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1.
Food Microbiol ; 86: 103352, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31703865

RESUMO

Shiga toxin-producing Escherichia (E.) coli (STEC) pathogens are responsible for the outbreaks of serious diseases in humans, including haemolytic uraemic syndrome (HUS), bloody diarrhoea (BD) and diarrhoea (D), and they pose a significant public health concern. Wild ruminants are an important environmental reservoir of foodborne pathogens that can cause serious illnesses in humans and contaminate fresh products. There is a general scarcity of published data about wildlife as a reservoir of foodborne pathogens in Poland, which is why the potential epidemiological risk associated with red deer, roe deer and fallow deer as reservoirs of STEC/AE-STEC strains was evaluated in this study. The aim of the study was to investigate the prevalence of STEC strains in red deer (Cervus elaphus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) populations in north-eastern Poland, and to evaluate the potential health risk associated with wild ruminants carrying STEC/AE-STEC strains. We examined 252 rectal swabs obtained from 134 roe deer (Capreolus capreolus), 97 red deer (Cervus elaphus) and 21 fallow deer (Dama dama) in north-eastern Poland. The samples were enriched in modified buffered peptone water. Polymerase chain reaction (PCR) assays were conducted to determine the virulence profile of stx1, stx2 and eae or aggR genes, to identify the subtypes of stx1 and stx2 genes, and to perform O and H serotyping. E. coli O157:H7 isolates were detected in the rectal swabs collected from 1/134 roe deer (0.75%) and 4/97 red deer (4.1%), and they were not detected in fallow deer (Dama dama). The remaining E. coli serogroups, namely O26, O103, O111 and O145 that belong to the "top five" non-O157 serogroups, were detected in 15/134 roe deer (11.19%), 18/97 red deer (18.56%) and 2/21 fallow deer (9.52%). STEC/AE-STEC strains were detected in 33 roe deer isolates (24.63%), 21 red deer isolates (21.65%) and 2 fallow deer isolates (9.52%). According to the most recent FAO/WHO report, stx2a and eae genes are the primary virulence traits associated with HUS, and these genes were identified in one roe deer isolate and one red deer isolate. Stx2 was the predominant stx gene, and it was detected in 78.79% of roe deer and in 71.43% of red deer isolates. The results of this study confirmed that red deer and roe deer in north-eastern Poland are carriers of STEC/AE-STEC strains that are potentially pathogenic for humans. This is the first report documenting the virulence of STEC/AE-STEC strains from wild ruminants in Poland.


Assuntos
Cervos/microbiologia , Reservatórios de Doenças/microbiologia , Escherichia coli Shiga Toxigênica/isolamento & purificação , Animais , Animais Selvagens/classificação , Animais Selvagens/microbiologia , Cervos/classificação , Reservatórios de Doenças/classificação , Polônia , Toxina Shiga/metabolismo , Escherichia coli Shiga Toxigênica/classificação , Escherichia coli Shiga Toxigênica/genética , Escherichia coli Shiga Toxigênica/metabolismo , Fatores de Virulência/genética , Fatores de Virulência/metabolismo
2.
BMC Evol Biol ; 19(1): 199, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31684869

RESUMO

BACKGROUND: Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes. RESULTS: We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat. CONCLUSIONS: Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa.


Assuntos
Cervos/classificação , Cervos/genética , Hibridização Genética , Animais , Evolução Biológica , DNA Mitocondrial/genética , Ecologia , Éxons , Feminino , Fluxo Gênico , Marcadores Genéticos , Genética Populacional , Masculino , Repetições de Microssatélites , Noroeste dos Estados Unidos , Polimorfismo de Nucleotídeo Único , Seleção Genética
3.
J Genet ; 98(2)2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31204725

RESUMO

Burgeoning pressures of habitat loss is a major cause of herbivore decline across India, forcing them to coexist with humans in non-protected areas. Their conservation in such landscapes is challenging due to paucity of ecological and demographic information. The northern subspecies of swamp deer, Rucervus duvaucelii duvaucelii, is one such herbivore that lives across human dominated landscapes in Terai region and upper Gangetic plains of north India. Here, we describe species-specific molecular markers and a cervid-specific molecular sexing assay for swamp deer and four other coexisting cervids sambar, chital, barking deer and hog deer. Our markers show species-specific band patterns and a high success rate of 88.21% in large number of field collected referencesamples for all species. Faecal pellets from pilot swamp deer survey samples from upper Ganges basin show 93.81% success rate, and only 5.5% misidentification based on morphological characteristics. Our cervid-specific molecular sexing multiplex assay accurately ascertained 81.15% samples to respective sexes. These molecular approaches provide an easy, quick and cheap option to generate critical information on herbivore population parameters and aid their conservation in this mosaic of protected and non-protected grassland habitats.


