Publications

axl as a mediator of cellular growth and survival.	the control of cellular growth and proliferation is key to the maintenance of homeostasis. survival, proliferation, and arrest are regulated, in part, by growth arrest specific 6 (gas6) through binding to members of the tam receptor tyrosine kinase family. activation of the tam receptors leads to downstream signaling through common kinases, but the exact mechanism within each cellular context varies and remains to be completely elucidated. deregulation of the tam family, due to its central role ...	25344858
the transcriptome of the bowhead whale balaena mysticetus reveals adaptations of the longest-lived mammal.	mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. the bowhead whale balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. it is also one of the two largest animals and the most cold-adapted baleen whale species. here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its tran ...	25411232
reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos.	nuclear landscapes were studied during preimplantation development of bovine embryos, generated either by in vitro fertilization (ivf), or generated as cloned embryos by somatic cell nuclear transfer (scnt) of bovine fetal fibroblasts, using 3-dimensional confocal laser scanning microscopy (3d-clsm) and structured illumination microscopy (3d-sim). nuclear landscapes of ivf and scnt embryonic nuclei were compared with each other and with fibroblast nuclei. we demonstrate that reprogramming of fib ...	25482066
farmers' perceptions and knowledge of cattle adaptation to heat stress and tick resistance in the eastern cape, south africa.	the objective of this study was to determine the perceptions and knowledge of farmers of heat stress and tick resistance in cattle. a cross-sectional survey was conducted and 110 farmers in four villages in the sour and sweet velds of the eastern cape province, south africa were interviewed. the associations among area (municipality), gender, age, level of education, employment and religion were computed using chi-square tests. the majority of the respondents had on average 4 bulls, 4 cows, 4 he ...	25358328
testicular cell indices and peripheral blood testosterone concentrations in relation to age and semen quality in crossbred (holstein friesian×tharparkar) bulls.	present study analyzed the changes in peripheral blood testosterone concentrations and testicular cytogram in relation to age and semen quality in crossbred males. three different age groups of crossbred males viz. bull calves (6 months, n = 5), young bulls (15 months, n = 5) and adult bulls (4 to 6 years, n = 8) were utilized for the study. testicular fine needle aspiration cytology technique was used to quantify testicular cytology and their indices. peripheral blood testosterone concentration ...	25358314
genomic heritability of bovine growth using a mixed model.	this study investigated heritability for bovine growth estimated with genomewide single nucleotide polymorphism (snp) information obtained from a dna microarray chip. three hundred sixty seven korean cattle were genotyped with the illumina bovinesnp50 beadchip, and 39,112 snps of 364 animals filtered by quality assurance were analyzed to estimate heritability of body weights at 6, 9, 12, 15, 18, 21, and 24 months of age. restricted maximum likelihood estimate of heritability was obtained using c ...	25358309
esophageal cancer-related gene 4 at the interface of injury, inflammation, infection, and malignancy.	in humans, esophageal cancer-related gene 4 (ecrg4) is encoded by four exons in the c2orf40 locus of chromosome 2. translation of ecrg4 messenger ribonucleic acid produces a 148 amino acid-secreted 17 kda protein that is then processed to 14, ten, eight, six, four, and two kda peptides, depending on the cell in which the gene is expressed. as hypermethylation at the c2orf40 locus inhibits ecrg4 gene expression in many epithelial cancers, several investigators have speculated that ecrg4 is a cand ...	25580077
recombinant lactococcus lactis fails to secrete bovine chymosine.	bovine chymosin is an important milk-clotting agent used in the manufacturing of cheeses. currently, the production of recombinant proteins by genetically modified organisms is widespread, leading to greatly reduced costs. lactococcus (l.) lactis, the model lactic acid bacterium, was considered a good candidate for heterologous chymosin production for the following reasons: (1) it is considered to be a gras (generally regarded as safe) microorganism, (2) only one protease is present on its surfa ...	25482140
a genome wide association study on age at first calving using high density single nucleotide polymorphism chips in hanwoo (bos taurus coreanae).	age at first calving is an important trait for achieving earlier reproductive performance. to detect quantitative trait loci (qtl) for reproductive traits, a genome wide association study was conducted on the 96 hanwoo cows that were born between 2008 and 2010 from 13 sires in a local farm (juk-am hanwoo farm, suncheon, korea) and genotyped with the illumina 50k bovine single nucleotide polymorphism (snp) chips. phenotypes were regressed on additive and dominance effects for each snp using a sim ...	25178291
characterization of the cellular localization of c4orf34 as a novel endoplasmic reticulum resident protein.	human genome projects have enabled whole genome mapping and improved our understanding of the genes in humans. however, many unknown genes remain to be functionally characterized. in this study, we characterized human chromosome 4 open reading frame 34 gene (hc4orf34). hc4orf34 was highly conserved from invertebrate to mammalian cells and ubiquitously expressed in the organs of mice, including the heart and brain. interestingly, hc4orf34 is a novel er-resident, type i transmembrane protein. muta ...	24499674
progress on low susceptibility mechanisms of transmissible spongiform encephalopathies.	transmissible spongiform encephalopathies (tses), also known as prion diseases, are a group of fatal neurodegenerative diseases detected in a wide range of mammalian species. the "protein-only" hypothesis of tse suggests that prions are transmissible particles devoid of nucleic acid and the primary pathogenic event is thought to be the conversion of cellular prion protein (prp(c)) into the disease-associated isoform (prp(sc)). according to susceptibility to tses, animals can be classified into s ...	25297084
genes that are uniquely stress regulated in salt overly sensitive (sos) mutants.	repetitive rounds of differential subtraction screening, followed by nucleotide sequence determination and northern-blot analysis, identified 84 salt-regulated (160 mm nacl for 4 h) genes in arabidopsis wild-type (col-0 gl1) seedlings. probes corresponding to these 84 genes and acp1, rd22bp1, myb2, stz, and pal were included in an analysis of salt responsive gene expression profiles in gl1 and the salt-hypersensitive mutant sos3. six of 89 genes were expressed differentially in wild-type and sos ...	11351099
