Publications

radiocaesium levels in game in the czech republic.	the paper summarizes results of monitoring of (137)cs activities in game species roaming in the woods over the territory of the czech republic for the time interval of 1986-2012. geometric means and other statistical characteristics were estimated from the data sets on the assumption of log-normal distribution of the data from the time interval 2004-2012 where the character of data distribution had displayed no significant change. geometric means (in bq/kg) in meat were: wild boar 5.1, red deer ...	25464037
first wave of cultivators spread to cyprus at least 10,600 y ago.	early neolithic sedentary villagers started cultivating wild cereals in the near east 11,500 y ago [pre-pottery neolithic a (ppna)]. recent discoveries indicated that cyprus was frequented by late ppna people, but the earliest evidence until now for both the use of cereals and neolithic villages on the island dates to 10,400 y ago. here we present the recent archaeological excavation at klimonas, which demonstrates that established villagers were living on cyprus between 11,100 and 10,600 y ago. ...	22566638
identification of mosquito avian-derived blood meals by polymerase chain reaction-heteroduplex analysis.	a polymerase chain reaction (pcr) heteroduplex assay (hda) was developed to identify avian derived mosquito blood meals to the species level. the assay used primers amplifying a fragment of the cytochrome b gene from vertebrate but not invertebrate species. in culex tarsalis fed on quail, pcr products derived from the quail cytochrome b gene were detected seven days post-engorgement. in an analysis of wild-caught mosquitoes, 85% of blood-fed mosquitoes produced detectable pcr products. heterodup ...	12201598
voltage-gated proton channels: molecular biology, physiology, and pathophysiology of the h(v) family.	voltage-gated proton channels (h(v)) are unique, in part because the ion they conduct is unique. h(v) channels are perfectly selective for protons and have a very small unitary conductance, both arguably manifestations of the extremely low h(+) concentration in physiological solutions. they open with membrane depolarization, but their voltage dependence is strongly regulated by the ph gradient across the membrane (δph), with the result that in most species they normally conduct only outward curr ...	23589829
aedes taeniorhynchus vectorial capacity informs a pre-emptive assessment of west nile virus establishment in galápagos.	increased connectivity with the mainland has led to the arrival of many invasive species to the galápagos islands, including novel pathogens, threatening the archipelago's unique fauna. here we consider the potential role of the mosquito aedes taeniorhynchus in maintaining the flavivirus west nile virus [wnv] should it reach the islands. we report on three components of vectorial capacity - vector competency, distributional abundance and host-feeding. in contrast to usa strains, galápagos a. tae ...	23519190
serologic study of pig-associated viral zoonoses in laos.	we conducted a serologic survey of four high-priority pig-associated viral zoonoses, japanese encephalitis virus (jev), hepatitis e virus (hev), nipah virus (niv), and swine influenza virus (siv), in laos. we collected blood from pigs at slaughter during may 2008-january 2009 in four northern provinces. japanese encephalitis virus hemagglutination inhibition seroprevalence was 74.7% (95% confidence interval [ci] = 71.5-77.9%), jev igm seroprevalence was 2.3% (95% ci = 1.2-3.2%), and hev seroprev ...	22665622
molecular characterization and seroprevalence in pigs of sc0806, a cat que virus isolated from mosquitoes in sichuan province, china.	the simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. cat que virus (cqv), a simbu serogroup virus of the genus orthobunyavirus (family bunyaviridae), was first isolated in 2004 from mosquitoes during surveillance of arbovirus activity in acute pediatric encephalitis in northern vietnam. we report here the complete genome sequence of sc0806 isolated from mosquitoes (culex tritaeniorhynchus) in ...	26186514
phylogenetic analysis of poly and non structural protein in japanese encephalitis virus with other related viral families.	japanese encephalitis (je) causes inflammation of brain. the mortality rate due to je is 30% while 10 -15 % of patients make full recovery. the disease spreads through infected mosquito bites breeding in rice fields and feeds on pigs, birds, and ducks.	25205875
identification of a novel coronavirus in bats.	exotic wildlife can act as reservoirs of diseases that are endemic in the area or can be the source of new emerging diseases through interspecies transmission. the recent emergence of severe acute respiratory syndrome-associated coronavirus (sars-cov) highlights the importance of virus surveillance in wild animals. here, we report the identification of a novel bat coronavirus through surveillance of coronaviruses in wildlife. analyses of the rna sequence from the orf1b and s-gene regions indicat ...	15681402
a real-time reverse transcriptase polymerase chain reaction for detection and quantification of vesiculovirus.	vesiculoviruses (vsv) are zoonotic viruses that cause vesicular stomatitis disease in cattle, horses and pigs, as well as sporadic human cases of acute febrile illness. therefore, diagnosis of vsv infections by reliable laboratory techniques is important to allow a proper case management and implementation of strategies for the containment of virus spread. we show here a sensitive and reproducible real-time reverse transcriptase polymerase chain reaction (rt-pcr) for detection and quantification ...	27276185
rising trends of neurocysticercosis: a serological report from tertiary-care hospital in south india.	taenia solium is a common two-host parasitic cestode, residing in both humans (definitive) and pigs (intermediate). invasion of this parasitic cyst into central nervous system leads to a condition known as neurocysticercosis (ncc). the world health organization (who) considers ncc as one of the "most neglected" tropical zoonotic diseases. the disease is presented with pleomorphic clinical manifestations, of which epilepsy is the most common. diagnosis of ncc is carried out by serological tests a ...	27722103
monoclonal and polyclonal antibodies specific for foot and mouth disease virus type a and type o vp1.	the foot and mouth disease virus (fmdv) is an rna virus composed of single stranded positive sense rna. fmdv has been known to infect cloven-hoofed animals, including pigs, cattle, and sheep. fmdv is rapidly spreading outward to neighboring regions, often leading to a high mortality rate. thus, early diagnosis of fmdv is critical to suppress propagation of fmdv and minimize economic losses. in this study, we report the generation and characterization of polyclonal and six monoclonal antibodies a ...	23098303
