Publications

tissues expression, polymorphisms identification of fcrn gene and its relationship with serum classical swine fever virus antibody level in pigs.	neonatal fc receptor (fcrn) gene encodes a receptor that binds the fc region of monomeric immunoglobulin g (igg) and is responsible for igg transport and stabilization. in this report, the 8,900 bp porcine fcrn genomic dna structure was identified and putative fcrn protein included 356 amino acids. alignment and phylogenetic analysis of the porcine fcrn amino acid sequences with their homologies of other species showed high identity. tissues expression of fcrn mrna was detected by real time quan ...	25049667
the effects of sequence length and oligonucleotide mismatches on 5' exonuclease assay efficiency.	although increasingly used for dna quantification, little is known of the dynamics of the 5' exonuclease assay, particularly in relation to amplicon length and mismatches at oligonucleotide binding sites. in this study we used seven assays targeting the c-myc proto-oncogene to examine the effects of sequence length, and report a marked reduction in efficiency with increasing fragment length. three of the assays were further tested on 15 mammalian species to gauge the effect of sequence differenc ...	12384613
protein sequence signatures support the african clade of mammals.	dna sequence evidence supports a superordinal clade of mammals that comprises elephants, sea cows, hyraxes, aardvarks, elephant shrews, golden moles, and tenrecs, which all have their origins in africa, and therefore are dubbed afrotheria. morphologically, this appears an unlikely assemblage, which challenges-by including golden moles and tenrecs-the monophyly of the order lipotyphla (insectivora). we here identify in three proteins unique combinations of apomorphous amino acid replacements that ...	11114173
characterization and repeat analysis of the compact genome of the freshwater pufferfish tetraodon nigroviridis.	tetraodon nigroviridis is a freshwater pufferfish 20-30 million years distant from fugu rubripes. the genome of both tetraodontiforms is compact, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. the previously uncharacterized tetraodon genome is described here together with a detailed analysis of its repeat content and organization. we report the sequencing of 46 megabases of bacterial artificial chromosome (bac) end sequences, which repr ...	10899143
compositional differences within and between eukaryotic genomes.	eukaryotic genome similarity relationships are inferred using sequence information derived from large aggregates of genomic sequences. comparisons within and between species sample sequences are based on the profile of dinucleotide relative abundance values (the profile is rhoxy = fxy/fxfy for all xy, where fx denotes the frequency of the nucleotide x and fxy denotes the frequency of the dinucleotide xy, both computed from the sequence concatenated with its inverted complement). previous s ...	9294192
genbank.	genbank (r) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. most submissions are made using the web-based bankit or standalone sequin programs and accession numbers are assigned by genbank staff upon receipt. daily data exchange with the embl data library in europe and the dna data bank of japan en ...	17202161
quantitative pcr method for sensitive detection of ruminant fecal pollution in freshwater and evaluation of this method in alpine karstic regions.	a quantitative taqman minor-groove binder real-time pcr assay was developed for the sensitive detection of a ruminant-specific genetic marker in fecal members of the phylum bacteroidetes. the qualitative and quantitative detection limits determined were 6 and 20 marker copies per pcr, respectively. tested ruminant feces contained an average of 4.1 x 10(9) marker equivalents per g, allowing the detection of 1.7 ng of feces per filter in fecal suspensions. the marker was detected in water samples ...	16885315
the potential role of sexual conflict and sexual selection in shaping the genomic distribution of mito-nuclear genes.	mitochondrial interactions with the nuclear genome represent one of life's most important co-evolved mutualisms. in many organisms, mitochondria are maternally inherited, and in these cases, co-transmission between the mitochondrial and nuclear genes differs across different parts of the nuclear genome, with genes on the x chromosome having two-third probability of co-transmission, compared with one-half for genes on autosomes. these asymmetrical inheritance patterns of mitochondria and differen ...	24682150
gonadotropin-releasing hormone receptor in the teleost haplochromis burtoni: structure, location, and function.	gnrh acts via gnrh receptors (gnrh-r) in the pituitary to cause the release of gonadotropins that regulate vertebrate reproduction. in the teleost fish, haplochromis burtoni, reproduction is socially regulated through the hypothalamus-pituitary-gonadal axis, making the pituitary gnrh-r a likely site of action for this control. as a first step toward understanding the role of gnrh-r in the social control of reproduction, we cloned and sequenced candidate gnrh-r complementary dnas from h. burtoni ...	11316736
cloning and sequence analysis of wild argali isg15 cdna.	the complete coding sequence of wild argali isg15 cdna was generated by rapid amplification of cdna ends. the isg15 cdna was 642 bp with an open reading frame of 474 bp, which encoded a 17.47 kda protein composed of 157 amino acids. its amino acid sequence shared 97.9%, 80.8%, 91.4%, 94.3%, 78.3% identity with those of isg15cdna from ovis aries (accession no. nm001009735.1), capra hircus (accession no. hq329186.1), bos taurus (accession no. bc102318.1), bubalus bubalis (accession no. hm543269.1) ...	25049988
segmented filamentous bacteria: commensal microbes with potential effects on research.	segmented filamentous bacteria (sfb) are commensal bacteria that were first identified in the ilea of mice and rats. morphologically similar bacteria occur in a broad range of host species, but all strains have been refractory to in vitro culture thus far. although sfb were once considered innocuous members of the intestinal microbiota of laboratory rodents, they are now known to affect the development of the immune system in rodents and, subsequently, the phenotype of models of both enteric and ...	24674582
domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives.	studies of domesticated animals have led to the suggestion that domestication could have significant effects on patterns of molecular evolution. in particular, analyses of mitochondrial genome sequences from domestic dogs and yaks have yielded higher ratios of non-synonymous to synonymous substitutions in the domesticated lineages than in their wild relatives. these results are important because they imply that changes to selection or population size operating over a short timescale can cause si ...	24459286
influences of different large mammalian fauna on dung beetle diversity in beech forests.	this paper focuses on biological relationships between mammalian species richness and the community structure of dung beetles in cool-temperate forests in the northernmost part of mainland japan. the composition of beetle assemblages was evaluated at 3 sites in undisturbed beech forests with different mammalian fauna. in spring and summer 2009, beetles were collected at each site using pitfall traps baited with feces from japanese macaques, macaca fuscata blyth (primates: cercopithecidae); asiat ...	23909510
