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Beichman AC, Koepfli KP, Li G, Murphy W, Dobrynin P, Kliver S, Tinker MT, Murray MJ, Johnson J, Lindblad-Toh K, Karlsson EK, Lohmueller KE, Wayne RK. Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. Mol Biol Evol 2019; 36:2631-2655. [PMID: 31212313 PMCID: PMC7967881 DOI: 10.1093/molbev/msz101] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.
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Affiliation(s)
- Annabel C Beichman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Gang Li
- College of Life Science, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Pasha Dobrynin
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Martin T Tinker
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | | | - Jeremy Johnson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kerstin Lindblad-Toh
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elinor K Karlsson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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52
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Wong J, Layton D, Wheatley AK, Kent SJ. Improving immunological insights into the ferret model of human viral infectious disease. Influenza Other Respir Viruses 2019; 13:535-546. [PMID: 31583825 PMCID: PMC6800307 DOI: 10.1111/irv.12687] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
Ferrets are a well-established model for studying both the pathogenesis and transmission of human respiratory viruses and evaluation of antiviral vaccines. Advanced immunological studies would add substantial value to the ferret models of disease but are hindered by the low number of ferret-reactive reagents available for flow cytometry and immunohistochemistry. Nevertheless, progress has been made to understand immune responses in the ferret model with a limited set of ferret-specific reagents and assays. This review examines current immunological insights gained from the ferret model across relevant human respiratory diseases, with a focus on influenza viruses. We highlight key knowledge gaps that need to be bridged to advance the utility of ferrets for immunological studies.
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Affiliation(s)
- Julius Wong
- Department of Microbiology and ImmunologyPeter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVic.Australia
| | - Daniel Layton
- CSIRO Health and BiosecurityAustralian Animal Health LaboratoriesGeelongVic.Australia
| | - Adam K. Wheatley
- Department of Microbiology and ImmunologyPeter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVic.Australia
| | - Stephen J. Kent
- Department of Microbiology and ImmunologyPeter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVic.Australia
- Melbourne Sexual Health Centre and Department of Infectious DiseasesAlfred Hospital and Central Clinical SchoolMonash UniversityMelbourneVic.Australia
- ARC Centre for Excellence in Convergent Bio‐Nano Science and TechnologyUniversity of MelbourneParkvilleVic.Australia
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53
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Belser JA, Eckert AM, Huynh T, Gary JM, Ritter JM, Tumpey TM, Maines TR. A Guide for the Use of the Ferret Model for Influenza Virus Infection. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 190:11-24. [PMID: 31654637 DOI: 10.1016/j.ajpath.2019.09.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 12/09/2022]
Abstract
As influenza viruses continue to jump species barriers to cause human infection, assessments of disease severity and viral replication kinetics in vivo provide crucial information for public health professionals. The ferret model is a valuable resource for evaluating influenza virus pathogenicity; thus, understanding the most effective techniques for sample collection and usage, as well as the full spectrum of attainable data after experimental inoculation in this species, is paramount. This is especially true for scheduled necropsy of virus-infected ferrets, a standard component in evaluation of influenza virus pathogenicity, as necropsy findings can provide important information regarding disease severity and pathogenicity that is not otherwise available from the live animal. In this review, we describe the range of influenza viruses assessed in ferrets, the measures of experimental disease severity in this model, and optimal sample collection during necropsy of virus-infected ferrets. Collectively, this information is critical for assessing systemic involvement after influenza virus infection in mammals.
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Affiliation(s)
- Jessica A Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia.
| | - Alissa M Eckert
- Division of Communication Services, Office of the Associate Director for Communication, Atlanta, Georgia
| | - Thanhthao Huynh
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Joy M Gary
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jana M Ritter
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Terrence M Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia
| | - Taronna R Maines
- Influenza Division, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia
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54
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Rosen BH, Evans TIA, Moll SR, Gray JS, Liang B, Sun X, Zhang Y, Jensen-Cody CW, Swatek AM, Zhou W, He N, Rotti PG, Tyler SR, Keiser NW, Anderson PJ, Brooks L, Li Y, Pope RM, Rajput M, Hoffman EA, Wang K, Harris JK, Parekh KR, Gibson-Corley KN, Engelhardt JF. Infection Is Not Required for Mucoinflammatory Lung Disease in CFTR-Knockout Ferrets. Am J Respir Crit Care Med 2019; 197:1308-1318. [PMID: 29327941 DOI: 10.1164/rccm.201708-1616oc] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Classical interpretation of cystic fibrosis (CF) lung disease pathogenesis suggests that infection initiates disease progression, leading to an exuberant inflammatory response, excessive mucus, and ultimately bronchiectasis. Although symptomatic antibiotic treatment controls lung infections early in disease, lifelong bacterial residence typically ensues. Processes that control the establishment of persistent bacteria in the CF lung, and the contribution of noninfectious components to disease pathogenesis, are poorly understood. OBJECTIVES To evaluate whether continuous antibiotic therapy protects the CF lung from disease using a ferret model that rapidly acquires lethal bacterial lung infections in the absence of antibiotics. METHODS CFTR (cystic fibrosis transmembrane conductance regulator)-knockout ferrets were treated with three antibiotics from birth to several years of age and lung disease was followed by quantitative computed tomography, BAL, and histopathology. Lung disease was compared with CFTR-knockout ferrets treated symptomatically with antibiotics. MEASUREMENTS AND MAIN RESULTS Bronchiectasis was quantified from computed tomography images. BAL was evaluated for cellular differential and features of inflammatory cellular activation, bacteria, fungi, and quantitative proteomics. Semiquantitative histopathology was compared across experimental groups. We demonstrate that lifelong antibiotics can protect the CF ferret lung from infections for several years. Surprisingly, CF animals still developed hallmarks of structural bronchiectasis, neutrophil-mediated inflammation, and mucus accumulation, despite the lack of infection. Quantitative proteomics of BAL from CF and non-CF pairs demonstrated a mucoinflammatory signature in the CF lung dominated by Muc5B and neutrophil chemoattractants and products. CONCLUSIONS These findings implicate mucoinflammatory processes in the CF lung as pathogenic in the absence of clinically apparent bacterial and fungal infections.
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Affiliation(s)
- Bradley H Rosen
- 1 Department of Anatomy & Cell Biology.,2 Department of Medicine
| | | | | | | | - Bo Liang
- 1 Department of Anatomy & Cell Biology
| | | | | | | | | | | | - Nan He
- 1 Department of Anatomy & Cell Biology
| | - Pavana G Rotti
- 1 Department of Anatomy & Cell Biology.,4 Department of Biomedical Engineering, College of Engineering, and
| | | | | | | | | | | | | | | | | | - Kai Wang
- 7 Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa; and
| | - J Kirk Harris
- 8 Department of Pediatrics, University of Colorado, Aurora, Colorado
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55
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Fan H, Hu Y, Shan L, Yu L, Wang B, Li M, Wu Q, Wei F. Synteny search identifies carnivore Y chromosome for evolution of male specific genes. Integr Zool 2019; 14:224-234. [PMID: 30019860 DOI: 10.1111/1749-4877.12352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The explosive accumulation of mammalian genomes has provided a valuable resource to characterize the evolution of the Y chromosome. Unexpectedly, the Y-chromosome sequence has been characterized in only a small handful of species, with the majority being model organisms. Thus, identification of Y-linked scaffolds from unordered genome sequences is becoming more important. Here, we used a syntenic-based approach to generate the scaffolds of the male-specific region of the Y chromosome (MSY) from the genome sequence of 6 male carnivore species. Our results identified 14, 15, 9, 28, 14 and 11 Y-linked scaffolds in polar bears, pacific walruses, red pandas, cheetahs, ferrets and tigers, covering 1.55 Mbp, 2.62 Mbp, 964 Kb, 1.75 Mb, 2.17 Mbp and 1.84 Mb MSY, respectively. All the candidate Y-linked scaffolds in 3 selected species (red pandas, polar bears and tigers) were successfully verified using polymerase chain reaction. We re-annotated 8 carnivore MSYs including these 6 Y-linked scaffolds and domestic dog and cat MSY; a total of 11 orthologous genes conserved in at least 7 of the 8 carnivores were identified. These 11 Y-linked genes have significantly higher evolutionary rates compared with their X-linked counterparts, indicating less purifying selection for MSY genes. Taken together, our study shows that the approach of synteny search is a reliable and easily affordable strategy to identify Y-linked scaffolds from unordered carnivore genomes and provides a preliminary evolutionary study for carnivore MSY genes.
