F, Casas I. Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network. Int J Mol Sci 2023; 24:ijms24108573. [PMID: 37239920 DOI: 10.3390/ijms24108573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Millions of SARS-CoV-2 whole genome sequences have been generated to date. However, good quality data and adequate surveillance systems are required to contribute to meaningful surveillance in public health. In this context, the network of Spanish laboratories for coronavirus (RELECOV) was created with the main goal of promoting actions to speed up the detection, analyses, and evaluation of SARS-CoV-2 at a national level, partially structured and financed by an ECDC-HERA-Incubator action (ECDC/GRANT/2021/024). A SARS-CoV-2 sequencing quality control assessment (QCA) was developed to evaluate the network's technical capacity. QCA full panel results showed a lower hit rate for lineage assignment compared to that obtained for variants. Genomic data comprising 48,578 viral genomes were studied and evaluated to monitor SARS-CoV-2. The developed network actions showed a 36% increase in sharing viral sequences. In addition, analysis of lineage/sublineage-defining mutations to track the virus showed characteristic mutation profiles for the Delta and Omicron variants. Further, phylogenetic analyses strongly correlated with different variant clusters, obtaining a robust reference tree. The RELECOV network has made it possible to improve and enhance the genomic surveillance of SARS-CoV-2 in Spain. It has provided and evaluated genomic tools for viral genome monitoring and characterization that make it possible to increase knowledge efficiently and quickly, promoting the genomic surveillance of SARS-CoV-2 in Spain.
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Affiliation(s)
- Sonia Vázquez-Morón
- Respiratory Viruses and Influenza Unit, National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
| | - María Iglesias-Caballero
- Respiratory Viruses and Influenza Unit, National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
| | - José Antonio Lepe
- Microbiology Service, Hospital Universitario Virgen del Rocio, 41013 Sevilla, Spain
| | - Federico Garcia
- Microbiology Service, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs. Granada, 18016 Granada, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28029 Madrid, Spain
| | - Santiago Melón
- Microbiology Service, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - José M Marimon
- Microbiology Service, Instituto de Investigación Sanitaria Biodonostia, Hospital Universitario Donostia, 20014 Donostia-San Sebastian, Spain
| | - Darío García de Viedma
- Microbiology Service, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Maria Dolores Folgueira
- Microbiology Department, Hospital Universitario 12 de Octubre, Biomedical Research Institute imas12, 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
| | - Juan Carlos Galán
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
- Microbiology Service, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Carla López-Causapé
- Microbiology Service, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Rafael Benito-Ruesca
- Microbiology Service, Hospital Clínico Universitario Lozano Blesa, Departamento de Microbiología, Facultad de Medicina, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Julia Alcoba-Florez
- Microbiology Service, Hospital Universitario Ntra. Sra de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Fernando Gonzalez Candelas
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), 46020 Valencia, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Miguel Fajardo
- Microbiology Service, Hospital Universitario de Badajoz, 06080 Badajoz, Spain
| | - Carmen Ezpeleta
- Complejo Hospitalario de Navarra and Navarra De Servicios Y Tecnologías S A (NASERTIC), 31008 Pamplona, Spain
| | - Fernando Lázaro
- Microbiology Service, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Sonia Pérez Castro
- Microbiology Service, Complexo Hospitalario Universitario de Vigo, 36204 Vigo, Spain
| | - Isabel Cuesta
- Bioinformatics Unit, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
| | - Angel Zaballos
- Genomics Unit, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
| | - Francisco Pozo
- Respiratory Viruses and Influenza Unit, National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
| | - Inmaculada Casas
- Respiratory Viruses and Influenza Unit, National Centre for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, 28029 Madrid, Spain
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Gong J, Chen XF, Fan X, Xu J, Zhang H, Li RY, Chen SCA, Kong F, Zhang S, Sun ZY, Kang M, Liao K, Guo DW, Wan Z, Hu ZD, Chu YZ, Zhao HM, Zou GL, Shen C, Geng YY, Wu WW, Wang H, Zhao F, Lu X, He LH, Liu GM, Xu YC, Zhang JZ, Xiao M. Emergence of Antifungal Resistant Subclades in the Global Predominant Phylogenetic Population of Candida albicans. Microbiol Spectr 2023; 11:e0380722. [PMID: 36700687 PMCID: PMC9927326 DOI: 10.1128/spectrum.03807-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Candida albicans remains the most common species causing invasive candidiasis. In this study, we present the population structure of 551 global C. albicans strains. Of these, the antifungal susceptibilities of 370 strains were tested. Specifically, 66.6% of the azole-nonsusceptible (NS)/non-wild-type (NWT) strains that were tested belonged to Clade 1. A phylogenetic analysis, a principal components analysis, the population structure, and a loss of heterozygosity events revealed two nested subclades in Clade 1, namely, Clade 1-R and Clade 1-R-α, that exhibited higher azole-NS/NWT rates (75.0% and 100%, respectively). In contrast, 6.4% (21/326) of the non-Clade 1-R isolates were NS/NWT to at least 1 of 4 azoles. Notably, all of the Clade 1-R-α isolates were pan-azole-NS/NWT that carried unique A114S and Y257H double substitutions in Erg11p and had the overexpression of ABC-type efflux pumps introduced by the substitution A736V in transcript factor Tac1p. It is worth noting that the Clade 1-R and Clade 1-R-α isolates were from different cities that are distributed over a large geographic span. Our study demonstrated the presence of specific phylogenetic subclades that are associated with antifungal resistance among C. albicans Clade 1, which calls for public attention on the monitoring of the future spread of these clones. IMPORTANCE Invasive candidiasis is the most common human fungal disease among hospitalized patients, and Candida albicans is the predominant pathogen. Considering the large number of infected cases and the limited alternative therapies, the azole-resistance of C. albicans brings a huge clinical threat. Here, our study suggested that antifungal resistance in C. albicans could also be associated with phylogenetic lineages. Specifically, it was revealed that more than half of the azole-resistant C. albicans strains belonged to the same clade. Furthermore, two nested subclades of the clade exhibited extremely high azole-resistance. It is worth noting that the isolates of two subclades were from different cities that are distributed over a large geographic span in China. This indicates that the azole-resistant C. albicans subclades may develop into serious public health concerns.
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Affiliation(s)
- Jie Gong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin-Fei Chen
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Juan Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Han Zhang
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Ruo-Yu Li
- Department of Dermatology, Beijing University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Beijing University, Beijing, China
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Shu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zi-Yong Sun
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mei Kang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kang Liao
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Da-Wen Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhe Wan
- Department of Dermatology, Beijing University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Zhi-Dong Hu
- Department of Clinical Laboratory, Tianjin Medical University General Hospital, Tianjin, China
| | - Yun-Zhuo Chu
- Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hong-Mei Zhao
- Department of Clinical Laboratory, The People's Hospital of Liaoning Province, Shenyang, Liaoning, China
| | - Gui-Ling Zou
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Chong Shen
- Center for Statistical Science, and Department of Industrial Engineering, Tsinghua University, Beijing, China
| | - Yuan-Yuan Geng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei-Wei Wu
- Department of Dermatology, the Fifth People's Hospital of Hainan Province, Haikou, Hainan, China
| | - He Wang
- Dynamiker Sub-center of Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Disease, Tianjin, China
| | - Fei Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li-Hua He
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Gui-Ming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Jian-Zhong Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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Adaptive Evolution of the Fox Coronavirus Based on Genome-Wide Sequence Analysis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9627961. [PMID: 35463975 PMCID: PMC9020971 DOI: 10.1155/2022/9627961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 01/01/2022] [Accepted: 03/18/2022] [Indexed: 11/17/2022]
Abstract
Purpose. To report the first complete fox coronavirus (CoV) genome sequence obtained through genome-wide amplifications and to understand the adaptive evolution of fox CoV. Methods. Anal swab samples were collected from 35 foxes to detect the presence of CoV and obtain the virus sequence. Phylogenetic analysis was conducted using MrBayes. The possibility of recombination within these sequences was assessed using GARD. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Data Monkey platforms. Results. Of the 35 samples, two were positive, and complete genome sequences for the viruses were obtained. Phylogenetic analysis, using Bayesian methods, of these sequences, together with other CoV sequences, revealed that the fox CoV sequences clustered with canine coronavirus (CCoV) sequences, with sequences from other carnivores more distantly related. In contrast to the feline, ferret and mink CoV sequences that clustered into species-specific clades, the fox CoV fell within the CCoV clade. Minimal evidence for recombination was found among the sequences. A total of 7, 3, 14, and 2 positively selected sites were identified in the M, N, S, and 7B genes, respectively, with 99, 111, and 581 negatively selected sites identified in M, N, and S genes, respectively. Conclusion. The complete genome sequence of fox CoV has been obtained for the first time. The results suggest that the genome sequence of fox CoV may have experienced adaptive evolution in the genes replication, entry, and virulence. The number of sites in each gene that experienced negative selection is far greater than the number that underwent positive selection, suggesting that most of the sequence is highly conserved and important for viral survive. However, positive selection at a few sites likely aided these viruses to adapt to new environments.