the tigr gene indices: analysis of gene transcript sequences in highly sampled eukaryotic species.	while genome sequencing projects are advancing rapidly, est sequencing and analysis remains a primary research tool for the identification and categorization of gene sequences in a wide variety of species and an important resource for annotation of genomic sequence. the tigr gene indices (http://www.tigr.org/tdb/tgi. shtml) are a collection of species-specific databases that use a highly refined protocol to analyze est sequences in an attempt to identify the genes represented by that data and to ...	11125077
transposable elements in sexual and ancient asexual taxa.	sexual reproduction allows deleterious transposable elements to proliferate in populations, whereas the loss of sex, by preventing their spread, has been predicted eventually to result in a population free of such elements [hickey, d. a. (1982) genetics 101, 519-531]. we tested this expectation by screening representatives of a majority of animal phyla for line-like and gypsy-like reverse transcriptases and mariner/tc1-like transposases. all species tested positive for reverse transcriptases exc ...	11121049
coevolution of head, neck, and tail domains of myosin heavy chains.	myosins, a large family of actin-based motors, have one or two heavy chains with one or more light chains associated with each heavy chain. the heavy chains have a (generally) n-terminal head domain with an atpase and actin-binding site, followed by a neck domain to which the light chains bind, and a c-terminal tail domain through which the heavy chains self-associate and/or bind the myosin to its cargo. approximately 140 members of the myosin superfamily have been grouped into 17 classes based ...	11058170
docosahexaenoic acid-containing phospholipid molecular species in brains of vertebrates.	the fatty acid composition of phospholipids and the contents of docosahexaenoic acid (dha)-containing diacyl phosphatidylcholine and diacyl phosphatidylethanolamine molecular species were determined from brains of five fresh-water fish species from a boreal region adapted to 5 degrees c, five fresh-water fish species from a temperate region acclimated to 5 degrees c, five fresh-water fish species from a temperate region acclimated to 20 degrees c, and three fresh water fish species from a subtro ...	10823917
smart: a web-based tool for the study of genetically mobile domains.	smart (a simple modular architecture research tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://smart.embl-heidelberg.de ). more than 400 domain families found in signalling, extra-cellular and chromatin-associated proteins are detectable. these domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. each domain found in a non-re ...	10592234
adaptive evolution of color vision of the comoran coelacanth (latimeria chalumnae).	the coelacanth, a "living fossil," lives near the coast of the comoros archipelago in the indian ocean. living at a depth of about 200 m, the comoran coelacanth receives only a narrow range of light, at about 480 nm. to detect the entire range of "color" at this depth, the coelacanth appears to use only two closely related paralogous rh1 and rh2 visual pigments with the optimum light sensitivities (lambdamax) at 478 nm and 485 nm, respectively. the lambdamax values are shifted about 20 nm toward ...	10339578
association of a missense change in the d2 dopamine receptor with myoclonus dystonia.	hereditary autosomal dominant myoclonus dystonia (md) is a movement disorder characterized by involuntary lightning jerks and dystonic movements and postures alleviated by alcohol. although various large families with md have been described, no positive linkage has been found to a chromosomal location. we report a family with eight members with md. linkage analysis identified a 23-centimorgan region on chromosome 11q23 that cosegregates with the disease state (maximum multipoint logarithm of odd ...	10220438
hot spots in cold adaptation: localized increases in conformational flexibility in lactate dehydrogenase a4 orthologs of antarctic notothenioid fishes.	to elucidate mechanisms of enzymatic adaptation to extreme cold, we determined kinetic properties, thermal stabilities, and deduced amino acid sequences of lactate dehydrogenase a4 (a4-ldh) from nine antarctic (-1.86 to 1 degree c) and three south american (4 to 10 degree c) notothenioid teleosts. higher michaelis-menten constants (km) and catalytic rate constants (kcat) distinguish orthologs of antarctic from those of south american species, but no relationship exists between adaptation tempera ...	9736762
the gastrulation defective gene of drosophila melanogaster is a member of the serine protease superfamily.	the establishment of dorsal-ventral polarity in the oocyte involves two sets of genes. one set belongs to the gurken-torpedo signaling pathway and affects the development of the egg chorion as well as the polarity of the embryo. the second set of genes affects only the dorsal-ventral polarity of the embryo but not the eggshell. gastrulation defective is one of the earliest acting of this second set of maternally required genes. we have cloned and characterized the gastrulation defective gene and ...	9618496
calx, a na-ca exchanger gene of drosophila melanogaster.	we have cloned calx, a gene that encodes a na-ca exchanger of drosophila melanogaster. calx encodes two repeated motifs, calx-alpha and calx-beta, that overlap domains required for exchanger activity and regulation. calx has multiple transcripts in adults, including at least one expressed in the retina. the calx genomic locus comprises >/=35 kb between the atpalpha and rudimentary-like genes in chromosomal region 93b. in xenopus oocytes, microinjected calx crna induces calcium uptake like that o ...	9294196
molecular architecture of g protein-coupled receptors.	this review of the current literature on mutations in g protein-coupled receptors (gpcrs) of the rhodopsin-related family intends to draw inferences from amino acid sequences for single receptors and multiple sequence alignments with regard to the molecular architecture of this class of receptors. for this purpose a comprehensive list of mutations within the transmembrane helical regions (tms; over 390 mutations from 38 different receptor subtypes) and their effects on function was compiled, and ...	21921973
y chromosome variants in cattle bos taurus and bos indicus.		22896221
analysis of the genetic variation for adaptation to a short thermal stress on young « bos taurus » cattle.		22896137
[not available].		22896549
[not available].		22896420