identification of recently selected mutations driven by artificial selection in hanwoo (korean cattle).	hanwoo have been subjected over the last seventy years to intensive artificial selection with the aim of improving meat production traits such as marbling and carcass weight. in this study, we performed a signature of selection analysis to identify recent positive selected regions driven by a long-term artificial selection process called a breeding program using whole genome snp data. in order to investigate homozygous regions across the genome, we estimated ies (integrated extended haplotype ho ...	25049829
house infestation dynamics and feeding sources of triatoma dimidiata in central veracruz, mexico.	chagas disease is endemic in the state of veracruz, mexico, and we investigated here the dynamics of house infestation by chagas disease vectors to understand disease transmission and design effective control interventions. bug collections in 42 rural villages confirmed the widespread distribution of triatoma dimidiata in central veracruz. unexpectedly, collection data further indicated a clear pattern of seasonal infestation by mostly adult bugs. analysis of feeding sources with a polymerase ch ...	22492153
congruency between biophysical data from multiple platforms and molecular dynamics simulation of the double-super helix model of nascent high-density lipoprotein.	the predicted structure and molecular trajectories from >80 ns molecular dynamics simulation of the solvated double-super helix (dsh) model of nascent high-density lipoprotein (hdl) were determined and compared with experimental data on reconstituted nascent hdl obtained from multiple biophysical platforms, including small angle neutron scattering (sans) with contrast variation, hydrogen-deuterium exchange tandem mass spectrometry (h/d-ms/ms), nuclear magnetic resonance spectroscopy (nmr), cross ...	20687589
mechanisms and modifications of naturally occurring host defense peptides for anti-hiv microbicide development.	despite advances in the treatment of hiv infection, heterosexual transmission of hiv remains high, and vaccines to prevent hiv acquisition have been unfruitful. vaginal microbicides, on the other hand, have demonstrated considerable potential for hiv prevention, and a variety of compounds have been screened for their activity and safety as anti-hiv microbicides. among these are the naturally occurring host defense peptides, small peptides from diverse lineages with intrinsic antiviral activity. ...	22264047
in silico investigation of lactoferrin protein characterizations for the prediction of anti-microbial properties.	lactoferrin (lf) is an iron-binding multi-functional glycoprotein which has numerous physiological functions such as iron transportation, anti-microbial activity and immune response. in this study, different in silico approaches were exploited to investigate lf protein properties in a number of mammalian species. results showed that the iron-binding site, dna and rna-binding sites, signal peptides and transferrin motifs in the lf structure were highly conserved. examined sequences showed three c ...	27843978
genomic organization and evolution of ruminant lysozyme c genes.	ruminant stomach lysozyme is a long established model of adaptive gene evolution. evolution of stomach lysozyme function required changes in the site of expression of the lysozyme c gene and changes in the enzymatic properties of the enzyme. in ruminant mammals, these changes were associated with a change in the size of the lysozyme c gene family. the recent release of near complete genome sequences from several ruminant species allows a more complete examination of the evolution and diversifica ...	25730456
association of quantitative interferon-γ responses with the progression of naturally acquired mycobacterium bovis infection in wild european badgers (meles meles).	bovine tuberculosis is one of the biggest challenges facing cattle farming in great britain. european badgers (meles meles) are a reservoir host for the causal agent, mycobacterium bovis. there have been significant recent advances in diagnostic testing for tuberculosis in humans, cattle and badgers, with the development of species-specific assays for interferon-γ (ifn-γ), an important cytokine in tuberculous infections. using data collected from longitudinal studies of naturally infected wild b ...	25109384
molecular phylogeny of pseudocapillaroides xenopi (moravec et cosgrov 1982) and development of a quantitative pcr assay for its detection in aquarium sediment.	we used high-fidelity pcr to amplify a portion of the small ribosomal subunit (18s rrna) of pseudocapillaroides xenopi, a nematode that parasitizes the skin of xenopus laevis. the 1113-bp amplicon was cloned, sequenced, and aligned with sequences from 22 other nematodes in the order trichocephalida; caenorhabditis elegans was used as the outgroup. maximum-likelihood and bayesian inference phylogenetic analyses clustered p. xenopi in a clade containing only members of the genus capillaria. our an ...	25650974
p53 shapes genome-wide and cell type-specific changes in microrna expression during the human dna damage response.	the human dna damage response (ddr) triggers profound changes in gene expression, whose nature and regulation remain uncertain. although certain micro-(mi)rna species including mir34, mir-18, mir-16 and mir-143 have been implicated in the ddr, there is as yet no comprehensive description of genome-wide changes in the expression of mirnas triggered by dna breakage in human cells. we have used next-generation sequencing (ngs), combined with rigorous integrative computational analyses, to describe ...	25486198
an evolutionary relationship between stearoyl-coa desaturase (scd) protein sequences involved in fatty acid metabolism.	stearoyl-coa desaturase (scd) is a key enzyme that converts saturated fatty acids (sfas) to monounsaturated fatty acids (mufas) in fat biosynthesis. despite being crucial for interpreting scds' roles across species, the evolutionary relationship of scd proteins across species has yet to be elucidated. this study aims to present this evolutionary relationship based on amino acid sequences.	26989730
an iranian familial amyotrophic lateral sclerosis pedigree with p.val48phe causing mutation in sod1: a genetic and clinical report.	amyotrophic lateral sclerosis (als), a fatal progressive neurodegenerative disorder, is the most common motor neuron disease in european populations. approximately 10% of als cases are familial (fals) and the other patients are considered as sporadic als (sals). among many als causing genes that have been identified, mutations in sod1 and c9orf72 are the most common genetic causes of the disease. in iranian patients, it has been shown that sod1, as compared to c9orf72, plays a much more prominen ...	25729540