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Wang F, Tekle YI. Variation of natural selection in the Amoebozoa reveals heterogeneity across the phylogeny and adaptive evolution in diverse lineages. Front Ecol Evol 2022; 10:851816. [PMID: 36874909 PMCID: PMC9980437 DOI: 10.3389/fevo.2022.851816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The evolution and diversity of the supergroup Amoebozoa is complex and poorly understood. The supergroup encompasses predominantly amoeboid lineages characterized by extreme diversity in phenotype, behavior and genetics. The study of natural selection, a driving force of diversification, within and among species of Amoebozoa will play a crucial role in understanding the evolution of the supergroup. In this study, we searched for traces of natural selection based on a set of highly conserved protein-coding genes in a phylogenetic framework from a broad sampling of amoebozoans. Using these genes, we estimated substitution rates and inferred patterns of selective pressure in lineages and sites with various models. We also examined the effect of selective pressure on codon usage bias and potential correlations with observed biological traits and habitat. Results showed large heterogeneity of selection across lineages of Amoebozoa, indicating potential species-specific optimization of adaptation to their diverse ecological environment. Overall, lineages in Tubulinea had undergone stronger purifying selection with higher average substitution rates compared to Discosea and Evosea. Evidence of adaptive evolution was observed in some representative lineages and in a gene (Rpl7a) within Evosea, suggesting potential innovation and beneficial mutations in these lineages. Our results revealed that members of the fast-evolving lineages, Entamoeba and Cutosea, all underwent strong purifying selection but had distinct patterns of codon usage bias. For the first time, this study revealed an overall pattern of natural selection across the phylogeny of Amoebozoa and provided significant implications on their distinctive evolutionary processes.
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Affiliation(s)
- Fang Wang
- Department of Biology, Spelman College, Atlanta, GA, United States
| | - Yonas I Tekle
- Department of Biology, Spelman College, Atlanta, GA, United States
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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9
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Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function. mBio 2021; 12:mBio.00605-21. [PMID: 33975934 PMCID: PMC8262981 DOI: 10.1128/mbio.00605-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate intracellular pathogen Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted infections and blindness globally. To date, Ct urogenital strains are considered tryptophan prototrophs, utilizing indole for tryptophan synthesis within a closed-conformation tetramer comprised of two α (TrpA)- and two β (TrpB)-subunits. In contrast, ocular strains are auxotrophs due to mutations in TrpA, relying on host tryptophan pools for survival. It has been speculated that there is strong selective pressure for urogenital strains to maintain a functional operon. Here, we performed genetic, phylogenetic, and novel functional modeling analyses of 595 geographically diverse Ct ocular, urethral, vaginal, and rectal strains with complete operon sequences. We found that ocular and urogenital, but not lymphogranuloma venereum, TrpA-coding sequences were under positive selection. However, vaginal and urethral strains exhibited greater nucleotide diversity and a higher ratio of nonsynonymous to synonymous substitutions [Pi(a)/Pi(s)] than ocular strains, suggesting a more rapid evolution of beneficial mutations. We also identified nonsynonymous amino acid changes for an ocular isolate with a urogenital backbone in the intergenic region between TrpR and TrpB at the exact binding site for YtgR-the only known iron-dependent transcription factor in Chlamydia-indicating that selective pressure has disabled the response to fluctuating iron levels. In silico effects on protein stability, ligand-binding affinity, and tryptophan repressor (TrpR) affinity for single-stranded DNA (ssDNA) measured by calculating free energy changes (ΔΔG) between Ct reference and mutant tryptophan operon proteins were also analyzed. We found that tryptophan synthase function was likely suboptimal compared to other bacterial tryptophan prototrophs and that a diversity of urogenital strain mutations rendered the synthase nonfunctional or inefficient. The novel mutations identified here affected active sites in an orthosteric manner but also hindered α- and β-subunit allosteric interactions from distant sites, reducing efficiency of the tryptophan synthase. Importantly, strains with mutant proteins were inclined toward energy conservation by exhibiting an altered affinity for their respective ligands compared to reference strains, indicating greater fitness. This is not surprising as l-tryptophan is one of the most energetically costly amino acids to synthesize. Mutations in the tryptophan repressor gene (trpR) among urogenital strains were similarly detrimental to function. Our findings indicate that urogenital strains are evolving more rapidly than previously recognized with mutations that impact tryptophan operon function in a manner that is energetically beneficial, providing a novel host-pathogen evolutionary mechanism for intracellular survival.IMPORTANCE Chlamydia trachomatis (Ct) is a major global public health concern causing sexually transmitted and ocular infections affecting over 130 million and 260 million people, respectively. Sequelae include infertility, preterm birth, ectopic pregnancy, and blindness. Ct relies on available host tryptophan pools and/or substrates to synthesize tryptophan to survive. Urogenital strains synthesize tryptophan from indole using their intact tryptophan synthase (TS). Ocular strains contain a trpA frameshift mutation that encodes a truncated TrpA with loss of TS function. We found that TS function is likely suboptimal compared to other tryptophan prototrophs and that urogenital stains contain diverse mutations that render TS nonfunctional/inefficient, evolve more rapidly than previously recognized, and impact operon function in a manner that is energetically beneficial, providing an alternative host-pathogen evolutionary mechanism for intracellular survival. Our research has broad scientific appeal since our approach can be applied to other bacteria that may explain evolution/survival in host-pathogen interactions.
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10
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Yuan Y, He J, Gong L, Li W, Jiang L, Liu J, Chen Q, Yu J, Hou S, Shi Y, Lu S, Zhang Z, Ge Y, Sa N, He L, Wu J, Sun Y, Liu Z. Molecular epidemiology of SARS-CoV-2 clusters caused by asymptomatic cases in Anhui Province, China. BMC Infect Dis 2020; 20:930. [PMID: 33287717 PMCID: PMC7719853 DOI: 10.1186/s12879-020-05612-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/11/2020] [Indexed: 01/25/2023] Open
Abstract
Background COVID-19 is a newly emerging disease caused by a novel coronavirus (SARS-CoV-2), which spread globally in early 2020. Asymptomatic carriers of the virus contribute to the propagation of this disease, and the existence of asymptomatic infection has caused widespread fear and concern in the control of this pandemic. Methods In this study, we investigated the origin and transmission route of SARS-CoV-2 in Anhui’s two clusters, analyzed the role and infectiousness of asymptomatic patients in disease transmission, and characterized the complete spike gene sequences in the Anhui strains. Results We conducted an epidemiological investigation of two clusters caused by asymptomatic infections sequenced the spike gene of viruses isolated from 12 patients. All cases of the two clusters we investigated had clear contact histories, both from Wuhan, Hubei province. The viruses isolated from two outbreaks in Anhui were found to show a genetically close link to the virus from Wuhan. In addition, new single nucleotide variations were discovered in the spike gene. Conclusions Both clusters may have resulted from close contact and droplet-spreading and asymptomatic infections were identified as the initial cause. We also analyzed the infectiousness of asymptomatic cases and the challenges to the current epidemic to provided information for the development of control strategies.
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Affiliation(s)
- Yuan Yuan
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Jun He
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Lei Gong
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Weiwei Li
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Liangliang Jiang
- Maanshan Center for Disease Control and Prevention, 849, Jiangdong Avenue, Maanshan, China
| | - Jiang Liu
- Huainan Center for Disease Control and Prevention, Linchang Avenue, Huainan, China
| | - Qingqing Chen
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Junling Yu
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Sai Hou
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Yonglin Shi
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Siqi Lu
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Zhuhui Zhang
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Yinglu Ge
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Nan Sa
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China
| | - Lan He
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Jiabing Wu
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China
| | - Yong Sun
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China. .,Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China.
| | - Zhirong Liu
- Anhui Provincial Center for Disease Control and Prevention, 12560, Fanhua Avenue, Hefei, China.
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11
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Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9089768. [PMID: 32923488 PMCID: PMC7453238 DOI: 10.1155/2020/9089768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/19/2020] [Accepted: 07/30/2020] [Indexed: 11/21/2022]
Abstract
Purpose We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus. Methods Ascites samples from 31 cats with suspected FIP and feces samples from 8 healthy cats were screened for the presence of FCoV. Partial viral genome sequences, including parts of the nsp12-nsp14, S, N, and 7b genes, were obtained and aligned with additional sequences obtained from the GenBank database. Bayesian phylogenetic analysis was conducted, and the possibility of recombination within these sequences was assessed. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Datamonkey platforms. Results Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. Fewer than 3 recombination breakpoints were detected in the nsp12-nsp14, S, N, and 7b genes, suggesting that analyses for positive selection could be conducted. A total of 4, 12, 4, and 4 positively selected sites were detected in the nsp12-nsp14, S, N, and 7b genes, respectively, with the previously described site 245 of the S gene, which distinguishes FIPV from FECV, being a positive selection site. Conversely, 106, 168, 25, and 17 negative selection sites in the nsp12-14, S, N, and 7b genes, respectively, were identified. Conclusion Our study provides evidence that the FCoV genes encoding replicative, entry, and virulence proteins potentially experienced adaptive evolution. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. A few of the sites showing evidence of positive selection might be associated with the more severe pathology of FIPV or help these viruses survive other harmful conditions.