Assuntos
Cervos/classificação , Cervos/genética , Ecossistema , Genética Populacional , Animais , Feminino , Geografia , Humanos , Índia , Masculino , Tipagem Molecular , Reação em Cadeia da Polimerase , Dinâmica Populacional , Especificidade da Espécie
4.
Mol Ecol Resour ; 19(5): 1205-1217, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31058463

RESUMO

Estimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree-free estimation of trait heritabilities in wild populations. However, until now, most quantitative genetic studies based on a genomic relatedness matrix (GRM) have focused on long-term monitored populations for which traditional pedigrees were also available, and have often had access to knowledge of genome sequence and variability. Here, we investigated the potential of RAD-sequencing for estimating heritability in a free-ranging roe deer (Capreolous capreolus) population for which no prior genomic resources were available. We propose a step-by-step analytical framework to optimize the quality and quantity of the genomic data and explore the impact of the single nucleotide polymorphism (SNP) calling and filtering processes on the GRM structure and GRM-based heritability estimates. As expected, our results show that sequence coverage strongly affects the number of recovered loci, the genotyping error rate and the amount of missing data. Ultimately, this had little effect on heritability estimates and their standard errors, provided that the GRM was built from a minimum number of loci (above 7,000). Genomic relatedness matrix-based heritability estimates thus appear robust to a moderate level of genotyping errors in the SNP data set. We also showed that quality filters, such as the removal of low-frequency variants, affect the relatedness structure of the GRM, generating lower h2 estimates. Our work illustrates the huge potential of RAD-sequencing for estimating GRM-based heritability in virtually any natural population.


Assuntos
Cervos/classificação , Cervos/genética , Genética Populacional/métodos , Técnicas de Genotipagem/métodos , Linhagem , Análise de Sequência de DNA/métodos , Animais , Genótipo , Polimorfismo de Nucleotídeo Único , Característica Quantitativa Herdável
5.
BMC Genomics ; 20(1): 384, 2019 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-31101010

RESUMO

BACKGROUND: Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. METHODS: In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. RESULTS: A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii, C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii, C. unicolor, C. albirostris, C. elaphus and C. nippon. Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis, C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China), and C. c. songaricus/C. c. sibiricus (distributed in northwest of China). Among them, C. e. yarkandensis was molecularly the most primitive subclade, with a differentiation dating back to 0.8-2.2 Myr ago. D statistical analysis showed that there was high probability of interspecific gene exchange between C. albirostris and C. eldii, C. albirostris and C. unicolor, C. nippon and C. unicolor, and there might be 2 migration events among 5 species in the genus Cervus. CONCLUSIONS: Our results provided new insight to the genetic diversity and phylogeny of Cervus deer. In view of the current status of these populations, their conservation category will need to be reassessed.


Assuntos
Cervos/classificação , Cervos/genética , Variação Genética , Estudo de Associação Genômica Ampla , Genoma , Genômica/métodos , Filogenia , Animais , Evolução Biológica , Sequenciamento de Nucleotídeos em Larga Escala
6.
J Pharm Biomed Anal ; 165: 18-23, 2019 Feb 20.
Artigo em Inglês | MEDLINE | ID: mdl-30500596

RESUMO

Many species of velvet antler have been used as traditional medicine for thousands of years; however, as medicinal materials, velvet antler derived from different animals have different clinical effects. To distinguish the differences and homologies, ultra-performance liquid chromatography-quadruple-time of flight mass spectrometry (UPLC-QTOF-MS) coupled with principal component analysis (PCA) was developed and applied to identify these antler samples derived from Cervus nippon Temminck, Cervus elaphus Linnaeus and Rangifer tarandus Linnaeus, which were first tested and compared at the molecular level of protein. The UPLC-MS data of the trypsin digested samples were subjected to PCA, and the potential markers based on peptide were depicted to illustrate their differences. With the integrated strategy combining UPLC-QTOF-MS with PCA, the results from this study indicated that the proposed methods could be successfully applied to distinguish reindeer antler from sika deer antler and red deer antler, which were prescribed in the Chinese Pharmacopoeia (2015 edition).