vertebrate hosts of aedes aegypti and aedes mediovittatus (diptera: culicidae) in rural puerto rico.	the distribution of aedes (stegomyia) aegypti (l.), the main vector of dengue viruses (denv) worldwide, overlaps with aedes (gymnometopa) mediovittatus (coquillett), the caribbean treehole mosquito, in urban, suburban, and rural areas. ae. mediovittatus is a competent vector of denv with high rates of vertical denv transmission in the laboratory. this study determined whether ae. mediovittatus feeds on humans and compared its feeding patterns with co-occurring ae. aegypti in two rural communitie ...	22897052
transmission routes of african swine fever virus to domestic pigs: current knowledge and future research directions.	african swine fever (asf) is a major threat to the pig industry in europe. since 2007, asf outbreaks have been ongoing in the caucasus, eastern europe and the baltic countries, causing severe economic losses for many pig farmers and pork producers. in addition, the number of asf cases in wild boar populations has dramatically increased over the past few years. evidence supports direct contact with infectious domestic pigs and wild boars, and consumption of contaminated feed, as the main transmis ...	26966305
molecular characterization and expression of a heat shock protein gene (hsp90) from the carmine spider mite, tetranychus cinnabarinus (boisduval).	in this study, the cdna of tetranychus cinnabarinus (boisduval) (acarina: tetranychidae) hsp90 (designated tchsp90) was cloned using a combination of the homology cloning and rapid amplification of cdna ends (race) approaches. the full-length cdna of tchsp90 is 2595 bp, including a 5′-untranslated region (utr) of 177 bp, 3′-utr of 249 bp, and an open reading frame (orf) of 2169 bp. the orf encodes a polypeptide of 722 amino acids with a predicted molecular weight of 83.45 kda and a theoretical i ...	20874569
wild boars as hosts of human-pathogenic anaplasma phagocytophilum variants.		23171572
wild boars as hosts of human-pathogenic anaplasma phagocytophilum variants.	to investigate the potential of wild boars to host anaplasma phagocytophilum, we analyzed bacterial 16s rrna and ank genes. dna sequencing identified several a. phagocytophilum variants, including a predominance of strains known to cause human disease. boars are thus hosts for a. phagocytophilum, notably, strains associated with human granulocytic anaplasmosis.	22607827
unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes.	we have shown previously by southern blot analysis that bov-b long interspersed nuclear elements (lines) are present in different viperidae snake species. to address the question as to whether bov-b lines really have been transmitted horizontally between vertebrate classes, the analysis has been extended to a larger number of vertebrate, invertebrate, and plant species. in this paper, the evolutionary origin of bov-b lines is shown unequivocally to be in squamata. the previously proposed horizon ...	9724768
the role of game (wild boar and roe deer) in the spread of tick-borne encephalitis in the czech republic.	in the czech republic, the incidence of human tick-borne encephalitis (tbe) has been increasing over the last two decades. at the same time, populations of game have also shown an upward trend. in this country, the ungulate game is the main host group of hosts for ixodes ricinus female ticks. this study examined the potential contribution of two most widespread game species (roe deer [capreolus capreolus] and wild boar [sus scrofa]) to the high incidence of tbe in the czech republic, using the a ...	25409271
using the dfci gene index databases for biological discovery.	the dfci gene index web pages provide access to analyses of ests and gene sequences for nearly 114 species, as well as a number of resources derived from these. each species-specific database is presented using a common format with a home page. a variety of methods exist that allow users to search each species-specific database. methods implemented currently include nucleotide or protein sequence queries using wu-blast, text-based searches using various sequence identifiers, searches by gene, ti ...	20205187
evolution of air breathing: oxygen homeostasis and the transitions from water to land and sky.	life originated in anoxia, but many organisms came to depend upon oxygen for survival, independently evolving diverse respiratory systems for acquiring oxygen from the environment. ambient oxygen tension (po2) fluctuated through the ages in correlation with biodiversity and body size, enabling organisms to migrate from water to land and air and sometimes in the opposite direction. habitat expansion compels the use of different gas exchangers, for example, skin, gills, tracheae, lungs, and their ...	23720333
spotted fever group rickettsiae in questing ticks, central spain.		23763913
emerging protozoal pathogens in india: how prepared are we to face the threat?	emerging protozoal pathogens have become a major threat to human health. the number of protozoal pathogens causing human disease has been on the rise since the last two to three decades. significant increase in the number of immunocompromised people, increase in international travel, deforestation, and widespread urban dwellings are some of the factors contributing to this changing epidemiology of protozoal diseases. apart from naegleria and acanthamoeba, other free-living amoebae like balamuthi ...	23508066
arrestins: ubiquitous regulators of cellular signaling pathways.	in vertebrates, the arrestins are a family of four proteins that regulate the signaling and trafficking of hundreds of different g-protein-coupled receptors (gpcrs). arrestin homologs are also found in insects, protochordates and nematodes. fungi and protists have related proteins but do not have true arrestins. structural information is available only for free (unbound) vertebrate arrestins, and shows that the conserved overall fold is elongated and composed of two domains, with the core of eac ...	17020596
vasa genes: emerging roles in the germ line and in multipotent cells.	sexually reproducing metazoans establish a cell lineage during development that is ultimately dedicated to gamete production. work in a variety of animals suggests that a group of conserved molecular determinants act in this germ line maintenance and function. the most universal of these genes are vasa and vasa-like dead-box rna helicase genes. however, recent evidence indicates that vasa genes also function in other cell types, distinct from the germ line. here we evaluate our current understan ...	20586054