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Affiliation(s)
- Huizhong Fan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Lei Shan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lijun Yu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Min Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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56
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Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology 2019; 16:6. [PMID: 30845962 PMCID: PMC6407205 DOI: 10.1186/s12977-019-0468-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 01/20/2023] Open
Abstract
Background Vertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids. Results We identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within Canis, including 58 insertions that were absent from the reference assembly. Insertions were found throughout the dog genome including within and near gene models. By comparison of orthologous occupied sites, we characterized element prevalence across 332 genomes including all nine extant canid species, revealing evolutionary patterns of ERV-Fc segregation among species as well as subpopulations. Conclusions Sequence analysis revealed common disruptive mutations, suggesting a predominant form of ERV-Fc spread by trans complementation of defective proviruses. ERV-Fc activity included multiple circulating variants that infected canid ancestors from the last 20 million to within 1.6 million years, with recent bursts of germline invasion in the sublineage leading to wolves and dogs. Electronic supplementary material The online version of this article (10.1186/s12977-019-0468-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Abigail S Jarosz
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Robert J Gifford
- Centre for Virus Research, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Malika L Day
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Ave., Ann Arbor, MI, 48109, USA
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57
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Yu M, Sun X, Tyler SR, Liang B, Swatek AM, Lynch TJ, He N, Yuan F, Feng Z, Rotti PG, Choi SH, Shahin W, Liu X, Yan Z, Engelhardt JF. Highly Efficient Transgenesis in Ferrets Using CRISPR/Cas9-Mediated Homology-Independent Insertion at the ROSA26 Locus. Sci Rep 2019; 9:1971. [PMID: 30760763 PMCID: PMC6374392 DOI: 10.1038/s41598-018-37192-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 12/03/2018] [Indexed: 11/09/2022] Open
Abstract
The domestic ferret (Mustela putorius furo) has proven to be a useful species for modeling human genetic and infectious diseases of the lung and brain. However, biomedical research in ferrets has been hindered by the lack of rapid and cost-effective methods for genome engineering. Here, we utilized CRISPR/Cas9-mediated, homology-independent insertion at the ROSA26 "safe harbor" locus in ferret zygotes and created transgenic animals expressing a dual-fluorescent Cre-reporter system flanked by PhiC31 and Bxb1 integrase attP sites. Out of 151 zygotes injected with circular transgene-containing plasmid and Cas9 protein loaded with the ROSA26 intron-1 sgRNA, there were 23 births of which 5 had targeted integration events (22% efficiency). The encoded tdTomato transgene was highly expressed in all tissues evaluated. Targeted integration was verified by PCR analyses, Southern blot, and germ-line transmission. Function of the ROSA26-CAG-LoxPtdTomatoStopLoxPEGFP (ROSA-TG) Cre-reporter was confirmed in primary cells following Cre expression. The Phi31 and Bxb1 integrase attP sites flanking the transgene will also enable rapid directional insertion of any transgene without a size limitation at the ROSA26 locus. These methods and the model generated will greatly enhance biomedical research involving lineage tracing, the evaluation of stem cell therapy, and transgenesis in ferret models of human disease.
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Affiliation(s)
- Miao Yu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- College of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China
| | - Xingshen Sun
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Scott R Tyler
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Bo Liang
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Anthony M Swatek
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Thomas J Lynch
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Nan He
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Feng Yuan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Zehua Feng
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Pavana G Rotti
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Soon H Choi
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Weam Shahin
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Xiaoming Liu
- College of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China.
| | - Ziying Yan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
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58
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Hu J, Yin H, Li B, Yang H. Identification of Transcriptional Metabolic Dysregulation in Subtypes of Pituitary Adenoma by Integrated Bioinformatics Analysis. Diabetes Metab Syndr Obes 2019; 12:2441-2451. [PMID: 31819570 PMCID: PMC6885545 DOI: 10.2147/dmso.s226056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pituitary adenoma (PA) is a prevalent intracranial tumor. Metabolites differ between pituitary tumor and healthy tissues or among different tumor subtypes. However, the transcriptional changes in metabolic enzymes, which are usually seemed as targets for metabolic therapy, remain unidentified. METHODS Using microarray data for 160 samples from the Gene Expression Omnibus database, across the four most common tumor subtypes, we present the integrated identification of differentially expressed genes (DEGs) between tumors and controls. RESULTS Subtype-specific DEGs revealed 1081 prolactin tumor-specific DEGs, 437 nonfunctioning tumor-specific DEGs, and 217 common DEGs among the four subtypes. Functional enrichment showed that a lot of biological functions related to metabolism had changed. Twenty-one prolactin and twenty-three nonfunctioning tumor-specific metabolic-related DEGs are mainly involved in fatty acid and nucleotide metabolism, redox reaction, and gluconeogenesis. Eighteen metabolic-related DEGs enriched in the metabolism of xenobiotics by the cytochrome P450 pathway, sulfur metabolism, retinoid metabolism, and glucose homeostasis were abnormal in all subtypes of PA. CONCLUSION Based on a comprehensive bioinformatics analysis of the available PA-related transcriptomics data, we identified specific DEGs related to metabolism, and some of them might be new attractive therapeutic targets. Especially, PDK4 and PCK1 might be new attractive biomarkers and therapeutic targets.
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Affiliation(s)
- Jintao Hu
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, People’s Republic of China
| | - Huachun Yin
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, People’s Republic of China
- College of Life Sciences, Chongqing Normal University, Chongqing, People’s Republic of China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing, People’s Republic of China
- Correspondence: Bo Li; Hui Yang Email ;
| | - Hui Yang
- Department of Neurosurgery, Xinqiao Hospital, The Army Medical University, Chongqing, People’s Republic of China
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Stronen AV, Iacolina L, Ruiz-Gonzalez A. Rewilding and conservation genomics: How developments in (re)colonization ecology and genomics can offer mutual benefits for understanding contemporary evolution. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2018.e00502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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60
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Ekblom R, Brechlin B, Persson J, Smeds L, Johansson M, Magnusson J, Flagstad Ø, Ellegren H. Genome sequencing and conservation genomics in the Scandinavian wolverine population. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:1301-1312. [PMID: 29935028 DOI: 10.1111/cobi.13157] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 06/01/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42 Gb draft sequence representing >85% of the genome and including >21,000 protein-coding genes. We then performed whole-genome resequencing of 10 Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (Ne ) from 10,000 well before the last glaciation to <500 after this period. Current Ne appeared even lower. The genome-wide FIS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.
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Affiliation(s)
- Robert Ekblom
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Birte Brechlin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Jens Persson
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden
| | - Linnéa Smeds
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Malin Johansson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Jessica Magnusson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | | | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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61
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Cross RW, Speranza E, Borisevich V, Widen SG, Wood TG, Shim RS, Adams RD, Gerhardt DM, Bennett RS, Honko AN, Johnson JC, Hensley LE, Geisbert TW, Connor JH. Comparative Transcriptomics in Ebola Makona-Infected Ferrets, Nonhuman Primates, and Humans. J Infect Dis 2018; 218:S486-S495. [PMID: 30476250 PMCID: PMC6249602 DOI: 10.1093/infdis/jiy455] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The domestic ferret is a uniformly lethal model of infection for 3 species of Ebolavirus known to be pathogenic in humans. Reagents to systematically analyze the ferret host response to infection are lacking; however, the recent publication of a draft ferret genome has opened the potential for transcriptional analysis of ferret models of disease. In this work, we present comparative analysis of longitudinally sampled blood taken from ferrets and nonhuman primates infected with lethal doses of the Makona variant of Zaire ebolavirus. Strong induction of proinflammatory and prothrombotic signaling programs were present in both ferrets and nonhuman primates, and both transcriptomes were similar to previously published datasets of fatal cases of human Ebola virus infection.
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Affiliation(s)
- Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Emily Speranza
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Massachusetts
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Steven G Widen
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
| | - Thomas G Wood
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
| | - Rebecca S Shim
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Ricky D Adams
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Dawn M Gerhardt
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Richard S Bennett
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Anna N Honko
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - John H Connor
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Massachusetts
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Starbæk SMR, Brogaard L, Dawson HD, Smith AD, Heegaard PMH, Larsen LE, Jungersen G, Skovgaard K. Animal Models for Influenza A Virus Infection Incorporating the Involvement of Innate Host Defenses: Enhanced Translational Value of the Porcine Model. ILAR J 2018; 59:323-337. [DOI: 10.1093/ilar/ily009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Abstract
Influenza is a viral respiratory disease having a major impact on public health. Influenza A virus (IAV) usually causes mild transitory disease in humans. However, in specific groups of individuals such as severely obese, the elderly, and individuals with underlying inflammatory conditions, IAV can cause severe illness or death. In this review, relevant small and large animal models for human IAV infection, including the pig, ferret, and mouse, are discussed. The focus is on the pig as a large animal model for human IAV infection as well as on the associated innate immune response. Pigs are natural hosts for the same IAV subtypes as humans, they develop clinical disease mirroring human symptoms, they have similar lung anatomy, and their respiratory physiology and immune responses to IAV infection are remarkably similar to what is observed in humans. The pig model shows high face and target validity for human IAV infection, making it suitable for modeling many aspects of influenza, including increased risk of severe disease and impaired vaccine response due to underlying pathologies such as low-grade inflammation. Comparative analysis of proteins involved in viral pattern recognition, interferon responses, and regulation of interferon-stimulated genes reveals a significantly higher degree of similarity between pig, ferret, and human compared with mice. It is concluded that the pig is a promising animal model displaying substantial human translational value with the ability to provide essential insights into IAV infection, pathogenesis, and immunity.