Assuntos
Chifres de Veado/química , Cromatografia Líquida de Alta Pressão/métodos , Cervos , Espectrometria de Massas/métodos , Animais , Cervos/classificação , Masculino , Medicina Tradicional Chinesa , Análise de Componente Principal , Especificidade da Espécie
7.
J Food Drug Anal ; 26(4): 1275-1282, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30249326

RESUMO

Velvet antler (VA), the unossified antler from members of the family Cervidae, has been used in traditional Chinese medicines and health foods for over 2000 years in enhancement of kidney function and treatment or prevention of cardiovascular, immunological and gynaecological disease. The aim of this study was to investigate the anti-inflammatory effect of velvet antler water extracts from Formosan sambar deer (Rusa unicolor swinhoei, SVAE) and red deer (Cervus elaphus, RVAE). Results indicated that both SVAE and RVAE significantly reduced the pro-inflammatory cytokines tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) productions in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells at concentrations above 200 µg mL-1. SVAE seems to demonstrate a better anti-inflammatory effect than that of RVAE in vitro. Both SVAE and RAVE also enhanced the anti-inflammatory cytokine IL-10 production in LPS-stimulated RAW 264.7 cells. The results of MTT assay indicated that SVAE and RVAE did not exhibit any cytotoxicity in LPS-stimulated RAW 264.7 cells. Two-dimensional (2D) gel electrophoresis analysis revealed that the levels of 6 specific proteins were different between these two velvet antlers samples. Furthermore, the storage period was the major factor affecting the anti-inflammatory activity of SAVE. In this study, we demonstrated the difference of anti-inflammatory effect and the protein profile between SVAE and RVAE. SVAE showed better anti-inflammatory potential than RVAE. In the future, the anti-inflammatory active components and their related mechanisms should be further investigated.


Assuntos
Anti-Inflamatórios/farmacologia , Chifres de Veado/química , Cervos/classificação , Proteínas/química , Animais , Anti-Inflamatórios/química , Anti-Inflamatórios/isolamento & purificação , Chifres de Veado/metabolismo , Eletroforese em Gel Bidimensional , Interleucina-6/imunologia , Macrófagos/efeitos dos fármacos , Macrófagos/imunologia , Medicina Tradicional Chinesa , Camundongos , Proteínas/isolamento & purificação , Células RAW 264.7 , Fator de Necrose Tumoral alfa/genética , Fator de Necrose Tumoral alfa/imunologia
8.
PLoS One ; 13(1): e0189278, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29304165

RESUMO

In north-eastern France, red deer (Cervus elaphus L.) populations were rebuilt from a few hundred individuals, which have subsisted in remote valleys of the Vosges mountains, and to a lesser extent from individuals escaped from private enclosures; at present times, this species occupies large areas, mainly in the Vosges Mountains. In this study, we examined the population dynamics of red deer in the Vosges Mountains using ancient and contemporary mitochondrial DNA (mtDNA) from 140 samples (23 ancient + 117 modern) spanning the last 7'000 years. In addition, we reconstructed the feeding habits and the habitat of red deer since the beginning of agriculture applying isotopic analyses in order to establish a basis for current environmental management strategies. We show that past and present red deer in the Vosges Mountains belong to mtDNA haplogroup A, suggesting that they originated from the Iberian refugium after the last glacial maximum (LGM). Palaeogenetic analysis of ancient bone material revealed the presence of two distinct haplotypes with different temporal distributions. Individuals belonging to the two haplotype groups apparently occupied two different habitats over at least 7'000 years. AM6 correlates with an ecological type that feeds in densely forested mountain landscapes, while AM235 correlates with feeding in lowland landscapes, composed of a mixture of meadows and riverine, herb-rich woodlands. Our results suggest that red deer of north-eastern France was able to adapt, over the long term, to these different habitat types, possibly due to efficient ethological barriers. Modern haplotype patterns support the historical record that red deer has been exposed to strong anthropogenic influences as a major game species.