assessment of gel-coated delayed self-gripping mesh.	mesh hernia repair is one of the most frequently performed procedures in general surgery. recently, use of the self-gripping mesh demonstrated a beneficial effect on postoperative pain in inguinal hernia repairs. however, in intra-abdominal placement, the use of this novel mesh requires greater laparoscopic skill and dexterity because of the mesh's tendency to fold and adhere to itself and to any surrounding tissues. we hypothesized that gel-like coverage of a self-gripping mesh with a water-sol ...	25516704
evolution of klk4 and enamel maturation in eutherians.	kallikrein-related peptidase 4 (klk4) is a secreted serine protease that degrades residual enamel proteins to facilitate their removal by ameloblasts, which increases mineralization and hardens the enamel. mutations in human klk4 cause hypomaturation amelogenesis imperfecta. enamel formed by klk4 null mice is normal in thickness and prism structure, but the enamel layer retains proteins, is hypomineralized, and undergoes rapid attrition following tooth eruption. we searched multiple databases, r ...	25153384
endogenous retroviruses in domestic animals.	endogenous retroviruses (ervs) are genomic elements that are present in a wide range of vertebrates. although the study of ervs has been carried out mainly in humans and model organisms, recently, domestic animals have become important, and some species have begun to be analyzed to gain further insight into ervs. due to the availability of complete genomes and the development of new computer tools, ervs can now be analyzed from a genome-wide viewpoint. in addition, more experimental work is bein ...	25132796
identification of a novel mutation in a chinese family with nance-horan syndrome by whole exome sequencing.	nance-horan syndrome (nhs) is a rare x-linked disorder characterized by congenital nuclear cataracts, dental anomalies, and craniofacial dysmorphisms. mental retardation was present in about 30% of the reported cases. the purpose of this study was to investigate the genetic and clinical features of nhs in a chinese family.	25091991
seasonal oscillation of liver-derived hibernation protein complex in the central nervous system of non-hibernating mammals.	mammalian hibernation elicits profound changes in whole-body physiology. the liver-derived hibernation protein (hp) complex, consisting of hp-20, hp-25 and hp-27, was shown to oscillate circannually, and this oscillation in the central nervous system (cns) was suggested to play a role in hibernation. the hp complex has been found in hibernating chipmunks but not in related non-hibernating tree squirrels, leading to the suggestion that hibernation-specific genes may underlie the origin of hiberna ...	25079892
cloning the sterol carrier protein 2 genes of japanese toad (bufo japonicus formosus) and chinese toad (bufo gargarizans) and its tissue expression analysis.	in this study, to clarify the bioactive polypeptides included in the skins and secretions of bufo, we screened the japanese toad (bufo japonicus formosus) skin cdna liary by colony polymerase chain reaction (pcr), and obtained a transcript of 1 075 bp consisting of 1 37 bp 5' untranslated region (utr), 515 bp 3' utr and a 423 bp open reading frame (orf) encoding a polypeptide of 140 amino acid residues (genbank accession number: kf359945). homolog analysis showed a 70%-96% homology with sterol c ...	25297079
therapeutic uses of animal biles in traditional chinese medicine: an ethnopharmacological, biophysical chemical and medicinal review.	forty-four different animal biles obtained from both invertebrates and vertebrates (including human bile) have been used for centuries for a host of maladies in traditional chinese medicine (tcm) beginning with dog, ox and common carp biles approximately in the zhou dynasty (c. 1046-256 bce). overall, different animal biles were prescribed principally for the treatment of liver, biliary, skin (including burns), gynecological and heart diseases, as well as diseases of the eyes, ears, nose, mouth ...	25110425
proteome changes in biceps femoris muscle of iranian one-humped camel and their effect on meat quality traits.	in this study physicochemical and quality traits of biceps femoris and longissimus thoracis muscles of male and female iranian one-humped camel were determined during 14 days of refrigeration storage. analysis of variance of the results showed that only shear force and temperature were affected by the gender (p<0.05). anatomical location of the muscle influenced the meat properties except for drip loss (p<0.05). also, except for cooking loss, ageing influenced the physicochemical and quality pro ...	27956864
a comparative study of the morphometry of sperm head components in cattle, sheep, and pigs with a computer-assisted fluorescence method.	the aim of this study was to compare the sperm nuclear and acrosomal morphometry of three species of domestic artiodactyls; cattle (bos taurus), sheep (ovis aries), and pigs (sus scrofa). semen smears of twenty ejaculates from each species were fixed and labeled with a propidium iodide-pisum sativum agglutinin (pi/psa) combination. digital images of the sperm nucleus, acrosome, and whole sperm head were captured and analyzed. the use of the pi/psa combination and casa-morph fluorescence-based me ...	27624987
mycobacterium bovis infection in a wild sow (sus scrofa): first case in korea.	mycobacterium (m.) bovis causes tuberculosis and has a broad host range, including humans, livestock, and wild animals. m. bovis infection of wild boar has been reported in several european countries. we report here the first case of m. bovis infection in a domesticated wild sow in korea. granulomatous and necrotizing lesions with small numbers of acid-fast bacilli were observed in nodules of the lung of wild sow. furthermore, the m. bovis isolate from the wild sow had spoligotype sb0140 and a n ...	26726026
determinants involved in subtype-specific functions of rat trace amine-associated receptors 1 and 4.	the trace amine-associated receptor (taar) family displays high species- and subtype-specific pharmacology. several trace amines such as β-phenylethylamine (β-pea), p-tyramine and tryptamine are agonists at ta(1) but poorly activate rat and mouse taar4.	23072560
agr genes, missing in amniotes, are involved in the body appendages regeneration in frog tadpoles.	previous studies have shown that agr genes, which encode thioredoxin domain-containing secreted proteins, play a critical role in limb regeneration in salamanders. to determine the evolutionary conservation of agr function, it is important to examine whether agrs play a similar role in species with a different type of regeneration. here, we refined the phylogeny of agrs, revealing three subfamilies: ag1, agr2 and agr3. importantly, we established that ag1 was lost in higher vertebrates, which co ...	23412115
myosin light chains: teaching old dogs new tricks.	the myosin holoenzyme is a multimeric protein complex consisting of heavy chains and light chains. myosin light chains are calmodulin family members which are crucially involved in the mechanoenzymatic function of the myosin holoenzyme. this review examines the diversity of light chains within the myosin superfamily, discusses interactions between the light chain and the myosin heavy chain as well as regulatory and structural functions of the light chain as a subunit of the myosin holoenzyme. it ...	26155737
