Publications

combining untargeted and targeted proteomic strategies for discrimination and quantification of cashmere fibers.	cashmere is regarded as a specialty and luxury fiber due to its scarcity and high economic value. for fiber quality assessment, it is technically very challenging to distinguish and quantify the cashmere fiber from yak or wool fibers because of their highly similar physical appearance and substantial protein sequence homology. to address this issue, we propose a workflow combining untargeted and targeted proteomics strategies for selecting, verifying and quantifying biomarkers for cashmere texti ...	2016	26789629
bovine viral diarrhea virus in zoos: a perspective from the veterinary team.	the many different species in close proximity make zoological collections a unique environment for disease transmission. bovine viral diarrhea virus (bvdv) is of special concern with zoos due to the numerous exotic ruminant species that this virus can infect. bvdv occurs as both a non-cytopathic and a cytopathic strain both of which are capable of infecting exotic ruminants. the cytopathic strain causes mucosal disease (md) and death. infection with the non-cytopathic strain may produce persiste ...	2016	26779151
continental island formation and the archaeology of defaunation on zanzibar, eastern africa.	with rising sea levels at the end of the pleistocene, land-bridge or continental islands were formed around the world. many of these islands have been extensively studied from a biogeographical perspective, particularly in terms of impacts of island creation on terrestrial vertebrates. however, a majority of studies rely on contemporary faunal distributions rather than fossil data. here, we present archaeological findings from the island of zanzibar (also known as unguja) off the eastern african ...	2016	26901050
establishment and characterization of a telomerase-immortalized sheep trophoblast cell line.	the primary sheep trophoblast cells (stcs) have a finite lifespan in culture. this feature limits the scope for long-term in vitro studies with stcs. this study was an attempt to establish and characterize a telomerase-immortalized sheep trophoblast cell line. stcs were isolated and purified by using percoll and specific immunoaffinity purification, respectively. the purified stcs were transfected with a plasmid carrying sequences of human telomerase reverse transcriptase (htert) to create immor ...	2016	26998488
variations in t cell transcription factor sequence and expression associated with resistance to the sheep nematode teladorsagia circumcincta.	this study used selected lambs that varied in their resistance to the gastrointestinal parasite teladorsagia circumcincta. infection over 12 weeks identified susceptible (high adult worm count, awc; high fecal egg count, fec; low body weight, bw; low iga) and resistant sheep (no/low awc and fec, high bw and high iga). resistance is mediated largely by a th2 response and iga and ige antibodies, and is a heritable characteristic. the polarization of t cells and the development of appropriate immun ...	2016	26890074
transcriptomics modeling of the late-gestation fetal pituitary response to transient hypoxia.	the late-gestation fetal sheep responds to hypoxia with physiological, neuroendocrine, and cellular responses that aid in fetal survival. the response of the fetus to hypoxia represents a coordinated effort to maximize oxygen transfer from the mother and minimize wasteful oxygen consumption by the fetus. while there have been many studies aimed at investigating the coordinated physiological and endocrine responses to hypoxia, and while immunohistochemical or in situ hybridization studies have re ...	2016	26859870
rabies in the baltic states: decoding a process of control and elimination.	rabies is a fatal zoonosis that still causes nearly 70, 000 human deaths every year. in europe, the oral rabies vaccination (orv) of red foxes (vulpes vulpes) was developed in the late 1970s and has demonstrated its effectiveness in the eradication of the disease in western and some central european countries. following the accession of the three baltic countries--estonia, latvia and lithuania--to the european union in 2004, subsequent financial support has allowed the implementation of regular ...	2016	26849358
transcriptomic determinants of scrapie prion propagation in cultured ovine microglia.	susceptibility to infection by prions is highly dependent on the amino acid sequence and host expression of the cellular prion protein (prpc); however, cellular expression of a genetically susceptible prpc is insufficient. as an example, it has been shown in cultured cells that permissive and resistant sublines derived from the same parental population often have similar expression levels of prpc. thus, additional cellular factors must influence susceptibility to prion infection. the aim of this ...	2016	26807844
post-entry blockade of small ruminant lentiviruses by wild ruminants.	small ruminant lentivirus (srlv) infection causes losses in the small ruminant industry due to reduced animal production and increased replacement rates. infection of wild ruminants in close contact with infected domestic animals has been proposed to play a role in srlv epidemiology, but studies are limited and mostly involve hybrids between wild and domestic animals. in this study, srlv seropositive red deer, roe deer and mouflon were detected through modified elisa tests, but virus was not suc ...	2016	26738942
transcript profiling in the milk of dairy ewes fed extruded linseed.	the identification of genes regulating milk secretion by mammary glands is a key-step for exploiting changes in milk composition induced by different diet regimens. linseed supplementation is a reliable feeding strategy to enhance polyunsaturated fatty acid content in milk fat from sheep, increasing milk quality and nutraceutical value. to investigate the molecular bases of diet induced differences in milk composition, we collected milk from dairy ewes at 90 day of lactation and after 3 weeks of ...	2016	27920979
nature vs. nurture: evidence for social learning of conflict behaviour in grizzly bears.	the propensity for a grizzly bear to develop conflict behaviours might be a result of social learning between mothers and cubs, genetic inheritance, or both learning and inheritance. using non-invasive genetic sampling, we collected grizzly bear hair samples during 2011-2014 across southwestern alberta, canada. we targeted private agricultural lands for hair samples at grizzly bear incident sites, defining an incident as an occurrence in which the grizzly bear caused property damage, obtained an ...	2016	27851753
structure of the mis12 complex and molecular basis of its interaction with cenp-c at human kinetochores.	kinetochores, multisubunit protein assemblies, connect chromosomes to spindle microtubules to promote chromosome segregation. the 10-subunit kmn assembly (comprising knl1, mis12, and ndc80 complexes, designated knl1c, mis12c, and ndc80c) binds microtubules and regulates mitotic checkpoint function through ndc80c and knl1c, respectively. mis12c, on the other hand, connects the kmn to the chromosome-proximal domain of the kinetochore through a direct interaction with cenp-c. the structural basis f ...	2016	27881301