Assuntos
Cervos/genética , Agricultura/história , Animais , DNA Mitocondrial/genética , DNA Mitocondrial/isolamento & purificação , Cervos/classificação , Dieta/história , Ecossistema , França , Variação Genética , Haplótipos , História do Século XX , História do Século XXI , História Antiga , História Medieval , Filogeografia , Dinâmica Populacional/história
9.
Mitochondrial DNA A DNA Mapp Seq Anal ; 29(2): 266-272, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-28071968

RESUMO

Deer antler velvet is widely used as a vitalizing, tonifying, haemopoietic and strengthening agent for debilitated persons in East Asia. To develop a rapid and sensitive method for the identification of the biological source or origin in antler velvet products, a molecular approach was applied using PCR-restriction fragment length polymorphism analysis. The cytochrome b gene sequences of nine cervidae species were analyzed, and a Dde I restriction endonuclease recognition site was found only in sika deer and red deer, the official origin of deer velvet in Chinese pharmacopoeia. A specific primer was designed, and rapid PCR amplified products were subjected to restriction digestion using a fast RFLP procedure. Sika deer and red deer showed two bands of 161 and 102 bp, in contrast to the undigested state of 263 from other antlers. The established PCR-RFLP method was applied in commercial velvet products, and a high frequency of substitution (50%) was revealed in collected commercial samples. The method was successful in detecting contaminated and adulterated antler products in Chinese patent drugs, and the whole detection process was accomplished within 1-1.5 h.


Assuntos
Chifres de Veado , Citocromos b/genética , Cervos/genética , Reação em Cadeia da Polimerase/métodos , Substituição de Aminoácidos , Animais , Cervos/classificação , Polimorfismo de Fragmento de Restrição , Controle de Qualidade
10.
Gigascience ; 7(2)2018 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-29267854

RESUMO

Background: Milu, also known as Père David's deer (Elaphurus davidianus), was widely distributed in East Asia but recently experienced a severe bottleneck. Only 18 survived by the end of the 19th century, and the current population of 4500 individuals was propagated from just 11 kept by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. To aid efforts to explore these phenomena, we constructed a draft genome of the species. Findings: In total, we generated 321.86 gigabases (Gb) of raw DNA sequence from whole-genome sequencing of a male milu deer using an Illumina HiSeq 2000 platform. Assembly yielded a final genome with a scaffold N50 size of 3.03 megabases (Mb) and a total length of 2.52 Gb. Moreover, we identified 20 125 protein-coding genes and 988.1 Mb of repetitive sequences. In addition, homology-based searches detected 280 rRNA, 1335 miRNA, 1441 snRNA, and 893 tRNA sequences in the milu genome. The divergence time between E. davidianus and Bos taurus was estimated to be about 28.20 million years ago (Mya). We identified 167 species-specific genes and 293 expanded gene families in the milu lineage. Conclusions: We report the first reference genome of milu, which will provide a valuable resource for studying the species' demographic history of severe bottleneck and the genetic mechanism(s) of special phenotypic evolution.


Assuntos
Evolução Biológica , Mapeamento Cromossômico/métodos , Cervos/genética , Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Animais , Bovinos , Cervos/classificação , Masculino , MicroRNAs/classificação , MicroRNAs/genética , Fases de Leitura Aberta , Filogenia , Proteínas/classificação , Proteínas/genética , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA Nuclear Pequeno/classificação , RNA Nuclear Pequeno/genética , RNA de Transferência/classificação , RNA de Transferência/genética , Sequenciamento Completo do Genoma
11.
PLoS One ; 12(11): e0187559, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29112970