identification and characterisation of micrornas in young adults of angiostrongylus cantonensis via a deep-sequencing approach.	angiostrongylus cantonensis is an important causative agent of eosinophilic meningitis and eosinophilic meningoencephalitis in humans. micrornas (mirnas) are small non-coding rnas that participate in a wide range of biological processes. this study employed a deep-sequencing approach to study mirnas from young adults of a. cantonensis. based on 16,880,456 high-quality reads, 252 conserved mature mirnas including 10 antisense mirnas that belonging to 90 families, together with 10 antisense mirnas ...	24037191
invhogen: a database of homologous invertebrate genes.	classification of proteins into families of homologous sequences constitutes the basis of functional analysis or of evolutionary studies. here we present invertebrate homologous genes (invhogen), a database combining the available invertebrate protein genes from uniprot (consisting of swiss-prot and trembl) into gene families. for each family invhogen provides a multiple protein alignment, a maximum likelihood based phylogenetic tree and taxonomic information about the sequences. it is possible ...	16381884
molecular evolution, structure, and function of peroxidasins.	peroxidasins represent the subfamily 2 of the peroxidase-cyclooxygenase superfamily and are closely related to chordata peroxidases (subfamily 1) and peroxinectins (subfamily 3). they are multidomain proteins containing a heme peroxidase domain with high homology to human lactoperoxidase that mediates one- and two-electron oxidation reactions. additional domains of the secreted and glycosylated metalloproteins are type c-like immunoglobulin domains, typical leucine-rich repeats, as well as a von ...	22976969
a phylogenetic study of drosophila splicing assembly chaperone rnp-4f associated u4-/u6-snrna secondary structure.	the rnp-4f gene in drosophila melanogaster encodes nuclear protein rnp-4f. this encoded protein is represented by homologs in other eukaryotic species, where it has been shown to function as an intron splicing assembly factor. here, rnp-4f is believed to initially bind to a recognition sequence on u6-snrna, serving as a chaperone to facilitate its association with u4-snrna by intermolecular hydrogen bonding. rna conformations are a key factor in spliceosome function, so that elucidation of chang ...	25419488
pedf - a noninhibitory serpin with neurotrophic activity.	the pigment epithelium-derived factor (pedf) is a glycoprotein with a molecular weight of 50 kda belonging to the noninhibitory serpin family. it regulates several physiological processes, such as stimulation of retinoblastoma cell differentiation into neuron cells, and facilitation of the growth and viability of photoreceptor cells and neurons of the central nervous system. moreover, this factor protects neuronal cells against apoptosis. pedf is not only a neurotrophic factor, but also a natura ...	22649652
mutations and polymorphisms in gusb gene in mucopolysaccharidosis vii (sly syndrome).	mucopolysaccharidosis vii (mps vii; sly syndrome) is an autosomal recessive disorder caused by a deficiency of beta-glucuronidase (gus, ec 3.2.1.31; gusb). gus is required to degrade glycosaminoglycans (gags), including heparan sulfate (hs), dermatan sulfate (ds), and chondroitin-4,6-sulfate (cs). accumulation of undegraded gags in lysosomes of affected tissues leads to mental retardation, short stature, hepatosplenomegaly, bone dysplasia, and hydrops fetalis. we summarize information on the 49 ...	19224584
the peptidoglycan recognition proteins (pgrps).	peptidoglycan recognition proteins (pgrps) are innate immunity molecules present in insects, mollusks, echinoderms, and vertebrates, but not in nematodes or plants. pgrps have at least one carboxy-terminal pgrp domain (approximately 165 amino acids long), which is homologous to bacteriophage and bacterial type 2 amidases. insects have up to 19 pgrps, classified into short (s) and long (l) forms. the short forms are present in the hemolymph, cuticle, and fat-body cells, and sometimes in epidermal ...	16930467
edema and tetraparesis in a miniature pig after allogeneic hematopoietic cell transplantation.	a 3-mo-old, 12-kg, intact, miniature pig presented with severe neurologic signs on day 8 after hematopoietic cell transplantation. this pig had received an immunosuppressive regimen before transplantation that included an anticd3 immunotoxin for t-cell depletion, 100 cgy of total-body irradiation, and cyclosporine for 45 d. the pig began exhibiting erythematous lesions on posttransplantation day 7. he also demonstrated increased conscious proprioceptive deficits and recumbency but normal mentati ...	23043783
cloning of porcine platelet glycoprotein ibα and comparison with the human homolog.	glycoprotein ib-ix-v (gpib-ix-v) is a platelet adhesion receptor complex that initiates platelet aggregation. glycoprotein ibα (gpibα) is the central component of the gpib-ix-v complex, anchoring the complex to the cytoskeleton and harboring the binding site for von willebrand factor (vwf). previous studies suggest that the coagulation function in pigs differs from that in humans, especially with respect to the interaction between vwf and platelets. however, we have little knowledge about the fu ...	23043782
leptospira infection prevalence in small mammal host populations on three hawaiian islands.	we describe the geographic distribution and variation in host-pathogen specificity for leptospira-infected small mammals collected concurrently from three hawaiian islands over a period of 14 years: 1990-2003. four serogroups (icterohaemorrhagiae, ballum, sejroe, and australis) were identified from the 15,171 animals tested. serogroup prevalence differed across host species and islands (p < 0.0001 for each), but not across years. the host associations and biogeographic patterns of leptospira in ...	22855767
hepatitis e virus in pork production chain in czech republic, italy, and spain, 2010.	we evaluated the prevalence of hepatitis e virus (hev) in the pork production chain in czech republic, italy, and spain during 2010. a total of 337 fecal, liver, and meat samples from animals at slaughterhouses were tested for hev by real-time quantitative pcr. overall, hev was higher in italy (53%) and spain (39%) than in czech republic (7.5%). hev was detected most frequently in feces in italy (41%) and spain (39%) and in liver (5%) and meat (2.5%) in czech republic. of 313 sausages sampled at ...	22840221
contraceptive effect and potential side-effects of deslorelin acetate implants in rats (rattus norvegicus): preliminary observations.	during the last ten years, numerous species have been treated with deslorelin implants to induce contraception. the aims of the study were 1) to assess contraceptive efficacy of 4.7 mg subcutaneous deslorelin implants in rats, 2) to determine the latency of contraceptive effect, and 3) to determine potential side effects. three experimental females were implanted and their estrous cycle was studied by vaginal smear. two weeks after implantation, a male whose fertility was previously assessed wit ...	23277700