observation of c.260a > g mutation in superoxide dismutase 1 that causes p.asn86ser in iranian amyotrophic lateral sclerosis patient and absence of genotype/phenotype correlation.	amyotrophic lateral sclerosis (als) is the most common motor neuron disorder in european populations. als can be sporadic als (sals) or familial als (fals). among 20 known als genes, mutations in c9orf72 and superoxide dismutase 1 (sod1) are the most common genetic causes of the disease. whereas c9orf72 mutations are more common in western populations, the contribution of sod1 to als in iran is more than c9orf72. at present, a clear genotype/phenotype correlation for als has not been identified. ...	26622980
molecular cloning, characterization and expression of the energy homeostasis-associated gene in piglet.	the energy homeostasis-associated (enho) gene encodes a secreted protein, adropin, which regulates the expression of hepatic lipogenic genes and adipose tissue peroxisome proliferator-activated receptor γ, a major regulator of lipogenesis. in the present study, the porcine (sus scrofa) homologue of the enho gene, which was named penho, was amplified by reverse transcriptase polymerase chain reaction (rt-pcr) using oligonucleotide primers derived from in silico sequences. the gene sequence was su ...	26055914
molecular evolution of the hyaluronan synthase 2 gene in mammals: implications for adaptations to the subterranean niche and cancer resistance.	the naked mole-rat (nmr) heterocephalus glaber is a unique and fascinating mammal exhibiting many unusual adaptations to a subterranean lifestyle. the recent discovery of their resistance to cancer and exceptional longevity has opened up new and important avenues of research. part of this resistance to cancer has been attributed to the fact that nmrs produce a modified form of hyaluronan--a key constituent of the extracellular matrix--that is thought to confer increased elasticity of the skin as ...	25948568
structure-activity relationships for α-calcitonin gene-related peptide.	calcitonin gene-related peptide (cgrp) is a member of the calcitonin (ct) family of peptides. it is a widely distributed neuropeptide implicated in conditions such as neurogenic inflammation. with other members of the ct family, it shares an n-terminal disulphide-bonded ring which is essential for biological activity, an area of potential α-helix, and a c-terminal amide. cgrp binds to the calcitonin receptor-like receptor (clr) in complex with receptor activity-modifying protein 1 (ramp1), a mem ...	23186257
mutation analysis of mitogen activated protein kinase 1 gene in indian cases of 46,xy disorder of sex development.	determination of sex is the result of cascade of molecular events that cause undifferentiated bipotential gonad to develop as a testis or an ovary. a series of genes such as sry, steroidogenic factor-1 (sf1), ar, srd5 α, desert hedgehog (dhh) etc., have been reported to have a significant role in development of sex in the fetus and secondary sexual characteristics at the time of puberty. recently, mitogen activated protein kinase kinase kinase 1 (map3k1) gene was found to be associated with 46, ...	24497709
identification of bloodmeal sources and trypanosoma cruzi infection in triatomine bugs (hemiptera: reduviidae) from residential settings in texas, the united states.	the host-vector-parasite interactions in chagas disease peridomestic transmission cycles in the united states are not yet well understood. trypanosoma cruzi (kinetoplastida: trypanosomatidae) infection prevalence and bloodmeal sources were determined for adult and immature triatomine (hemiptera: reduviidae) specimens collected from residential settings in central texas. sequenced cytochrome b dna segments obtained from triatomine digestive tract identified nine vertebrate hosts and one invertebr ...	24180119
the drug target genes show higher evolutionary conservation than non-target genes.	although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. we compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein- ...	26716901
comparative and evolutionary insights into cd4 gene across mammalian and avian taxa.	the present day genetic architecture of a species bears much significance to its closely related species which is due to species-specific differences, shaped by different evolutionary forces across time scale. with the availability of whole genome sequence of several closely related species, it is now possible to infer evolutionary patterns of genes and genomes in specific lineages. to this respect, cd4 gene, primarily responsible for defensive mechanism in human, is conserved across a few taxa, ...	26767121
decreasing sleep requirement with increasing numbers of neurons as a driver for bigger brains and bodies in mammalian evolution.	mammals sleep between 3 and 20 h d(-1), but what regulates daily sleep requirement is unknown. while mammalian evolution has been characterized by a tendency towards larger bodies and brains, sustaining larger bodies and brains requires increasing hours of feeding per day, which is incompatible with a large sleep requirement. mammalian evolution, therefore, must involve mechanisms that tie increasing body and brain size to decreasing sleep requirements. here i show that daily sleep requirement d ...	26400745
ecological consequences of human niche construction: examining long-term anthropogenic shaping of global species distributions.	the exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by homo sapiens a crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. such data suggest that, by the late pleistocene, humans had be ...	27274046
microsporidial spores in fecal samples of some domesticated animals living in giza, egypt.	the aim of the present work was to investigate the prevalence and species of intestinal microsporidiosis among animals in giza, egypt.	28096853
complex tissue-specific patterns and distribution of multiple rage splice variants in different mammals.	the receptor for advanced glycosylation end products (rage) is a multiligand receptor involved in diverse cell signaling pathways. previous studies show that this gene expresses several splice variants in human, mouse, and dog. alternative splicing (as) plays an important role in expanding transcriptomic and proteomic diversity, and it has been related to disease. as is also one of the main evolutionary mechanisms in mammalian genomes. however, limited information is available regarding the as o ...	24273313
the first chameleon transcriptome: comparative genomic analysis of the oxphos system reveals loss of cox8 in iguanian lizards.	recently, we found dramatic mitochondrial dna divergence of israeli chamaeleo chamaeleon populations into two geographically distinct groups. we aimed to examine whether the same pattern of divergence could be found in nuclear genes. however, no genomic resource is available for any chameleon species. here we present the first chameleon transcriptome, obtained using deep sequencing (solid). our analysis identified 164,000 sequence contigs of which 19,000 yielded unique blastx hits. to test the e ...	24009133
solutions to peto's paradox revealed by mathematical modelling and cross-species cancer gene analysis.	whales have 1000-fold more cells than humans and mice have 1000-fold fewer; however, cancer risk across species does not increase with the number of somatic cells and the lifespan of the organism. this observation is known as peto's paradox. how much would evolution have to change the parameters of somatic evolution in order to equalize the cancer risk between species that differ by orders of magnitude in size? analysis of previously published models of colorectal cancer suggests that a two- to ...	26056366