RESUMO

The Cervidae family comprises more than fifty species divided into three subfamilies: Capreolinae, Cervinae and Hydropotinae. A characteristic attribute for the species included in this family is the great karyotype diversity, with the chromosomal numbers ranging from 2n = 6 observed in female Muntiacus muntjak vaginalis to 2n = 70 found in Mazama gouazoubira as a result of numerous Robertsonian and tandem fusions. This work reports chromosomal homologies between cattle (Bos taurus, 2n = 60) and nine cervid species using a combination of whole chromosome and region-specific paints and BAC clones derived from cattle. We show that despite the great diversity of karyotypes in the studied species, the number of conserved chromosomal segments detected by 29 cattle whole chromosome painting probes was 35 for all Cervidae samples. The detailed analysis of the X chromosomes revealed two different morphological types within Cervidae. The first one, present in the Capreolinae is a sub/metacentric X with the structure more similar to the bovine X. The second type found in Cervini and Muntiacini is an acrocentric X which shows rearrangements in the proximal part that have not yet been identified within Ruminantia. Moreover, we characterised four repetitive sequences organized in heterochromatic blocks on sex chromosomes of the reindeer (Rangifer tarandus). We show that these repeats gave no hybridization signals to the chromosomes of the closely related moose (Alces alces) and are therefore specific to the reindeer.


Assuntos
Bovinos/genética , Cervos/genética , Hibridização in Situ Fluorescente/métodos , Cariotipagem , Animais , Evolução Biológica , Bovinos/classificação , Cervos/classificação , Filogenia
12.
J Gen Virol ; 98(7): 1932-1942, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28708047

RESUMO

Chronic wasting disease (CWD) is the only naturally occurring transmissible spongiform encephalopathy affecting free-ranging wildlife populations. Transmission of CWD occurs by direct contact or through contaminated environments; however, little is known about the temporal patterns of CWD prion excretion and shedding in wild cervids. We tested the urine and faeces of three species of captive cervids (elk, mule and white-tailed deer) at 6, 12, 18 and 24 months after oral inoculation to evaluate the temporal, species- and genotype-specific factors affecting the excretion of CWD prions. Although none of the animals exhibited clinical signs of CWD during the study, we determined that all three cervid species were excreting CWD prions by 6 months post-inoculation. Faecal samples were consistently positive for CWD prions for all three cervid species (88 %), and were more likely to be positive than urine samples (28 %). Cervids with genotypes encoding for the prion protein (PRNP) that were considered to be more susceptible to CWD were more likely to excrete CWD prions (94 %) than cervids with genotypes considered to be less susceptible (64 %). All cervids with CWD prions in their urine also had positive faeces (n=5), but the converse was not true. Our study is the first to demonstrate CWD prion excretion in urine by asymptomatic elk and mule deer. Our results indicate that the excretion of CWD prions in faeces and, to a lesser extent, urine may provide an important avenue for depositing prions in the environment.


Assuntos
Animais Selvagens/metabolismo , Cervos/metabolismo , Príons/metabolismo , Doença de Emaciação Crônica/metabolismo , Animais , Animais Selvagens/genética , Cervos/classificação , Cervos/genética , Fezes/química , Príons/genética , Doença de Emaciação Crônica/genética
13.
J Am Assoc Lab Anim Sci ; 56(4): 350-360, 2017 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-28724483

RESUMO

Between 1940 and 2004, more than 335 emerging infectious disease events were reported in the scientific literature. The majority (60%) of these events involved zoonoses, most of which (72%) were of wildlife origin or had an epidemiologically important wildlife host. Because this trend of increasing emerging diseases likely will continue, understanding the pathogenesis, transmission, and diagnosis of these diseases in the relevant wildlife host is paramount. Achieving this goal often requires using wild animals as research subjects, which are vastly different from the traditional livestock or laboratory animals used by most universities and institutions. Using wildlife in infectious disease research presents many challenges but also provides opportunities to answer questions impossible to address by using traditional models. Cervid species, especially white-tailed deer (Odocoileus virginianus), elk (Cervus canadensis), and red deer (Cervus elaphus), are hosts or sentinels for several important pathogens, some of which are zoonotic. The long history of infectious disease research using white-tailed deer, conducted at ever-increasing levels of sophisticated biosecurity, demonstrates that this type of research can be conducted safely and that valuable insights can be gained. The greatest challenges to using wildlife in infectious disease research include animal source, facility design, nutrition, animal handling, and enrichment and other practices that both facilitate animal care and enhance animal wellbeing. The study of Mycobacterium bovis infection in white-tailed deer at the USDA's National Animal Disease Center serves to illustrate one approach to address these challenges.