amassin, an olfactomedin protein, mediates the massive intercellular adhesion of sea urchin coelomocytes.	sea urchins have a fluid-filled body cavity, the coelom, containing four types of immunocytes called coelomocytes. within minutes after coelomic fluid is removed from the body cavity, a massive cell-cell adhesion of coelomocytes occurs. this event is referred to as clotting. clotting is thought to be a defense mechanism against loss of coelomic fluid if the body wall is punctured, and it may also function in the cellular encapsulation of foreign material and microbes. here we show that this inte ...	12591917
functional specialization of maize mitochondrial aldehyde dehydrogenases.	the maize (zea mays) rf2a and rf2b genes both encode homotetrameric aldehyde dehydrogenases (aldhs). the rf2a protein was shown previously to accumulate in the mitochondria. in vitro import experiments and aldh assays on mitochondrial extracts from rf2a mutant plants established that the rf2b protein also accumulates in the mitochondria. rna gel-blot analyses and immunohistolocation experiments revealed that these two proteins have only partially redundant expression patterns in organs and cell ...	12481049
arabidopsis contains ancient classes of differentially expressed actin-related protein genes.	actin-related proteins (arps) share less than 60% amino acid sequence homology with conventional actins and have roles in diverse cytoskeletal processes in the cytoplasm and nucleus. the genome of arabidopsis was explored for possible arp gene family members. eight potential arp gene sequences were found dispersed on three of the five arabidopsis chromosomes. atarp2 and atarp3 are protein orthologs of their similarly named counterparts in other kingdoms. atarp4, atarp5, and atarp6 are orthologs ...	11891255
knockout of arabidopsis accelerated-cell-death11 encoding a sphingosine transfer protein causes activation of programmed cell death and defense.	we describe the lethal, recessive accelerated-cell-death11 arabidopsis mutant (acd11). cell death in acd11 exhibits characteristics of animal apoptosis monitored by flow cytometry, and acd11 constitutively expresses defense-related genes that accompany the hypersensitive response normally triggered by avirulent pathogens. global transcriptional changes during programmed cell death (pcd) and defense activation in acd11 were monitored by cdna microarray hybridization. the pcd and defense pathways ...	11850411
autophagy in the eukaryotic cell.		12455967
substitution rates in alpha-helical transmembrane proteins.	it has been shown previously that some membrane proteins have a conserved core of amino acid residues. this idea not only serves to orient helices during model building exercises but may also provide insight into the structural role of residues mediating helix-helix interactions. using experimentally determined high-resolution structures of alpha-helical transmembrane proteins we show that, of the residues within the hydrophobic transmembrane spans, the residues at lipid and subunit interfaces a ...	11714918
switch1 (swi1): a novel protein required for the establishment of sister chromatid cohesion and for bivalent formation at meiosis.	we have characterized a new gene, swi1, involved in sister chromatid cohesion during both male and female meiosis in arabidopsis thaliana. a first allele, swi1.1, was obtained as a t-dna tagged mutant and was described previously as abnormal exclusively in female meiosis. we have isolated a new allele, swi1.2, which is defective for both male and female meiosis. in swi1.2 male meiosis, the classical steps of prophase were not observed, especially because homologs do not synapse. chromatid arms a ...	11459834
triatoma sanguisuga blood meals and potential for chagas disease, louisiana, usa.	to evaluate human risk for chagas disease, we molecularly identified blood meal sources and prevalence of trypanosoma cruzi infection among 49 triatoma sanguisuga kissing bugs in louisiana, usa. humans accounted for the second most frequent blood source. of the bugs that fed on humans, ≈40% were infected with t. cruzi, revealing transmission potential.	25418456
a piece of cake.		25185714
comparison digestibility and protozoa population of khuzestan water buffalo and holstein cow.	the major aim of this study was to compare the morphology and activity of rumen protozoa of khuzestan water buffalo and holstein cow using in vitro digestibility and gas production parameters of steam treated sugarcane pith. rumen fluid obtained from two buffalo and cow steers fed the same diet, 30:70 concentrate: forage. to separate rumen protozoa, antibiotic solution and fungicides were added to rumen fluid. the results of present experiment indicated that the neutral detergent fiber (ndf; 7.8 ...	25610581
myosin heavy chain 15 is associated with bovine pulmonary arterial pressure.	bovine pulmonary hypertension, brisket disease, causes significant morbidity and mortality at elevations above 2,000 m. mean pulmonary arterial pressure (mpap) is moderately heritable, with inheritance estimated to lie within a few major genes. invasive mpap measurement is currently the only tool available to identify cattle at risk of hypoxia-induced pulmonary hypertension. a genetic test could allow selection of cattle suitable for high altitude without the need for invasive testing. in this s ...	25621163
application of top-down and bottom-up systems approaches in ruminant physiology and metabolism.	systems biology is a computational field that has been used for several years across different scientific areas of biological research to uncover the complex interactions occurring in living organisms. applications of systems concepts at the mammalian genome level are quite challenging, and new complimentary computational/experimental techniques are being introduced. most recent work applying modern systems biology techniques has been conducted on bacteria, yeast, mouse, and human genomes. howev ...	23372424
evolution of mhc class i genes in the european badger (meles meles).	the major histocompatibility complex (mhc) plays a central role in the adaptive immune system and provides a good model with which to understand the evolutionary processes underlying functional genes. trans-species polymorphism and orthology are both commonly found in mhc genes; however, mammalian mhc class i genes tend to cluster by species. concerted evolution has the potential to homogenize different loci, whereas birth-and-death evolution can lead to the loss of orthologs; both processes res ...	22957169