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Affiliation(s)
- Sofie M R Starbæk
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Louise Brogaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Harry D Dawson
- Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
| | - Allen D Smith
- Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
| | - Peter M H Heegaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars E Larsen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gregers Jungersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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Peng C, Niu L, Deng J, Yu J, Zhang X, Zhou C, Xing J, Li J. Can-SINE dynamics in the giant panda and three other Caniformia genomes. Mob DNA 2018; 9:32. [PMID: 30455747 PMCID: PMC6230240 DOI: 10.1186/s13100-018-0137-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs. Results We found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes. In particular, SINEC1_AMe, SINEC1B_AMe and SINEC_C1 are the top three most abundant Can-SINE subfamilies in the panda and polar bear genomes. Transposition in transposition analysis indicates that SINEC1_AMe and SINEC1B_AMe are the most active subfamilies in the panda and the polar bear genomes. SINEC2A1_CF and SINEC1A_CF subfamilies show a higher retrotransposition activity in the dog genome, and MVB2 subfamily is the most active Can-SINE in the ferret genome. As the giant panda is an endangered icon species, we then focused on the identification of panda specific Can-SINEs. With the panda-associated two-way genome alignments, we identified 250 putative panda-specific (PPS) elements (139 SINEC1_AMes and 111 SINEC1B_AMes) that inserted in the panda genome but were absent at the orthologous regions of the other three genomes. Further investigation of these PPS elements allowed us to identify a new Can-SINE subfamily, the SINEC1_AMe2, which was distinguishable from the current SINEC1_AMe consensus by four non-CpG sites. SINEC1_AMe2 has a high copy number (> 100,000) in the panda and polar bear genomes and the vast majority (> 96%) of the SINEC1_AMe2 elements have divergence rates less than 10% in both genomes. Conclusions Our results suggest that Can-SINEs show lineage-specific retransposition activity in the four genomes and have an important impact on the genomic landscape of different Caniformia lineages. Combining these observations with results from the COSEG, Network, and target site duplication analysis, we suggest that SINEC1_AMe2 is a young mobile element subfamily and currently active in both the panda and polar bear genomes.
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Affiliation(s)
- Changjun Peng
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
| | - Lili Niu
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Jiabo Deng
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Jianqiu Yu
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Xueyan Zhang
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
| | - Chuang Zhou
- 3Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan China
| | - Jinchuan Xing
- 4Department of Genetics, Human Genetic Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Jing Li
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
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Belser JA, Maines TR, Tumpey TM. Importance of 1918 virus reconstruction to current assessments of pandemic risk. Virology 2018; 524:45-55. [PMID: 30142572 PMCID: PMC9036538 DOI: 10.1016/j.virol.2018.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/25/2018] [Accepted: 08/09/2018] [Indexed: 01/13/2023]
Abstract
Reconstruction of the 1918 influenza virus has facilitated considerable advancements in our understanding of this extraordinary pandemic virus. However, the benefits of virus reconstruction are not limited to this one strain. Here, we provide an overview of laboratory studies which have evaluated the reconstructed 1918 virus, and highlight key discoveries about determinants of virulence and transmissibility associated with this virus in mammals. We further discuss recent and current pandemic threats from avian and swine reservoirs, and provide specific examples of how reconstruction of the 1918 pandemic virus has improved our ability to contextualize research employing novel and emerging strains. As influenza viruses continue to evolve and pose a threat to human health, studying past pandemic viruses is key to future preparedness efforts.
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Affiliation(s)
- Jessica A Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Taronna R Maines
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Terrence M Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Abstract
The domestic ferret (Mustela putorius furo) recently emerged as a novel model for human pancreatic diseases. To investigate whether the ferret would be appropriate to study hereditary pancreatitis associated with increased trypsinogen autoactivation, we purified and cloned the trypsinogen isoforms from the ferret pancreas and studied their functional properties. We found two highly expressed isoforms, anionic and cationic trypsinogen. When compared to human cationic trypsinogen (PRSS1), ferret anionic trypsinogen autoactivated only in the presence of high calcium concentrations but not in millimolar calcium, which prevails in the secretory pathway. Ferret cationic trypsinogen was completely defective in autoactivation under all conditions tested. However, both isoforms were readily activated by enteropeptidase and cathepsin B. We conclude that ferret trypsinogens do not autoactivate as their human paralogs and cannot be used to model the effects of trypsinogen mutations associated with human hereditary pancreatitis. Intra-pancreatic trypsinogen activation by cathepsin B can occur in ferrets, which might trigger pancreatitis even in the absence of trypsinogen autoactivation.
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Cross RW, Fenton KA, Geisbert TW. Small animal models of filovirus disease: recent advances and future directions. Expert Opin Drug Discov 2018; 13:1027-1040. [DOI: 10.1080/17460441.2018.1527827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Robert W. Cross
- Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Karla A. Fenton
- Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas W. Geisbert
- Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
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Abstract
Since the initial report in 1911, the domestic ferret has become an invaluable biomedical research model. While widely recognized for its utility in influenza virus research, ferrets are used for a variety of infectious and noninfectious disease models due to the anatomical, metabolic, and physiological features they share with humans and their susceptibility to many human pathogens. However, there are limitations to the model that must be overcome for maximal utility for the scientific community. Here, we describe important recent advances that will accelerate biomedical research with this animal model.
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Gustafson KD, Hawkins MG, Drazenovich TL, Church R, Brown SA, Ernest HB. Founder events, isolation, and inbreeding: Intercontinental genetic structure of the domestic ferret. Evol Appl 2018; 11:694-704. [PMID: 29875811 PMCID: PMC5979634 DOI: 10.1111/eva.12565] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/02/2017] [Indexed: 12/30/2022] Open
Abstract
Domestication and breeding for human-desired morphological traits can reduce population genetic diversity via founder events and artificial selection, resulting in inbreeding depression and genetic disorders. The ferret (Mustela putorius furo) was domesticated from European polecats (M. putorius), transported to multiple continents, and has been artificially selected for several traits. The ferret is now a common pet, a laboratory model organism, and feral ferrets can impact native biodiversity. We hypothesized global ferret trade resulted in distinct international genetic clusters and that ferrets transported to other continents would have lower genetic diversity than ferrets from Europe because of extreme founder events and no hybridization with wild polecats or genetically diverse ferrets. To assess these hypotheses, we genotyped 765 ferrets at 31 microsatellites from 11 countries among the continents of North America, Europe, and Australia and estimated population structure and genetic diversity. Fifteen M. putorius were genotyped for comparison. Our study indicated ferrets exhibit geographically distinct clusters and highlights the low genetic variation in certain countries. Australian and North American clusters have the lowest genetic diversities and highest inbreeding metrics whereas the United Kingdom (UK) cluster exhibited intermediate genetic diversity. Non-UK European ferrets had high genetic diversity, possibly a result of introgression with wild polecats. Notably, Hungarian ferrets had the highest genetic diversity and Hungary is the only country sampled with two wild polecat species. Our research has broad social, economic, and biomedical importance. Ferret owners and veterinarians should be made aware of potential inbreeding depression. Breeders in North America and Australia would benefit by incorporating genetically diverse ferrets from mainland Europe. Laboratories using ferrets as biomedical organisms should consider diversifying their genetic stock and incorporating genetic information into bioassays. These results also have forensic applications for conserving the genetics of wild polecat species and for identifying and managing sources of feral ferrets causing ecosystem damage.
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Affiliation(s)
- Kyle D. Gustafson
- Wildlife Genomics and Disease Ecology LaboratoryVeterinary SciencesUniversity of WyomingLaramieWYUSA
| | - Michelle G. Hawkins
- Department of Medicine and EpidemiologySchool of Veterinary Medicine, University of California–DavisDavisCAUSA
| | - Tracy L. Drazenovich
- Department of Medicine and EpidemiologySchool of Veterinary Medicine, University of California–DavisDavisCAUSA
| | | | | | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology LaboratoryVeterinary SciencesUniversity of WyomingLaramieWYUSA
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Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high latitudes. Commun Biol 2018; 1:51. [PMID: 30271934 PMCID: PMC6123727 DOI: 10.1038/s42003-018-0058-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/20/2018] [Indexed: 01/19/2023] Open
Abstract
At high latitudes, climatic shifts hypothetically initiate recurrent episodes of divergence by isolating populations in glacial refugia—ice-free regions that enable terrestrial species persistence. Upon glacial recession, populations subsequently expand and often come into contact with other independently diverging populations, resulting in gene flow. To understand how recurrent periods of isolation and contact may have impacted evolution at high latitudes, we investigated introgression dynamics in the stoat (Mustela erminea), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two spatio-temporally distinct episodes of introgression coincident with large-scale climatic shifts: contemporary introgression in a mainland contact zone and ancient contact ~200 km south of the contemporary zone, in the archipelagos along North America’s North Pacific Coast. Repeated episodes of gene flow highlight the central role of cyclic climates in structuring high-latitude diversity, through refugial divergence and introgressive hybridization. When introgression is followed by allopatric isolation (e.g., insularization) it may ultimately expedite divergence. Jocelyn Colella et al. report whole-genome sequences of 10 stoats (Mustela erminea) from four regions of glacial refugia. They find evidence for two past introgressive events between lineages that coincide with interglacial periods, a pattern that may extend to other high–latitude species.