Assuntos
Criação de Animais Domésticos , Cervos , Mycobacterium bovis/fisiologia , Tuberculose/veterinária , Animais , Animais Selvagens , Pesquisa Biomédica , Contenção de Riscos Biológicos/veterinária , Cervos/classificação , Feminino , Masculino
14.
Zhongguo Zhong Yao Za Zhi ; 42(23): 4588-4592, 2017 Dec.
Artigo em Chinês | MEDLINE | ID: mdl-29376256

RESUMO

For rapid identification of Cervus nippon, C. elaphus and their hybridize samples, the specific PCR for mutual authentication of them was established based on the SNPs in COI and SRY sequence. C. nippon, C. elaphus and their hybridize samples were collected from different origins, total DNA of 24 identified samples were extracted, and the COI and SRY gene was seqenced. SNPs in the COI and SRY sequences of the samples were found by Clustul X 2.1 program. Primers for identifying C. nippon and C. elaphus were designed according to the SNP site, two multi-PCR reaction system were established to identify them. In addition, 24 samples which were randomly collected in different herbal medicine market were identified. The band special for C. nippon (232 bp)and band special for C. elaphus (518 bp) based on COI sequence,and the band special for C. nippon (803 bp)and band special for C. elaphus (425 bp) based on SRY sequence, were found using multi-PCR reaction, and three of the twenty-four samples were identified as the hybridize samples. The multi-PCR reaction system could be used to identify C. nippon, C. elaphus and their hybridize samples.


Assuntos
Cervos/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Genes sry , Animais , DNA , Primers do DNA , Cervos/classificação , Reação em Cadeia da Polimerase , Polimorfismo de Nucleotídeo Único
15.
Mitochondrial DNA A DNA Mapp Seq Anal ; 28(6): 835-842, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-27937071

RESUMO

The Hangul (Cervus elaphus hanglu) is a "Least Concern" deer species, and it is the only survivor of the Red Deer group in the Indian subcontinent. The phylogenetic status of the Hangul relative to the other members of the family Cervidae is not known because sequence data are not available in public databases. Therefore, this study was carried out to determine the phylogenetic status and delineate the genetic boundaries of the Hangul with respect to the other Red Deer subspecies on the basis of cytochrome b gene sequence data (ca 421 bp). There are three major monophyletic groups of the Red Deer in the phylogenetic tree, which are referred to as the western (Hap-01 to Hap-10), eastern (Hap-11 to Hap-20) and tarim (Hap-21 to Hap-25) groups. The overall haplotype diversity and per-site nucleotide diversity were 0.9771 (±0.0523) and 0.0388 (±0.00261), respectively. In the phylogenetic tree, the Hangul clustered with the tarim group (Yarkand and Bactrian Red Deer) with a strong bootstrap support (92%) and was found to be genetically closer to the Bactrian Red Deer than to the Yarkand Red Deer. Our molecular analysis supported the idea that the Hangul diverged from the Bactrian Red Deer and migrated to India from Tajikistan approximately 1.2 MYA.


Assuntos
Cervos/genética , Genes Mitocondriais , Variação Genética , Filogenia , Animais , Citocromos b/genética , Cervos/classificação , Cervos/metabolismo , Haplótipos , Índia , Filogeografia , Análise de Sequência de DNA
16.
ISME J ; 11(3): 691-703, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27959345

RESUMO

Ruminants have co-evolved with their gastrointestinal microbial communities that digest plant materials to provide energy for the host. Some arctic and boreal ruminants have already shown to be vulnerable to dietary shifts caused by changing climate, yet we know little about the metabolic capacity of the ruminant microbiome in these animals. Here, we use meta-omics approaches to sample rumen fluid microbial communities from Alaskan moose foraging along a seasonal lignocellulose gradient. Winter diets with increased hemicellulose and lignin strongly enriched for BS11, a Bacteroidetes family lacking cultivated or genomically sampled representatives. We show that BS11 are cosmopolitan host-associated bacteria prevalent in gastrointestinal tracts of ruminants and other mammals. Metagenomic reconstruction yielded the first four BS11 genomes; phylogenetically resolving two genera within this previously taxonomically undefined family. Genome-enabled metabolic analyses uncovered multiple pathways for fermenting hemicellulose monomeric sugars to short-chain fatty acids (SCFA), metabolites vital for ruminant energy. Active hemicellulosic sugar fermentation and SCFA production was validated by shotgun proteomics and rumen metabolites, illuminating the role BS11 have in carbon transformations within the rumen. Our results also highlight the currently unknown metabolic potential residing in the rumen that may be vital for sustaining host energy in response to a changing vegetative environment.