revealing the glycation sites in synthetic neoglycoconjugates formed by conjugation of the antigenic monosaccharide hapten of vibrio cholerae o1, serotype ogawa with the bsa protein carrier using lc-esi-qqtof-ms/ms.	in this manuscript, we present the determination of glycation sites in synthetic neoglycoconjugates formed by conjugation of the antigenic monosaccharide hapten of vibrio cholerae o1 serotype ogawa to bsa using nano- liquid chromatography electrospray ionization quadrupole time-of-flight tandem mass spectroscopy (lc-esi-qqtof-ms/ms). the matrix-assisted laser desorption/ionization-tof/tof-ms/ms analyses of the tryptic digests of the glycoconjugates having a hapten:bsa ratio of 4.3:1, 6.6:1 and 1 ...	22791257
familial cortical myoclonus with a mutation in nol3.	myoclonus is characterized by sudden, brief involuntary movements, and its presence is debilitating. we identified a family suffering from adult onset, cortical myoclonus without associated seizures. we performed clinical, electrophysiological, and genetic studies to define this phenotype.	22926851
lipoic acid metabolism of plasmodium--a suitable drug target.	α-lipoic acid (6,8-thioctic acid; la) is a vital co-factor of α-ketoacid dehydrogenase complexes and the glycine cleavage system. in recent years it was shown that biosynthesis and salvage of la in plasmodium are necessary for the parasites to complete their complex life cycle. la salvage requires two lipoic acid protein ligases (lpla1 and lpla2). lpla1 is confined to the mitochondrion while lpla2 is located in both the mitochondrion and the apicoplast. lpla1 exclusively uses salvaged la and lip ...	22607141
a case series of survival outcomes in patients with advanced-stage iiib/iv non-small-cell lung cancer treated with hangam-plus.	non-small-cell lung cancer (nsclc) represents approximately 80% of all lung cancers. unfortunately, at their time of diagnosis, most patients have advanced to unresectable disease with a very poor prognosis. the oriental herbal medicine hangam-plus(hap) has been developed for antitumor purposes, and several previous studies have reported its therapeutic effects. in this study, the efficacy of hap was evaluated as a third-line treatment for advanced-stage iiib/iv nsclc.	25780640
molecular characterization of selected local and exotic cattle using rapd marker.	in order to develop specific genetic markers and determine the genetic diversity of bangladeshi native cattle (pabna, red chittagong) and exotic breeds (sahiwal), randomly amplified polymorphic dna (rapd) analysis was performed using 12 primers. genomic dna was extracted from 20 cattle (local and exotic) blood samples and extracted dna was observed by gel electrophoresis. among the random primers three were matched and found to be polymorphic. genetic relations between cattle's were determined b ...	25049622
molecular characterization and tissue-specific expression of a novel fkbp38 gene in the cashmere goat (capra hircus).	as a member of a subclass of immunophilins, it is controversial that fkbp38 acts an upstream regulator of mtor signaling pathway, which control the process of cell-growth, proliferation and differentiation. in order to explore the relationship between fkbp38 and mtor in the cashmere goat (capra hircus) cells, a full-length cdna was cloned (genbank accession number jf714970) and expression pattern was analyzed. the cloned fkbp38 gene is 1,248 bp in length, containing an open reading frame (orf) f ...	25049623
identification of a heat shock cognate protein 70 gene in chinese soft-shell turtle (pelodiscus sinensis) and its expression profiles under thermal stress.	the heat shock cognate protein 70 (hsc70) is a member of a 70-kda heat shock protein (hsp70) family that functions as molecular chaperones. in this study, a novel hsc70 gene from chinese soft-shelled turtle (pelodiscus sinensis) (thsc70) was identified. the thsc70 full-length complementary dna (cdna) is 2272 bp long with a 1941-bp open reading frame (orf) encoding 646 amino acids. three characteristic signature regions of the hsp70 family, two major domains of an adenosine triphosphate (atp)/gua ...	22661209
an ankyring-binding motif is necessary and sufficient for targeting nav1.6 sodium channels to axon initial segments and nodes of ranvier.	neurons are highly polarized cells with functionally distinct axonal and somatodendritic compartments. voltage-gated sodium channels na(v)1.2 and na(v)1.6 are highly enriched at axon initial segments (aiss) and nodes of ranvier, where they are necessary for generation and propagation of action potentials. previous studies using reporter proteins in unmyelinated cultured neurons suggest that an ankyring-binding motif within intracellular loop 2 (l2) of sodium channels is sufficient for targeting ...	22623668
constitutive activity of trpml2 and trpml3 channels versus activation by low extracellular sodium and small molecules.	the transient receptor potential channels trpml2 and trpml3 (mcoln2 and mcoln3) are nonselective cation channels. they are widely expressed in mammals. however, little is known about their physiological function(s) and activation mechanism(s). trpml3 can be activated or rather de-inhibited by exposing it first to sodium-free extracellular solution and subsequently to high extracellular sodium. trpml3 can also be activated by a variety of small chemical compounds identified in a high throughput s ...	22753890
alix binds a ypx(3)l motif of the gpcr par1 and mediates ubiquitin-independent escrt-iii/mvb sorting.	the sorting of signaling receptors to lysosomes is an essential regulatory process in mammalian cells. during degradation, receptors are modified with ubiquitin and sorted by endosomal sorting complex required for transport (escrt)-0, -i, -ii, and -iii complexes into intraluminal vesicles (ilvs) of multivesicular bodies (mvbs). however, it remains unclear whether a single universal mechanism mediates mvb sorting of all receptors. we previously showed that protease-activated receptor 1 (par1), a ...	22547407
determination of glycation sites by tandem mass spectrometry in a synthetic lactose-bovine serum albumin conjugate, a vaccine model prepared by dialkyl squarate chemistry.	neoglycoconjugate vaccines synthesized by the squaric acid spacer method allow single point attachment of the carbohydrate antigen to the protein carrier. however, the localization of the carbohydrate antigen sites of conjugation on the protein carrier has been an elusive task difficult to achieve.	22368054
daily sperm production and evaluation of morphological reproductive parameters of murrah buffaloes in an extensive breeding system.	the development of male sexual maturity varies among buffaloes. the murrah buffalo is considered the most important and efficient milk and fat producer, but aspects of its reproductive biology are still unknown. the present study aimed to evaluate the daily sperm production (dsp) and spermatogenesis in developing murrah buffalo bulls by evaluation of the seminiferous tubules, testicular morphometry and using light microscopy and scanning electron microscopy. the testes of murrah buffalo bulls at ...	22670218