how many papillomavirus species can go undetected in papilloma lesions?	a co-infection comprising to at least seven papillomavirus (pv) types was detected by next generation sequencing (ngs) of randomly primed rolling circle amplification (rca) products of a bovine (bos taurus) papilloma lesion from the brazilian amazon region. six putative new pv types that could not be detected by commonly used pcr protocols were identified. their overall l1 nucleotide identities were less than 90% compared to described pv species and types. l1 nucleotide blast sequence hits showe ...	2016	27808255
itraq-based quantitative proteomic analysis of the potentiated and dormant antler stem cells.	as the only known organ that can completely regenerate in mammals, deer antler is of real significance in the field of regenerative medicine. recent studies have shown that the regenerative capacity of the antlers comes from the pedicle periosteum and the cells resident in the periosteum possess the attributes of stem cells. currently, the molecular mechanism of antler regeneration remains unclear. in the present study, we compared the potentiated and dormant antler stem cells using isobaric tag ...	2016	27792145
early cave art and ancient dna record the origin of european bison.	the two living species of bison (european and american) are among the few terrestrial megafauna to have survived the late pleistocene extinctions. despite the extensive bovid fossil record in eurasia, the evolutionary history of the european bison (or wisent, bison bonasus) before the holocene (<11.7 thousand years ago (kya)) remains a mystery. we use complete ancient mitochondrial genomes and genome-wide nuclear dna surveys to reveal that the wisent is the product of hybridization between the e ...	2016	27754477
judgement bias in goats (capra hircus): investigating the effects of human grooming.	animal emotional states can be investigated by evaluating their impact on cognitive processes. in this study, we used a judgement bias paradigm to determine if short-term positive human-animal interaction (grooming) induced a positive affective state in goats. we tested two groups of goats and trained them to discriminate between a rewarded and a non-rewarded location over nine training days. during training, the experimental group (n = 9) was gently groomed by brushing their heads and backs for ...	2016	27761311
rnf213 rare variants in slovakian and czech moyamoya disease patients.	rnf213/mysterin has been identified as a susceptibility gene for moyamoya disease, a cerebrovascular disease characterized by occlusive lesions in the circle of willis. the p.r4810k (rs112735431) variant is a founder polymorphism that is strongly associated with moyamoya disease in east asia. many non-p.r4810k rare variants of rnf213 have been identified in white moyamoya disease patients, although the ethnic mutations have not been investigated in this population. in the present study, we scree ...	2016	27736983
lab-on-a-chip-based pcr-rflp assay for the detection of malayan box turtle (cuora amboinensis) in the food chain and traditional chinese medicines.	the malayan box turtle (cuora amboinensis) (mbt) is a vulnerable and protected turtle species, but it is a lucrative item in the illegal wildlife trade because of its great appeal as an exotic food item and in traditional medicine. although several polymerase chain reaction (pcr) assays to identify mbt by various routes have been documented, their applicability for forensic authentication remains inconclusive due to the long length of the amplicon targets, which are easily broken down by natural ...	2016	27716792
a novel method for alignment-free dna sequence similarity analysis based on the characterization of complex networks.	determination of sequence similarity is one of the major steps in computational phylogenetic studies. one of the major tasks of computational biologists is to develop novel mathematical descriptors for similarity analysis. dna clustering is an important technology that automatically identifies inherent relationships among large-scale dna sequences. the comparison between the dna sequences of different species helps determine phylogenetic relationships among species. alignment-free approaches hav ...	2016	27746676
coprophilous mucorales (ex zygomycota) from three areas in the semi-arid of pernambuco, brazil.	mucorales comprises fungi commonly isolated as saprobes from soil, dung, stored grains and plants. although these fungi have been studied in several countries, there are relatively a few reports of them in semi-arid areas. therefore, the aims of the present study were to assess and compare the mucorales communities in dung from different species and breeds of herbivores in the semi-arid of pernambuco, based on the frequency of occurrence and species richness of these fungi. samples of dung colle ...	2016	27769884
characterization of a very rare case of living ewe-buck hybrid using classical and molecular cytogenetics.	the natural occurrence of live hybrid offsprings between sheep and goats has been documented in literature, however all the studies have reported the mating of goats with rams, whereas the reciprocal cross was never documented. this study reports on a very rare case of interspecies hybridization occurred between a ewe (2n = 54, xx) and a buck (2n = 60, xy). the hybrid, born in a german flock under natural conditions, is characterised by an intermediate karyotype (2n = 57, xx). the cba-banding ha ...	2016	27698378
use of fgf-2 and fgf-18 to direct bone marrow stromal stem cells to chondrogenic and osteogenic lineages.	intervertebral disc degeneration/low back pain is the number one global musculoskeletal condition in terms of disability and socioeconomic impact.	2016	28116125
a new look at the ltr retrotransposon content of the chicken genome.	ltr retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. a novel ltr retrotransposon classification pipeline, locatr, was developed and subsequently utilised to re-examine the chicken ltr retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact.	2016	27577548
intron length coevolution across mammalian genomes.	although they do not contribute directly to the proteome, introns frequently contain regulatory elements and can extend the protein coding potential of the genome through alternative splicing. for some genes, the contribution of introns to the time required for transcription can also be functionally significant. we have previously shown that intron length in genes associated with developmental patterning is often highly conserved. in general, sets of genes that require precise coordination in th ...	2016	27550903
a whole mitochondria analysis of the tyrolean iceman's leather provides insights into the animal sources of copper age clothing.	the attire of the tyrolean iceman, a 5,300-year-old natural mummy from the ötzal italian alps, provides a surviving example of ancient manufacturing technologies. research into his garments has however, been limited by ambiguity surrounding their source species. here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. results indicate that the majority of the samples orig ...	2016	27537861
deciphering the wisent demographic and adaptive histories from individual whole-genome sequences.	as the largest european herbivore, the wisent (bison bonasus) is emblematic of the continent wildlife but has unclear origins. here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. we estimate that the wisent and bovine species diverged from 1.7 × 10(6) to 850,000 years before present (ybp) through a speciation process involving an extended period of limited gene flow. our data further support the ...	2016	27436010