pancreatic islet plasticity: interspecies comparison of islet architecture and composition.	the pancreatic islet displays diverse patterns of endocrine cell arrangement. the prototypic islet, with insulin-secreting beta-cells forming the core surrounded by other endocrine cells in the periphery, is largely based on studies of normal rodent islets. recent reports on large animals, including humans, show a difference in islet architecture, in which the endocrine cells are randomly distributed throughout the islet. this particular species difference has raised concerns regarding the inter ...	20657742
evolution and spectral tuning of visual pigments in birds and mammals.	variation in the types and spectral characteristics of visual pigments is a common mechanism for the adaptation of the vertebrate visual system to prevailing light conditions. the extent of this diversity in mammals and birds is discussed in detail in this review, alongside an in-depth consideration of the molecular changes involved. in mammals, a nocturnal stage in early evolution is thought to underlie the reduction in the number of classes of cone visual pigment genes from four to only two, w ...	19720655
beyond the mouse monopoly: studying the male germ line in domestic animal models.	spermatogonial stem cells (sscs) are the foundation of spermatogenesis and essential to maintain the continuous production of spermatozoa after the onset of puberty in the male. the study of the male germ line is important for understanding the process of spermatogenesis, unravelling mechanisms of stemness maintenance, cell differentiation, and cell-to-cell interactions. the transplantation of sscs can contribute to the preservation of the genome of valuable individuals in assisted reproduction ...	25991701
the nature of nurture in a wild mammal's fitness.	genetic variation in fitness is required for the adaptive evolution of any trait but natural selection is thought to erode genetic variance in fitness. this paradox has motivated the search for mechanisms that might maintain a population's adaptive potential. mothers make many contributions to the attributes of their developing offspring and these maternal effects can influence responses to natural selection if maternal effects are themselves heritable. maternal genetic effects (mges) on fitness ...	25833849
improved bleeding scores using gelfoam(®) powder with incremental concentrations of bovine thrombin in a swine liver lesion model.	topical hemostatic agents are used intra-operatively to prevent uncontrolled bleeding. gelfoam(®) powder contains a hemostatic agent prepared from purified pork skin gelatin, the efficacy of which is increased when combined with thrombin. however, the effect of increasing concentrations of thrombin on resultant hemostasis is not known. this study sought to evaluate the ability of various concentrations of thrombin in combination with gelfoam powder to control bleeding using a swine liver lesion ...	27334382
animal performance and carcass characteristics of bulls (1/2 purunã vs 1/2 canchim) slaughtered at 16 and 22 months old, and three different weights.	current study aimed to evaluate the performance of bulls (1/2 purunã vs 1/2 canchim) slaughtered at two ages and three different weights. one hundred and thirteen bulls were divided into two slaughter ages (16 and 22 months) and three different slaughter weights (light, 422 kg; medium, 470 kg; and heavy, 550 kg). the body weight was higher for bulls slaughtered at 16 months. daily gain, carcass weight and dressing were higher for bulls slaughtered at 16 months. feed intake was higher for bulls s ...	25715688
organogenesis in deep time: a problem in genomics, development, and paleontology.	the fossil record is a unique repository of information on major morphological transitions. increasingly, developmental, embryological, and functional genomic approaches have also conspired to reveal evolutionary trajectory of phenotypic shifts. here, we use the vertebrate appendage to demonstrate how these disciplines can mutually reinforce each other to facilitate the generation and testing of hypotheses of morphological evolution. we discuss classical theories on the origins of paired fins, r ...	25901307
translation attenuation via 3' terminal codon usage in bovine csn1s2 is responsible for the difference in αs2- and β-casein profile in milk.	the rate of secretion of αs2-casein into bovine milk is approximately 25% of that of β-casein, yet mammary expression of their respective mrna transcripts (csn1s2 and csn2) is not different. our objective was to identify molecular mechanisms that explain the difference in translation efficiency between csn1s2 and csn2. cell-free translational efficiency of csn2 was 5 times that of csn1s2. transcripts of csn1s2 distributed into heavier polysomes than csn2 transcripts, indicating an attenuation of ...	25826667
comparative genomics reveals conservation of filaggrin and loss of caspase-14 in dolphins.	the expression of filaggrin and its stepwise proteolytic degradation are critical events in the terminal differentiation of epidermal keratinocytes and in the formation of the skin barrier to the environment. here, we investigated whether the evolutionary transition from a terrestrial to a fully aquatic lifestyle of cetaceans, that is dolphins and whales, has been associated with changes in genes encoding filaggrin and proteins involved in the processing of filaggrin. we used comparative genomic ...	25739514
a protocol to correct for intra- and interspecific variation in tail hair growth to align isotope signatures of segmentally cut tail hair to a common time line.	in recent years, segmental stable isotope analysis of hair has been a focus of research in animal dietary ecology and migration. to correctly assign tail hair segments to seasons or even julian dates, information on tail hair growth rates is a key parameter, but is lacking for most species.	26044272
dominance rank is associated with body condition in outdoor-living domestic horses (equus caballus).	the aim of our study was to explore the association between dominance rank and body condition in outdoor group-living domestic horses, equus caballus. social interactions were recorded using a video camera during a feeding test, applied to 203 horses in 42 herds. dominance rank was assigned to 194 individuals. the outcome variable body condition score (bcs) was recorded using a 9-point scale. the variables age and height were recorded and considered as potential confounders or effect modifiers. ...	25937683
derivation and characterization of bovine induced pluripotent stem cells by transposon-mediated reprogramming.	induced pluripotent stem cells (ipscs) are a seminal breakthrough in stem cell research and are promising tools for advanced regenerative therapies in humans and reproductive biotechnology in farm animals. ipscs are particularly valuable in species in which authentic embryonic stem cell (esc) lines are yet not available. here, we describe a nonviral method for the derivation of bovine ipscs employing sleeping beauty (sb) and piggybac (pb) transposon systems encoding different combinations of rep ...	25826726