catalytic residues and a predicted structure of tetrahydrobiopterin-dependent alkylglycerol mono-oxygenase.	alkylglycerol mono-oxygenase (ec 1.14.16.5) forms a third, distinct, class among tetrahydrobiopterin-dependent enzymes in addition to aromatic amino acid hydroxylases and nitric oxide synthases. its protein sequence contains the fatty acid hydroxylase motif, a signature indicative of a di-iron centre, which contains eight conserved histidine residues. membrane enzymes containing this motif, including alkylglycerol mono-oxygenase, are especially labile and so far have not been purified to homogen ...	22220568
leucine signaling in the pathogenesis of type 2 diabetes and obesity.	epidemiological evidence points to increased dairy and meat consumption, staples of the western diet, as major risk factors for the development of type 2 diabetes (t2d). this paper presents a new concept and comprehensive review of leucine-mediated cell signaling explaining the pathogenesis of t2d and obesity by leucine-induced over-stimulation of mammalian target of rapamycin complex 1 (mtorc1). mtorc1, a pivotal nutrient-sensitive kinase, promotes growth and cell proliferation in response to g ...	22442749
bioinformatic identification of novel methyltransferases.	methylation of dna, protein, and even rna species are integral processes in epigenesis. enzymes that catalyze these reactions using the donor s-adenosylmethionine fall into several structurally distinct classes. the members in each class share sequence similarity that can be used to identify additional methyltransferases. here, we characterize these classes and in silico approaches to infer protein function. computational methods such as hidden markov model profiling and the multiple motif scann ...	20582239
evolutionary dynamics of rhodopsin type 2 opsins in vertebrates.	among the five groups of visual pigments in vertebrates, the rhodopsin type 2 (rh2) group shows the largest number of gene duplication events. we have isolated three intact and one nonfunctional rh2 opsin genes each from northern lampfish (stenobrachius leucopsarus) and scabbardfish (lepidopus fitchi). using the deduced amino acid sequences of these and other representative rh2 opsin genes in vertebrates, we have estimated the divergence times and evolutionary rates of amino acid substitution at ...	19759234
transcriptome and protein domain analyses in aplysia nervous system with evolutionary implications.	the sea hare aplysia is a powerful model organism for studying the structure and function of the nervous system. recently, the genomic characterization of aplysia has been facilitated: a large scale est sequences was acquired by sequencing cdna libraries from a. californica and a parallel est database of the closely related species a. kurodai was reported. these est databases provide useful tools for both molecular biology and bioinformatics. in our previous report, we demonstrated the utility o ...	19721878
sequencing and phylogenetic analysis of the pyrgilauda ruficollis (aves, passeridae) complete mitochondrial genome.	in this study, both long pcr and conserved primers walking sequencing methods were used to determine the complete sequence of the of pyrgilauda ruficollis mitochondrial genome (kc836121). the results showed that the complete mitochondrial genome of p. ruficollis is 1 6909 bp in length with 55.0% a+t content, harboring the typical 37 genes. the mitogenome had the same gene order with that of podoces hendersoni. all protein coding genes started with atg codon, except nd3 with gtg. for the stop cod ...	24668650
mimivirus circulation among wild and domestic mammals, amazon region, brazil.	to investigate circulation of mimiviruses in the amazon region of brazil, we surveyed 513 serum samples from domestic and wild mammals. neutralizing antibodies were detected in 15 sample pools, and mimivirus dna was detected in 9 pools of serum from capuchin monkeys and in 16 pools of serum from cattle.	24564967
structural biology of the macroautophagy machinery.	macroautophagy is a conserved degradative process mediated through formation of a unique double-membrane structure, the autophagosome. the discovery of autophagy-related (atg) genes required for autophagosome formation has led to the characterization of approximately 20 genes mediating this process. recent structural studies of the atg proteins have provided the molecular basis for their function. here we summarize the recent progress in elucidating the structural basis for autophagosome formati ...	27656195
replicative capacity of mers coronavirus in livestock cell lines.	replicative capacity of middle east respiratory syndrome coronavirus (mers-cov) was assessed in cell lines derived from livestock and peridomestic small mammals on the arabian peninsula. only cell lines originating from goats and camels showed efficient replication of mers-cov. these results provide direction in the search for the intermediate host of mers-cov.	24457147
the genomes of the south american opossum (monodelphis domestica) and platypus (ornithorhynchus anatinus) encode a more complete purine catabolic pathway than placental mammals.	the end product of purine catabolism varies amongst vertebrates and is a consequence of independent gene inactivation events that have truncated the purine catabolic pathway. mammals have traditionally been grouped into two classes based on their end product of purine catabolism: most mammals, whose end product is allantoin due to an ancient loss of allantoinase (alln), and the hominoids, whose end product is uric acid due to recent inactivations of urate oxidase (uox). however little is known a ...	20161190
gene expression during the oocyte-to-embryo transition in mammals.	the seminal question in modern developmental biology is the origins of new life arising from the unification of sperm and egg. the roots of this question begin from 19th to 20th century embryologists studying fertilization and embryogenesis. although the revolution of molecular biology has yielded significant insight into the complexity of this process, the overall orchestration of genes, molecules, and cells is still not fully formed. early mammalian development, specifically the oocyte-to-embr ...	19363788
identification and analysis of biomarkers for mismatch repair proteins: a bioinformatic approach.	mismatch repair is a highly conserved process from prokaryotes to eukaryotes. defects in mismatch repair can lead to mutations in human homologues of the mut proteins and affect genomic stability which can result in microsatellite instability (mi). mi is implicated in most human cancers and majority of hereditary nonpolyposis colorectal cancers (hnpccs) are attributed to defects in mlh1.	23225975