biological parameters of rhipicephalus (boophilus) microplus (acari: ixodidae) fed on rabbits, sheep, and cattle.	in order to determine the effect of various hosts on feeding performance of rhipicephalus (boophilus) microplus, we used 3 mammalian species as hosts, cattle (qinchuan), sheep (t an), and rabbits (japanese white rabbit) for infest-ing ticks. five hundreds of r. microplus larvae were exposed to each animal (3 animals/host species). tick recoveries were 11.0%, 0.47%, and 5.5% from cattle, sheep, and rabbits, respectively. the averages of tick feeding periods were not significantly different on cat ...	2016	27417084
zinc finger domain of the prdm9 gene on chromosome 1 exhibits high diversity in ruminants but its paralog prdm7 contains multiple disruptive mutations.	prdm9 is the sole hybrid sterility gene identified so far in vertebrates. prdm9 gene encodes a protein with an immensely variable zinc-finger (zf) domain that determines the site of meiotic recombination hotspots genome-wide. in this study, the terminal zf domain of prdm9 on bovine chromosome 1 and its paralog on chromosome 22 were characterized in 225 samples from five ruminant species (cattle, yak, mithun, sheep and goat). we found extraordinary variation in the number of prdm9 zinc fingers (6 ...	2016	27203728
methanogen diversity in indigenous and introduced ruminant species on the tibetan plateau.	host factors are regarded as important in shaping the archaeal community in the rumen but few controlled studies have been performed to demonstrate this across host species under the same environmental conditions. a study was designed to investigate the structure of the methanogen community in the rumen of two indigenous (yak and tibetan sheep) and two introduced domestic ruminant (cattle and crossbred sheep) species raised and fed under similar conditions on the high altitude tibetan plateau. t ...	2016	27274707
serological survey of coxiella burnetii at the wildlife-livestock interface in the eastern pyrenees, spain.	coxiella burnetii is a zoonotic bacterium that infects a wide range of animal species and causes the disease q fever. both wild and domestic ruminants may be relevant in the epidemiology of c. burnetii infection. in order to investigate the significance of the ruminant host community in the alpine and subalpine ecosystems of the eastern pyrenees, northeastern spain, in the epidemiology of q fever, a serological survey was performed on samples from 599 wild and 353 sympatric domestic ruminants.	2016	27121001
mib-mip is a mycoplasma system that captures and cleaves immunoglobulin g.	mycoplasmas are "minimal" bacteria able to infect humans, wildlife, and a large number of economically important livestock species. mycoplasma infections include a spectrum of clinical manifestations ranging from simple fever to fulminant inflammatory diseases with high mortality rates. these infections are mostly chronic, suggesting that mycoplasmas have developed means to evade the host immune response. here we present and functionally characterize a two-protein system from mycoplasma mycoides ...	2016	27114507
the hibernating south american marsupial, dromiciops gliroides, displays torpor-sensitive microrna expression patterns.	when faced with adverse environmental conditions, the marsupial dromiciops gliroides uses either daily or seasonal torpor to support survival and is the only known hibernating mammal in south america. as the sole living representative of the ancient order microbiotheria, this species can provide crucial information about the evolutionary origins and biochemical mechanisms of hibernation. hibernation is a complex energy-saving strategy that involves changes in gene expression that are elicited in ...	2016	27090740
mlva and mlst typing of brucella from qinghai, china.	the qinghai-tibet plateau (qtp) of china is an extensive pastoral and semi-pastoral area, and because of poverty and bad hygiene conditions, brucella is highly prevalent in this region. in order to adequately prevent this disease in the qtp region it is important to determine the identity of brucella species that caused the infection.	2016	27072820
absence of nucleolus formation in raccoon dog-porcine interspecies somatic cell nuclear transfer embryos results in embryonic developmental failure.	interspecies somatic cell nuclear transfer (iscnt) can be a solution for preservation of endangered species that have limited oocytes. it has been reported that blastocyst production by iscnt is successful even if the genetic distances between donors and recipients are large. in particular, domestic pig oocytes can support the development of canine to porcine iscnt embryos. therefore, we examined whether porcine oocytes may be suitable recipient oocytes for korean raccoon dog iscnt. we investiga ...	2016	27064112
using mobile sequencers in an academic classroom.	the advent of mobile dna sequencers has made it possible to generate dna sequencing data outside of laboratories and genome centers. here, we report our experience of using the minion, a mobile sequencer, in a 13-week academic course for undergraduate and graduate students. the course consisted of theoretical sessions that presented fundamental topics in genomics and several applied hackathon sessions. in these hackathons, the students used minion sequencers to generate and analyze their own dat ...	2016	27054412
ketamine decreases inflammatory and immune pathways after transient hypoxia in late gestation fetal cerebral cortex.	transient hypoxia in pregnancy stimulates a physiological reflex response that redistributes blood flow and defends oxygen delivery to the fetal brain. we designed the present experiment to test the hypotheses that transient hypoxia produces damage of the cerebral cortex and that ketamine, an antagonist ofnmdareceptors and a known anti-inflammatory agent, reduces the damage. late gestation, chronically catheterized fetal sheep were subjected to a 30-min period of ventilatory hypoxia that decreas ...	2016	27033443
neuromedin b and its receptor: gene cloning, tissue distribution and expression levels of the reproductive axis in pigs.	neuromedin b is one member of a family of bombesin-like peptides, which performs a variety of physiological functions via their receptor (nmbr) in most mammals. however, the genes encoding nmb and nmbr and their functions especially reproduction of the pigs are currently not fully understood. to research the physiological functions of nmb, we cloned and analyzed the nmb and nmbr genes, and systematically investigated the expression levels of nmb and nmbr mrna using relative real-time pcr and the ...	2016	27010315
cloning and expression of yak active chymosin in pichia pastoris.	rennet, a complex of enzymes found in the stomachs of ruminants, is an important component for cheese production. in our study, we described that yak chymosin gene recombinant pichia pastoris strain could serve as a novel source for rennet production. yaks total rna was extracted from the abomasum of an unweaned yak. the yak preprochymosin, prochymosin, and chymosin genes from total rna were isolated using gene specific primers based on cattle chymosin gene sequence respectively and analyzed the ...	2016	27004812