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12
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Reyes-Corral M, Sørensen NM, Thrasivoulou C, Dasgupta P, Ashmore JF, Ahmed A. Differential Free Intracellular Calcium Release by Class II Antiarrhythmics in Cancer Cell Lines. J Pharmacol Exp Ther 2019; 369:152-162. [PMID: 30655298 DOI: 10.1124/jpet.118.254375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/02/2019] [Indexed: 12/31/2022] Open
Abstract
Class II antiarrhythmics or β-blockers are antisympathetic nervous system agents that act by blocking β-adrenoceptors. Despite their common clinical use, little is known about the effects of β-blockers on free intracellular calcium (Ca2+ i), an important cytosolic second messenger and a key regulator of cell function. We investigated the role of four chemical analogs, commonly prescribed β-blockers (atenolol, metoprolol, propranolol, and sotalol), on Ca2+ i release and whole-cell currents in mammalian cancer cells (PC3 prostate cancer and MCF7 breast cancer cell lines). We discovered that only propranolol activated free Ca2+ i release with distinct kinetics, whereas atenolol, metoprolol, and sotalol did not. The propranolol-induced Ca2+ i release was significantly inhibited by the chelation of extracellular calcium with ethylene glycol tetraacetic acid (EGTA) and by dantrolene, an inhibitor of the endoplasmic reticulum (ER) ryanodine receptor channels, and it was completely abolished by 2-aminoethoxydiphenyl borate, an inhibitor of the ER inositol-1,4,5-trisphosphate (IP3) receptor channels. Exhaustion of ER stores with 4-chloro-m-cresol, a ryanodine receptor activator, or thapsigargin, a sarco/ER Ca2+ ATPase inhibitor, precluded the propranolol-induced Ca2+ i release. Finally, preincubation of cells with sotalol or timolol, nonselective blockers of β-adrenoceptors, also reduced the Ca2+ i release activated by propranolol. Our results show that different β-blockers have differential effects on whole-cell currents and free Ca2+ i release and that propranolol activates store-operated Ca2+ i release via a mechanism that involves calcium-induced calcium release and putative downstream transducers such as IP3 The differential action of class II antiarrhythmics on Ca2+ i release may have implications on the pharmacology of these drugs.
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Affiliation(s)
- Marta Reyes-Corral
- Centre for Stem Cells and Regenerative Medicine (M.R.-C., A.A.) and MRC Centre for Transplantation (P.D.), King's College London, London, United Kingdom; Sophion Bioscience A/S, Ballerup, Denmark (N.M.S.); and Departments of Cell and Developmental Biology (C.T.) and Neuroscience, Physiology and Pharmacology, and The Ear Institute (J.F.A.), University College London, London, United Kingdom
| | - Naja M Sørensen
- Centre for Stem Cells and Regenerative Medicine (M.R.-C., A.A.) and MRC Centre for Transplantation (P.D.), King's College London, London, United Kingdom; Sophion Bioscience A/S, Ballerup, Denmark (N.M.S.); and Departments of Cell and Developmental Biology (C.T.) and Neuroscience, Physiology and Pharmacology, and The Ear Institute (J.F.A.), University College London, London, United Kingdom
| | - Christopher Thrasivoulou
- Centre for Stem Cells and Regenerative Medicine (M.R.-C., A.A.) and MRC Centre for Transplantation (P.D.), King's College London, London, United Kingdom; Sophion Bioscience A/S, Ballerup, Denmark (N.M.S.); and Departments of Cell and Developmental Biology (C.T.) and Neuroscience, Physiology and Pharmacology, and The Ear Institute (J.F.A.), University College London, London, United Kingdom
| | - Prokar Dasgupta
- Centre for Stem Cells and Regenerative Medicine (M.R.-C., A.A.) and MRC Centre for Transplantation (P.D.), King's College London, London, United Kingdom; Sophion Bioscience A/S, Ballerup, Denmark (N.M.S.); and Departments of Cell and Developmental Biology (C.T.) and Neuroscience, Physiology and Pharmacology, and The Ear Institute (J.F.A.), University College London, London, United Kingdom
| | - Jonathan F Ashmore
- Centre for Stem Cells and Regenerative Medicine (M.R.-C., A.A.) and MRC Centre for Transplantation (P.D.), King's College London, London, United Kingdom; Sophion Bioscience A/S, Ballerup, Denmark (N.M.S.); and Departments of Cell and Developmental Biology (C.T.) and Neuroscience, Physiology and Pharmacology, and The Ear Institute (J.F.A.), University College London, London, United Kingdom
| | - Aamir Ahmed
- Centre for Stem Cells and Regenerative Medicine (M.R.-C., A.A.) and MRC Centre for Transplantation (P.D.), King's College London, London, United Kingdom; Sophion Bioscience A/S, Ballerup, Denmark (N.M.S.); and Departments of Cell and Developmental Biology (C.T.) and Neuroscience, Physiology and Pharmacology, and The Ear Institute (J.F.A.), University College London, London, United Kingdom
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13
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Esmaelizad M, Mayahi V. Analysis of natural recombination and host-related evolutionary dynamics of avian avulavirus 1 isolates based on positive and negative selection from 1948 to 2017. Arch Virol 2019; 164:717-724. [DOI: 10.1007/s00705-018-04130-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/08/2018] [Indexed: 12/26/2022]
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14
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Zhang QL, Zhang L, Yang XZ, Wang XT, Li XP, Wang J, Chen JY, Yuan ML. Comparative transcriptomic analysis of Tibetan Gynaephora to explore the genetic basis of insect adaptation to divergent altitude environments. Sci Rep 2017; 7:16972. [PMID: 29208990 PMCID: PMC5717227 DOI: 10.1038/s41598-017-17051-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/21/2017] [Indexed: 01/01/2023] Open
Abstract
Adaptation of insects to different altitudes remain largely unknown, especially those endemic to the Tibetan Plateau (TP). Here, we generated the transcriptomes of Gynaephora menyuanensis and G. alpherakii, inhabiting different high altitudes on the TP, and used these and the previously available transcriptomic and genomic sequences from low-altitude insects to explore potential genetic basis for divergent high-altitude adaptation in Gynaephora. An analysis of 5,869 orthologous genes among Gynaephora and other three low-altitude insects uncovered that fast-evolving genes and positively selected genes (PSGs) in the two Gynaephora species were enriched in energy metabolism and hypoxia response categories (e.g. mitochondrion, oxidation-reduction process, and response to oxidative stress). Particularly, mTOR signaling pathway involving hypoxia was enriched by PSGs, indicating this well-known pathway in mammal hypoxia adaptation may be an important signaling system in Gynaephora. Furthermore, some PSGs were associated with response to hypoxia (e.g. cytochrome proteins), cold (e.g. dehydrogenase) and DNA repair (e.g. DNA repair proteins). Interestingly, several insect-specific genes that were associated with exoskeleton and cuticle development (e.g. chitinase and ecdysteroids) had experienced positive selection, suggesting the specific adaptive mechanisms in insects. This study is favourable for understanding the adaptive evolution of Gynaephora and even TP insects to divergent altitudes.
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Affiliation(s)
- Qi-Lin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China.,Evo-devo Institute, School of Life Science, Nanjing University, Nanjing 210023, China; Nanjing Institute of Geology and Paleontology, Nanjing, 210008, China
| | - Li Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of, Agriculture, China
| | - Xing-Zhuo Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of, Agriculture, China
| | - Xiao-Tong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xiao-Peng Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Juan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jun-Yuan Chen
- Evo-devo Institute, School of Life Science, Nanjing University, Nanjing 210023, China; Nanjing Institute of Geology and Paleontology, Nanjing, 210008, China.
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China. .,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of, Agriculture, China.
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15
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Vogl W, Lyon K, Adams A, Piva M, Nassour V. The endoplasmic reticulum, calcium signaling and junction turnover in Sertoli cells. Reproduction 2017; 155:R93-R104. [PMID: 29066527 DOI: 10.1530/rep-17-0281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/12/2017] [Accepted: 10/23/2017] [Indexed: 12/19/2022]
Abstract
The endoplasmic reticulum (ER) forms a continuous network throughout morphologically differentiated Sertoli cells. It is an integral component of intercellular adhesion junctions in this cell type, as well as forming membrane contact sites with the plasma membrane and intracellular organelles. One of the major functions of the ER in cells generally is maintaining calcium homeostasis and generating calcium signals. In this review, we discuss what is currently known about the overall pattern of distribution of the ER in Sertoli cells and the location of calcium regulatory machinery in the various subdomains of the organelle. Current data are consistent with the hypothesis that calcium signaling by the ER of Sertoli cells may play a significant role in events related to junction remodeling that occur in the seminiferous epithelium during spermatogenesis.
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Affiliation(s)
- Wayne Vogl
- Department of Cellular and Physiological SciencesUniversity of British Columbia, British Columbia, Canada .,Department of Obstetrics and GynaecologyUniversity of British Columbia, British Columbia, Canada
| | - Kevin Lyon
- Department of Obstetrics and GynaecologyUniversity of British Columbia, British Columbia, Canada
| | - Arlo Adams
- Department of Cellular and Physiological SciencesUniversity of British Columbia, British Columbia, Canada
| | - Matthew Piva
- Department of Cellular and Physiological SciencesUniversity of British Columbia, British Columbia, Canada
| | - Vanessa Nassour
- Department of Cellular and Physiological SciencesUniversity of British Columbia, British Columbia, Canada
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16
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Trinh JT, Székely T, Shao Q, Balázsi G, Zeng L. Cell fate decisions emerge as phages cooperate or compete inside their host. Nat Commun 2017; 8:14341. [PMID: 28165024 PMCID: PMC5303824 DOI: 10.1038/ncomms14341] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023] Open
Abstract
The system of the bacterium Escherichia coli and its virus, bacteriophage lambda, is paradigmatic for gene regulation in cell-fate development, yet insight about its mechanisms and complexities are limited due to insufficient resolution of study. Here we develop a 4-colour fluorescence reporter system at the single-virus level, combined with computational models to unravel both the interactions between phages and how individual phages determine cellular fates. We find that phages cooperate during lysogenization, compete among each other during lysis, and that confusion between the two pathways occasionally occurs. Additionally, we observe that phage DNAs have fluctuating cellular arrival times and vie for resources to replicate, enabling the interplay during different developmental paths, where each phage genome may make an individual decision. These varied strategies could separate the selection for replication-optimizing beneficial mutations during lysis from sequence diversification during lysogeny, allowing rapid adaptation of phage populations for various environments.