reproductive performance of holstein dairy cows grazing in dry-summer subtropical climatic conditions: effect of heat stress and heat shock on meiotic competence and in vitro fertilization.	the present study was designed to evaluate how environmental factors in a dry-summer subtropical climate in terceira-azores (situated in the north atlantic ocean: 38° 43' n 27° 12' w) can affect dairy cow (holstein) fertility, as well as seasonal influence on in vitro oocytes maturation and embryos development. impact of heat shock (hs) effects on in vitro oocyte's maturation and further embryo development after in vitro fertilization (ivf) was also evaluated. for such purpose the result of the ...	25656191
stories and challenges of genome wide association studies in livestock - a review.	undoubtedly livestock is one of the major contributors to the economy of any country. the economic value of livestock includes meat, dairy products, fiber, fertilizer etc. understanding and identifying the associations of quantitative trait loci (qtl) with the economically important traits is believed to substantially benefit the livestock industry. the past two decades have seen a flurry of interest in mapping the qtl associated with traits of economic importance on the genome. with the availab ...	26194229
four members of heat shock protein 70 family in korean rose bitterling (rhodeus uyekii).	heat shock protein (hsp) 70, the highly conserved stress protein families, plays important roles in protecting cells against heat and other stresses in most animal species. in the present study, we identified and characterized four hsp70 (ruhsp4, ruhsc70, ruhsp12a, rugrp78) family proteins based on the expressed sequence tag (est) analysis of the korean rose bitterling r. uyekii cdna library. the deduced ruhsp70 family has high amino acid identities of 72-99% with those of other species. phyloge ...	27004270
physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the united residue (unres) force field for protein simulations.	the united residue (unres) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interaction sites, namely, a united peptide group (p) located halfway between the two neighboring α-carbon atoms (cαs), which serve only as geometrical points, and a united side chain (sc) attached to the respective cα. owing to this simplification, millisecond molecular dynamics simulations of large systems can be performed. while unres predicts overall folds well, ...	25691834
sequencing and characterization of divergent marbling levels in the beef cattle (longissimus dorsi muscle) transcriptome.	marbling is an important trait regarding the quality of beef. analysis of beef cattle transcriptome and its expression profile data are essential to extend the genetic information resources and would support further studies on beef cattle. rna sequencing was performed in beef cattle using the illumina high-seq2000 platform. approximately 251.58 million clean reads were generated from a high marbling (h) group and low marbling (l) group. approximately 80.12% of the 19,994 bovine genes (protein co ...	25557810
single nucleotide polymorphism in the coding region of bovine chemerin gene and their associations with carcass traits in japanese black cattle.	chemerin, highly expressed in adipose and liver tissues, regulates glucose and lipid metabolism and immunity in these tissues in ruminants and mice. our previous reports showed that chemerin is involved in adipogenesis and lipid metabolism in adipose tissue as an adipokine. the aim of the present study was to identify single nucleotide polymorphisms (snps) in the coding region of the chemerin gene and to analyze their effects on carcass traits and intramuscular fatty acid compositions in japanes ...	26104515
influence of temperature and humidity on pregnancy rate of murrah buffaloes under subtropical climate.	heat stress has adverse effects on fertility of dairy animals. decline in fertility is linearly associated with an increase in combination of both temperature and humidity. the purpose of this study was to investigate the relationship between temperature humidity index (thi) and the pregnancy rate of murrah buffaloes in a subtropical climate. the effects of genetic and non-genetic factors viz., sire, parity, period of calving and age group at first calving were found non-significant on pregnancy ...	26104398
multiple linkage disequilibrium mapping methods to validate additive quantitative trait loci in korean native cattle (hanwoo).	the efficiency of genome-wide association analysis (gwas) depends on power of detection for quantitative trait loci (qtl) and precision for qtl mapping. in this study, three different strategies for gwas were applied to detect qtl for carcass quality traits in the korean cattle, hanwoo; a linkage disequilibrium single locus regression method (ldrm), a combined linkage and linkage disequilibrium analysis (ldla) and a bayescπ approach. the phenotypes of 486 steers were collected for weaning weight ...	26104396
african indigenous cattle: unique genetic resources in a rapidly changing world.	at least 150 indigenous african cattle breeds have been named, but the majority of african cattle populations remain largely uncharacterized. as cattle breeds and populations in africa adapted to various local environmental conditions, they acquired unique features. we know now that the history of african cattle was particularly complex and while several of its episodes remain debated, there is no doubt that african cattle population evolved dramatically over time. today, we find a mosaic of gen ...	26104394
modelling pasture-based automatic milking system herds: the impact of large herd on milk yield and economics.	the aim of this modelling study was to investigate the effect of large herd size (and land areas) on walking distances and milking interval (mi), and their impact on milk yield and economic penalties when 50% of the total diets were provided from home grown feed either as pasture or grazeable complementary forage rotation (cfr) in an automatic milking system (ams). twelve scenarios consisting of 3 ams herds (400, 600, 800 cows), 2 levels of pasture utilisation (current ams utilisation of 15.0 t ...	26104411
invader probes: harnessing the energy of intercalation to facilitate recognition of chromosomal dna for diagnostic applications.	development of probes capable of recognizing specific regions of chromosomal dna has been a long-standing goal for chemical biologists. current strategies such as pna, triplex-forming oligonucleotides, and polyamides are subject to target choice limitations and/or necessitate non-physiological conditions, leaving a need for alternative approaches. toward this end, we have recently introduced double-stranded oligonucleotide probes that are energetically activated for dna recognition through modif ...	26240741
distribution and frequencies of post-transcriptional modifications in trnas.	functional trna molecules always contain a wide variety of post-transcriptionally modified nucleosides. these modifications stabilize trna structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mrnas during translation. their presence in functionally important regions of trna is conserved in all domains of life. however, the identities of many of these modified residues depend much on the phylogeny of organisms the trnas are found in, attesting for domain ...	25611331