a phage tubulin assembles dynamic filaments by an atypical mechanism to center viral dna within the host cell.	tubulins are essential for the reproduction of many eukaryotic viruses, but historically, bacteriophage were assumed not to require a cytoskeleton. here, we identify a tubulin-like protein, phuz, from bacteriophage 201φ2-1 and show that it forms filaments in vivo and in vitro. the phuz structure has a conserved tubulin fold, with an unusual, extended c terminus that we demonstrate to be critical for polymerization in vitro and in vivo. longitudinal packing in the crystal lattice mimics packing o ...	22726436
comparative epigenomic annotation of regulatory dna.	despite the explosive growth of genomic data, functional annotation of regulatory sequences remains difficult. here, we introduce "comparative epigenomics"-interspecies comparison of dna and histone modifications-as an approach for annotation of the regulatory genome. we measured in human, mouse, and pig pluripotent stem cells the genomic distributions of cytosine methylation, h2a.z, h3k4me1/2/3, h3k9me3, h3k27me3, h3k27ac, h3k36me3, transcribed rnas, and p300, taf1, oct4, and nanog binding. we ...	22682255
use of ¹⁸f-fluorodeoxyglucose positron emission tomography-computed tomography in a miniature pig (sus scrofa domestica) with pneumonia.	a 1-y-old male miniature pig housed in our laboratory facility was evaluated for weight loss and rough coat condition. cbc results revealed neutrophilia. radiography of the thoracic area showed increased opacity throughout the thoracic cavity except for the right caudal lobe. ¹⁸f-labeled fluorodeoxyglucose positron emission tomography-computed tomography (fdg-pet-ct) revealed elevated standard uptake values in the area corresponding to the radiologic findings. follow-up thoracic radiography take ...	22776053
complete absence of the αgal xenoantigen and isoglobotrihexosylceramide in α1,3galactosyltransferase knock-out pigs.	anti-galα1,3galβ-r natural antibodies are responsible for hyperacute rejection in pig-to-primate xenotransplantation. although the generation of pigs lacking the α1,3galactosyltransferase (galt) has overcome hyperacute rejection, antibody-mediated rejection is still a problem. it is possible that other enzymes synthesize antigens similar to galα1,3gal epitopes that are recognized by xenoreactive antibodies. the glycosphingolipid isoglobotrihexosylceramide (igb₃) represents such a candidate expre ...	22702471
differential limb loading in miniature pigs (sus scrofa domesticus): a test of chondral modeling theory.	variation in mechanical loading is known to influence chondrogenesis during joint formation. however, the interaction among chondrocyte behavior and variation in activity patterns is incompletely understood, hindering our knowledge of limb ontogeny and function. here, the role of endurance exercise in the development of articular and physeal cartilage in the humeral head was examined in 14 miniature swine (sus scrofa domesticus). one group was subjected to graded treadmill running over a period ...	22496283
genetic architecture of body size in mammals.	much of the heritability for human stature is caused by mutations of small-to-medium effect. this is because detrimental pleiotropy restricts large-effect mutations to very low frequencies.	22546202
acute electrocardiographic st segment elevation may predict hypotension in a swine model of severe cyanide toxicity.	cyanide causes severe cardiac toxicity resulting in tachycardia, hypotension, and cardiac arrest; however, the clinical diagnosis can be difficult to make. a clinical finding that may precede or predict cyanide-induced hypotension may be a trigger to provide treatment earlier and improve outcomes in cyanide toxicity. our primary objective was to determine if there is a clinically significant change in st segment deviation measured on ecg during intravenous cyanide infusion that may predict cyani ...	22528590
novel reptilian uncoupling proteins: molecular evolution and gene expression during cold acclimation.	many animals upregulate metabolism in response to cold. uncoupling proteins (ucps) increase proton conductance across the mitochondrial membrane and can thereby alleviate damage from reactive oxygen species that may form as a result of metabolic upregulation. our aim in this study was to determine whether reptiles (crocodylus porosus) possess ucp genes. if so, we aimed to place reptilian ucp genes within a phylogenetic context and to determine whether the expression of ucp genes is increased dur ...	18230589
is chernobyl radiation really causing negative individual and population-level effects on barn swallows?		18042513
prey synchronize their vigilant behaviour with other group members.	it is generally assumed that an individual of a prey species can benefit from an increase in the number of its group's members by reducing its own investment in vigilance. but what behaviour should group members adopt in relation to both the risk of being preyed upon and the individual investment in vigilance? most models assume that individuals scan independently of one another. it is generally argued that it is more profitable for each group member owing to the cost that coordination of indivi ...	17341457
discrimination of infant isolation calls by female greater spear-nosed bats, phyllostomus hastatus.	in colonial species, recognition of offspring should be under strong selection. for accurate identification to occur offspring must emit individually distinctive signals and parents must be able to discriminate between signals. female greater spear-nosed bats (phyllostomus hastatus) roost in stable social groups and use infant vocalizations, termed isolation calls, to locate and identify their young. in this study, we investigate both the production and perception of isolation calls in p. hastat ...	18311319
the nested structure of a scavenger community.	scavenging is a widespread phenomenon in vertebrate communities which has rarely been accounted for, in spite of playing an essential role in food webs by enhancing nutrient recycling and community stability. most studies on scavenger assemblages have often presented an oversimplified view of carrion foraging. here, we applied for the first time the concept of nestedness to the study of a species-rich scavenger community in a forest ecosystem (białowieza primeval forest, poland) following a netw ...	17301021
mapping ancestral genomes with massive gene loss: a matrix sandwich problem.	ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of dna segments present in exactly one exemplar in every considered species. complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. it follows that some ancestors are inaccessible by these methods, such as t ...	21685079