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Abstract
The development of novel therapeutics and vaccines to treat or prevent disease caused by filoviruses, such as Ebola and Marburg viruses, depends on the availability of animal models that faithfully recapitulate clinical hallmarks of disease as it is observed in humans. In particular, small animal models (such as mice and guinea pigs) are historically and frequently used for the primary evaluation of antiviral countermeasures, prior to testing in nonhuman primates, which represent the gold-standard filovirus animal model. In the past several years, however, the filovirus field has witnessed the continued refinement of the mouse and guinea pig models of disease, as well as the introduction of the hamster and ferret models. We now have small animal models for most human-pathogenic filoviruses, many of which are susceptible to wild type virus and demonstrate key features of disease, including robust virus replication, coagulopathy, and immune system dysfunction. Although none of these small animal model systems perfectly recapitulates Ebola virus disease or Marburg virus disease on its own, collectively they offer a nearly complete set of tools in which to carry out the preclinical development of novel antiviral drugs.
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Affiliation(s)
- Logan Banadyga
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Street, Winnipeg, MB R3E 0J9, Canada
| | - Gary Wong
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Street, Winnipeg, MB R3E 0J9, Canada
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People’s Hospital, 29 Bulan Road, Longgang District, Shenzhen, China, 518000
| | - Xiangguo Qiu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Street, Winnipeg, MB R3E 0J9, Canada
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Leon AJ, Borisevich V, Boroumand N, Seymour R, Nusbaum R, Escaffre O, Xu L, Kelvin DJ, Rockx B. Host gene expression profiles in ferrets infected with genetically distinct henipavirus strains. PLoS Negl Trop Dis 2018; 12:e0006343. [PMID: 29538374 PMCID: PMC5868854 DOI: 10.1371/journal.pntd.0006343] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/26/2018] [Accepted: 02/24/2018] [Indexed: 02/05/2023] Open
Abstract
Henipavirus infection causes severe respiratory and neurological disease in humans that can be fatal. To characterize the pathogenic mechanisms of henipavirus infection in vivo, we performed experimental infections in ferrets followed by genome-wide gene expression analysis of lung and brain tissues. The Hendra, Nipah-Bangladesh, and Nipah-Malaysia strains caused severe respiratory and neurological disease with animals succumbing around 7 days post infection. Despite the presence of abundant viral shedding, animal-to-animal transmission did not occur. The host gene expression profiles of the lung tissue showed early activation of interferon responses and subsequent expression of inflammation-related genes that coincided with the clinical deterioration. Additionally, the lung tissue showed unchanged levels of lymphocyte markers and progressive downregulation of cell cycle genes and extracellular matrix components. Infection in the brain resulted in a limited breadth of the host responses, which is in accordance with the immunoprivileged status of this organ. Finally, we propose a model of the pathogenic mechanisms of henipavirus infection that integrates multiple components of the host responses.
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Affiliation(s)
- Alberto J. Leon
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Viktoriya Borisevich
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Nahal Boroumand
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Robert Seymour
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Rebecca Nusbaum
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Olivier Escaffre
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Luoling Xu
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, PRC
- * E-mail: (DJK); (BR)
| | - Barry Rockx
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States of America
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail: (DJK); (BR)
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72
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Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Jones SJM. The Genome of the Northern Sea Otter (Enhydra lutris kenyoni). Genes (Basel) 2017; 8:genes8120379. [PMID: 29232880 PMCID: PMC5748697 DOI: 10.3390/genes8120379] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 11/21/2022] Open
Abstract
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419.
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Affiliation(s)
- Samantha J Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | | | - Gregory A Taylor
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Simon Chan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Steven Bilobram
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Caleb Choo
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Adrian Ally
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Noreen Dhalla
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Angela K Y Tam
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Armelle Troussard
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Daniel Paulino
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Robin J N Coope
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
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Cai Z, Petersen B, Sahana G, Madsen LB, Larsen K, Thomsen B, Bendixen C, Lund MS, Guldbrandtsen B, Panitz F. The first draft reference genome of the American mink (Neovison vison). Sci Rep 2017; 7:14564. [PMID: 29109430 PMCID: PMC5674041 DOI: 10.1038/s41598-017-15169-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/23/2017] [Indexed: 01/28/2023] Open
Abstract
The American mink (Neovison vison) is a semiaquatic species of mustelid native to North America. It's an important animal for the fur industry. Many efforts have been made to locate genes influencing fur quality and color, but this search has been impeded by the lack of a reference genome. Here we present the first draft genome of mink. In our study, two mink individuals were sequenced by Illumina sequencing with 797 Gb sequence generated. Assembly yielded 7,175 scaffolds with an N50 of 6.3 Mb and length of 2.4 Gb including gaps. Repeat sequences constitute around 31% of the genome, which is lower than for dog and cat genomes. The alignments of mink, ferret and dog genomes help to illustrate the chromosomes rearrangement. Gene annotation identified 21,053 protein-coding sequences present in mink genome. The reference genome's structure is consistent with the microsatellite-based genetic map. Mapping of well-studied genes known to be involved in coat quality and coat color, and previously located fur quality QTL provide new knowledge about putative candidate genes for fur traits. The draft genome shows great potential to facilitate genomic research towards improved breeding for high fur quality animals and strengthen our understanding on evolution of Carnivora.
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Affiliation(s)
- Zexi Cai
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark.
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Lone B Madsen
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Knud Larsen
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Bo Thomsen
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Christian Bendixen
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
| | - Frank Panitz
- Section for Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark
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74
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Animal and model systems for studying cystic fibrosis. J Cyst Fibros 2017; 17:S28-S34. [PMID: 28939349 DOI: 10.1016/j.jcf.2017.09.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/31/2017] [Accepted: 09/01/2017] [Indexed: 01/07/2023]
Abstract
The cystic fibrosis (CF) field is the beneficiary of five species of animal models that lack functional cystic fibrosis transmembrane conductance regulator (CFTR) channel. These models are rapidly informing mechanisms of disease pathogenesis and CFTR function regardless of how faithfully a given organ reproduces the human CF phenotype. New approaches of genetic engineering with RNA-guided nucleases are rapidly expanding both the potential types of models available and the approaches to correct the CFTR defect. The application of new CRISPR/Cas9 genome editing techniques are similarly increasing capabilities for in vitro modeling of CFTR functions in cell lines and primary cells using air-liquid interface cultures and organoids. Gene editing of CFTR mutations in somatic stem cells and induced pluripotent stem cells is also transforming gene therapy approaches for CF. This short review evaluates several areas that are key to building animal and cell systems capable of modeling CF disease and testing potential treatments.
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75
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Yang S, Zhang G, Liu W, Wang Z, Zhang J, Yang D, Chen YE, Sun H, Li Y. SysFinder: A customized platform for search, comparison and assisted design of appropriate animal models based on systematic similarity. J Genet Genomics 2017; 44:251-258. [PMID: 28529081 DOI: 10.1016/j.jgg.2017.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/02/2017] [Accepted: 05/03/2017] [Indexed: 11/17/2022]
Abstract
Animal models are increasingly gaining values by cross-comparisons of response or resistance to clinical agents used for patients. However, many disease mechanisms and drug effects generated from animal models are not transferable to human. To address these issues, we developed SysFinder (http://lifecenter.sgst.cn/SysFinder), a platform for scientists to find appropriate animal models for translational research. SysFinder offers a "topic-centered" approach for systematic comparisons of human genes, whose functions are involved in a specific scientific topic, to the corresponding homologous genes of animal models. Scientific topic can be a certain disease, drug, gene function or biological pathway. SysFinder calculates multi-level similarity indexes to evaluate the similarities between human and animal models in specified scientific topics. Meanwhile, SysFinder offers species-specific information to investigate the differences in molecular mechanisms between humans and animal models. Furthermore, SysFinder provides a user-friendly platform for determination of short guide RNAs (sgRNAs) and homology arms to design a new animal model. Case studies illustrate the ability of SysFinder in helping experimental scientists. SysFinder is a useful platform for experimental scientists to carry out their research in the human molecular mechanisms.
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Affiliation(s)
- Shuang Yang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Bioinformation Technology, Shanghai 200235, China
| | - Guoqing Zhang
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
| | - Wan Liu
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Y Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA.
| | - Hong Sun
- Biomedical Information Research Center, Children's Hospital of Shanghai, Shanghai 200040, China.
| | - Yixue Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Bioinformation Technology, Shanghai 200235, China; Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China.