influence of condensed tannins from ficus bengalensis leaves on feed utilization, milk production and antioxidant status of crossbred cows.	this study was conducted to examine the effects of condensed tannins (ct) from ficus bengalensis leaves on the feed utilization, milk production and health status of crossbred cows. eighteen crossbred dairy cows at their second and mid lactation (avg. bw 351.6±10.6 kg) were randomly divided into two groups of nine each in a completely randomized block design and fed two iso-nitrogenous supplements formulated to contain 0% and 1.5% ct through dried and ground leaves of ficus bengalensis. the diet ...	25049960
persistence of oxytocin receptors in the bovine uterus during the first 7 d after calving: an immunohistochemical study.	persistence of the oxytocin receptor (otr) in the bovine uterus during the first 7 d after calving was investigated by means of immunohistochemical staining. immunoreactive otrs were present in different locations in the uterus on almost all days except day 2, when staining was seen only in the endothelium of blood vessels in the endometrium and myometrium. this finding supports the hypothesis that oxytocin may be ecbolic in cows through the 1st week post partum, but further studies are required ...	24396185
regulation of actin by ion-linked equilibria.	actin assembly, filament mechanical properties, and interactions with regulatory proteins depend on the types and concentrations of salts in solution. salts modulate actin through both nonspecific electrostatic effects and specific binding to discrete sites. multiple cation-binding site classes spanning a broad range of affinities (nanomolar to millimolar) have been identified on actin monomers and filaments. this review focuses on discrete, low-affinity cation-binding interactions that drive po ...	24359734
grazing behavior and locomotion of young bulls receiving different nutritional plans in a tropical pasture.	the objectives of this study were to compare visual observation and an electronic grazing time method and to evaluate the effects of nutritional plans on intake, grazing behavior and horizontal and vertical locomotion of young bulls in a tropical pasture. thirty-nine nellore young bulls with an average body weight of 345±9.3 kg kept in pasture were used. the experimental treatments consisted of: restricted: animals kept in a plot with a low mass of forage receiving mineral mixture only; control: ...	25049762
life history constrains biochemical development in the highly specialized odontocete echolocation system.	the vertebrate head has undergone enormous modification from the features borne by early ancestors. the growth of skull bones has been well studied in many species, yet little is known about corresponding soft tissue development. among mammals, some of the most unusual examples of cranial evolution exist in the toothed whales (odontocetes). specialized fat bodies in toothed whale heads play important roles in sound transmission and reception. these fat bodies contain unique endogenous lipids, wi ...	18611851
pantothenate kinase 2 mutation with eye-of-the-tiger sign on magnetic resonance imaging in three siblings.	pantothenate kinase associated neurodegeneration (pkan) is the most prevalent type of neurodegeneration with brain iron accumulation (nbia) disorders characterized by extrapyramidal signs, and 'eye-of-the-tiger' on t2 brain magnetic resonance imaging (mri) characterized by hypointensity in globus pallidus and a hyperintensity in its core. all pkan patients have homozygous or compound heterozygous mutation in pank2 gene.	24250886
predicting monoamine oxidase inhibitory activity through ligand-based models.	the evolution of bio- and cheminformatics associated with the development of specialized software and increasing computer power has produced a great interest in theoretical in silico methods applied in drug rational design. these techniques apply the concept that "similar molecules have similar biological properties" that has been exploited in medicinal chemistry for years to design new molecules with desirable pharmacological profiles. ligand-based methods are not dependent on receptor structur ...	23231398
proteome degradation in fossils: investigating the longevity of protein survival in ancient bone.	we report the use of proteomics techniques to study how the fossil bone proteome changes in complexity over one million years.	24519823
genetics of taste receptors.	taste receptors function as one of the interfaces between internal and external milieus. taste receptors for sweet and umami (t1r [taste receptor, type 1]), bitter (t2r [taste receptor, type 2]), and salty (enac [epithelial sodium channel]) have been discovered in the recent years, but transduction mechanisms of sour taste and enac-independent salt taste are still poorly understood. in addition to these five main taste qualities, the taste system detects such noncanonical "tastes" as water, fat, ...	23886383
protein cysteines map to functional networks according to steady-state level of oxidation.	the cysteine (cys) proteome serves critical roles in protein structure, function and regulation, and includes key targets in oxidative mechanisms of disease. thioredoxins maintain cys residues in thiol forms, and previous research shows that the redox potential of thioredoxin in mitochondria and nuclei is more reduced than cytoplasm, suggesting that proteins in these compartments may have different steady-state oxidation. this study measured fractional oxidation of 641 peptidyl cys residues from ...	22605892
johanson-blizzard syndrome.	johanson-blizzard syndrome (jbs) is a rare autosomal recessive disease characterized by exocrine pancreatic insufficiency, hypoplastic or aplastic nasal alae, cutis aplasia on the scalp, and other features including developmental delay, failure to thrive, hearing loss, mental retardation, hypothyroidism, dental abnormalities, and anomalies in cardiac and genitourinary systems. more than 60 cases of this syndrome have been reported to date. we describe the case of a male infant with typical sympt ...	22072859
high-altitude pulmonary hypertension in cattle (brisket disease): candidate genes and gene expression profiling of peripheral blood mononuclear cells.	high-altitude pulmonary hypertension (haph) is a consequence of chronic alveolar hypoxia, leading to hypoxic vasoconstriction and remodeling of the pulmonary circulation. brisket disease in cattle is a naturally occurring animal model of hypoxic pulmonary hypertension. genetically susceptible cattle develop severe pulmonary hypertension and right heart failure at altitudes >7,000 ft. no information currently exists regarding the identity of the pathways and gene(s) responsible for haph or influe ...	22530101