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Affiliation(s)
- Jimmy T. Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
| | - Tamás Székely
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
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17
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Kamau LM, Skilton RA, Githaka N, Kiara H, Kabiru E, Shah T, Musoke AJ, Bishop RP. Extensive polymorphism of Ra86 genes in field populations of Rhipicephalus appendiculatus from Kenya. Ticks Tick Borne Dis 2016; 7:772-781. [PMID: 27051976 DOI: 10.1016/j.ttbdis.2016.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
Abstract
Commercial vaccines based on recombinant forms of the Bm86 tick gut antigen are used to control the southern cattle tick, Rhipicephalus microplus, a 1-host species, in Australia and Latin America. We describe herein sequence polymorphism in genes encoding Ra86 homologues of Bm86 in the brown ear tick, Rhipicephalus appendiculatus, isolated from four Kenyan field populations and one laboratory colony. Sequencing of 19 Ra86 sequences defined two alleles differentiated by indels, encoding 693 amino acids (aa) and 654 aa respectively, from the Muguga laboratory reference strain. Ra86 sequences were also determined from gut cDNA from four field populations of R. appendiculatus collected in different livestock production systems in Kenya. Analysis of approximately 20 Ra86 sequences from each of the four field sites in central and Western Kenya; Makuyu, Kiambu, Kakamega and Uasin Gishu, revealed three additional size types differentiated by 39-49 amino acid indels resulting in a total of 5 indel-defined genotypes. The 693 aa type 5 was isolated only from the laboratory tick stock; genotypes 1, 2 and 3 were identified in ticks from the four Kenyan field sites and appeared to be derivatives of the shorter RA86 genotype found in Muguga laboratory stock genotype 4. By contrast no large indels have yet been observed between R. microplus sequences from Australia, South America or Africa. Evidence that selection contributes to the observed sequence variation was provided by analysis of ratio of synonymous and non-synonymous substitutions and application of the selective neutrality and neutral evolution tests to the primary data. Phylogenetic analysis clustered sequences from all Ra86 size types and Bm86, into four major clades based on amino acid substitutions, but there was no evidence that these groupings correlated with geographical separation of R. appendiculatus populations.
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Affiliation(s)
- L M Kamau
- Department of Zoological Sciences, Kenyatta University, P.O. Box 43844, Nairobi, Kenya; International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - R A Skilton
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - N Githaka
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya.
| | - H Kiara
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - E Kabiru
- Department of Zoological Sciences, Kenyatta University, P.O. Box 43844, Nairobi, Kenya
| | - T Shah
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - A J Musoke
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
| | - R P Bishop
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
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18
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Genetic drift of human coronavirus OC43 spike gene during adaptive evolution. Sci Rep 2015; 5:11451. [PMID: 26099036 PMCID: PMC4476415 DOI: 10.1038/srep11451] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/26/2015] [Indexed: 11/08/2022] Open
Abstract
Coronaviruses (CoVs) continuously threaten human health. However, to date, the evolutionary mechanisms that govern CoV strain persistence in human populations have not been fully understood. In this study, we characterized the evolution of the major antigen-spike (S) gene in the most prevalent human coronavirus (HCoV) OC43 using phylogenetic and phylodynamic analysis. Among the five known HCoV-OC43 genotypes (A to E), higher substitution rates and dN/dS values as well as more positive selection sites were detected in the S gene of genotype D, corresponding to the most dominant HCoV epidemic in recent years. Further analysis showed that the majority of substitutions were located in the S1 subunit. Among them, seven positive selection sites were chronologically traced in the temporal evolution routes of genotype D, and six were located around the critical sugar binding region in the N-terminal domain (NTD) of S protein, an important sugar binding domain of CoV. These findings suggest that the genetic drift of the S gene may play an important role in genotype persistence in human populations, providing insights into the mechanisms of HCoV-OC43 adaptive evolution.
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Veldhuis NA, Poole DP, Grace M, McIntyre P, Bunnett NW. The G Protein–Coupled Receptor–Transient Receptor Potential Channel Axis: Molecular Insights for Targeting Disorders of Sensation and Inflammation. Pharmacol Rev 2014; 67:36-73. [DOI: 10.1124/pr.114.009555] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Bachmann NL, Fraser TA, Bertelli C, Jelocnik M, Gillett A, Funnell O, Flanagan C, Myers GSA, Timms P, Polkinghorne A. Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum. BMC Genomics 2014; 15:667. [PMID: 25106440 PMCID: PMC4137089 DOI: 10.1186/1471-2164-15-667] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced. RESULTS Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the origin of these point mutations. CONCLUSIONS The genomic data revealed that variation between C. pecorum strains were mainly due to the accumulation of SNPs, some of which cause gene inactivation. The identification of these genetic differences will provide the basis for further studies to understand the biology and evolution of this important animal pathogen.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs 4558, Queensland, Australia.
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Nilius B, Szallasi A. Transient Receptor Potential Channels as Drug Targets: From the Science of Basic Research to the Art of Medicine. Pharmacol Rev 2014; 66:676-814. [DOI: 10.1124/pr.113.008268] [Citation(s) in RCA: 348] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Abstract
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from those expected under neutral evolution and described statistically by Kingman's coalescent. While differences in the statistical structure of genealogies have long been used as a test for the presence of selection, the full extent of the information that they contain has not been exploited. Here we demonstrate that the shape of the reconstructed genealogical tree for a moderately large number of random genomic samples taken from a fitness diverse, but otherwise unstructured, asexual population can be used to predict the relative fitness of individuals within the sample. To achieve this we define a heuristic algorithm, which we test in silico, using simulations of a Wright-Fisher model for a realistic range of mutation rates and selection strength. Our inferred fitness ranking is based on a linear discriminator that identifies rapidly coalescing lineages in the reconstructed tree. Inferred fitness ranking correlates strongly with actual fitness, with a genome in the top 10% ranked being in the top 20% fittest with false discovery rate of 0.1-0.3, depending on the mutation/selection parameters. The ranking also enables us to predict the genotypes that future populations inherit from the present one. While the inference accuracy increases monotonically with sample size, samples of 200 nearly saturate the performance. We propose that our approach can be used for inferring relative fitness of genomes obtained in single-cell sequencing of tumors and in monitoring viral outbreaks.
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Teso S, Passerini A. Joint probabilistic-logical refinement of multiple protein feature predictors. BMC Bioinformatics 2014; 15:16. [PMID: 24428894 PMCID: PMC3929554 DOI: 10.1186/1471-2105-15-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 11/06/2013] [Indexed: 11/24/2022] Open
Abstract
Background Computational methods for the prediction of protein features from sequence are a long-standing focus of bioinformatics. A key observation is that several protein features are closely inter-related, that is, they are conditioned on each other. Researchers invested a lot of effort into designing predictors that exploit this fact. Most existing methods leverage inter-feature constraints by including known (or predicted) correlated features as inputs to the predictor, thus conditioning the result. Results By including correlated features as inputs, existing methods only rely on one side of the relation: the output feature is conditioned on the known input features. Here we show how to jointly improve the outputs of multiple correlated predictors by means of a probabilistic-logical consistency layer. The logical layer enforces a set of weighted first-order rules encoding biological constraints between the features, and improves the raw predictions so that they least violate the constraints. In particular, we show how to integrate three stand-alone predictors of correlated features: subcellular localization (Loctree [J Mol Biol 348:85–100, 2005]), disulfide bonding state (Disulfind [Nucleic Acids Res 34:W177–W181, 2006]), and metal bonding state (MetalDetector [Bioinformatics 24:2094–2095, 2008]), in a way that takes into account the respective strengths and weaknesses, and does not require any change to the predictors themselves. We also compare our methodology against two alternative refinement pipelines based on state-of-the-art sequential prediction methods. Conclusions The proposed framework is able to improve the performance of the underlying predictors by removing rule violations. We show that different predictors offer complementary advantages, and our method is able to integrate them using non-trivial constraints, generating more consistent predictions. In addition, our framework is fully general, and could in principle be applied to a vast array of heterogeneous predictions without requiring any change to the underlying software. On the other hand, the alternative strategies are more specific and tend to favor one task at the expense of the others, as shown by our experimental evaluation. The ultimate goal of our framework is to seamlessly integrate full prediction suites, such as Distill [BMC Bioinformatics 7:402, 2006] and PredictProtein [Nucleic Acids Res 32:W321–W326, 2004].
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Affiliation(s)
- Stefano Teso
- Department of Information Engineering and Computer Science, Università degli Studi di Trento, Trento, Italy.
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Abstract
The rate of evolution of the human papillomavirus 16 (HPV16) genome is low. However, the ability of the E6 oncoprotein to interact with distinct p53 variants causes selective pressure on the E6 gene. In addition, intratypic recombination events in the HPV16 E6 and E7 genes have been characterized as extraordinary phenomena during the evolutionary history of virus. In the present study, we identified two new sequence variants through nucleotide analysis of the E6-E7 region of the HPV16 genome. Maximum-likelihood and empirical Bayesian methods were used in order to identify positive selection at particular residues of the E6 and E7 genes. Using the single recombination breakpoint (SBP) method, we found evidence of recombination events in the E6 ORF. Nucleotide sequence analysis showed that the new sequence variants are phylogenetically distant from the other members of the population. Our results indicate that new evolutionary intermediates of HPV16 might be formed either though positive selective pressure or through recombination events by multiple infections with distinct HPV16 variants.