rinq: reference-based indexing for network queries.	we consider the problem of similarity queries in biological network databases. given a database of networks, similarity query returns all the database networks whose similarity (i.e. alignment score) to a given query network is at least a specified similarity cutoff value. alignment of two networks is a very costly operation, which makes exhaustive comparison of all the database networks with a query impractical. to tackle this problem, we develop a novel indexing method, named rinq (reference-b ...	21685064
physiological roles of mitogen-activated-protein-kinase-activated p38-regulated/activated protein kinase.	mitogen-activated protein kinases (mapks) are a family of proteins that constitute signaling pathways involved in processes that control gene expression, cell division, cell survival, apoptosis, metabolism, differentiation and motility. the mapk pathways can be divided into conventional and atypical mapk pathways. the first group converts a signal into a cellular response through a relay of three consecutive phosphorylation events exerted by mapk kinase kinases, mapk kinase, and mapk. atypical m ...	21666810
the physiological costs of reproduction in small mammals.	life-history trade-offs between components of fitness arise because reproduction entails both gains and costs. costs of reproduction can be divided into ecological and physiological costs. the latter have been rarely studied yet are probably a dominant component of the effect. a deeper understanding of life-history evolution will only come about once these physiological costs are better understood. physiological costs may be direct or indirect. direct costs include the energy and nutrient demand ...	17686735
an engineering approach to modelling, decision support and control for sustainable systems.	engineering research and development contributes to the advance of sustainable agriculture both through innovative methods to manage and control processes, and through quantitative understanding of the operation of practical agricultural systems using decision models. this paper describes how an engineering approach, drawing on mathematical models of systems and processes, contributes new methods that support decision making at all levels from strategy and planning to tactics and real-time contr ...	17656345
mechanical influences on suture development and patency.	in addition to their role in skull growth, sutures are sites of flexibility between the more rigid bones. depending on the suture, predominant loading during life may be either tensile or compressive. loads are transmitted across sutures via collagenous fibers and a fluid-rich extracellular matrix and can be quasi-static (growth of neighboring tissues) or intermittent (mastication). the mechanical properties of sutures, while always viscoelastic, are therefore quite different for tensile versus ...	18391494
regioselectivity of catechol o-methyltransferase confers enhancement of catalytic activity.	catechol o-methyltransferase (comt) metabolizes catechol moieties by methylating a single hydroxyl group at the meta- or para- hydroxyl position. hydrophobic amino acids near the active site of comt influence the regioselectivity of this reaction. our sequence analysis highlights their importance by showing that these residues are highly conserved throughout evolution. reaction barriers calculated in the gas phase reveal a lower barrier during methylation at the meta- position, suggesting that t ...	21731105
characterization of the porcine testis-expressed gene 11 (tex11).	testis expressed gene 11 (tex11) is essential for meiosis and male fertility in the mouse. currently, little is known about the control of spermatogenesis in non-rodent animal models such as pigs. here, we characterized the sequence and expression profile of the porcine tex11 gene. we showed that the porcine tex11 is an x-linked gene that is exclusively expressed in germ cells in the adult pig testis. the expression of porcine tex11 is correlated with the onset of meiosis and the expression patt ...	22319663
measurement of macrophage growth and differentiation.	this unit provides protocols for measuring the abundance and growth of macrophage precursors in agar cultures and the proliferation of isolated mature macrophages in vitro, by either direct cell counting or by dna measurement. methods for the immunohistochemical identification of macrophages and the determination of their proliferative status in vivo by immunofluorescence are also included. it also describes methods for characterization of macrophage differentiation through the immunofluorescenc ...	21400680
activation of pparγ2 by pparγ1 through a functional ppre in transdifferentiation of myoblasts to adipocytes induced by epa.	pparγ and wnt signaling are central positive and negative regulators of adipogenesis, respectively. here we identified that, eicosapentaenoic acid (epa) could effectively induce the transdifferentiation of myoblasts into adipocytes through modulation of both pparγ expression and wnt signaling. during the early stage of transdifferentiation, epa activates pparδ and pparγ1, which in turn targets β-catenin to degradation and down-regulates wnt/β-catenin signaling, such that the myogenic fate of myo ...	25892270
ccm2-ccm3 interaction stabilizes their protein expression and permits endothelial network formation.	mutations in the essential adaptor proteins ccm2 or ccm3 lead to cerebral cavernous malformations (ccm), vascular lesions that most frequently occur in the brain and are strongly associated with hemorrhagic stroke, seizures, and other neurological disorders. ccm2 binds ccm3, but the molecular basis of this interaction, and its functional significance, have not been elucidated. here, we used x-ray crystallography and structure-guided mutagenesis to show that an α-helical ld-like motif within ccm2 ...	25825518
the advantage of objects over images in discrimination and reversal learning by kea, nestor notabilis.	studies investigating the same paradigm but employing different methods are often directly compared in the literature. one such paradigm used to assess behavioural flexibility in animals is reversal learning. commonly, these studies require individuals to learn the reward contingency of either solid objects presented on the ground or images presented on a touchscreen. once learned, these contingencies are swapped. researchers often refer to trials required to reach learning criteria from differe ...	25745190