wild ungulate decision-making and the role of tiny refuges in human-dominated landscapes.	wildlife conservation in human-dominated landscapes requires that we understand how animals, when making habitat-use decisions, obtain diverse and dynamically occurring resources while avoiding risks, induced by both natural predators and anthropogenic threats. little is known about the underlying processes that enable wild animals to persist in densely populated human-dominated landscapes, particularly in developing countries. in a complex, semi-arid, fragmented, human-dominated agricultural la ...	2016	26985668
data on phylogenetic analyses of gazelles (genus gazella) based on mitochondrial and nuclear intron markers.	the data provided is related to the article "phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus gazella" [1]. the data is based on 48 tissue samples of all nine extant species of the genus gazella, namely gazella gazella, gazella arabica, gazella bennettii, gazella cuvieri, gazella dorcas, gazella leptoceros, gazella marica, gazella spekei, and gazella subgutturosa and four related taxa (saiga tatarica, a ...	2016	27054158
diet switching by mammalian herbivores in response to exotic grass invasion.	invasion by exotic grasses is a severe threat to the integrity of grassland ecosystems all over the world. because grasslands are typically grazed by livestock and wildlife, the invasion is a community process modulated by herbivory. we hypothesized that the invasion of native south american grasslands by eragrostis plana nees, an exotic tussock-forming grass from africa, could be deterred by grazing if grazers switched dietary preferences and included the invasive grass as a large proportion of ...	2016	26919613
the habitat of coccidioides spp. and the role of animals as reservoirs and disseminators in nature.	coccidioidomycosis, a potentially fatal fungal infection, is considered an emergent mycotic disease because of the increased incidence of fungal infections registered over recent years. infection occurs through the inhalation of arthroconidia from two main species of coccidioides: coccidioides immitis and c. posadasii, which are both endemic to arid and semi-arid regions of north america. coccidioides species not only infect humans but can also infect other mammals (land, aquatic, wild or domest ...	2016	27724885
species identification of bovine, ovine and porcine type 1 collagen; comparing peptide mass fingerprinting and lc-based proteomics methods.	collagen is one of the most ubiquitous proteins in the animal kingdom and the dominant protein in extracellular tissues such as bone, skin and other connective tissues in which it acts primarily as a supporting scaffold. it has been widely investigated scientifically, not only as a biomedical material for regenerative medicine, but also for its role as a food source for both humans and livestock. due to the long-term stability of collagen, as well as its abundance in bone, it has been proposed a ...	2016	27023524
vertebrate bacterial gut diversity: size also matters.	one of the central issues in microbial ecology is to understand the parameters that drive diversity. among these parameters, size has often been considered to be the main driver in many different ecosystems. surprisingly, the influence of size on gut microbial diversity has not yet been investigated, and so far in studies reported in the literature only the influences of age, diet, phylogeny and digestive tract structures have been considered. this study explicitly challenges the underexplored r ...	2016	27008566
identification and evolutionary analysis of potential candidate genes in a human eating disorder.	the purpose of this study was to find genes linked with eating disorders and associated with both metabolic and neural systems. our operating hypothesis was that there are genetic factors underlying some eating disorders resting in both those pathways. specifically, we are interested in disorders that may rest in both sleep and metabolic function, generally called night eating syndrome (nes). a meta-analysis of the gene expression omnibus targeting the mammalian nervous system, sleep, and obesit ...	2016	27088090
in silico assessment of primers for edna studies using primertree and application to characterize the biodiversity surrounding the cuyahoga river.	analysis of environmental dna (edna) enables the detection of species of interest from water and soil samples, typically using species-specific pcr. here, we describe a method to characterize the biodiversity of a given environment by amplifying edna using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. we tested this approach on 91 water samples of 40 ml collected along the cuyahoga river (ohio, usa). we amplified edna using 12 primer pairs ...	2016	26965911
genome-wide search for host association factors during ovine progressive pneumonia virus infection.	ovine progressive pneumonia virus (oppv) is an important virus that causes serious diseases in sheep and goats with a prevalence of 36% in the usa. although oppv was discovered more than half of a century ago, little is known about the infection and pathogenesis of this virus. in this report, we used rna-seq technology to conduct a genome-wide probe for cellular factors that are associated with oppv infection. a total of approximately 22,000 goat host genes were detected of which 657 were found ...	2016	26950733
organization and characteristics of the major histocompatibility complex class ii region in the yangtze finless porpoise (neophocaena asiaeorientalis asiaeorientalis).	little is known about the major histocompatibility complex (mhc) in the genome of yangtze finless porpoise (neophocaena asiaeorientalis asiaeorientalis) (yfp) or other cetaceans. in this study, a high-quality yfp bacterial artificial chromosome (bac) library was constructed. we then determined the organization and characterization of yfp mhc class ii region by screening the bac library, followed by sequencing and assembly of positive bac clones. the yfp mhc class ii region consists of two segreg ...	2016	26932528
identification of a novel single nucleotide polymorphism in porcine beta-defensin-1 gene.	porcine beta-defensin-1 (pbd-1) gene plays an important role in the innate immunity of pigs. the peptide encoded by this gene is an antimicrobial peptide that has direct activity against a wide range of microbes. this peptide is involved in the co-creation of an antimicrobial barrier in the oral cavity of pigs. the objective of the present study was to detect polymorphisms, if any, in exon-1 and exon-2 regions of pbd-1 gene in large white yorkshire (lwy) and native ankamali pigs of kerala, india ...	2016	26950860
conserved mir-26b enhances ovarian granulosa cell apoptosis through has2-ha-cd44-caspase-3 pathway by targeting has2.	the hyaluronan synthase 2 (has2)-hyaluronic acid (ha)-cd44-caspase-3 pathway is involved in ovarian granulosa cell (gc) functions in mammals. has2 is a key enzyme required for ha synthesis and is the key factor in this pathway. however, the regulation of has2 and the has2-mediated pathway by micrornas in gcs is poorly understood. here, we report that mir-26b regulates porcine gc (pgc) apoptosis through the has2-ha-cd44-caspase-3 pathway by binding directly to the 3'- untranslated region of has2 ...	2016	26887530