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Directional evolution of Chlamydia trachomatis towards niche-specific adaptation. J Bacteriol 2012; 194:6143-53. [PMID: 22961851 DOI: 10.1128/jb.01291-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
On behalf of the host-pathogen "arms race," a cutting-edge approach for elucidating genotype-phenotype relationships relies on the identification of positively selected loci involved in pathoadaptation. We studied the obligate intracellular bacterium Chlamydia trachomatis, for which same-species strains display a nearly identical core and pan genome, while presenting a wide range of tissue tropism and ecological success. We sought to evaluate the evolutionary patterns underlying species separation (divergence) and C. trachomatis serovar radiation (polymorphism) and to establish genotype-phenotype associations. By analyzing 60 Chlamydia strains, we detected traces of Muller's ratchet as a result of speciation and identified positively selected genes and codons hypothetically involved in the infection of different human cell types (e.g., columnar epithelial cells of ocular or genital mucosae and mononuclear phagocytes) and also events likely driving pathogenic and ecological success dissimilarities. In general, these genes code for proteins involved in immune response elicitation, proteolysis, and the subversion of host-cell functions, and also for proteins with unknown function(s). Several genes are potentially involved in more than one adaptive process, suggesting multiple functions or a distinct modus operandi for a specific function, and thus should be considered as crucial research targets. In addition, six of the nine genes encoding the putative antigen/adhesin polymorphic membrane proteins seem to be under positive selection along specific serovars, which sustains an essential biological role of this extra-large paralogue family in chlamydial pathobiology. This study provides insight into how evolutionary inferences illuminate ecological processes such as adaptation to different niches, pathogenicity, or ecological success driven by arms races.
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Morgan CC, Shakya K, Webb A, Walsh TA, Lynch M, Loscher CE, Ruskin HJ, O'Connell MJ. Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. BMC Evol Biol 2012; 12:114. [PMID: 22788692 PMCID: PMC3563467 DOI: 10.1186/1471-2148-12-114] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/22/2012] [Indexed: 12/17/2022] Open
Abstract
Background Cancer, much like most human disease, is routinely studied by utilizing model organisms. Of these model organisms, mice are often dominant. However, our assumptions of functional equivalence fail to consider the opportunity for divergence conferred by ~180 Million Years (MY) of independent evolution between these species. For a given set of human disease related genes, it is therefore important to determine if functional equivalency has been retained between species. In this study we test the hypothesis that cancer associated genes have different patterns of substitution akin to adaptive evolution in different mammal lineages. Results Our analysis of the current literature and colon cancer databases identified 22 genes exhibiting colon cancer associated germline mutations. We identified orthologs for these 22 genes across a set of high coverage (>6X) vertebrate genomes. Analysis of these orthologous datasets revealed significant levels of positive selection. Evidence of lineage-specific positive selection was identified in 14 genes in both ancestral and extant lineages. Lineage-specific positive selection was detected in the ancestral Euarchontoglires and Hominidae lineages for STK11, in the ancestral primate lineage for CDH1, in the ancestral Murinae lineage for both SDHC and MSH6 genes and the ancestral Muridae lineage for TSC1. Conclusion Identifying positive selection in the Primate, Hominidae, Muridae and Murinae lineages suggests an ancestral functional shift in these genes between the rodent and primate lineages. Analyses such as this, combining evolutionary theory and predictions - along with medically relevant data, can thus provide us with important clues for modeling human diseases.
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Affiliation(s)
- Claire C Morgan
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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Liang B, Luo M, Scott-Herridge J, Semeniuk C, Mendoza M, Capina R, Sheardown B, Ji H, Kimani J, Ball BT, Van Domselaar G, Graham M, Tyler S, Jones SJM, Plummer FA. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1. PLoS One 2011; 6:e26745. [PMID: 22039546 PMCID: PMC3198814 DOI: 10.1371/journal.pone.0026745] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 10/03/2011] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. METHODOLOGY/PRINCIPAL FINDINGS HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB) sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL) and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. CONCLUSIONS/SIGNIFICANCE Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies.
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Affiliation(s)
- Binhua Liang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
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Wroe R, Chan HS, Bornberg‐Bauer E. A structural model of latent evolutionary potentials underlying neutral networks in proteins. HFSP JOURNAL 2010; 1:79-87. [DOI: 10.2976/1.2739116/10.2976/1] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 04/20/2007] [Indexed: 11/19/2022]
Affiliation(s)
- Richard Wroe
- a Faculty of Life Sciences , University of Manchester , United Kingdom
- b MRC Centre for Neurodegeneration Research , Kings College , London, United Kingdom
| | - Hue Sun Chan
- c Department of Biochemistry, and Department of Medical Genetics & Microbiology, Faculty of Medicine , University of Toronto , Toronto, Canada
| | - Erich Bornberg‐Bauer
- d Institute for Evolution and Biodiversity, School of Biological Sciences , University of Münster , Huefferstrasse 1, Münster, D48 149, Germany E-mail:
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Bindels RJ. 2009 Homer W. Smith Award: Minerals in Motion: From New Ion Transporters to New Concepts. J Am Soc Nephrol 2010; 21:1263-9. [DOI: 10.1681/asn.2010010001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Bamshad M, Stephens JC. Assessing human variation data for signatures of natural selection. Cold Spring Harb Protoc 2009; 2009:pdb.top61. [PMID: 20150073 DOI: 10.1101/pdb.top61] [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: 05/28/2023]
Abstract
In this article, we highlight some of the different types of natural selection, their effects on patterns of DNA variation, and some of the statistical tests that are commonly used to detect such effects. We also explain some of the relative strengths and weaknesses of different strategies that can be used to detect signatures of natural selection at individual loci. These strategies are illustrated by their application to empirical data from gene variants that are often associated with differences in disease susceptibility. We briefly outline some of the methods proposed to scan the genome for evidence of selection. Finally, we discuss some of the problems associated with identifying signatures of selection and with making inferences about the nature of the selective process.
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Miller PJ, Kim LM, Ip HS, Afonso CL. Evolutionary dynamics of Newcastle disease virus. Virology 2009; 391:64-72. [PMID: 19564032 DOI: 10.1016/j.virol.2009.05.033] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 03/27/2009] [Accepted: 05/22/2009] [Indexed: 12/26/2022]
Abstract
A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in viruses of low virulence, suggesting that an increase in virulence may accelerate the rate of NDV evolution.
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Affiliation(s)
- Patti J Miller
- Southeast Poultry Research Laboratories, USDA ARS, Southeast Poultry Research Laboratory, Athens, GA 30605, USA
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Wang J, Lu ZH, Gabius HJ, Rohowsky-Kochan C, Ledeen RW, Wu G. Cross-linking of GM1 ganglioside by galectin-1 mediates regulatory T cell activity involving TRPC5 channel activation: possible role in suppressing experimental autoimmune encephalomyelitis. THE JOURNAL OF IMMUNOLOGY 2009; 182:4036-45. [PMID: 19299701 DOI: 10.4049/jimmunol.0802981] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several animal autoimmune disorders are suppressed by treatment with the GM1 cross-linking units of certain toxins such as B subunit of cholera toxin (CtxB). Due to the recent observation of GM1 being a binding partner for the endogenous lectin galectin-1 (Gal-1), which is known to ameliorate symptoms in certain animal models of autoimmune disorders, we tested the hypothesis that an operative Gal-1/GM1 interplay induces immunosuppression in a manner evidenced by both in vivo and in vitro systems. Our study of murine experimental autoimmune encephalomyelitis (EAE) indicated suppressive effects by both CtxB and Gal-1 and further highlighted the role of GM1 in demonstrating enhanced susceptibility to EAE in mice lacking this ganglioside. At the in vitro level, polyclonal activation of murine regulatory T (Treg) cells caused up-regulation of Gal-1 that was both cell bound and released to the medium. Similar activation of murine CD4(+) and CD8(+) effector T (Teff) cells resulted in significant elevation of GM1 and GD1a, the neuraminidase-reactive precursor to GM1. Activation of Teff cells also up-regulated TRPC5 channels which mediated Ca(2+) influx upon GM1 cross-linking by Gal-1 or CtxB. This involved co-cross-linking of heterodimeric integrin due to close association of these alpha(4)beta(1) and alpha(5)beta(1) glycoproteins with GM1. Short hairpin RNA (shRNA) knockdown of TRPC5 in Teff cells blocked contact-dependent proliferation inhibition by Treg cells as well as Gal-1/CtxB-triggered Ca(2+) influx. Our results thus indicate GM1 in Teff cells to be the primary target of Gal-1 expressed by Treg cells, the resulting co-cross-linking and TRPC5 channel activation contributing importantly to the mechanism of autoimmune suppression.