ungulate preference for burned patches reveals strength of fire-grazing interaction.	the interactions between fire and grazing are widespread throughout fire-dependent landscapes. the utilization of burned areas by grazing animals establishes the fire-grazing interaction, but the preference for recently burned areas relative to other influences (water, topography, etc.) is unknown. in this study, we determine the strength of the fire-grazing interaction by quantifying the influence of fire on ungulate site selection. we compare the preference for recently burned patches relative ...	22393490
a ben-domain-containing protein associates with heterochromatin and represses transcription.	in eukaryotes, higher order chromatin structure governs crucial cellular processes including dna replication, transcription and post-transcriptional gene regulation. specific chromatin-interacting proteins play vital roles in the maintenance of chromatin structure. we have identified bend3, a quadruple ben domain-containing protein that is highly conserved amongst vertebrates. bend3 colocalizes with hp1 and h3 trimethylated at k9 at heterochromatic regions in mammalian cells. using an in vivo ge ...	21914818
genetic integration of molar cusp size variation in baboons.	many studies of primate diversity and evolution rely on dental morphology for insight into diet, behavior, and phylogenetic relationships. consequently, variation in molar cusp size has increasingly become a phenotype of interest. in 2007 we published a quantitative genetic analysis of mandibular molar cusp size variation in baboons. those results provided more questions than answers, as the pattern of genetic integration did not fit predictions from odontogenesis. to follow up, we expanded our ...	20034010
stabilization of the spectrin-like domains of nesprin-1α by the evolutionarily conserved "adaptive" domain.	nesprins are located at the outer and inner membranes of the nuclear envelope and help link the cytoskeleton to the nucleoskeleton. nesprin-1α, located at the inner nuclear membrane, binds to a-type lamins and emerin and has homology to spectrin-repeat proteins. however, the mechanical and thermodynamic properties of the spectrin-like repeats (slrs) of nesprin-1α and the potential structural contributions of the unique central domain were untested. in other spectrin superfamily proteins, tandem ...	20563238
a versatile telemetry system for continuous measurement of heart rate, body temperature and locomotor activity in free-ranging ruminants.	1. measuring physiological and behavioural parameters in free-ranging animals - and therefore under fully natural conditions - is of general biological concern but difficult to perform.2. we have developed a minimally invasive telemetry system for ruminants that is capable of measuring heart rate (hr), body temperature (t(b)) and locomotor activity (la). a ruminal transmitter unit was per os placed into the reticulum and therefore located in close proximity to the heart. the unit detected hr by ...	22428081
preparation and evaluation of a novel therapeutic dairy-based drink for phenylketonuria.	people with phenylketonuria need to eat a special diet which contains a low level of phenylalanine. most of these special diets have high protein levels which contain phenylalanine. control of phenylalanine levels in the early years of life is crucial and remains important throughout childhood, especially for cognitive function and behavior.	22624117
molecular characterization of xenopus lamin liv reveals differences in the lamin composition of sperms in amphibians and mammals.	lamins are nuclear intermediate filament proteins. they are involved in most nuclear activities and are essential for retaining the mechano-elastic properties of the nucleus. somatic cells of vertebrates express lamins a, b1 and b2 while lamin liii, a major component of the amphibian oocyte lamina is absent in mammals. the organization of the lamina of germ cells differs significantly from that of somatic cells. mammalian spermatogenic cells express two short lamins, c2 and b3, that are splice i ...	21327107
mass spectrometric analysis, automated identification and complete annotation of o-linked glycopeptides.	complex mixtures containing o-linked glycopeptides bearing sa(1-0)galgalnac structures, or single galnac units were subjected to collision-induced dissociation (cid) and electron transfer dissociation (etd) analysis on a linear ion trap-orbitrap mass spectrometer and the resulting data was analyzed using the protein prospector software. an overview of the structural information provided by the different fragmentation techniques, as well as their limitations, is presented. we illustrate the impor ...	20530845
chromosome territories.	chromosome territories (cts) constitute a major feature of nuclear architecture. in a brief statement, the possible contribution of nuclear architecture studies to the field of epigenomics is considered, followed by a historical account of the ct concept and the final compelling experimental evidence of a territorial organization of chromosomes in all eukaryotes studied to date. present knowledge of nonrandom ct arrangements, of the internal ct architecture, and of structural interactions with o ...	20300217
analysis of the phosphoproteome of chlamydomonas reinhardtii provides new insights into various cellular pathways.	the unicellular flagellated green alga chlamydomonas reinhardtii has emerged as a model organism for the study of a variety of cellular processes. posttranslational control via protein phosphorylation plays a key role in signal transduction, regulation of gene expression, and control of metabolism. thus, analysis of the phosphoproteome of c. reinhardtii can significantly enhance our understanding of various regulatory pathways. in this study, we have grown c. reinhardtii cultures in the presence ...	16524901
the unholy trinity: taxonomy, species delimitation and dna barcoding.	recent excitement over the development of an initiative to generate dna sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'dna barcoding' initiative should proceed. it is critical that these two issues are clarified and resolved, before the use of dna as a tool for taxonomy and species delimitation can be universalized. the first issue concerns how dna data are to be used in the context of this initiative; this is the dna barc ...	16214748
trample: the transmembrane protein labelling environment.	trample (http://gpcr.biocomp.unibo.it/biodec/) is a web application server dedicated to the detection and the annotation of transmembrane protein sequences. trample includes different state-of-the-art algorithms for the prediction of signal peptides, transmembrane segments (both beta-strands and alpha-helices), secondary structure and fast fold recognition. trample also includes a complete content management system to manage the results of the predictions. each user of the server has his/her own ...	15980454