a comparison of postnatal arterial patterns in a growth series of giraffe (artiodactyla: giraffa camelopardalis).	nearly all living artiodactyls (even-toed ungulates) possess a derived cranial arterial pattern that is highly distinctive from most other mammals. foremost among a suite of atypical arterial configurations is the functional and anatomical replacement of the internal carotid artery with an extensive, subdural arterial meshwork called the carotid rete. this interdigitating network branches from the maxillary artery and is housed within the cavernous venous sinus. as the cavernous sinus receives c ...	2016	26925324
dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention.	the bovine lungworm, dictyocaulus viviparus (order strongylida), is an important parasite of livestock that causes substantial economic and production losses worldwide. here we report the draft genome, variome, and developmental transcriptome of d. viviparus. the genome (161 mb) is smaller than those of related bursate nematodes and encodes fewer proteins (14,171 total). in the first genome-wide assessment of genomic variation in any parasitic nematode, we found a high degree of sequence variabi ...	2016	26856411
cryptosporidium proliferans n. sp. (apicomplexa: cryptosporidiidae): molecular and biological evidence of cryptic species within gastric cryptosporidium of mammals.	the morphological, biological, and molecular characteristics of cryptosporidium muris strain ts03 are described, and the species name cryptosporidium proliferans n. sp. is proposed. cryptosporidium proliferans obtained from a naturally infected east african mole rat (tachyoryctes splendens) in kenya was propagated under laboratory conditions in rodents (scid mice and southern multimammate mice, mastomys coucha) and used in experiments to examine oocyst morphology and transmission. dna from the p ...	2016	26771460
assessing the effects of indigenous migration on zootherapeutic practices in the semiarid region of brazil.	human migration implies adaptations to new environments, such as ways to benefit from the available biodiversity. this study focused on the use of animal-derived remedies, and we investigated the effects of migration on the traditional medical system of the indigenous truká people. this ethnic group lives in northeast brazil and is currently distributed in four distinct villages. in these villages, the zootherapeutic knowledge of 54 indigenous people was determined through semi-structured questi ...	2016	26745882
snp miniplexes for individual identification of random-bred domestic cats.	phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (snps) analyses of fur. this study developed miniplexes using snps with high discriminating power for random-bred domestic cats, focusing on individual and phenotypic identification. seventy-eight snps were investigated using a multiplex pcr followed by a fluorescently labeled single base extension (sbe) technique (snapshot(®) ). the snp miniplexes were evaluated for reliability, reproducibil ...	2016	27122395
the ensembl gene annotation system.	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 ultimatel ...	2016	27337980
a comprehensive in silico analysis of non-synonymous and regulatory snps of human mbl2 gene.	mannose binding lectin (mbl) is a liver derived protein which plays an important role in innate immunity. mannose binding lectin gene 2 (mbl2) polymorphisms are reported to be associated with various diseases. in spite of being exhaustively studied molecule, no attempt has been made till date to comprehensively and systematically analyze the snps of mbl2 gene. the present study was carried out to identify and prioritize the snps of mbl2 gene for further genotyping and functional studies. to pred ...	2016	27390651
cross-reactivity of porcine immunoglobulin a antibodies with fecal immunoglobulins of wild boar (sus scrofa) and other animal species.	fecal samples obtained from wild boar habitats are useful for the surveillance of diseases in wild boar populations; however, it is difficult to determine the species of origin of feces collected in natural habitats. in this study, a fecal iga elisa was evaluated as a method for identifying the porcine species from fecal samples. both domestic pigs (sus scrofa domestica) and wild boars (sus scrofa coreanus) showed significantly higher levels of fecal iga than other animal species. additionally, ...	2016	27340389
nucleocytoplasmic human o-glcnac transferase is sufficient for o-glcnacylation of mitochondrial proteins.	o-linked n-acetylglucosamine modification (o-glcnacylation) is a nutrient-dependent protein post-translational modification (ptm), dynamically and reversibly driven by two enzymes: o-glcnac transferase (ogt) and o-glcnacase (oga) that catalyse the addition and the removal of the o-glcnac moieties to/from serine and threonine residues of target proteins respectively. increasing evidence suggests involvement of o-glcnacylation in many biological processes, including transcription, signalling, neur ...	2016	27048592
if-combined smrna fish reveals interaction of mcpip1 protein with ier3 mrna.	mcpip1 and ier3 are recently described proteins essential for maintenance of immune homeostasis. ier3 is involved in the regulation of apoptosis and differentiation and has been shown lately to protect activated t cells and macrophages from apoptosis. mcpip1 is an rnase critical for controlling inflammation-related mrnas. mcpip1 interacts with and degrades a set of stem-loop-containing mrnas (including il-6). our results demonstrate the involvement of mcpip1 in the regulation of ier3 mrna levels ...	2016	27256408
the emergence of sarcoptic mange in australian wildlife: an unresolved debate.	due to its suspected increase in host range and subsequent global diversification, sarcoptes scabiei has important implications at a global scale for wildlife conservation and animal and human health. the introduction of this pathogen into new locations and hosts has been shown to produce high morbidity and mortality, a situation observed recently in australian and north american wildlife.of the seven native animal species in australia known to be infested by s. scabiei, the bare-nosed wombat (v ...	2016	27255333
geve: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes.	in mammals, approximately 10% of genome sequences correspond to endogenous viral elements (eves), which are derived from ancient viral infections of germ cells. although most eves have been inactivated, some open reading frames (orfs) of eves obtained functions in the hosts. however, eve orfs usually remain unannotated in the genomes, and no databases are available for eve orfs. to investigate the function and evolution of eves in mammalian genomes, we developed eve orf databases for 20 genomes ...	2016	27242033
erythrocyte glutathione transferase: a general probe for chemical contaminations in mammals.	glutathione transferases (gsts) are enzymes devoted to the protection of cells against many different toxins. in erythrocytes, the isoenzyme (e-gst) mainly present is gstp1-1, which is overexpressed in humans in case of increased blood toxicity, as it occurs in nephrophatic patients or in healthy subjects living in polluted areas. the present study explores the possibility that e-gst may be used as an innovative and highly sensitive biomarker of blood toxicity also for other mammals. all distinc ...	2016	27551520