functional characterization of a vesicular glutamate transporter in an interneuron that makes excitatory and inhibitory synaptic connections in a molluscan neural circuit.	understanding circuit function requires the characterization of component neurons and their neurotransmitters. previous work on radula protraction in the aplysia feeding circuit demonstrated that critical neurons initiate feeding via cholinergic excitation. in contrast, it is less clear how retraction is mediated at the interneuronal level. in particular, glutamate involvement was suggested, but was not directly confirmed. here we study a suspected glutamatergic retraction interneuron, b64. we u ...	26085636
stable isotopes suggest low site fidelity in bar-headed geese (anser indicus) in mongolia: implications for disease transmission.	population connectivity is an important consideration in studies of disease transmission and biological conservation, especially with regard to migratory species. determining how and when different subpopulations intermingle during different phases of the annual cycle can help identify important geographical regions or features as targets for conservation efforts and can help inform our understanding of continental-scale disease transmission. in this study, stable isotopes of hydrogen and carbon ...	27695389
vertebrate hepatic lipase genes and proteins: a review supported by bioinformatic studies.	hepatic lipase (gene: lipc; enzyme: hl; e.c.3.1.1.3) is one of three members of the triglyceride lipase family that contributes to vascular lipoprotein degradation and serves a dual role in triglyceride hydrolysis and in facilitating receptor-mediated lipoprotein uptake into the liver. amino acid sequences, protein structures, and gene locations for vertebrate lipc (or lipc for mouse and rat) genes and proteins were sourced from previous reports and vertebrate genome databases. lipc was distinct ...	22408368
proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup.	we have sequenced the complete mitochondrial genome of the extinct american mastodon (mammut americanum) from an alaskan fossil that is between 50,000 and 130,000 y old, extending the age range of genomic analyses by almost a complete glacial cycle. the sequence we obtained is substantially different from previously reported partial mastodon mitochondrial dna sequences. by comparing those partial sequences to other proboscidean sequences, we conclude that we have obtained the first sequence of m ...	17676977
genetic polymorphisms and the risk of infection following esophagectomy. positive association with tnf-alpha gene -308 genotype.	to examine the association of single nucleotide polymorphisms (snps) in inflammation-related genes in the development of infections following esophagectomy.	17592300
apigenin blocks ikkα activation and suppresses prostate cancer progression.	ikkα has been implicated as a key regulator of oncogenesis and driver of the metastatic process; therefore is regarded as a promising therapeutic target in anticancer drug development. in spite of the progress made in the development of ikk inhibitors, no potent ikkα inhibitor(s) have been identified. our multistep approach of molecular modeling and direct binding has led to the identification of plant flavone apigenin as a specific ikkα inhibitor. here we report apigenin, in micro molar range, ...	26435478
kappa-alpha plot derived structural alphabet and blosum-like substitution matrix for rapid search of protein structure database.	we present a novel protein structure database search tool, 3d-blast, that is useful for analyzing novel structures and can return a ranked list of alignments. this tool has the features of blast (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (kappa, alpha) plot derived structural alphabet and a new substitution matrix. 3d-blast searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequenc ...	17335583
determination of cancer risk associated with germ line brca1 missense variants by functional analysis.	germ line inactivating mutations in brca1 confer susceptibility for breast and ovarian cancer. however, the relevance of the many missense changes in the gene for which the effect on protein function is unknown remains unclear. determination of which variants are causally associated with cancer is important for assessment of individual risk. we used a functional assay that measures the transactivation activity of brca1 in combination with analysis of protein modeling based on the structure of br ...	17308087
the role of maternal antibodies in the emergence of severe disease as a result of fragmentation.	population fragmentation is a major problem for the conservation of mammalian species. since the spread of an infectious disease is related to the intensity of contacts between individuals, fragmentation destabilizes the way the parasites circulate in their host population. recently, zinkernagel has proposed that a reduction in the frequency of infections by a parasite could lead to the emergence of severe forms of the disease, previously avoided because the disease was contracted early in life ...	17251137
variability of the mechanical properties of bone, and its evolutionary consequences.	the relative variabilities (coefficient of variation (cv)) of 10 different mechanical properties of compact bone were determined from 2166 measurements. all measures of variability were made on a minimum of four specimens from any bone. three pre-yield properties had a cv of about 12%. six post-yield properties had cvs varying from 24 to 46%. pre-yield properties increase as a function of mineral content, whereas post-yield properties decrease. these differences give insight into mechanical phen ...	17254981
qgrs mapper: a web-based server for predicting g-quadruplexes in nucleotide sequences.	the quadruplex structures formed by guanine-rich nucleic acid sequences have received significant attention recently because of growing evidence for their role in important biological processes and as therapeutic targets. g-quadruplex dna has been suggested to regulate dna replication and may control cellular proliferation. sequences capable of forming g-quadruplexes in the rna have been shown to play significant roles in regulation of polyadenylation and splicing events in mammalian transcripts ...	16845096
mechanisms directing the nuclear localization of the ctbp family proteins.	the c-terminal binding protein (ctbp) family includes four proteins (ctbp1 [ctbp1-l], ctbp3/bars [ctbp1-s], ctbp2, and ribeye) which are implicated both in transcriptional repression and in intracellular trafficking. however, the precise mechanisms by which different ctbp proteins are targeted to different subcellular regions remains unknown. here, we report that the nuclear import of the various ctbp proteins and splice isoforms is differentially regulated. we show that ctbp2 contains a unique ...	16782877