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76
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Establishing the ferret as a gyrencephalic animal model of traumatic brain injury: Optimization of controlled cortical impact procedures. J Neurosci Methods 2017; 285:82-96. [PMID: 28499842 DOI: 10.1016/j.jneumeth.2017.05.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/04/2017] [Accepted: 05/07/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Although rodent TBI studies provide valuable information regarding the effects of injury and recovery, an animal model with neuroanatomical characteristics closer to humans may provide a more meaningful basis for clinical translation. The ferret has a high white/gray matter ratio, gyrencephalic neocortex, and ventral hippocampal location. Furthermore, ferrets are amenable to behavioral training, have a body size compatible with pre-clinical MRI, and are cost-effective. NEW METHODS We optimized the surgical procedure for controlled cortical impact (CCI) using 9 adult male ferrets. We used subject-specific brain/skull morphometric data from anatomical MRIs to overcome across-subject variability for lesion placement. We also reflected the temporalis muscle, closed the craniotomy, and used antibiotics. We then gathered MRI, behavioral, and immunohistochemical data from 6 additional animals using the optimized surgical protocol: 1 control, 3 mild, and 1 severely injured animals (surviving one week) and 1 moderately injured animal surviving sixteen weeks. RESULTS The optimized surgical protocol resulted in consistent injury placement. Astrocytic reactivity increased with injury severity showing progressively greater numbers of astrocytes within the white matter. The density and morphological changes of microglia amplified with injury severity or time after injury. Motor and cognitive impairments scaled with injury severity. COMPARISON WITH EXISTING METHOD(S) The optimized surgical methods differ from those used in the rodent, and are integral to success using a ferret model. CONCLUSIONS We optimized ferret CCI surgery for consistent injury placement. The ferret is an excellent animal model to investigate pathophysiological and behavioral changes associated with TBI.
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Abstract
Ferrets have become more popular as household pets and as animal models in biomedical research in the past 2 decades. The average life span of ferrets is about 5-11 years with onset of geriatric diseases between 3-4 years including endocrinopathies, neoplasia, gastrointestinal diseases, cardiomyopathy, splenomegaly, renal diseases, dental diseases, and cataract. Endocrinopathies are the most common noninfectious disease affecting middle-aged and older ferrets. Spontaneous neoplasms affecting the endocrine system of ferrets appear to be increasing in prevalence with a preponderance toward proliferative lesions in the adrenal cortex and pancreatic islet cells. Diet, gonadectomy, and genetics may predispose ferrets to an increased incidence of these endocrinopathies. These functional proliferative lesions cause hypersecretion of hormones that alter the physiology and metabolism of the affected ferrets resulting in a wide range of clinical manifestations. However, there is an apparent dearth of information available in the literature about the causal relationship between aging and neoplasia in ferrets. This review provides a comprehensive overview of the anatomy and physiology of endocrine organs, disease incidence, age at diagnosis, clinical signs, pathology, and molecular markers available for diagnosis of various endocrine disorders in ferrets.
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Affiliation(s)
- V Bakthavatchalu
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - S Muthupalani
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - R P Marini
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
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78
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Hutchinson EB, Schwerin SC, Radomski KL, Sadeghi N, Jenkins J, Komlosh ME, Irfanoglu MO, Juliano SL, Pierpaoli C. Population based MRI and DTI templates of the adult ferret brain and tools for voxelwise analysis. Neuroimage 2017; 152:575-589. [PMID: 28315740 PMCID: PMC6409125 DOI: 10.1016/j.neuroimage.2017.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/27/2017] [Accepted: 03/05/2017] [Indexed: 01/26/2023] Open
Abstract
Non-invasive imaging has the potential to play a crucial role in the characterization and translation of experimental animal models to investigate human brain development and disorders, especially when employed to study animal models that more accurately represent features of human neuroanatomy. The purpose of this study was to build and make available MRI and DTI templates and analysis tools for the ferret brain as the ferret is a well-suited species for pre-clinical MRI studies with folded cortical surface, relatively high white matter volume and body dimensions that allow imaging with pre-clinical MRI scanners. Four ferret brain templates were built in this study – in-vivo MRI and DTI and ex-vivo MRI and DTI – using brain images across many ferrets and region of interest (ROI) masks corresponding to established ferret neuroanatomy were generated by semi-automatic and manual segmentation. The templates and ROI masks were used to create a web-based ferret brain viewing software for browsing the MRI and DTI volumes with annotations based on the ROI masks. A second objective of this study was to provide a careful description of the imaging methods used for acquisition, processing, registration and template building and to demonstrate several voxelwise analysis methods including Jacobian analysis of morphometry differences between the female and male brain and bias-free identification of DTI abnormalities in an injured ferret brain. The templates, tools and methodological optimization presented in this study are intended to advance non-invasive imaging approaches for human-similar animal species that will enable the use of pre-clinical MRI studies for understanding and treating brain disorders.
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Affiliation(s)
- E B Hutchinson
- Section on Quantitative Imaging and Tissue Science, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - S C Schwerin
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - K L Radomski
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - N Sadeghi
- Section on Quantitative Imaging and Tissue Science, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - J Jenkins
- Section on Quantitative Imaging and Tissue Science, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Dept. of Electrical Engineering and Computer Science, The Catholic University of America, Washington D.C., USA
| | - M E Komlosh
- Section on Quantitative Imaging and Tissue Science, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - M O Irfanoglu
- Section on Quantitative Imaging and Tissue Science, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - S L Juliano
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - C Pierpaoli
- Section on Quantitative Imaging and Tissue Science, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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79
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Lindeberg H, Burchmore RJS, Kennedy MW. Pulse of inflammatory proteins in the pregnant uterus of European polecats ( Mustela putorius) leading to the time of implantation. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161085. [PMID: 28405395 PMCID: PMC5383852 DOI: 10.1098/rsos.161085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/22/2017] [Indexed: 06/07/2023]
Abstract
Uterine secretory proteins protect the uterus and conceptuses against infection, facilitate implantation, control cellular damage resulting from implantation, and supply pre-implantation embryos with nutrients. Unlike in humans, the early conceptus of the European polecat (Mustela putorius; ferret) grows and develops free in the uterus until implanting at about 12 days after mating. We found that the proteins appearing in polecat uteri changed dramatically with time leading to implantation. Several of these proteins have also been found in pregnant uteri of other eutherian mammals. However, we found a combination of two increasingly abundant proteins that have not been recorded before in pre-placentation uteri. First, the broad-spectrum proteinase inhibitor α2-macroglobulin rose to dominate the protein profile by the time of implantation. Its functions may be to limit damage caused by the release of proteinases during implantation or infection, and to control other processes around sites of implantation. Second, lipocalin-1 (also known as tear lipocalin) also increased substantially in concentration. This protein has not previously been recorded as a uterine secretion in pregnancy in any species. If polecat lipocalin-1 has similar biological properties to that of humans, then it may have a combined function in antimicrobial protection and transporting or scavenging lipids. The changes in the uterine secretory protein repertoire of European polecats is therefore unusual, and may be representative of pre-placentation supportive uterine secretions in mustelids (otters, weasels, badgers, mink, wolverines) in general.
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Affiliation(s)
- Heli Lindeberg
- Natural Resources Institute Finland (Luke), Green Technology, Halolantie 31 A, 71750 Maaninka, Finland
| | - Richard J. S. Burchmore
- Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow G61 1QH, Scotland, UK
| | - Malcolm W. Kennedy
- Institute of Biodiversity, Animal Health and Comparative Medicine, and the Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, Scotland, UK
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80
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Generation of Monoclonal Antibodies against Immunoglobulin Proteins of the Domestic Ferret ( Mustela putorius furo). J Immunol Res 2017; 2017:5874572. [PMID: 28286781 PMCID: PMC5329684 DOI: 10.1155/2017/5874572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/20/2016] [Accepted: 01/12/2017] [Indexed: 12/30/2022] Open
Abstract
The domestic ferret (Mustela putorius furo) serves as an animal model for the study of several viruses that cause human disease, most notably influenza. Despite the importance of this animal model, characterization of the immune response by flow cytometry (FCM) is severely hampered due to the limited number of commercially available reagents. To begin to address this unmet need and to facilitate more in-depth study of ferret B cells including the identification of antibody-secreting cells, eight unique murine monoclonal antibodies (mAb) with specificity for ferret immunoglobulin (Ig) were generated using conventional B cell hybridoma technology. These mAb were screened for reactivity against ferret peripheral blood mononuclear cells by FCM and demonstrate specificity for CD79β+ B cells. Several of these mAb are specific for the light chain of surface B cell receptor (BCR) and enable segregation of kappa and lambda B cells. Additionally, a mAb that yielded surface staining of nearly all surface BCR positive cells (i.e., pan ferret Ig) was generated. Collectively, these MαF-Ig mAb offer advancement compared to the existing portfolio of polyclonal anti-ferret Ig detection reagents and should be applicable to a wide array of immunologic assays including the identification of antibody-secreting cells by FCM.