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Affiliation(s)
- Jianfeng Wang
- Department of Neurology & Neurosciences, University of Medicine and Dentistry of New Jersey, Newark, 07103, USA
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So CH, Verma V, Alijaniaram M, Cheng R, Rashid AJ, O'Dowd BF, George SR. Calcium signaling by dopamine D5 receptor and D5-D2 receptor hetero-oligomers occurs by a mechanism distinct from that for dopamine D1-D2 receptor hetero-oligomers. Mol Pharmacol 2009; 75:843-54. [PMID: 19171671 DOI: 10.1124/mol.108.051805] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this report, we investigated whether the D5 dopamine receptor, given its structural and sequence homology with the D1 receptor, could interact with the D2 receptor to mediate a calcium signal similar to the G(q/11) protein-linked phospholipase C-mediated calcium signal resulting from the coactivation of D1 and D2 dopamine receptors within D1-D2 receptor heterooligomers. Fluorescent resonance energy transfer experiments demonstrated close colocalization of cell surface D5 and D2 receptors (<100 A), indicating hetero-oligomerization of D5 and D2 receptors in cells coexpressing both receptors. Coactivation of D5 and D2 receptors within the D5-D2 hetero-oligomers activated a calcium signal. However, unlike what is observed for D1 receptors, which activate extensive calcium mobilization only within a complex with the D2 receptors, a robust calcium signal was triggered by D5 receptors expressed alone. Hetero-oligomerization with the D2 receptor attenuated the ability of the D5 receptor to trigger a calcium signal. The D5 and D5-D2-associated calcium signals were G(q/11) protein-linked and phospholipase C-mediated but were also critically dependent on the influx of extracellular calcium through store-operated calcium channels, unlike the calcium release triggered by D1-D2 heterooligomers. Collectively, these results demonstrate that calcium signaling through D5-D2 receptor hetero-oligomers occurred through a distinct mechanism to achieve an increase in intracellular calcium levels.
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Affiliation(s)
- Christopher H So
- Department of Pharmacology, University of Toronto, and the Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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Thyagarajan B, Benn BS, Christakos S, Rohacs T. Phospholipase C-mediated regulation of transient receptor potential vanilloid 6 channels: implications in active intestinal Ca2+ transport. Mol Pharmacol 2008; 75:608-16. [PMID: 19073818 DOI: 10.1124/mol.108.052449] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transient receptor potential vanilloid 6 (TRPV6) channels play an important role in intestinal Ca(2+) transport. These channels undergo Ca(2+)-induced inactivation. Here we show that Ca(2+) flowing through these channels activates phospholipase C (PLC) leading to the depletion of phosphatidylinositol 4,5-bisphosphate (PIP(2)) and formation of inositol 1,4,5-trisphosphate in TRPV6-expressing cells. PIP(2) depletion was inhibited by the two structurally different PLC inhibitors 1-[6-[[17beta-methoxyestra-1,3,5(10)-trien-17-yl]amino]hexyl]-1H-pyrrole-2,5-dione (U73122) and edelfosine. Ca(2+)-induced inactivation of TRPV6 was also prevented by the PLC inhibitors in whole-cell patch-clamp experiments. Ca(2+) signals in TRPV6-expressing cells were transient upon restoration of extracellular Ca(2+) but were rendered more sustained by the PLC inhibitors. Finally, intestinal Ca(2+) transport in the everted duodenal sac assay was enhanced by edelfosine. These observations suggest that Ca(2+)-induced inactivation of TRPV6 limits intestinal Ca(2+) absorption and raise the possibility that Ca(2+) absorption can be enhanced pharmacologically by interfering with PLC activation.
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Affiliation(s)
- Baskaran Thyagarajan
- Department of Pharmacology and Physiology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07103, USA
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Nunes A, Nogueira PJ, Borrego MJ, Gomes JP. Chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race. Genome Biol 2008; 9:R153. [PMID: 18947394 PMCID: PMC2760880 DOI: 10.1186/gb-2008-9-10-r153] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 09/26/2008] [Accepted: 10/23/2008] [Indexed: 01/13/2023] Open
Abstract
Analysis of 15 serovars of Chlamydia trachomatis reveals an evolutionary arms race in pathogen-host interactions. Background The genomes of pathogens are thought to have evolved under selective pressure provided by the host in a coevolutionary arms race (the 'Red Queen's Hypothesis'). Traditionally, adaptation by pathogens is thought to rely not on whole chromosome dynamics but on gain/loss of specific genes, yielding differential abilities to infect distinct tissues. Thus, it is not known whether distinct host organs differently shape the genome of the same pathogen. We tested this hypothesis using Chlamydia trachomatis as model species, looking at 15 serovars that infect different organs: eyes, genitalia and lymph nodes. Results We analyzed over 51,000 base pairs from all serovars using various phylogenetic approaches and a non-phylogenetic indel-based algorithm to study the evolution of individual and concatenated loci. This survey comprised about 33% of all single nucleotide polymorphisms in C. trachomatis chromosomes. We present a model in which genome evolution indeed correlates with the cell type (epithelial versus lymph cells) and organ (eyes versus genitalia) that a serovar infects, illustrating an adaptation to physiologically distinct niches, and discarding genetic drift as the dominant evolutionary driving force. We show that radiation of serovars occurred primarily by accumulation of single nucleotide polymorphisms in intergenomic regions, housekeeping genes, and genes encoding hypothetical and cell envelope proteins. Furthermore, serovar evolution also correlates with ecological success, as the two most successful serovars showed a parallel evolution. Conclusion We identified a single nucleotide polymorphism-based tissue-specific arms race for strains in the same species, reflecting global chromosomal dynamics. Studying such tissue-specific arms race scenarios is crucial for understanding pathogen-host interactions during the course of infectious diseases, in order to dissect pathogen biology and develop preventive and therapeutic strategies.
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Affiliation(s)
- Alexandra Nunes
- Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, Lisbon, Portugal
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Abstract
The relationship between influenza antigenic drift and vaccination lies at the intersection of evolutionary biology and public health, and it must be viewed and analyzed in both contexts simultaneously. In this paper, 1 review what is known about the effects of antigenic drift on vaccination and the effects of vaccination on antigenic drift, and I suggest some simple ways to detect the presence of antigenic drift in seasonal influenza data. If antigenic drift occurs on the time scale of a single influenza season, it may be associated with the presence of herd immunity at the beginning of the season and may indicate a need to monitor for vaccine updates at the end of the season. The relationship between antigenic drift and vaccination must also be viewed in the context of the global circulation of influenza strains and the seeding of local and regional epidemics. In the data sets I consider--from New Zealand, New York, and France--antigenic drift can be statistically detected during some seasons, and seeding of epidemics appears to be endogenous sometimes and exogenous at other times. Improved detection of short-term antigenic drift and epidemic seeding would significantly benefit influenza monitoring efforts and vaccine selection.
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Affiliation(s)
- Maciej F Boni
- Resources for the Future, Washington, DC 20036, USA.
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Pepin KM, Domsic J, McKenna R. Genomic evolution in a virus under specific selection for host recognition. INFECTION GENETICS AND EVOLUTION 2008; 8:825-34. [PMID: 18804189 DOI: 10.1016/j.meegid.2008.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 08/01/2008] [Accepted: 08/06/2008] [Indexed: 10/21/2022]
Abstract
Genetic variation in viral structural proteins is often explained by evolutionary escape of strong host defenses through processes such as immune evasion, host switching, and tissue tropism. An understanding of the mechanisms driving evolutionary change in virus surface proteins is key to designing effective intervention strategies to disease emergence. This study investigated the predictability of virus genomic evolution in response to highly specific differences in host receptor structure. The bacteriophage PhiX174 was evolved on three E. coli mutant hosts, each differing only by a single sugar group in the lipopolysaccharides, used for phage attachment. Large phage populations were used in order to maximize the amount of sequence space explored by mutation, and thus the potential for parallel evolution. Repeatability was assessed by genome sequencing of multiple isolates from endpoint populations and by fitness of the endpoint population relative to its ancestor. Evolutionary lines showed similar magnitudes of fitness increase between treatments. Only one mutation, occurring in the internal DNA pilot protein H, was completely repeatable, and it appeared to be a necessary stepping stone toward further adaptive change. Substitutions in the surface accessible major capsid protein F appeared to be involved in capsid stability rather than specific interactions with host receptors, suggesting that non-specific alterations to capsid structure could be an important component of adaptation to novel hosts. 33% of mutations were synonymous and showed evidence of selection on codon usage. Lastly, results supported previous findings that evolving populations of small ssDNA viruses may maintain relatively high levels of genetic variation.
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Affiliation(s)
- Kim M Pepin
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA.
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Winn MP. 2007 Young Investigator Award: TRP'ing into a new era for glomerular disease. J Am Soc Nephrol 2008; 19:1071-5. [PMID: 18434567 DOI: 10.1681/asn.2007121292] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
FSGS is a pathologic lesion that frequently causes the nephrotic syndrome and ensuing renal failure. The cause remains unknown in the majority of individuals; however, in the past two decades, rare familial forms have been identified. It has been suggested that known genetic causes of the hereditary form of this disease account for upwards of 18% of cases. Mutations in five genes have been found to cause inherited nephrotic syndromes and FSGS. In this article, I discuss the phenotypic characteristics of hereditary FSGS and the transient receptor potential cation channel 6 (TRPC6) protein, which is the genetic impetus for an autosomal dominant form of FSGS. The TRP channels have been implicated in varied biologic functions such as mechanosensation, ion homeostasis, cell growth, and phospholipase C-dependent calcium entry into cells. The mutated ion channel causes an increase in calcium transients. Current evidence also suggests that blocking TRPC6 channels may be of therapeutic benefit in idiopathic FSGS, a disease with a generally poor prognosis. Preliminary experiments reveal that the commonly used immunosuppressive agent FK-506 can inhibit TRPC6 activity in vivo. This creates the intriguing possibility that blocking TRPC6 channels within the podocyte may translate into long-lasting clinical benefits in patients with FSGS.