macracanthorhynchus hirudinaceus eggs in canine coprolite from the sasanian era in iran (4(th)/5(th) century ce).	present paper is the second publication introducing the paleoparasitological findings from animal coprolites obtained from archeological site of chehrabad salt mine in northwestern iran. the current archeological site is located in northwest of iran, dated to the sassanian era (4(th)/5(th) century ce). in the summer 2012 the carnivore coprolite was obtained within the layers in the mine and were thoroughly analyzed for parasites using tsp rehydration technique. eggs of 0 were successfully retrie ...	26246822
determination of alkali-sensing parts of the insulin receptor-related receptor using the bioinformatic approach.	irr (insulin receptor-related receptor) is a receptor tyrosine kinase belonging to the insulin receptor family, which also includes insulin receptor and igf-ir receptor. we have previously shown that irr is activated by extracellular fluid with ph > 7.9 and regulates excess alkali excretion in the body. we performed a bioinformatic analysis of the ph-sensitive potential of all three members of the insulin receptor family of various animal species (from frog to man) and their chimeras with swappi ...	26085948
toxoplasmosis in mexico: epidemiological situation in humans and animals.	toxoplasmosis is a parasitic disease widely distributed throughout the world, infecting a wide variety of animal species including humans. in mexico, this parasite has been detected in different parts of the country, particularly in the tropical areas where the parasite can remain infective for long periods of time due to the environmental conditions (i.e. high temperature and humidity over the whole year). several epidemiological studies have been conducted in both human and animal populations, ...	25923887
differential expression of immunologic proteins in gingiva after socket preservation in mini pigs.	during healing following tooth extraction, inflammation and the immune response within the extraction socket are related to bone resorption.	26018311
gene expression profiling of myc-driven tumor signatures in porcine liver stem cells by transcriptome sequencing.	to identify the genes induced and regulated by the myc protein in generating tumors from liver stem cells.	25717234
multiple drivers of decline in the global status of freshwater crayfish (decapoda: astacidea).	rates of biodiversity loss are higher in freshwater ecosystems than in most terrestrial or marine ecosystems, making freshwater conservation a priority. however, prioritization methods are impeded by insufficient knowledge on the distribution and conservation status of freshwater taxa, particularly invertebrates. we evaluated the extinction risk of the world's 590 freshwater crayfish species using the iucn categories and criteria and found 32% of all species are threatened with extinction. the l ...	25561679
conserving the functional and phylogenetic trees of life of european tetrapods.	protected areas (pas) are pivotal tools for biodiversity conservation on the earth. europe has had an extensive protection system since natura 2000 areas were created in parallel with traditional parks and reserves. however, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. using high-resolution distribution data of all european tetrapods together with dated mole ...	25561666
managing wildlife populations with uncertainty: cormorants phalacrocorax carbo.	managing wildlife populations for conservation, control or harvesting involves uncertainty. nevertheless, decisions need to be made based on the available evidence. the two main sources of uncertainty in population modelling are parameter estimates and structural uncertainty. structural uncertainty in models is not included as often as parameter uncertainty.we present an approach where parameter and structural uncertainty (strength of density dependence) is included within a model, using the ove ...	19536342
neocartilage integration in temporomandibular joint discs: physical and enzymatic methods.	integration of engineered musculoskeletal tissues with adjacent native tissues presents a significant challenge to the field. specifically, the avascularity and low cellularity of cartilage elicit the need for additional efforts in improving integration of neocartilage within native cartilage. self-assembled neocartilage holds significant potential in replacing degenerated cartilage, though its stabilization and integration in native cartilage require further efforts. physical and enzymatic stab ...	25519993
cross-species fertilization: the hamster egg receptor, juno, binds the human sperm ligand, izumo1.	fertilization is the culminating event in sexual reproduction and requires the recognition and fusion of the haploid sperm and egg to form a new diploid organism. specificity in these recognition events is one reason why sperm and eggs from different species are not normally compatible. one notable exception is the unusual ability of zona-free eggs from the syrian golden hamster (mesocricetus auratus) to recognize and fuse with human sperm, a phenomenon that has been exploited to assess sperm qu ...	25533103
assessment of the role of sutures in a lizard skull: a computer modelling study.	sutures form an integral part of the functioning skull, but their role has long been debated among vertebrate morphologists and palaeontologists. furthermore, the relationship between typical skull sutures, and those involved in cranial kinesis, is poorly understood. in a series of computational modelling studies, complex loading conditions obtained through multibody dynamics analysis were imposed on a finite element model of the skull of uromastyx hardwickii, an akinetic herbivorous lizard. a f ...	18765341
aggressive monopolization of mobile carers by young of a cooperative breeder.	competition between young of the same brood or litter is of particular interest in the fields of behavioural and evolutionary ecology, because the competing individuals are likely to be closely related, where evolutionary theory predicts a greater degree of cooperation. studies of cooperative breeding species typically concentrate on who contributes care to rearing young, and assume a passive role of the young. relatively, little attention has been devoted to considering how intralitter competit ...	18647720
porcine liver carboxylesterase requires polyisoprenylation for high affinity binding to cysteinyl substrates.	the polyisoprenylation pathway enzymes have been the focus of numerous studies to better understand the roles of polyisoprenylated proteins in eukaryotic cells and to identify novel targets against diseases such as cancer. the final step of the pathway is a reversible reaction catalyzed by isoprenyl carboxylmethyl transferase (icmt) whose products are then hydrolyzed by polyisoprenylated methylated protein methyl esterase (pmpmease). unlike the other pathway enzymes, the esterase has received li ...	20664805