data on the evolutionary history of the v(d)j recombination-activating protein 1 - rag1 coupled with sequence and variant analyses.	rag1 protein is one of the key component of rag complex regulating the v(d)j recombination. there are only few studies for rag1 concerning evolutionary history, detailed sequence and mutational hotspots. herein, we present out datasets used for the recent comprehensive study of rag1 based on sequence, phylogenetic and genetic variant analyses (kumar et al., 2015) [1]. protein sequence alignment helped in characterizing the conserved domains and regions of rag1. it also aided in unraveling ancest ...	2016	27284568
behavioral ecology of captive species: using bibliographic information to assess pet suitability of mammal species.	which mammal species are suitable to be kept as pet? for answering this question many factors have to be considered. animals have many adaptations to their natural environment in which they have evolved that may cause adaptation problems and/or risks in captivity. problems may be visible in behavior, welfare, health, and/or human-animal interaction, resulting, for example, in stereotypies, disease, and fear. a framework is developed in which bibliographic information of mammal species from the w ...	2016	27243023
elemental analysis of bone, teeth, horn and antler in different animal species using non-invasive handheld x-ray fluorescence.	mineralized tissues accumulate elements that play crucial roles in animal health. although elemental content of bone, blood and teeth of human and some animal species have been characterized, data for many others are lacking, as well as species comparisons. here we describe the distribution of elements in horn (bovidae), antler (cervidae), teeth and bone (humerus) across a number of species determined by handheld x-ray fluorescence (xrf) to better understand differences and potential biological ...	2016	27196603
the brain of the domestic bos taurus: weight, encephalization and cerebellar quotients, and comparison with other domestic and wild cetartiodactyla.	the domestic bovine bos taurus is raised worldwide for meat and milk production, or even for field work. however the functional anatomy of its central nervous system has received limited attention and most of the reported data in textbooks and reviews are derived from single specimens or relatively old literature. here we report information on the brain of bos taurus obtained by sampling 158 individuals, 150 of which at local abattoirs and 8 in the dissecting room, these latter subsequently form ...	2016	27128674
mir-152 as a tumor suppressor microrna: target recognition and regulation in cancer.	micrornas (mirnas or mirs) are endogenous translation repressors of protein-coding genes that act by binding to the 3'-untranslated region of their target genes, and may contribute to tumorigenesis by functioning as oncogenes or tumor suppressor genes. mir-152, a member of the mir-148/152 family, is aberrantly expressed in various diseases, including various types of cancer. a growing body of evidence has demonstrated that mir-152 may act as a tumor suppressor gene by regulating its target genes ...	2016	27313716
blood meal sources of wild and domestic triatoma infestans (hemiptera: reduviidae) in bolivia: connectivity between cycles of transmission of trypanosoma cruzi.	chagas disease is a major public health problem in latin america. its etiologic agent, trypanosoma cruzi, is mainly transmitted through the contaminated faeces of blood-sucking insects called triatomines. triatoma infestans is the main vector in various countries in south america and recently, several foci of wild populations of this species have been described in bolivia and other countries. these wild populations are suspected of affecting the success of insecticide control campaigns being car ...	2016	27090297
assessing the role of livestock in big cat prey choice using spatiotemporal availability patterns.	livestock is represented in big cat diets throughout the world. husbandry approaches aim to reduce depredation, which may influence patterns of prey choice, but whether felids have a preference for livestock or not often remains unclear as most studies ignore livestock availability. we assessed prey choice of the endangered persian leopard (panthera pardus saxicolor) in golestan national park, iran, where conflict over livestock depredation occurs. we analyzed leopard diet (77 scats) and assesse ...	2016	27064680
mfppi - multi fasta protparam interface.	physico-chemical properties reflect the functional and structural characteristics of a protein. the comparative study of the physicochemical properties is important to know role of a protein in exploring its molecular evolution. a number of online and offline tools are available for calculating the physico-chemical properties of a single protein sequence. however, a tool is not available for a comparative study with graphical visualization of multi-fasta sequences. hence, we describe the develop ...	2016	28104964
molecular evolution of pten pseudogenes in mammals.	phosphatase and tensin homolog (pten) is a tumor-suppressor gene. pten pseudogene (ptenp) acts as an endogenous rna, which regulates its parental gene by competitively binding to the 3' utr of pten gene in the human. despite the importance of this pseudogene, little is known about the molecular evolution of ptenp in mammals. in this study, we identified 37 pseudogenes from 65 mammalian genomes. among them, 32 were from rodents or primates. phylogenetic analyse showed a complex evolutionary histo ...	2016	27936183
lactobacilli dominance and vaginal ph: why is the human vaginal microbiome unique?	the human vaginal microbiome is dominated by bacteria from the genus lactobacillus, which create an acidic environment thought to protect women against sexually transmitted pathogens and opportunistic infections. strikingly, lactobacilli dominance appears to be unique to humans; while the relative abundance of lactobacilli in the human vagina is typically >70%, in other mammals lactobacilli rarely comprise more than 1% of vaginal microbiota. several hypotheses have been proposed to explain human ...	2016	28008325
the complete genome sequence of the african buffalo (syncerus caffer).	the african buffalo (syncerus caffer) is an important role player in the savannah ecosystem. it has become a species of relevance because of its role as a wildlife maintenance host for an array of infectious and zoonotic diseases some of which include corridor disease, foot-and-mouth disease and bovine tuberculosis. to date, no complete genome sequence for s. caffer had been available for study and the genomes of other species such as the domestic cow (bos taurus) had been used as a proxy for an ...	2016	27927182
development of olfactory epithelium and associated structures in the green iguana, iguana iguana-light and scanning electron microscopic study.	the ontogenesis of the nasal cavity has been described in many mammalian species. the situation is different with reptiles, despite the fact that they have become relatively common as pets. in this study we focused on the ontogenesis of the olfactory epithelium, as well as other types of epithelia in the nasal cavity of pre-hatched green iguanas (iguana iguana). collection of samples began from day 67 of incubation and continued every four days until hatching. microscopic examination revealed th ...	2016	27920949