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Affiliation(s)
- Michelle P Winn
- Department of Medicine and Center for Human Genetics, Duke University Medical Center, Duke Box 2903, Durham, NC 27705, USA.
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Haag KL, Gottstein B, Ayala FJ. Taeniid history, natural selection and antigenic diversity: evolutionary theory meets helminthology. Trends Parasitol 2008; 24:96-102. [PMID: 18182327 DOI: 10.1016/j.pt.2007.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 10/31/2007] [Accepted: 11/05/2007] [Indexed: 10/22/2022]
Abstract
Large sets of nucleotide sequence data of parasitic helminths have been accumulated in the past two decades. Our ability to improve the health of people and animals using this knowledge has not increased proportionally, however. Evolutionary biology provides the background to understand how parasites adapt to their hosts, and computational molecular biology offers the tools to infer the mechanisms involved. The study of antigenic diversity, a way for parasites to overcome host defenses against parasites, has been neglected in helminths, yet such a study could contribute to the development of more efficient drugs, diagnostic tests and vaccines. This review focuses on the study of adaptive evolution as the cause of antigenic diversity in tapeworms and its potential applications.
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Affiliation(s)
- Karen L Haag
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970 RS, Brazil.
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40
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Wykes RCE, Lee M, Duffy SM, Yang W, Seward EP, Bradding P. Functional transient receptor potential melastatin 7 channels are critical for human mast cell survival. THE JOURNAL OF IMMUNOLOGY 2007; 179:4045-52. [PMID: 17785843 DOI: 10.4049/jimmunol.179.6.4045] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mast cells play a significant role in the pathophysiology of many diverse diseases such as asthma and pulmonary fibrosis. Ca2+ influx is essential for mast cell degranulation and release of proinflammatory mediators, while Mg2+ plays an important role in cellular homeostasis. The channels supporting divalent cation influx in human mast cells have not been identified, but candidate channels include the transient receptor potential melastatin (TRPM) family. In this study, we have investigated TRPM7 expression and function in primary human lung mast cells (HLMCs) and in the human mast cell lines LAD2 and HMC-1, using RT-PCR, patch clamp electrophysiology, and RNA interference. Whole cell voltage-clamp recordings revealed a nonselective cation current that activated spontaneously following loss of intracellular Mg2+. The current had a nonlinear current-voltage relationship with the characteristic steep outward rectification associated with TRPM7 channels. Reducing external divalent concentration from 3 to 0.3 mM dramatically increased the size of the outward current, whereas the current was markedly inhibited by elevated intracellular Mg2+ (6 mM). Ion substitution experiments revealed cation selectivity and Ca2+ permeability. RT-PCR confirmed the presence of mRNA for TRPM7 in HLMC, LAD2, and HMC-1 cells. Adenoviral-mediated knockdown of TRPM7 in HLMC with short hairpin RNA and in HMC-1 with short interfering RNA markedly reduced TRPM7 currents and induced cell death, an effect that was not rescued by raising extracellular Mg2+. In summary, HLMC and human mast cell lines express the nonselective cation channel TRPM7 whose presence is essential for cell survival.
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Affiliation(s)
- Rob C E Wykes
- Department of Infection, Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, United Kingdom
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41
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Wroe R, Chan HS, Bornberg-Bauer E. A structural model of latent evolutionary potentials underlying neutral networks in proteins. HFSP JOURNAL 2007. [PMID: 19404462 DOI: 10.2976/1.2739116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A central question in molecular evolution concerns the nature of phenotypic transitions, in particular, if neutral mutations hamper or somehow facilitate adaptability of proteins to new requirements. Proteins have been found to fluctuate between different structures, with frequencies of structures being proportional to their stability. Therefore, functional promiscuity may correspond to different structures with energies close to the ground state which then represent multiple selectable traits. We here postulate that these near-ground-state structures facilitate smooth transitions between phenotypes. Using a biophysical heteropolymer model with exhaustive mappings of sequences onto structures, we demonstrate that this is indeed possible because of a smooth gradient of stability along which any structural phenotype can be optimized and also because of mutational proximity of similar phenotypes in genotype space. Our model provides a biophysical rationalization of the intriguing, and otherwise puzzling experimental observation that adaptation to new requirements, e.g., latent function of a promiscuous enzyme, can proceed while the "old," phenotypically dominant function is maintained along a series of seemingly neutral mutations (see accompanying article). Thus pleiotropy may facilitate adaptation of latent traits before gene duplications and increase the effective adaptability of proteins.
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Du J, Sours-Brothers S, Coleman R, Ding M, Graham S, Kong DH, Ma R. Canonical transient receptor potential 1 channel is involved in contractile function of glomerular mesangial cells. J Am Soc Nephrol 2007; 18:1437-45. [PMID: 17389736 DOI: 10.1681/asn.2006091067] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Contractility of mesangial cells (MC) is tightly controlled by [Ca(2+)](i). Ca(2+) influx across the plasma membrane constitutes a major component of mesangial responses to vasoconstrictors. Canonical transient receptor potential 1 (TRPC1) is a Ca(2+)-permeable cation channel in a variety of cell types. This study was performed to investigate whether TRPC1 takes part in vasoconstrictor-induced mesangial contraction by mediating Ca(2+) entry. It was found that angiotensin II (AngII) evoked remarkable contraction of the cultured MC. Downregulation of TRPC1 using RNA interference significantly attenuated the contractile response. Infusion of AngII or endothelin-1 in rats caused a decrease in GFR. The GFR decline was significantly reduced by infusion of TRPC1 antibody that targets an extracellular domain in the pore region of TRPC1 channel. However, the treatment of TRPC1 antibody did not affect the AngII-induced vasopressing effect. Electrophysiologic experiments revealed that functional or biologic inhibition of TRPC1 significantly depressed AngII-induced channel activation. Fura-2 fluorescence-indicated that Ca(2+) entry in response to AngII stimulation was also dramatically inhibited by TRPC1 antibody and TRPC1-specific RNA interference. These results suggest that TRPC1 plays an important role in controlling contractile function of MC. Mediation of Ca(2+) entry might be the underlying mechanism for the TRPC1-associated MC contraction.
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Affiliation(s)
- Juan Du
- Department of Integrative Physiology, University of North Texas Health Science Center at Fort Worth, Fort Worth, Texas 76107, USA
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43
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Suárez-Castillo EC, García-Arrarás JE. Molecular evolution of the ependymin protein family: a necessary update. BMC Evol Biol 2007; 7:23. [PMID: 17302986 PMCID: PMC1805737 DOI: 10.1186/1471-2148-7-23] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 02/15/2007] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Ependymin (Epd), the predominant protein in the cerebrospinal fluid of teleost fishes, was originally associated with neuroplasticity and regeneration. Ependymin-related proteins (Epdrs) have been identified in other vertebrates, including amphibians and mammals. Recently, we reported the identification and characterization of an Epdr in echinoderms, showing that there are ependymin family members in non-vertebrate deuterostomes. We have now explored multiple databases to find Epdrs in different metazoan species. Using these sequences we have performed genome mapping, molecular phylogenetic analyses using Maximum Likelihood and Bayesian methods, and statistical tests of tree topologies, to ascertain the phylogenetic relationship among ependymin proteins. RESULTS Our results demonstrate that ependymin genes are also present in protostomes. In addition, as a result of the putative fish-specific genome duplication event and posterior divergence, the ependymin family can be divided into four groups according to their amino acid composition and branching pattern in the gene tree: 1) a brain-specific group of ependymin sequences that is unique to teleost fishes and encompasses the originally described ependymin; 2) a group expressed in non-brain tissue in fishes; 3) a group expressed in several tissues that appears to be deuterostome-specific, and 4) a group found in invertebrate deuterostomes and protostomes, with a broad pattern of expression and that probably represents the evolutionary origin of the ependymins. Using codon-substitution models to statistically assess the selective pressures acting over the ependymin protein family, we found evidence of episodic positive Darwinian selection and relaxed selective constraints in each one of the postduplication branches of the gene tree. However, purifying selection (with among-site variability) appears to be the main influence on the evolution of each subgroup within the family. Functional divergence among the ependymin paralog groups is well supported and several amino acid positions are predicted to be critical for this divergence. CONCLUSION Ependymin proteins are present in vertebrates, invertebrate deuterostomes, and protostomes. Overall, our analyses suggest that the ependymin protein family is a suitable target to experimentally test subfunctionalization in gene copies that originated after gene or genome duplication events.