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81
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Hoff MLM, Fabrizius A, Czech-Damal NU, Folkow LP, Burmester T. Transcriptome Analysis Identifies Key Metabolic Changes in the Hooded Seal (Cystophora cristata) Brain in Response to Hypoxia and Reoxygenation. PLoS One 2017; 12:e0169366. [PMID: 28046118 PMCID: PMC5207758 DOI: 10.1371/journal.pone.0169366] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/15/2016] [Indexed: 11/21/2022] Open
Abstract
The brain of diving mammals tolerates low oxygen conditions better than the brain of most terrestrial mammals. Previously, it has been demonstrated that the neurons in brain slices of the hooded seal (Cystophora cristata) withstand hypoxia longer than those of mouse, and also tolerate reduced glucose supply and high lactate concentrations. This tolerance appears to be accompanied by a shift in the oxidative energy metabolism to the astrocytes in the seal while in terrestrial mammals the aerobic energy production mainly takes place in neurons. Here, we used RNA-Seq to compare the effect of hypoxia and reoxygenation in vitro on brain slices from the visual cortex of hooded seals. We saw no general reduction of gene expression, suggesting that the response to hypoxia and reoxygenation is an actively regulated process. The treatments caused the preferential upregulation of genes related to inflammation, as found before e.g. in stroke studies using mammalian models. Gene ontology and KEGG pathway analyses showed a downregulation of genes involved in ion transport and other neuronal processes, indicative for a neuronal shutdown in response to a shortage of O2 supply. These differences may be interpreted in terms of an energy saving strategy in the seal's brain. We specifically analyzed the regulation of genes involved in energy metabolism. Hypoxia and reoxygenation caused a similar response, with upregulation of genes involved in glucose metabolism and downregulation of the components of the pyruvate dehydrogenase complex. We also observed upregulation of the monocarboxylate transporter Mct4, suggesting increased lactate efflux. Together, these data indicate that the seal brain responds to the hypoxic challenge by a relative increase in the anaerobic energy metabolism.
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Affiliation(s)
| | - Andrej Fabrizius
- Institute of Zoology, Biocenter Grindel, University of Hamburg, Hamburg, Germany
| | | | - Lars P. Folkow
- Department of Arctic and Marine Biology, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
| | - Thorsten Burmester
- Institute of Zoology, Biocenter Grindel, University of Hamburg, Hamburg, Germany
- * E-mail:
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82
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Bhoumik P, Del Rio-Espinola A, Hahne F, Moggs J, Grenet O. Translational Safety Genetics. Toxicol Pathol 2016; 45:119-126. [PMID: 27932582 DOI: 10.1177/0192623316675064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The emerging field of translational safety genetics is providing new opportunities to enhance drug discovery and development. Genetic variation in therapeutic drug targets, off-target interactors and relevant drug metabolism/disposition pathways can contribute to diverse drug pharmacologic and toxicologic responses between different animal species, strains and geographic origins. Recent advances in the sequencing of rodent, canine, nonhuman primate, and minipig genomes have dramatically improved the ability to select the most appropriate animal species for preclinical drug toxicity studies based on genotypic characterization of drug targets/pathways and drug metabolism and/or disposition, thus avoiding inconclusive or misleading animal studies, consistent with the principles of the 3Rs (replacement, reduction and refinement). The genetic background of individual animals should also be taken into consideration when interpreting phenotypic outcomes from toxicity studies and susceptibilities to spontaneous safety-relevant background findings.
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Affiliation(s)
- Priyasma Bhoumik
- 1 Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alberto Del Rio-Espinola
- 1 Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Florian Hahne
- 1 Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jonathan Moggs
- 1 Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Olivier Grenet
- 1 Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
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83
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Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. Viral factors in influenza pandemic risk assessment. eLife 2016; 5. [PMID: 27834632 PMCID: PMC5156527 DOI: 10.7554/elife.18491] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022] Open
Abstract
The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus. The goal would be to use genetic sequence and/or biological assays of viral traits to identify those non-human influenza viruses with the greatest risk of evolving into pandemic threats, and/or to understand drivers of such evolution, to prioritize pandemic prevention or response measures. We describe such efforts, identify progress and ongoing challenges, and discuss three specific traits of influenza viruses (hemagglutinin receptor binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency) that contribute to pandemic risk.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T. H Chan School of Public Health, Boston, United States.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Wendy Barclay
- Division of Infectious Disease, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Rahul Raman
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Charles J Russell
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, United States
| | - Jessica A Belser
- Centers for Disease Control and Prevention, Atlanta, United States
| | - Sarah Cobey
- Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, United States
| | - Peter M Kasson
- Department of Biomedical Engineering, University of Virginia, Charlottesville, United States.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States.,Fogarty International Center, National Institutes of Health, Bethesda, United States
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore.,National Public Health Laboratory, Communicable Diseases Division, Ministry of Health, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Steven Riley
- MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | | | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, United States
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, United States
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pablo R Murcia
- MRC-University of Glasgow Centre For Virus Research, Glasgow, United Kingdom
| | | | - Claus O Wilke
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, United States.,Department of Integrative Biology, The University of Texas at Austin, Austin, United States
| | - Colin A Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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84
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Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell Host Microbe 2016; 19:254-66. [PMID: 26867183 DOI: 10.1016/j.chom.2016.01.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 12/02/2015] [Accepted: 01/18/2016] [Indexed: 11/23/2022]
Abstract
Pandemic influenza viruses modulate proinflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data with virologic and histopathologic data uncovered relationships between host responses and phenotypic outcomes of viral infection. Proinflammatory lipid precursors in the trachea following 1918 infection correlated with severe tracheal lesions. Using an algorithm to infer cell quantity changes from gene expression data, we found enrichment of distinct T cell subpopulations in the trachea. There was also a predicted increase in inflammatory monocytes in the lung of 1918 virus-infected animals that was sustained throughout infection. This study presents a unique resource to the influenza research community and demonstrates the utility of an integrative systems approach for characterization of lipid metabolism alterations underlying respiratory responses to viruses.
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85
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Kim S, Cho YS, Kim HM, Chung O, Kim H, Jho S, Seomun H, Kim J, Bang WY, Kim C, An J, Bae CH, Bhak Y, Jeon S, Yoon H, Kim Y, Jun J, Lee H, Cho S, Uphyrkina O, Kostyria A, Goodrich J, Miquelle D, Roelke M, Lewis J, Yurchenko A, Bankevich A, Cho J, Lee S, Edwards JS, Weber JA, Cook J, Kim S, Lee H, Manica A, Lee I, O'Brien SJ, Bhak J, Yeo JH. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. Genome Biol 2016; 17:211. [PMID: 27802837 PMCID: PMC5090899 DOI: 10.1186/s13059-016-1071-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. RESULTS We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. CONCLUSIONS Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.
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Affiliation(s)
- Soonok Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Yun Sung Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Hak-Min Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Oksung Chung
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Hyunho Kim
- Geromics, Ulsan, 44919, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Hong Seomun
- Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Jeongho Kim
- Cheongju Zoo, Cheongju, 28311, Republic of Korea
| | - Woo Young Bang
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Changmu Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Junghwa An
- Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Chang Hwan Bae
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Youngjune Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Sungwon Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hyejun Yoon
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yumi Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - JeHoon Jun
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.,Geromics, Ulsan, 44919, Republic of Korea
| | - HyeJin Lee
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.,Geromics, Ulsan, 44919, Republic of Korea
| | - Suan Cho
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.,Geromics, Ulsan, 44919, Republic of Korea
| | - Olga Uphyrkina
- Institute of Biology & Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Aleksey Kostyria
- Institute of Biology & Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia
| | | | - Dale Miquelle
- Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY, 10460, USA.,Department of Ecology, Far Eastern Federal University, Ayaks, Russki Island, Vladivostok, 690950, Russia
| | - Melody Roelke
- Laboratory of Animal Sciences Program, Leídos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, 21702, USA
| | - John Lewis
- International Zoo Veterinary Group (UK) IZVG LLP, Station House, Parkwood Street, Keighley, BD21 4NQ, UK
| | - Andrey Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia
| | - Anton Bankevich
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Juok Cho
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Semin Lee
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jessica A Weber
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jo Cook
- Zoological Society of London, London, NW1 4RY, UK
| | - Sangsoo Kim
- Department of Bioinformatics & Life Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Ilbeum Lee
- Daejeon O-World, Daejeon, 35073, Republic of Korea
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia. .,Oceanographic Center 8000 N. Ocean Drive, Nova Southeastern University, Ft Lauderdale, FL, 33004, USA.
| | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea. .,Geromics, Ulsan, 44919, Republic of Korea.