evolutionary comparison provides evidence for pathogenicity of rmrp mutations.	cartilage-hair hypoplasia (chh) is a pleiotropic disease caused by recessive mutations in the rmrp gene that result in a wide spectrum of manifestations including short stature, sparse hair, metaphyseal dysplasia, anemia, immune deficiency, and increased incidence of cancer. molecular diagnosis of chh has implications for management, prognosis, follow-up, and genetic counseling of affected patients and their families. we report 20 novel mutations in 36 patients with chh and describe the associat ...	16244706
cloning and characterization of the glucosidase ii alpha subunit gene of trichoderma reesei: a frameshift mutation results in the aberrant glycosylation profile of the hypercellulolytic strain rut-c30.	we describe isolation and characterization of the gene encoding the glucosidase ii alpha subunit (giialpha) of the industrially important fungus trichoderma reesei. this subunit is the catalytic part of the glucosidase ii heterodimeric enzyme involved in the structural modification within the endoplasmic reticulum (er) of n-linked oligosaccharides present on glycoproteins. the gene encoding giialpha (gls2alpha) in the hypercellulolytic strain rut-c30 contains a frameshift mutation resulting in a ...	15932985
sperm competition and the evolution of male reproductive anatomy in rodents.	sperm competition is a pervasive selective force in evolution, shaping reproductive anatomy, physiology and behaviour. here, we present comparative evidence that varying sperm competition levels account for variation in the male reproductive anatomy of rodents, the largest and most diverse mammalian order. we focus on the sperm-producing testes and the accessory reproductive glands, which produce the seminal fluid fraction of the ejaculate. we demonstrate a positive association between relative ...	16024351
microrna: biological and computational perspective.	micrornas (mirnas) are endogenously expressed non-coding rnas of 20-24 nucleotides, which post-transcriptionally regulate gene expression in plants and animals. recently it has been recognized that mirnas comprise one of the abundant gene families in multicellular species, and their regulatory functions in various biological processes are widely spread. there has been a surge in the research activities in this field in the past few years. from the very beginning, computational methods have been ...	16393143
lz complexity distance of dna sequences and its application in phylogenetic tree reconstruction.	dna sequences can be treated as finite-length symbol strings over a four-letter alphabet (a, c, t, g). as a universal and computable complexity measure, lz complexity is valid to describe the complexity of dna sequences. in this study, a concept of conditional lz complexity between two sequences is proposed according to the principle of lz complexity measure. an lz complexity distance metric between two nonnull sequences is defined by utilizing conditional lz complexity. based on lz complexity d ...	16689687
nuclear dna amounts in angiosperms: progress, problems and prospects.	the nuclear dna amount in an unreplicated haploid chromosome complement (1c-value) is a key diversity character with many uses. angiosperm c-values have been listed for reference purposes since 1976, and pooled in an electronic database since 1997 (http://www.kew.org/cval/homepage). such lists are cited frequently and provide data for many comparative studies. the last compilation was published in 2000, so a further supplementary list is timely to monitor progress against targets set at the firs ...	15596457
comparability of whole-blood and plasma clozapine and norclozapine concentrations.		12848787
microtubule-kinesin interface mutants reveal a site critical for communication.	strict coordination of the two motor domains of kinesin is required for driving the processive movement of organelles along microtubules. glutamate 164 of the kinesin heavy chain was shown to be critical for kinesin function through in vivo genetics in drosophila melanogaster. the mutant motor e164k exhibited reduced steady-state atpase activity and higher affinity for both atp and microtubules. moreover, an alanine substitution at this position (e164a) caused similar defects. it became stalled ...	15005614
intranasal naltrexone and atipamezole for reversal of white-tailed deer immobilized with carfentanil and medetomidine.	carfentanil and medetomidine were used to immobilize 8 captive female white-tailed deer (odocoileus virginianus) using mean dosages [+/- standard deviation (s)] of 14.2 +/- 1.11 microg/kg carfentanil and 17.8 +/- 2.03 microg/kg of medetomidine. deer were reversed by intranasally or intramuscularly administered naltrexone and atipamezole. dosages of carfentanil and medetomidine proved reliable for immobilization of most, but not all deer, with a mean induction time of 13.3 +/- 3.13 min. effective ...	20676292
the myh7 p.r787h mutation causes hypertrophic cardiomyopathy in two unrelated families.	familial hypertrophic cardiomyopathy (fhc) is a mendelian disorder usually caused by mutations in any one of more than 12 genes, most of which encode sarcomere proteins. the disease exhibits extensive genetic heterogeneity, and it is important to identify mutations that result in adverse symptoms and/or lethality in affected individuals. an analysis of disease-causing mutations has been initiated in the indian population to determine prevalent mutations.	20664766
alone in the crowd: the structure and spread of loneliness in a large social network.	the discrepancy between an individual's loneliness and the number of connections in a social network is well documented, yet little is known about the placement of loneliness within, or the spread of loneliness through, social networks. the authors use network linkage data from the population-based framingham heart study to trace the topography of loneliness in people's social networks and the path through which loneliness spreads through these networks. results indicated that loneliness occurs ...	19968414
horner syndrome after carotid sheath surgery in a pig: anatomic study of cervical sympathetic chain.	in an experimental model, iatrogenic horner syndrome developed after a right carotid sheath surgery in an infant pig (sus scrofa). horner syndrome is a classic clinical triad consisting of ipsilateral eyelid ptosis, pupil miosis, and facial anhydrosis. this syndrome results from cervical sympathetic chain (csc) paresis and usually is acquired in humans. to determine whether the development of horner syndrome in this situation could be attributed to pig anatomy, we compared the anatomy of the csc ...	22330354