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Affiliation(s)
- Edna C Suárez-Castillo
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 00931, Puerto Rico
| | - José E García-Arrarás
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 00931, Puerto Rico
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Kawano T, Zhao P, Floreani CV, Nakajima Y, Kozasa T, Nakajima S. Interaction of Galphaq and Kir3, G protein-coupled inwardly rectifying potassium channels. Mol Pharmacol 2007; 71:1179-84. [PMID: 17296805 DOI: 10.1124/mol.106.032508] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Activation of substance P receptors, which are coupled to Galpha(q), inhibits the Kir3.1/3.2 channels, resulting in neuronal excitation. We have shown previously that this channel inactivation is not caused by reduction of the phosphatidylinositol 4,5-bisphosphate level in membrane. Moreover, Galpha(q) immunoprecipitates with Kir3.2 (J Physiol 564:489-500, 2005), suggesting that Galpha(q) interacts with Kir3.2. Positive immunoprecipitation, however, does not necessarily indicate direct interaction between the two proteins. Here, the glutathione transferase pull-down assay was used to investigate interaction between Galpha(q) and the K(+) channels. We found that Galpha(q) interacted with N termini of Kir3.1, Kir3.2, and Kir3.4. However, Galpha(q) did not interact with the C terminus of any Kir3 or with the C or N terminus of Kir2.1. TRPC6 is regulated by the signal initiated by Galpha(q). Immunoprecipitation, however, showed that Galpha(q) did not interact with TRPC6. Thus, the interaction between Galpha(q) and the Kir3 N terminus is quite specific. This interaction occurred in the presence of GDP or GDP-AlF(-)(4). The Galpha(q) binding could take place somewhere between residues 51 to 90 of Kir3.2; perhaps the segment between 81 to 90 residues is crucial. Gbetagamma, which is known to bind to N terminus of Kir3, did not compete with Galpha(q) for the binding, suggesting that these two binding regions are different. These findings agree with the hypothesis (J Physiol 564:489-500, 2005) that the signal to inactivate the Kir3 channel could be mainly transmitted directly from Galpha(q) to Kir3.
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Affiliation(s)
- Takeharu Kawano
- Departments of Anatomy & Cell Biology, College of Medicine, University of Illinois at Chicago, Illinois 60612, USA
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45
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Chibo D, Birch C. Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains. J Gen Virol 2006; 87:1203-1208. [PMID: 16603522 DOI: 10.1099/vir.0.81662-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Historically, coronaviruses have been recognized as a cause of minor respiratory infections in humans. However, the recent identification of three novel human coronaviruses, one causing severe acute respiratory syndrome (SARS), has prompted further examination of these viruses. Previous studies of geographically and chronologically distinct Human coronavirus 229E (HCoV-229E) isolates have found only limited variation within S gene nucleotide sequences. In contrast, analysis of the S genes of contemporary Human coronavirus OC43 variants identified in Belgium revealed two distinct viruses circulating during 2003 and 2004. Here, the S and N gene sequences of 25 HCoV-229E variants identified in Victoria, Australia, between 1979 and 2004 in patients with symptomatic infections were determined. Phylogenetic analysis showed clustering of the isolates into four groups, with evidence of increasing divergence with time. Evidence of positive selection in the S gene was also established.
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Affiliation(s)
- Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, 10 Wreckyn Street, North Melbourne, Victoria 3051, Australia
| | - Chris Birch
- Victorian Infectious Diseases Reference Laboratory, 10 Wreckyn Street, North Melbourne, Victoria 3051, Australia
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46
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Takezawa R, Cheng H, Beck A, Ishikawa J, Launay P, Kubota H, Kinet JP, Fleig A, Yamada T, Penner R. A Pyrazole Derivative Potently Inhibits Lymphocyte Ca2+Influx and Cytokine Production by Facilitating Transient Receptor Potential Melastatin 4 Channel Activity. Mol Pharmacol 2006; 69:1413-20. [PMID: 16407466 DOI: 10.1124/mol.105.021154] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
3,5-Bis(trifluoromethyl)pyrazole derivative (BTP2) or N-[4-3, 5-bis(trifluromethyl)pyrazol-1-yl]-4-methyl-1,2,3-thiadiazole-5-carboxamide (YM-58483) is an immunosuppressive compound that potently inhibits both Ca2+ influx and interleukin-2 (IL-2) production in lymphocytes. We report here that BTP2 dosedependently enhances transient receptor potential melastatin 4 (TRPM4), a Ca2+-activated nonselective (CAN) cation channel that decreases Ca2+ influx by depolarizing lymphocytes. The effect of BTP2 on TRPM4 occurs at low nanomolar concentrations and is highly specific, because other ion channels in T lymphocytes are not significantly affected, and the major Ca2+ influx pathway in lymphocytes, ICRAC, is blocked only at 100-fold higher concentrations. The efficacy of BTP2 in blocking IL-2 production is reduced approximately 100-fold when preventing TRPM4-mediated membrane depolarization, suggesting that the BTP2-mediated facilitation of TRPM4 channels represents the major mechanism for its immunosuppressive effect. Our results demonstrate that TRPM4 channels represent a previously unrecognized key element in lymphocyte Ca2+ signaling and that their facilitation by BTP2 supports cell membrane depolarization, which reduces the driving force for Ca2+ entry and ultimately causes the potent suppression of cytokine release.
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Affiliation(s)
- Ryuichi Takezawa
- Laboratory of Cell and Molecular Signalling, Center for Biomedical Research, The Queen's Medical Center, 1301 Punchbowl St., UHT 8, Honolulu, HI 96813, USA
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Winn MP, Daskalakis N, Spurney RF, Middleton JP. Unexpected Role ofTRPC6Channel in Familial Nephrotic Syndrome: Does It Have Clinical Implications? J Am Soc Nephrol 2006; 17:378-87. [PMID: 16396961 DOI: 10.1681/asn.2005090962] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Michelle P Winn
- Department of Medicine, Duke University Medical Center, Box 2903, Durham, NC 27710, USA.
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Aihara E, Hayashi M, Sasaki Y, Kobata A, Takeuchi K. Mechanisms underlying capsaicin-stimulated secretion in the stomach: comparison with mucosal acidification. J Pharmacol Exp Ther 2005; 315:423-32. [PMID: 15985616 DOI: 10.1124/jpet.105.087619] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The effects of capsaicin and mucosal acidification on gastric HCO3(-) secretion were compared in wild-type and prostacyclin (PGI2) IP receptor or prostaglandin E receptor EP1 or EP3 knockout C57BL/6 mice as well as rats. Under urethane anesthesia, the stomach was mounted on an ex vivo chamber, perfused with saline, and the secretion of HCO3(-) was measured at pH 7.0 using the pH-stat method. Capsaicin or 200 mM HCl was applied to the chamber for 10 min. Capsaicin increased the secretion of HCO3(-) in rats and wild-type mice, the response at 0.3 mg/ml being equivalent to that induced by acidification. This effect of capsaicin in rats was abolished by ablation of capsaicin-sensitive afferent neurons and attenuated by indomethacin, N(G)-nitro-L-arginine methylester (L-NAME), and capsazepine [transient receptor potential vanilloid type 1 (TRPV1) antagonist] but not FR172357 [3-bromo-8-[2,6-dichloro-3-[N[(E)-4-(N,N-dimethylcarbamoyl) cinnamidoacetyl]-N-methylamino]benzyloxy]-2-metylimidazo[1,2-a]pyridine; bradykinin B2 antagonist] or the EP1 antagonist. The acid-induced HCO3(-) secretion was attenuated by indomethacin, L-NAME, the EP1 antagonist, and sensory deafferentation, but not affected by capsazepine or FR172357. Prostaglandin E2 (PGE2), NOR-3 [(+/-)-(E)-ethyl-2-[(E)-hydroxyimino]-5-nitro-3-hexeneamine] (NO donor), and bradykinin stimulated the secretion of HCO3(-), and the effect of bradykinin was blocked by indomethacin and L-NAME as well as FR172357. The stimulatory effect of capsaicin disappeared in IP (-/-) mice, whereas that of acidification disappeared in EP1 (-/-) mice. Intragastric application of capsaicin increased mucosal PGI2 but not PGE2 levels in the rat stomach. These results suggested that both capsaicin and acid increase gastric HCO3(-) secretion via a common pathway, involving PG and NO as well as capsaicin-sensitive afferent neurons, yet their responses differ concerning TRPV1 or prostanoid receptor dependence.
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Affiliation(s)
- Eitaro Aihara
- Department of Pharmacology and Experimental Therapeutics, Kyoto Pharmaceutical University, Misasagi, Yamashina, Kyoto 607, Japan
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Abstract
A near constancy of the extracellular Ca(2+) and Mg(2+) concentration is required for numerous physiologic functions at the organ, tissue, and cellular levels. This suggests that minor changes in the extracellular concentration of these divalents must be detected to allow the appropriate correction by the homeostatic systems. The maintenance of the Ca(2+) and Mg(2+) balance is controlled by the concerted action of intestinal absorption, renal excretion, and exchange with bone. After years of research, rapid progress was made recently in identification and characterization of the Ca(2+) and Mg(2+) transport proteins that contribute to the delicate balance of divalent cations. Expression-cloning approaches in combination with knockout mice models and genetic studies in families with a disturbed Mg(2+) balance revealed novel Ca(2+) and Mg(2+) gatekeeper proteins that belong to the super family of the transient receptor potential (TRP) channels. These epithelial Ca(2+) (TRPV5 and TRPV6) and Mg(2+) channels (TRPM6 and TRPM7) form prime targets for hormonal control of the active Ca(2+) and Mg(2+) flux from the urine space or intestinal lumen to the blood compartment. This review describes the characteristics of epithelial Ca(2+) and Mg(2+) transport in general and highlights in particular the distinctive features and the physiologic relevance of these new epithelial Ca(2+) and Mg(2+) channels in (patho)physiologic situations.
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Affiliation(s)
- Joost G J Hoenderop
- Department of Physiology, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
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50
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Semovski S, Verheyen E, Sherbakov D. Simulating the evolution of neutrally evolving sequences in a population under environmental changes. Ecol Modell 2004. [DOI: 10.1016/j.ecolmodel.2003.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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