characterization of the canine mhc class i dla-88*50101 peptide binding motif as a prerequisite for canine t cell immunotherapy.	there are limitations in pre-clinical settings using mice as a basis for clinical development in humans. in cancer, similarities exist between humans and dogs; thus, the dog patient can be a link in the transition from laboratory research on mouse models to clinical trials in humans. knowledge of the peptides presented on mhc molecules is fundamental for the development of highly specific t cell-based immunotherapies. this information is available for human mhc molecules but is absent for the ca ...	2016	27893789
tgf-β signaling controls fshr signaling-reduced ovarian granulosa cell apoptosis through the smad4/mir-143 axis.	follicle-stimulating hormone receptor (fshr) and its intracellular signaling control mammalian follicular development and female infertility. our previous study showed that fshr is downregulated during follicular atresia of porcine ovaries. however, its role and regulation in follicular atresia remain unclear. here, we showed that fshr knockdown induced porcine granulosa cell (pgc) apoptosis and follicular atresia, and attenuated the levels of intracellular signaling molecules such as pka, akt a ...	2016	27882941
genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions.	throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. mongolian sheep is the common ancestor of the chinese short fat-tailed sheep. migration to different ecoregions leads to changes in selection pressures and results in microevolution. mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. genome-wide intraspecific variation is required to dissect the genetic basis of these trai ...	2016	27809776
golgi transport 1b regulates protein export from the endoplasmic reticulum in rice endosperm cells.	coat protein complex ii (copii) mediates the first step of anterograde transport of newly synthesized proteins from the endoplasmic reticulum (er) to other endomembrane compartments in eukaryotes. a group of evolutionarily conserved proteins (sar1, sec23, sec24, sec13, and sec31) constitutes the basic copii coat machinery; however, the details of how the copii coat assembly is regulated remain unclear. here, we report a protein transport mutant of rice (oryza sativa), named glutelin precursor ac ...	2016	27803308
piglets learn to use combined human-given visual and auditory signals to find a hidden reward in an object choice task.	although animals rarely use only one sense to communicate, few studies have investigated the use of combinations of different signals between animals and humans. this study assessed for the first time the spontaneous reactions of piglets to human pointing gestures and voice in an object-choice task with a reward. piglets (sus scrofa domestica) mainly use auditory signals-individually or in combination with other signals-to communicate with their conspecifics. their wide hearing range (42 hz to 4 ...	2016	27792731
cluster analysis of p53 binding site sequences reveals subsets with different functions.	p53 is an important regulator of cell cycle arrest, senescence, apoptosis and metabolism, and is frequently mutated in tumors. it functions as a tetramer, where each component dimer binds to a decameric dna region known as a response element. we identify p53 binding site subtypes and examine the functional and evolutionary properties of these subtypes. we start with over 1700 known binding sites and, with no prior labeling, identify two sets of response elements by unsupervised clustering. when ...	2016	27812278
l1base 2: more retrotransposition-active line-1s, more mammalian genomes.	line-1 (l1) insertions comprise as much as 17% of the human genome sequence, and similar proportions have been recorded for other mammalian species. given the established role of l1 retrotransposons in shaping mammalian genomes, it becomes an important task to track and annotate the sources of this activity: full length elements, able to encode the cis and trans acting components of the retrotransposition machinery. the l1base database (http://l1base.charite.de) contains annotated full-length se ...	2016	27924012
predation by red foxes (vulpes vulpes) at an outdoor piggery.	outdoor pig operations are an alternative to intensive systems of raising pigs; however for the majority of outdoor pork producers, issues of biosecurity and predation control require significant management and (or) capital investment. identifying and quantifying predation risk in outdoor pork operations has rarely been done, but such data would be informative for these producers as part of their financial and logistical planning. we quantified potential impact of fox predation on piglets bred o ...	2016	27740601
brain mass and encephalization quotients in the domestic industrial pig (sus scrofa).	in the present study we examined the brain of fetal, newborn, and adult pigs raised for meat production. the fresh and formalin-fixed weights of the brain have been recorded and used, together with body weight, to calculate the encephalization quotient (eq). the weight of the cerebellum has been used to calculate the cerebellar quotient (cq). the results have been discussed together with analogue data obtained in other terrestrial cetartiodactyla (including the domestic bovine, sheep, goat, and ...	2016	27351807
vertebrate tfpi-2 c-terminal peptides exert therapeutic applications against gram-negative infections.	tissue factor pathway inhibitor-2 (tfpi-2) is a serine protease inhibitor that exerts multiple physiological and patho-physiological activities involving the modulation of coagulation, angiogenesis, tumor invasion, and apoptosis. in previous studies we reported a novel role of human tfpi-2 in innate immunity by serving as a precursor for host defense peptides. here we employed a number of tfpi-2 derived peptides from different vertebrate species and found that their antibacterial activity is evo ...	2016	27349742
web-based bioinformatics workflows for end-to-end rna-seq data computation and analysis in agricultural animal species.	remarkable advances in next generation sequencing (ngs) technologies, bioinformatics algorithms and computational technologies have significantly accelerated genomic research. however, complicated ngs data analysis still remains as a major bottleneck. rna-seq, as one of the major area in the ngs field, also confronts great challenges in data analysis.	2016	27678198
evolution of digestive enzymes and rnase1 provides insights into dietary switch of cetaceans.	although cetaceans (whales, porpoises, and dolphins) have multi-chambered stomachs, feeding habits of modern cetaceans have dramatically changed from herbivorous to carnivorous. however, the genetic basis underlying this dietary switch remains unexplored. here, we present the first systematic investigation of 10 digestive enzymes genes (i.e., cyp7a1, ctrc, lipc, lipf, pnlip, pgc, prss1, si, slc5a1, and tmprss15) of representative cetaceans, and the evolutionary trajectory of rnase1 in cetartioda ...	2016	27651393