Assuntos
Bacteroidetes/metabolismo , Cervos/microbiologia , Microbioma Gastrointestinal , Polissacarídeos/metabolismo , Rúmen/microbiologia , Animais , Regiões Árticas , Bactérias/classificação , Bacteroidetes/classificação , Mudança Climática , Cervos/classificação , Digestão , Ácidos Graxos Voláteis/metabolismo , Fermentação , Lignina/metabolismo , Metagenômica/métodos , Filogenia , Estações do Ano
17.
Ecology ; 97(11): 3184-3194, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27870038

RESUMO

Stability in population dynamics is an emergent property of the interaction between direct and delayed density dependence, the strengths of which vary with environmental covariates. Analysis of variation across populations in the strength of direct and delayed density dependence can reveal variation in stability properties of populations at the species level. We examined the stability properties of 22 elk/red deer populations in a two-stage analysis. First, we estimated direct and delayed density dependence applying an AR(2) model in a Bayesian hierarchical framework. Second, we plotted the coefficients of direct and delayed density dependence in the Royama parameter plane. We then used a hierarchical approach to test the significance of environmental covariates of direct and delayed density dependence. Three populations exhibited highly stable and convergent dynamics with strong direct, and weak delayed, density dependence. The remaining 19 populations exhibited more complex dynamics characterized by multi-annual fluctuations. Most (15 of 19) of these exhibited a combination of weak to moderate direct and delayed density dependence. Best-fit models included environmental covariates in 17 populations (77% of the total). Of these, interannual variation in growing-season primary productivity and interannual variation in winter temperature were the most common, performing as the best-fit covariate in six and five populations, respectively. Interannual variation in growing-season primary productivity was associated with the weakest combination of direct and delayed density dependence, while interannual variation in winter temperature was associated with the strongest combination of direct and delayed density dependence. These results accord with a classic theoretical prediction that environmental variability should weaken population stability. They furthermore suggest that two forms of environmental variability, one related to forage resources and the other related to abiotic conditions, both reduce stability, but in opposing fashion: one through weakened direct density dependence and the other through strengthened delayed density dependence. Importantly, however, no single abiotic or biotic environmental factor emerged as generally predictive of the strengths of direct or delayed density dependence, nor of the stability properties emerging from their interaction. Our results emphasize the challenges inherent to ascribing primacy to drivers of such parameters at the species level and distribution scale.


Assuntos
Distribuição Animal/fisiologia , Cervos/fisiologia , Ecossistema , Animais , Teorema de Bayes , Cervos/classificação , Modelos Biológicos , Dinâmica Populacional , Especificidade da Espécie
18.
J Hered ; 107(7): 666-669, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27638816

RESUMO

The tule elk (Cervus elaphus nannodes) experienced a severe bottleneck in the 1800s, resulting in low genetic diversity. There is a need for high-resolution genetic assays that can be used to differentiate individual elk, including close relatives, with high confidence. An efficient assay requires multiple markers both polymorphic and that can be amplified in concert with other markers in multiplex reactions. To develop such markers, we employed 150-bp paired-end whole genome shotgun sequencing on an Illumina HiSeq3000 platform to discover dinucleotide microsatellite markers. After preliminary screening of these markers, we selected and screened 15 candidate loci and 5 existing tetra nucleotide markers in 56 tule elk. We combined these markers in 2 multiplex reactions and report primer concentrations and PCR conditions enabling their efficient amplification.