| | - Joo-Hong Yeo
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
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86
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Ali R, Blackburn RM, Kozlakidis Z. Next-Generation Sequencing and Influenza Virus: A Short Review of the Published Implementation Attempts. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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87
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DiPiazza A, Richards K, Batarse F, Lockard L, Zeng H, García-Sastre A, Albrecht RA, Sant AJ. Flow Cytometric and Cytokine ELISpot Approaches To Characterize the Cell-Mediated Immune Response in Ferrets following Influenza Virus Infection. J Virol 2016; 90:7991-8004. [PMID: 27356897 PMCID: PMC4988159 DOI: 10.1128/jvi.01001-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/18/2016] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Influenza virus infections represent a significant socioeconomic and public health burden worldwide. Although ferrets are considered by many to be ideal for modeling human responses to influenza infection and vaccination, efforts to understand the cellular immune response have been severely hampered by a paucity of standardized procedures and reagents. In this study, we developed flow cytometric and T cell enzyme-linked immunosorbent spot (ELISpot) approaches to characterize the leukocyte composition and antigen-specific T cell response within key lymphoid tissues following influenza virus infection in ferrets. Through a newly designed and implemented set of serological reagents, we used multiparameter flow cytometry to directly quantify the frequency of CD4(+) and CD8(+) T cells, Ig(+) B cells, CD11b(+) myeloid-derived cells, and major histocompatibility complex (MHC) class II-positive antigen-presenting cells (APCs) both prior to and after intranasal infection with A/California/04/09 (H1N1). We found that the leukocyte composition was altered at 10 days postinfection, with notable gains in the frequency of T cells and myeloid cells within the draining lymph node. Furthermore, these studies revealed that the antigen specificity of influenza virus-reactive CD4 and CD8 T cells was very broad, with recognition of the viral HA, NA, M1, NS1, and NP proteins, and that total reactivity to influenza virus postinfection represented approximately 0.1% of the circulating peripheral blood mononuclear cells (PBMC). Finally, we observed distinct patterns of reactivity between individual animals, suggesting heterogeneity at the MHC locus in ferrets within commercial populations, a finding of considerable interest in efforts to move the ferret model forward for influenza vaccine and challenge studies. IMPORTANCE Ferrets are an ideal animal model to study transmission, diseases, and vaccine efficacies of respiratory viruses because of their close anatomical and physiological resemblances to humans. However, a lack of reagents has limited our understanding of the cell-mediated immune response following infection and vaccination. In this study, we used cross-reactive and ferret-specific antibodies to study the leukocyte composition and antigen-specific CD4 and CD8 T cell responses following influenza A/California/04/09 (H1N1) virus infection. These studies revealed strikingly distinct patterns of reactivity between CD4 and CD8 T cells, which were overlaid with differences in protein-specific responses between individual animals. Our results provide a first, in-depth look at the T cell repertoire in response to influenza infection and suggest that there is considerable heterogeneity at the MHC locus, which is akin to that in humans and an area of intense research interest.
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Affiliation(s)
- Anthony DiPiazza
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Katherine Richards
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Frances Batarse
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Laura Lockard
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Hui Zeng
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, New York, USA Global Health and Emerging Pathogens Institute at Icahn School of Medicine, New York, New York, USA Department of Medicine, Icahn School of Medicine at Mt. Sinai, New York, New York, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, New York, USA Global Health and Emerging Pathogens Institute at Icahn School of Medicine, New York, New York, USA
| | - Andrea J Sant
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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88
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Complexities in Ferret Influenza Virus Pathogenesis and Transmission Models. Microbiol Mol Biol Rev 2016; 80:733-44. [PMID: 27412880 DOI: 10.1128/mmbr.00022-16] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ferrets are widely employed to study the pathogenicity, transmissibility, and tropism of influenza viruses. However, inherent variations in inoculation methods, sampling schemes, and experimental designs are often overlooked when contextualizing or aggregating data between laboratories, leading to potential confusion or misinterpretation of results. Here, we provide a comprehensive overview of parameters to consider when planning an experiment using ferrets, collecting data from the experiment, and placing results in context with previously performed studies. This review offers information that is of particular importance for researchers in the field who rely on ferret data but do not perform the experiments themselves. Furthermore, this review highlights the breadth of experimental designs and techniques currently available to study influenza viruses in this model, underscoring the wide heterogeneity of protocols currently used for ferret studies while demonstrating the wealth of information which can benefit risk assessments of emerging influenza viruses.
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89
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Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SMJ. The Ensembl gene annotation system. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw093. [PMID: 27337980 PMCID: PMC4919035 DOI: 10.1093/database/baw093] [Citation(s) in RCA: 677] [Impact Index Per Article: 84.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 12/12/2022]
Abstract
The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html.
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Affiliation(s)
- Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah Ayling
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Present addresses: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Laura Clarke
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Valery Curwen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Susan Fairley
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julio Fernandez Banet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Pfizer Inc, 10646 Science Center Dr, San Diego, CA 92121, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kevin Howe
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas Kähäri
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Institutionen för cell-och molekylärbiologi, Uppsala University, Husargatan 3, Uppsala 752 37, Sweden
| | - Felix Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Magali Ruffier
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Schuster
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna a-1090, Austria
| | - Y Amy Tang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jan-Hinnerk Vogel
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Simon White
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amonida Zadissa
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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90
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Cross RW, Mire CE, Borisevich V, Geisbert JB, Fenton KA, Geisbert TW. The Domestic Ferret (Mustela putorius furo) as a Lethal Infection Model for 3 Species of Ebolavirus. J Infect Dis 2016; 214:565-9. [PMID: 27354371 PMCID: PMC4957446 DOI: 10.1093/infdis/jiw209] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/13/2016] [Indexed: 12/05/2022] Open
Abstract
Small-animal models have been developed for several Filoviridae species; however, serial adaptation was required to produce lethal infection. These adapted viruses have sequence changes in several genes, including those that modulate the host immune response. Nonhuman primate models do not require adaptation of filoviruses. Here, we describe lethal models of disease for Bundibugyo, Sudan, and Zaire species of Ebolavirus in the domestic ferret, using wild-type nonadapted viruses. Pathologic features were consistent with disease in primates. Of particular importance, this is the only known small-animal model developed for Bundibugyo and the only uniformly lethal animal model for Bundibugyo.
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Affiliation(s)
- Robert W Cross
- Department of Microbiology and Immunology, Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | - Chad E Mire
- Department of Microbiology and Immunology, Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | - Viktoriya Borisevich
- Department of Microbiology and Immunology, Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | - Joan B Geisbert
- Department of Microbiology and Immunology, Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | - Karla A Fenton
- Department of Microbiology and Immunology, Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, Galveston National Laboratory, University of Texas Medical Branch at Galveston
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91
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Hekman JP, Johnson JL, Kukekova AV. Transcriptome Analysis in Domesticated Species: Challenges and Strategies. Bioinform Biol Insights 2016; 9:21-31. [PMID: 26917953 PMCID: PMC4756862 DOI: 10.4137/bbi.s29334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/21/2015] [Accepted: 12/26/2015] [Indexed: 12/13/2022] Open
Abstract
Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, we discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.
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Affiliation(s)
- Jessica P. Hekman
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Jennifer L. Johnson
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Anna V. Kukekova
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
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92
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Oh DY, Hurt AC. Using the Ferret as an Animal Model for Investigating Influenza Antiviral Effectiveness. Front Microbiol 2016; 7:80. [PMID: 26870031 PMCID: PMC4740393 DOI: 10.3389/fmicb.2016.00080] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/18/2016] [Indexed: 01/12/2023] Open
Abstract
The concern of the emergence of a pandemic influenza virus has sparked an increased effort toward the development and testing of novel influenza antivirals. Central to this is the animal model of influenza infection, which has played an important role in understanding treatment effectiveness and the effect of antivirals on host immune responses. Among the different animal models of influenza, ferrets can be considered the most suitable for antiviral studies as they display most of the human-like symptoms following influenza infections, they can be infected with human influenza virus without prior viral adaptation and have the ability to transmit influenza virus efficiently between one another. However, an accurate assessment of the effectiveness of an antiviral treatment in ferrets is dependent on three major experimental considerations encompassing firstly, the volume and titer of virus, and the route of viral inoculation. Secondly, the route and dose of drug administration, and lastly, the different methods used to assess clinical symptoms, viral shedding kinetics and host immune responses in the ferrets. A good understanding of these areas is necessary to achieve data that can accurately inform the human use of influenza antivirals. In this review, we discuss the current progress and the challenges faced in these three major areas when using the ferret model to measure influenza antiviral effectiveness.
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Affiliation(s)
- Ding Y Oh
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, MelbourneVIC, Australia; School of Applied and Biomedical Sciences, Federation University Australia, GippslandVIC, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, MelbourneVIC, Australia; Melbourne School of Population and Global Health, University of Melbourne, ParkvilleVIC, Australia
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93
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Ren B, McKinstry WJ, Pham T, Newman J, Layton DS, Bean AG, Chen Z, Laurie KL, Borg K, Barr IG, Adams TE. Structural and functional characterisation of ferret interleukin-2. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 55:32-38. [PMID: 26472619 PMCID: PMC7102629 DOI: 10.1016/j.dci.2015.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
While the ferret is a valuable animal model for a number of human viral infections, such as influenza, Hendra and Nipah, evaluating the cellular immune response following infection has been hampered by the lack of a number of species-specific immunological reagents. Interleukin 2 (IL-2) is one such key cytokine. Ferret recombinant IL-2 incorporating a C-terminal histidine tag was expressed and purified and the three-dimensional structure solved and refined at 1.89 Å by X-ray crystallography, which represents the highest resolution and first non-human IL-2 structure. While ferret IL-2 displays the classic cytokine fold of the four-helix bundle structure, conformational flexibility was observed at the second helix and its neighbouring region in the bundle, which may result in the disruption of the spatial arrangement of residues involved in receptor binding interactions, implicating subtle differences between ferret and human IL-2 when initiating biological functions. Ferret recombinant IL-2 stimulated the proliferation of ferret lymph node cells and induced the expression of mRNA for IFN-γ and Granzyme A.