species determination and quantitation in mixtures using mrm mass spectrometry of peptides applied to meat authentication.	we describe a simple protocol for identifying and quantifying the two components in binary mixtures of species possessing one or more similar proteins. central to the method is the identification of 'corresponding proteins' in the species of interest, in other words proteins that are nominally the same but possess species-specific sequence differences. when subject to proteolysis, corresponding proteins will give rise to some peptides which are likewise similar but with species-specific variants ...	2016	27685654
tp53 copy number expansion is associated with the evolution of increased body size and an enhanced dna damage response in elephants.	a major constraint on the evolution of large body sizes in animals is an increased risk of developing cancer. there is no correlation, however, between body size and cancer risk. this lack of correlation is often referred to as 'peto's paradox'. here, we show that the elephant genome encodes 20 copies of the tumor suppressor gene tp53 and that the increase in tp53 copy number occurred coincident with the evolution of large body sizes, the evolution of extreme sensitivity to genotoxic stress, and ...	2016	27642012
genome-wide identification and characterization of long non-coding rnas in developmental skeletal muscle of fetal goat.	long non-coding rnas (lncrnas) have been studied extensively over the past few years. large numbers of lncrnas have been identified in mouse, rat, and human, and some of them have been shown to play important roles in muscle development and myogenesis. however, there are few reports on the characterization of lncrnas covering all the development stages of skeletal muscle in livestock.	2016	27550073
molecular mechanisms of biological aging in intervertebral discs.	advanced age is the greatest risk factor for the majority of human ailments, including spine-related chronic disability and back pain, which stem from age-associated intervertebral disc degeneration (idd). given the rapid global rise in the aging population, understanding the biology of intervertebral disc aging in order to develop effective therapeutic interventions to combat the adverse effects of aging on disc health is now imperative. fortunately, recent advances in aging research have begun ...	2016	26890203
when the brain goes diving: transcriptome analysis reveals a reduced aerobic energy metabolism and increased stress proteins in the seal brain.	during long dives, the brain of whales and seals experiences a reduced supply of oxygen (hypoxia). the brain neurons of the hooded seal (cystophora cristata) are more tolerant towards low-oxygen conditions than those of mice, and also better survive other hypoxia-related stress conditions like a reduction in glucose supply and high concentrations of lactate. little is known about the molecular mechanisms that support the hypoxia tolerance of the diving brain.	2016	27507242
origin and timing of new zealand's earliest domestic chickens: polynesian commensals or european introductions?	human settlers transported chickens (gallus gallus domesticus) to most east polynesian archipelagos between ad 1000 and 1300; however, it has long been assumed that new zealand was an exception. despite the fact that chicken bones have been recovered from localities of early archaeological middens in new zealand, their age and genetic relationships have never been critically assessed. here, we test the assumption that chickens were not introduced to new zealand during prehistory through ancient ...	2016	27853601
development of primer pairs from molecular typing of rabies virus variants present in mexico.	nucleoprotein (n) gene from rabies virus (rabv) is a useful sequence target for variant studies. several specific rabv variants have been characterized in different mammalian hosts such as skunk, dog, and bats by using anti-nucleocapsid monoclonal antibodies (mabs) via indirect fluorescent antibody (ifa) test, a technique not available in many laboratories in mexico. in the present study, a total of 158 sequences of n gene from rabv were used to design eight pairs of primers (four external and f ...	2016	27563666
human hunting and nascent animal management at middle pre-pottery neolithic yiftah'el, israel.	the current view for the southern levant is that wild game hunting was replaced by herd management over the course of the pre-pottery neolithic b period, but there is significant debate over the timing, scale and origin of this transition. to date, most relevant studies focus either on wild game exploitation in the periods prior to domestication or on classic markers of domestication of domestic progenitor species over the course of the ppnb. we studied the faunal remains from the 2007-2008 exca ...	2016	27383247
molecular characterization and combined genotype association study of bovine cluster of differentiation 14 gene with clinical mastitis in crossbred dairy cattle.	the present study was undertaken with the objectives to characterize and to analyze combined genotypes of cluster of differentiation 14 (cd14) gene to explore its association with clinical mastitis in karan fries (kf) cows maintained in the national dairy research institute herd, karnal.	2016	27536026
molecular characterization of aquaporin 1 and aquaporin 3 from the gills of the african lungfish, protopterus annectens, and changes in their branchial mrna expression levels and protein abundance during three phases of aestivation.	african lungfishes can undergo long periods of aestivation on land during drought. during aestivation, lungfishes are confronted with desiccation and dehydration, and their gills become non-functional and covered with a thick layer of dried mucus. aquaporins (aqps) are a superfamily of integral membrane proteins which generally facilitate the permeation of water through plasma membranes. this study aimed to obtain the complete cdna coding sequences of aqp1 and aqp3 from the gills of protopterus ...	2016	27891097
ticks (acari: ixodidae) infesting cattle and some other domestic and wild hosts on the french mediterranean island of corsica.	corsica is a mountainous french island in the north-western mediterranean presenting a large diversity of natural environments where many interactions between domestic animals and wild fauna occur. despite a favourable context for ticks and tick-borne diseases (tbds), the tick fauna of corsica has not systematically been investigated.	2016	27842608
the influence of red deer space use on the distribution of ixodes ricinus ticks in the landscape.	many wingless ectoparasites have a limited capacity for active movement and are therefore primarily dependent on hitchhiking on their hosts for transportation. the distribution of the tick ixodes ricinus is expected to depend mainly on transportation by hosts and tick subsequent survival in areas where they drop off. in europe, the most important hosts of adult female i. ricinus are cervids. the extensive space use of large hosts provides a much larger dispersal potential for i. ricinus than tha ...	2016	27737695
contrasting emergence of lyme disease across ecosystems.	global environmental changes are causing lyme disease to emerge in europe. the life cycle of ixodes ricinus, the tick vector of lyme disease, involves an ontogenetic niche shift, from the larval and nymphal stages utilizing a wide range of hosts, picking up the pathogens causing lyme disease from small vertebrates, to the adult stage depending on larger (non-transmission) hosts, typically deer. because of this complexity the role of different host species for emergence of lyme disease remains co ...	2016	27306947