nuclear export is evolutionarily conserved in cvc paired-like homeobox proteins and influences protein stability, transcriptional activation, and extracellular secretion.	homeodomain transcription factors control a variety of essential cell fate decisions during development. to understand the developmental regulation by these transcription factors, we describe here the molecular analysis of paired-like cvc homeodomain protein (plc-hdp) trafficking. complementary experimental approaches demonstrated that plc-hdp family members are exported by the crm1 pathway and contain an evolutionary conserved leucine-rich nuclear export signal. importantly, inactivation of the ...	15767664
functional genomics analysis of singapore grouper iridovirus: complete sequence determination and proteomic analysis.	here we report the complete genome sequence of singapore grouper iridovirus (sgiv). sequencing of the random shotgun and restriction endonuclease genomic libraries showed that the entire sgiv genome consists of 140,131 nucleotide bp. one hundred sixty-two open reading frames (orfs) from the sense and antisense dna strands, coding for lengths varying from 41 to 1,268 amino acids, were identified. computer-assisted analyses of the deduced amino acid sequences revealed that 77 of the orfs exhibited ...	15507645
negative regulation of prolactin receptor stability and signaling mediated by scf(beta-trcp) e3 ubiquitin ligase.	ubiquitin-dependent degradation of hormone receptors is emerging as a key mechanism that regulates the magnitude and duration of hormonal effects on cells and tissues. the pituitary hormone prolactin (prl) is involved in regulating cell differentiation, proliferation, and survival. prl engages its receptor (prlr) to initiate various signaling cascades, including the phosphorylation and activation of stat5. we found that prl promotes interaction between prlr and the f-box protein beta-trcp2, whic ...	15082796
trome, trest and trgen: databases of predicted protein sequences.	we previously introduced two new protein databases (trest and trgen) of hypothetical protein sequences predicted from est and htg sequences, respectively. here, we present the updates made on these two databases plus a new database (trome), which uses alignments of est data to htg or full genomes to generate virtual transcripts and coding sequences. this new database is of higher quality and since it contains the information in a much denser format it is of much smaller size. these new databases ...	14681469
role of radical formation at tyrosine 193 in the allene oxide synthase domain of a lipoxygenase-aos fusion protein from coral.	coral allene oxide synthase (caos), a fusion protein with 8r-lipoxygenase in plexaura homomalla, is a hemoprotein with sequence similarity to catalases. caos reacts rapidly with the oxidant peracetic acid to form heme compound i and intermediate ii. concomitantly, an electron paramagnetic resonance (epr) signal with tyrosyl radical-like features, centered at a g-value of 2.004-2.005, is formed. the radical is identified as tyrosyl by changes in epr spectra when deuterated tyrosine is incorporate ...	12779342
molecular cloning and characterization of a new c-type lysozyme gene from yak mammary tissue.	milk lysozyme is the ubiquitous enzyme in milk of mammals. in this study, the cdna sequence of a new chicken-type (c-type) milk lysozyme gene (yml), was cloned from yak mammary gland tissue. a 444 bp open reading frames, which encodes 148 amino acids (16.54 kda) with a signal peptide of 18 amino acids, was sequenced. further analysis indicated that the nucleic acid and amino acid sequences identities between yak and cow milk lysozyme were 89.04% and 80.41%, respectively. recombinant yak milk lys ...	26580446
pftaa: a high affinity oligothiophene probe that detects filamentous tau in vivo and in cultured neurons.		26807101
molecular cytogenetics of tragelaphine and alcelaphine interspecies hybrids: hybridization, introgression and speciation in some african antelope.	hybridization can occur naturally among diverging lineages as part of the evolutionary process leading to complete reproductive isolation, or it can result from range shifts and habitat alteration through global warming and/or other anthropogenic influences. here we report a molecular cytogenetic investigation of hybridization between taxonomically distinct species of the alcelaphini (alcelaphus buselaphus 2n = 40 × damaliscus lunatus 2n = 36) and the tragelaphini (tragelaphus strepsiceros 2n = ...	26582842
effect of lipid sources with different fatty acid profiles on intake, nutrient digestion and ruminal fermentation of feedlot nellore steers.	the present study was conducted to determine the effect of lipid sources with different fatty acid profiles on nutrient digestion and ruminal fermentation. ten rumen and duodenal fistulated nellore steers (268 body weight±27 kg) were distributed in a duplicated 5×5 latin square. dietary treatments were as follows: without fat (wf), palm oil (po), linseed oil (lo), protected fat (pf; lactoplus), and whole soybeans (ws). the roughage feed was corn silage (600 g/kg on a dry matter [dm] basis) plus ...	26580282
physiological responses and lactation to cutaneous evaporative heat loss in bos indicus, bos taurus, and their crossbreds.	cutaneous evaporative heat loss in bos indicus and bos taurus has been well documented. nonetheless, how crossbreds with different fractional genetic proportions respond to such circumstances is of interest. a study to examine the physiological responses to cutaneous evaporative heat loss, also lactation period and milk yield, were conducted in sahiwal (bos indicus, n = 10, 444±64.8 kg, 9±2.9 years), holstein friesian (bos taurus, hf100% (n = 10, 488±97.9 kg, 6±2.8 years)) and the following cros ...	26580279
physiological roles of adipokines, hepatokines, and myokines in ruminants.	since the discovery of leptin secreted from adipocytes, specialized tissues and cells have been found that secrete the several peptides (or cytokines) that are characterized to negatively and positively regulate the metabolic process. different types of adipokines, hepatokines, and myokines, which act as cytokines, are secreted from adipose, liver, and muscle tissue, respectively, and have been identified and examined for their physiological roles in humans and disease in animal models. recently ...	26732322
neurotrophins and the immune system.	the neurotrophins are a family of polypeptide growth factors that are essential for the development and maintenance of the vertebrate nervous system. in recent years, data have emerged indicating that neurotrophins could have a broader role than their name might suggest. in particular, the putative role of ngf and its receptor trka in immune system homeostasis has become a much studied topic, whereas information on the other neurotrophins is scarce in this regard. this paper reviews what is know ...	12892403