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Affiliation(s)
- Bin Ren
- CSIRO Manufacturing, Parkville, VIC 3052, Australia
| | | | - Tam Pham
- CSIRO Manufacturing, Parkville, VIC 3052, Australia
| | - Janet Newman
- CSIRO Manufacturing, Parkville, VIC 3052, Australia
| | | | - Andrew G Bean
- CSIRO Health and Biosecurity, Geelong, VIC 3219, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute, Melbourne, VIC 3000, Australia
| | - Karen L Laurie
- WHO Collaborating Centre for Reference and Research on Influenza (VIDRL), Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Kathryn Borg
- WHO Collaborating Centre for Reference and Research on Influenza (VIDRL), Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza (VIDRL), Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
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94
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Abstract
Viral pathogenesis seeks to understand how a virus interacts with its host at multiple levels. Key questions include the source (an infected human, animal, or insect vector), the transmission mechanism, and how the virus is shed and transmitted. Following transmission, pathogenesis is governed by the initial site of replication, whether the virus disseminates within the host, and its tropism for specific tissues and organs. In turn, these steps are dictated by the structure and replication strategy of the virus. In addition to utilizing selected synthetic biochemical pathways in the host cell, viruses frequently reprogram host cells by inducing intracellular signaling pathways that render the cell more permissive. Host–virus interactions also control whether the infection is acute, chronic, latent, or transforming; how the virus interacts with the immune system; and the consequent pathophysiological response of the host. This chapter provides an overview of these basic concepts of viral pathogenesis, with emphasis on the interactions of viruses with their host cells and organisms.
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95
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Wisely SM, Ryder OA, Santymire RM, Engelhardt JF, Novak BJ. A Road Map for 21st Century Genetic Restoration: Gene Pool Enrichment of the Black-Footed Ferret. J Hered 2015; 106:581-92. [PMID: 26304983 PMCID: PMC4567841 DOI: 10.1093/jhered/esv041] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 06/07/2015] [Indexed: 12/15/2022] Open
Abstract
Interspecies somatic cell nuclear transfer (iSCNT) could benefit recovery programs of critically endangered species but must be weighed with the risks of failure. To weigh the risks and benefits, a decision-making process that evaluates progress is needed. Experiments that evaluate the efficiency and efficacy of blastocyst, fetal, and post-parturition development are necessary to determine the success or failure or species-specific iSCNT programs. Here, we use the black-footed ferret (Mustela nigripes) as a case study for evaluating this emerging biomedical technology as a tool for genetic restoration. The black-footed ferret has depleted genetic variation yet genome resource banks contain genetic material of individuals not currently represented in the extant lineage. Thus, genetic restoration of the species is in theory possible and could help reduce the persistent erosion of genetic diversity from drift. Extensive genetic, genomic, and reproductive science tools have previously been developed in black-footed ferrets and would aid in the process of developing an iSCNT protocol for this species. Nonetheless, developing reproductive cloning will require years of experiments and a coordinated effort among recovery partners. The information gained from a well-planned research effort with the goal of genetic restoration via reproductive cloning could establish a 21st century model for evaluating and implementing conservation breeding that would be applicable to other genetically impoverished species.
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Affiliation(s)
- Samantha M Wisely
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak).
| | - Oliver A Ryder
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - Rachel M Santymire
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - John F Engelhardt
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
| | - Ben J Novak
- From the Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611 USA (Wisely); San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, San Diego Zoo Global, Escondido, California, 92027 USA (Ryder); Davee Center for Epidemiology and Endocrinology, 2001 North Clark Street, Lincoln Park Zoo, Chicago, Illinois, 60614 USA (Santymire); Department of Anatomy and Cell Biology, 51 Newton Road, University of Iowa, Iowa City, Iowa, 52242 USA (Engelhardt); and Revive & Restore, The Long Now Foundation, 2 Marina Boulevard Building A, San Francisco, California, 94123 USA (Novak)
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96
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Howard JG, Lynch C, Santymire RM, Marinari PE, Wildt DE. Recovery of gene diversity using long-term cryopreserved spermatozoa and artificial insemination in the endangered black-footed ferret. Anim Conserv 2015. [DOI: 10.1111/acv.12229] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. G. Howard
- Smithsonian Conservation Biology Institute; National Zoological Park; Front Royal VA USA
| | - C. Lynch
- Animal Care Department; Riverbanks Zoo and Garden; Columbia SC USA
- Conservation and Science Department; Lincoln Park Zoo; Chicago IL USA
| | - R. M. Santymire
- Smithsonian Conservation Biology Institute; National Zoological Park; Front Royal VA USA
- Conservation and Science Department; Lincoln Park Zoo; Chicago IL USA
| | - P. E. Marinari
- Smithsonian Conservation Biology Institute; National Zoological Park; Front Royal VA USA
| | - D. E. Wildt
- Smithsonian Conservation Biology Institute; National Zoological Park; Front Royal VA USA
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97
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Empie K, Rangarajan V, Juul SE. Is the ferret a suitable species for studying perinatal brain injury? Int J Dev Neurosci 2015; 45:2-10. [PMID: 26102988 PMCID: PMC4793918 DOI: 10.1016/j.ijdevneu.2015.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/09/2015] [Accepted: 06/01/2015] [Indexed: 11/26/2022] Open
Abstract
Ferret brain architecture, composition, and development are similar to humans. Postnatal ferret brain development is comparable to that of premature infants. Ferrets have potential to model preterm and term neonatal brain injury. Ferrets may fulfill the need for an intermediate model species of neurodevelopment. Many opportunities exist to expand the use of ferrets as research subjects.
Complications of prematurity often disrupt normal brain development and/or cause direct damage to the developing brain, resulting in poor neurodevelopmental outcomes. Physiologically relevant animal models of perinatal brain injury can advance our understanding of these influences and thereby provide opportunities to develop therapies and improve long-term outcomes. While there are advantages to currently available small animal models, there are also significant drawbacks that have limited translation of research findings to humans. Large animal models such as newborn pig, sheep and nonhuman primates have complex brain development more similar to humans, but these animals are expensive, and developmental testing of sheep and piglets is limited. Ferrets (Mustela putorius furo) are born lissencephalic and undergo postnatal cortical folding to form complex gyrencephalic brains. This review examines whether ferrets might provide a novel intermediate animal model of neonatal brain disease that has the benefit of a gyrified, altricial brain in a small animal. It summarizes attributes of ferret brain growth and development that make it an appealing animal in which to model perinatal brain injury. We postulate that because of their innate characteristics, ferrets have great potential in neonatal neurodevelopmental studies.
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Affiliation(s)
- Kristen Empie
- Department of Neonatology, University of Washington, Seattle, USA
| | | | - Sandra E Juul
- Department of Neonatology, University of Washington, Seattle, USA.
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98
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Evolution of V genes from the TRV loci of mammals. Immunogenetics 2015; 67:371-84. [PMID: 26024913 DOI: 10.1007/s00251-015-0850-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
Information concerning the evolution of T lymphocyte receptors (TCR) can be deciphered from that part of the molecule that recognizes antigen presented by major histocompatibility complex (MHC), namely the variable (V) regions. The genes that code for these variable regions are found within the TCR loci. Here, we describe a study of the evolutionary origin of V genes that code for the α and β chains of the TCR loci of mammals. In particular, we demonstrate that most of the 35 TRAV and 25 TRBV conserved genes found in Primates are also found in other Eutheria, while in Marsupials, Monotremes, and Reptiles, these genes diversified in a different manner. We also show that in mammals, all TRAV genes are derived from five ancestral genes, while all TRBV genes originate from four such genes. In Reptiles, the five TRAV and three out of the four TRBV ancestral genes exist, as well as other V genes not found in mammals. We also studied the TRGV and TRDV loci from all mammals, and we show a relationship of the TRDV to the TRAV locus throughout evolutionary time.
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99
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Enkirch T, von Messling V. Ferret models of viral pathogenesis. Virology 2015; 479-480:259-70. [PMID: 25816764 PMCID: PMC7111696 DOI: 10.1016/j.virol.2015.03.017] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 01/28/2015] [Accepted: 03/02/2015] [Indexed: 11/26/2022]
Abstract
Emerging and well-known viral diseases remain one the most important global public health threats. A better understanding of their pathogenesis and mechanisms of transmission requires animal models that accurately reproduce these aspects of the disease. Here we review the role of ferrets as an animal model for the pathogenesis of different respiratory viruses with an emphasis on influenza and paramyxoviruses. We will describe the anatomic and physiologic characteristics that contribute to the natural susceptibility of ferrets to these viruses, and provide an overview of the approaches available to analyze their immune responses. Recent insights gained using this model will be highlighted, including the development of new prophylactic and therapeutic approaches. To provide decision criteria for the use of this animal model, its strengths and limitations will be discussed. Ferrets as models for respiratory virus pathogenesis. Ferrets as models for vaccine and drug efficacy assessment. Immunological tools for ferrets. Housing and handling of ferrets.
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Affiliation(s)
- T Enkirch
- Veterinary Medicine Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - V von Messling
- Veterinary Medicine Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany.
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