Assuntos
Cervos/classificação , Cervos/genética , Repetições de Microssatélites , Polimorfismo Genético , Alelos , Animais , Feminino , Frequência do Gene , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Masculino
19.
BMC Genomics ; 17(1): 618, 2016 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-27516089

RESUMO

BACKGROUND: B chromosomes are dispensable and variable karyotypic elements found in some species of animals, plants and fungi. They often originate from duplications and translocations of host genomic regions or result from hybridization. In most species, little is known about their DNA content. Here we perform high-throughput sequencing and analysis of B chromosomes of roe deer and brocket deer, the only representatives of Cetartiodactyla known to have B chromosomes. RESULTS: In this study we developed an approach to identify genomic regions present on chromosomes by high-throughput sequencing of DNA generated from flow-sorted chromosomes using degenerate-oligonucleotide-primed PCR. Application of this method on small cattle autosomes revealed a previously described KIT gene region translocation associated with colour sidedness. Implementing this approach to B chromosomes from two cervid species, Siberian roe deer (Capreolus pygargus) and grey brocket deer (Mazama gouazoubira), revealed dramatically different genetic content: roe deer B chromosomes consisted of two duplicated genomic regions (a total of 1.42-1.98 Mbp) involving three genes, while grey brocket deer B chromosomes contained 26 duplicated regions (a total of 8.28-9.31 Mbp) with 34 complete and 21 partial genes, including KIT and RET protooncogenes, previously found on supernumerary chromosomes in canids. Sequence variation analysis of roe deer B chromosomes revealed a high frequency of mutations and increased heterozygosity due to either amplification within B chromosomes or divergence between different Bs. In contrast, grey brocket deer B chromosomes were found to be more homogeneous and resembled autosomes in patterns of sequence variation. Similar tendencies were observed in repetitive DNA composition. CONCLUSIONS: Our data demonstrate independent origins of B chromosomes in the grey brocket and roe deer. We hypothesize that the B chromosomes of these two cervid species represent different stages of B chromosome sequences evolution: probably nascent and similar to autosomal copies in brocket deer, highly derived in roe deer. Based on the presence of the same orthologous protooncogenes in canids and brocket deer Bs we argue that genomic regions involved in B chromosome formation are not random. In addition, our approach is also applicable to the characterization of other evolutionary and clinical rearrangements.


Assuntos
Evolução Biológica , Cromossomos Humanos 4-5/química , Cromossomos de Mamíferos/química , Cervos/genética , Duplicação Gênica , Animais , Mapeamento Cromossômico , Primers do DNA/química , Cervos/classificação , Expressão Gênica , Heterozigoto , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Cariotipagem , Taxa de Mutação , Reação em Cadeia da Polimerase/métodos , Proteínas Proto-Oncogênicas c-kit/genética , Proteínas Proto-Oncogênicas c-ret/genética , Especificidade da Espécie
20.
Mol Ecol Resour ; 16(5): 1165-72, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27438092

RESUMO

Mule deer (Odocoileus hemionus) are an excellent nonmodel species for empirically testing hypotheses in landscape and population genomics due to their large population sizes (low genetic drift), relatively continuous distribution, diversity of occupied habitats and phenotypic variation. Because few genomic resources are currently available for this species, we used exon data from a cattle (Bos taurus) reference genome to direct targeted resequencing of 5935 genes in mule deer. We sequenced approximately 3.75 Mbp at minimum 20X coverage in each of the seven mule deer, identifying 23 204 single nucleotide polymorphisms (SNPs) within, or adjacent to, 6886 exons in 3559 genes. We found 91 SNP loci (from 69 genes) with putatively fixed allele frequency differences between the two major lineages of mule deer (mule deer and black-tailed deer), and our estimate of mean genetic divergence (genome-wide FST  = 0.123) between these lineages was consistent with previous findings using microsatellite loci. We detected an over-representation of gamete generation and amino acid transport genes among the genes with SNPs exhibiting potentially fixed allele frequency differences between lineages. This targeted resequencing approach using exon capture techniques has identified a suite of loci that can be used in future research to investigate the genomic basis of adaptation and differentiation between black-tailed deer and mule deer. This study also highlights techniques (and an exon capture array) that will facilitate population genomic research in other cervids and nonmodel organisms.


Assuntos
Cervos/classificação , Cervos/genética , Genética Populacional/métodos , Técnicas de Genotipagem/métodos , Polimorfismo de Nucleotídeo Único , Animais , Bovinos , DNA/química , DNA/genética , DNA/isolamento & purificação , Éxons , Sequenciamento de Nucleotídeos em Larga Escala , Repetições de Microssatélites , Hibridização de Ácido Nucleico
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