The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

Peng, Xinxia; Alföldi, Jessica; Gori, Kevin; Eisfeld, Amie J.; Tyler, Scott R.; Tisoncik-Go, Jennifer; Brawand, David; Law, G. Lynn; Škunca, Nives; Hatta, Masato; Gasper, David J.; Kelly, Sara; Chang, Jean; Thomas, Matthew; Johnson, Jeremy; Berlin, Aaron M.; Lara, Marcia; Russell, Pamela; Swofford, Ross; Turner-Maier, Jason; Young, Sarah; Hourlier, Thibaut; Aken, Bronwen; Searle, Steve; Sun, Xingshen; Yi, Yaling; Suresh, M.; Tumpey, Terrence M.; Siepel, Adam; Wisely, Samantha M.; Dessimoz, Christophe; Kawaoka, Yoshihiro; Birren, Bruce W.; Lindblad‐Toh, Kerstin; Palma, Federica Di; Engelhardt, John F.; Palermo, Robert E.; Katze, Michael G.

doi:10.1038/nbt.3079

Cited by 120 publications

(101 citation statements)

References 42 publications

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“…We confirmed that GCKR is also pseudogenized by frame-shift mutations in all other felids (leopard, tiger, lion, cheetah, snow leopard, and leopard cat; Additional file 2: Figure S7). Interestingly, GCKR genes of killer whale and domestic ferret (another obligate carnivore not used in this study) [37] were also pseudogenized by pre-matured and/or frame-shift mutations, whereas polar bear and Tasmanian devil have an intact GCKR (Additional file 3: Table S31). It has been suggested that carnivores may not need to remove excess glucose from the circulation, as they consume food containing large amounts of protein and little carbohydrate [36].…”

Section: Resultsmentioning

confidence: 99%

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

et al. 2016

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BackgroundThere 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.ResultsWe 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1071-4) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

et al. 2016

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“…Gene expression studies, using information gathered from the draft genome and cross-reactive probes for microarrays, have confirmed the biphasic kinetics of innate and adaptive immune responses following viral infection (42)(43)(44)(45). While limited, serological reagents (46,47) have been used in a number of applications, including immunohistochemical analyses to study pathological features of disease as it relates to the virus/host interface (48).…”

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confidence: 99%

Flow Cytometric and Cytokine ELISpot Approaches To Characterize the Cell-Mediated Immune Response in Ferrets following Influenza Virus Infection

DiPiazza

Richards

Batarse

et al. 2016

J Virol

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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. IMPORTANCEFerrets 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, indepth 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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“…There is no ‘perfect’ small mammalian model for influenza. A longstanding challenge of the ferret model has been limited availability of ferret-specific commercial reagents compared with other models, though recent sequencing of the ferret genome should improve this situation (Peng et al, 2014). Ethical considerations, and the size and cost of ferrets, necessitate generally small sample sizes in ferret experiments, limiting statistical power (Belser et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Viral factors in influenza pandemic risk assessment

Lipsitch

Barclay

Raman

et al. 2016

eLife

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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.DOI: http://dx.doi.org/10.7554/eLife.18491.001

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The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

Cited by 120 publications

References 42 publications

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Flow Cytometric and Cytokine ELISpot Approaches To Characterize the Cell-Mediated Immune Response in Ferrets following Influenza Virus Infection

Viral factors in influenza pandemic risk assessment

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