surgical porcine myocardial infarction model through permanent coronary occlusion.	using domestic pigs as an animal model, we here validated a reproducible and standardized myocardial infarction (mi) surgical model, to achieve the largest possible infarct extent with the lowest morbidity and mortality. to this end, we included several anesthetic and perisurgical precautions to minimize surgical complications. mortality and morbidity rates were compared among groups of pigs that underwent permanent occlusion at different locations of either the left circumflex or left anterior ...	22330353
analysis of correlated gene expression data on ordered categories.	a bootstrap based methodology is introduced for analyzing repeated measures/longitudinal microarray gene expression data over ordered categories. the proposed non-parametric procedure uses order-restricted inference to compare gene expressions among ordered experimental conditions. the null distribution for determining significance is derived by suitably bootstrapping the residuals. the procedure addresses two potential sources of correlation in the data, namely, (a) correlations among genes wit ...	21998487
the historical biogeography of mammalia.	palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. ancestral reconstruction methods are divided into parsimony versus bayesian/likelihood approaches. we compared ...	21807730
primary hyperoxaluria type iii gene hoga1 (formerly dhdpsl) as a possible risk factor for idiopathic calcium oxalate urolithiasis.	primary hyperoxaluria types i and ii (phi and phii) are rare monogenic causes of hyperoxaluria and calcium oxalate urolithiasis. recently, we described type iii, due to mutations in hoga1 (formerly dhdpsl), hypothesized to cause a gain of mitochondrial 4-hydroxy-2-oxoglutarate aldolase activity, resulting in excess oxalate.	21896830
antioxidant capacity develops with maturation in the deep-diving hooded seal.	maturation in hooded seals is characterized by the rapid development of their physiological diving capacity and is accompanied by increases in oxidant production but not oxidative damage. to test the hypothesis that the antioxidant system of hooded seals develops as they transition from a terrestrial to an aquatic environment, we obtained the complete cdna sequence that encodes the nf-e2-related factor 2 (nrf2), a central regulator of the antioxidant response, and compared nrf2 mrna and protein ...	21832133
extension of a three-helix bundle domain of myosin vi and key role of calmodulins.	the molecular motor protein myosin vi moves toward the minus-end of actin filaments with a step size of 30-36 nm. such large step size either drastically limits the degree of complex formation between dimer subunits to leave enough length for the lever arms, or requires an extension of the lever arms' crystallographically observed structure. recent experimental work proposed that myosin vi dimerization triggers the unfolding of the protein's proximal tail domain which could drive the needed leve ...	21689530
a rab32-dependent pathway contributes to salmonella typhi host restriction.	unlike other salmonellae, the intracellular bacterial human pathogen salmonella typhi exhibits strict host specificity. the molecular bases for this restriction are unknown. here we found that the expression of a single type iii secretion system effector protein from broad-host salmonella typhimurium allowed salmonella typhi to survive and replicate within macrophages and tissues from mice, a nonpermissive host. this effector proteolytically targeted rab32, which controls traffic to lysosome-rel ...	23162001
[the genus tunga jarocki, 1838 (siphonaptera: tungidae). i: taxonomy, phylogeny, ecology and pathogenicity].	this is the first review of the taxonomy and geographical range of the 12 known species of the genus tunga. their biology and pathogenic roles are considered, with particular emphasis on their phylogeny, chorology, phenology, sex-ratio, and dermecos.	23193514
analyses of pig genomes provide insight into porcine demography and evolution.	for 10,000 years pigs and humans have shared a close and complex relationship. from domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. here we present the assembly and analysis of the genome sequence of a female domestic duroc pig (sus scrofa) and a comparison with the genomes of wild and domestic pigs from europe and asia. wild pigs emerged in south east asia and subsequently spread across eurasia. our results reveal a deep phylogenetic split between eu ...	23151582
who wants food? individual characteristics in raven yells.	discriminating between different individuals is considered as prerequisite for any forms of social knowledge. in birds, discriminating between conspecifics based on individual characteristics has been tested mainly in the auditory domain with territorial calls and songs for neighbour and kin discrimination but little is known about discriminating between signallers in food calls. ravens utilize a large set of calls and show individually distinctive call repertoires. moreover, they show advanced ...	23162139
clinical islet xenotransplantation: how close are we?		23172951
a whole genome association study on meat quality traits using high density snp chips in a cross between korean native pig and landrace.	a whole genome association (wga) study was performed to detect significant polymorphisms for meat quality traits in an f2 cross population (n = 478) that were generated with korean native pig sires and landrace dams in national livestock research institute, songwhan, korea. the animals were genotyped using illumina porcine 60k snp beadchips, in which a set of 46,865 snps were available for the wga analyses on ten carcass quality traits; live weight, crude protein, crude lipids, crude ash, water ...	25049513
protein profile in corpus luteum during pregnancy in korean native cows.	steroidogenesis requires coordination of the anabolic and catabolic pathways of lipid metabolism, but the profile of proteins associated with progesterone synthesis in cyclic and pregnant corpus luteum (cl) is not well-known in cattle. in experiment 1, plasma progesterone level was monitored in cyclic cows (n = 5) and pregnant cows (n = 6; until d-90). a significant decline in the plasma progesterone level occurred at d-19 of cyclic cows. progesterone level in abbatoir-derived luteal tissues was ...	25049514
microrna mir-98 inhibits tumor angiogenesis and invasion by targeting activin receptor-like kinase-4 and matrix metalloproteinase-11.	angiogenesis and invasion are essential processes for solid tumor growth and dissemination. the tumor development process can be dependent on the activation of a series of signaling pathways, including growth factor-activated pathways. micrornas have been shown to be critical for tumorigenesis, but their roles in cancer angiogenesis, invasion and other signaling pathways important for tumor development are still unclear in the context of tumor biology. we investigated the role of microrna mir-98 ...	23211491