no oxygen? no problem! intrinsic brain tolerance to hypoxia in vertebrates.	many vertebrates are challenged by either chronic or acute episodes of low oxygen availability in their natural environments. brain function is especially vulnerable to the effects of hypoxia and can be irreversibly impaired by even brief periods of low oxygen supply. this review describes recent research on physiological mechanisms that have evolved in certain vertebrate species to cope with brain hypoxia. four model systems are considered: freshwater turtles that can survive for months trapped ...	24671961
insights into the evolution of longevity from the bowhead whale genome.	the bowhead whale (balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. these animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. in addi ...	25565328
structural comparison of bacterial multidrug efflux pumps of the major facilitator superfamily.	the biological membrane is an efficient barrier against water-soluble substances. solute transporters circumvent this membrane barrier by transporting water-soluble solutes across the membrane to the other sides. these transport proteins are thus required for all living organisms. microorganisms, such as bacteria, effectively exploit solute transporters to acquire useful nutrients for growth or to expel substances that are inhibitory to their growth. overall, there are distinct types of related ...	27065631
proteomic analysis of engineered cartilage.	tissue engineering holds promise for the treatment of damaged and diseased tissues, especially for those tissues that do not undergo repair and regeneration readily in situ. many techniques are available for cell and tissue culturing and differentiation of chondrocytes using a variety of cell types, differentiation methods, and scaffolds. in each case, it is critical to demonstrate the cellular phenotype and tissue composition, with particular attention to the extracellular matrix molecules that ...	26445845
effect of heifer frame score on growth, fertility, and economics.	a non-traditional forage-based protocol was employed to evaluate replacement heifer growth, fertility, and economics between small frame (sf, 3.50; n = 50) and large frame (lf, 5.56; n = 50) heifers using three increasing gain growth phases. preceding an 85 d growing-breeding period (phase 3; p3) the heifers were managed as a common group for phases 1 and 2 (p1 and p2). during p1, heifers grazed common fields of unharvested corn and corn residue (total digestible nutrients [tdn] 56%) with supple ...	25557677
molecular characterization and expression analysis of insulin-like growth factor-1 and insulin-like growth factor binding protein-1 genes in qinghai-tibet plateau bos grunniens and lowland bos taurus.	insulin-like growth factor-1 (igf-1) and insulin-like growth factor binding protein-1 (igfbp-1) play a pivotal role in regulating cellular hypoxic response. in this study, we cloned and characterized the genes encoding igf-1 and igfbp-1 to improve the current knowledge on their roles in highland bos grunniens (yak). we also compared their expression levels in the liver and kidney tissues between yaks and lowland cattle. we obtained full-length 465 bp igf-1 and 792 bp igfbp-1, encoding 154 amino ...	25557672
hydrophilic/hydrophobic characters of antimicrobial peptides derived from animals and their effects on multidrug resistant clinical isolates.	multidrug resistant (mdr) pathogen infections are serious threats to hospitalized patients because of the limited therapeutic options. a novel group of antibiotic candidates, antimicrobial peptides (amps), have recently shown powerful activities against both gram-negative and gram-positive bacteria. unfortunately, the viability of using these amps in clinical settings remains to be seen, since most still need to be evaluated prior to clinical trials and not all of amps are potent against mdr cli ...	25730460
positional changes of a pluripotency marker gene during structural reorganization of fibroblast nuclei in cloned early bovine embryos.	cloned bovine preimplantation embryos were generated by somatic cell nuclear transfer (scnt) of bovine fetal fibroblasts with a silent copy of the pluripotency reporter gene gof, integrated at a single site of a chromosome 13. gof combines the regulatory oct4/pou5f1 sequence with the coding sequence for egfp. egfp expression served as a marker for pluripotency gene activation and was consistently detected in preimplantation embryos with 9 and more cells. three-dimensional radial nuclear position ...	25495180
nucleotide sequence conservation of novel and established cis-regulatory sites within the tyrosine hydroxylase gene promoter.	tyrosine hydroxylase (th) is the rate-limiting enzyme in catecholamine biosynthesis and its gene proximal promoter ( < 1 kb upstream from the transcription start site) is essential for regulating transcription in both the developing and adult nervous systems. several putative regulatory elements within the th proximal promoter have been reported, but evolutionary conservation of these elements has not been thoroughly investigated. since many vertebrate species are used to model development, func ...	25774193
molecular characterization and tissue distribution of estrogen receptor genes in domestic yak.	estrogen and its receptors are essential hormones for normal reproductive function in males and females during developmental stage. to better understand the effect of estrogen receptor (er) gene in yak (bos grunniens), reverse transcription-polymerase chain reaction (pcr) was carried out to clone erα and erβ genes. bioinformatics methods were used to analyze the evolutionary relationship between yaks and other species, and real-time pcr was performed to identify the mrna expression of erα and er ...	25358360
leveraging existing data for prioritization of the ecological risks of human and veterinary pharmaceuticals to aquatic organisms.	medicinal innovation has led to the discovery and use of thousands of human and veterinary drugs. with this comes the potential for unintended effects on non-target organisms exposed to pharmaceuticals inevitably entering the environment. the impracticality of generating whole-organism chronic toxicity data representative of all species in the environment has necessitated prioritization of drugs for focused empirical testing as well as field monitoring. current prioritization strategies typicall ...	25405975
avian scavengers and the threat from veterinary pharmaceuticals.	veterinary use of the non-steroidal anti-inflammatory drug diclofenac on domesticated ungulates caused populations of resident gyps vultures in the indian sub-continent to collapse. the birds died when they fed on carrion from treated animals. veterinary diclofenac was banned in 2006 and meloxicam was advocated as a 'vulture-safe' alternative. we examine the effectiveness of the 2006 ban, whether meloxicam has replaced diclofenac, and the impact of these changes on vultures. drug residue data fr ...	25405963
rabies surveillance in the united states during 2013.	during 2013, 53 reporting jurisdictions reported 5,865 rabid animals and 3 human rabies cases to the cdc, representing a 4.8% decrease from the 6,162 rabid animals and 1 human case reported in 2012. ninety-two percent of reported rabid animals were wildlife. relative contributions by the major animal groups were as follows: 1,898 raccoons (32.4%), 1,598 bats (27.2%), 1,447 skunks (24.7%), 344 foxes (5.9%), 247 cats (4.2%), 86 cattle (1.5%), and 89 dogs (1.5%). one human case was reported from ma ...	25356711