[A database of available DNA tests in the dog]

For genetic counseling this report presents a database of canine hereditary diseases and coat color characteristics, which have been solved on the molecular level.The database facilitates access to appropriate diagnostic laboratories for specific phenotypes. The recent decoding of the dog genome provides ideal conditions for the molecular genetic analysis of hereditary traits and diseases. Therefore the authors would like to encourage veterinary surgeons in particular to report cases to assist the molecular analysis of further phenotypes in future.

Molecular characterization of the equine collagen, type IX, alpha 2 (COL9A2) gene on horse chromosome 2p16-->p15

The mammalian collagen, type IX, alpha 2 gene (COL9A2) encodes the alpha-2 chain of type IX collagen and is located on horse chromosome 2p16-->p14 harbouring a quantitative trait locus for osteochondrosis. We isolated a bacterial artificial chromosome (BAC) clone containing the equine COL9A2 gene and determined the complete genomic sequence of this gene. Cloning and characterization of equine COL9A2 revealed that the equine gene consists of 32 exons spanning approximately 15 kb. The COL9A2 transcript encodes a single protein of 688 amino acids. Thirty two single nucleotide polymorphisms (SNPs) equally distributed in the gene were detected in a mutation scan of eight unrelated Hanoverian warmblood stallions, including one SNP that affects the amino acid sequence of COL9A2. Comparative analyses between horse, human, mouse and rat indicate that the chromosomal location of equine COL9A2 is in agreement with known chromosomal synteny relationships. The comparison of the gene structure and transcript revealed a high degree of conservation towards the other mammalian COL9A2 genes. We chose three informative SNPs for association and linkage disequilibrium tests in three to five paternal half-sib families of Hanoverian warmblood horses consisting of 44 to 75 genotyped animals. The test statistics did not reach the significance threshold of 5% and so we could not show an association of COL9A2 with equine osteochondrosis.

Molecular diagnostics for gonorrhoea: implications for antimicrobial resistance and the threat of untreatable gonorrhoea

This Essay from Nicola Low and colleagues discusses the importance of the nucleic acid amplification tests for rapid detection of N. gonorrhoeae and its resistance determinants, as well as the importance of ensuring their rational use, as priorities for controlling both gonorrhoea and antimicrobial resistance. Please see later in the article for the Editors' Summary.

Molecular epidemiology of vancomycin-resistant Enterococcus faecium: a prospective, multicenter study in South American hospitals.

Enterococcus faecium has emerged as an important nosocomial pathogen worldwide, and this trend has been associated with the dissemination of a genetic lineage designated clonal cluster 17 (CC17). Enterococcal isolates were collected prospectively (2006 to 2008) from 32 hospitals in Colombia, Ecuador, Perú, and Venezuela and subjected to antimicrobial susceptibility testing. Genotyping was performed with all vancomycin-resistant E. faecium (VREfm) isolates by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. All VREfm isolates were evaluated for the presence of 16 putative virulence genes (14 fms genes, the esp gene of E. faecium [espEfm], and the hyl gene of E. faecium [hylEfm]) and plasmids carrying the fms20-fms21 (pilA), hylEfm, and vanA genes. Of 723 enterococcal isolates recovered, E. faecalis was the most common (78%). Vancomycin resistance was detected in 6% of the isolates (74% of which were E. faecium). Eleven distinct PFGE types were found among the VREfm isolates, with most belonging to sequence types 412 and 18. The ebpAEfm-ebpBEfm-ebpCEfm (pilB) and fms11-fms19-fms16 clusters were detected in all VREfm isolates from the region, whereas espEfm and hylEfm were detected in 69% and 23% of the isolates, respectively. The fms20-fms21 (pilA) cluster, which encodes a putative pilus-like protein, was found on plasmids from almost all VREfm isolates and was sometimes found to coexist with hylEfm and the vanA gene cluster. The population genetics of VREfm in South America appear to resemble those of such strains in the United States in the early years of the CC17 epidemic. The overwhelming presence of plasmids encoding putative virulence factors and vanA genes suggests that E. faecium from the CC17 genogroup may disseminate in the region in the coming years.

Liquid lead and Lithium. A Comprehensive molecular dynamics study

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. One of the main issues in these programs is the problem of liquid metals breeder blanket behavior. Structural material of the blanket should meet high requirements because of extreme operating conditions. Therefore the knowledge of eutectic properties like optimal composition, physical and thermodynamic behavior or diffusion coefficients of Tritium are extremely necessary for current designs. In particular, the knowledge of the function linking the tritium concentration dissolved in liquid materials with the tritium partial pressure at a liquid/gas interface in equilibrium, CT=f(PT), is of basic importance because it directly impacts all functional properties of a blanket determining: tritium inventory, tritium permeation rate and tritium extraction efficiency. Nowadays, understanding the structure and behavior of this compound is a real goal in fusion engineering and materials science. Simulations of liquids can provide much information to the community; not only supplementing experimental data, but providing new tests of theories and ideas, making specific predictions that require experimental tests, and ultimately helping to lead to the deeper understanding and better predictive behavior.

Molecular mechanisms of cocaine reward: Combined dopamine and serotonin transporter knockouts eliminate cocaine place preference

Cocaine blocks uptake by neuronal plasma membrane transporters for dopamine (DAT), serotonin (SERT), and norepinephrine (NET). Cocaine reward/reinforcement has been linked to actions at DAT or to blockade of SERT. However, knockouts of neither DAT, SERT, or NET reduce cocaine reward/reinforcement, leaving substantial uncertainty about cocaine's molecular mechanisms for reward. Conceivably, the molecular bases of cocaine reward might display sufficient redundancy that either DAT or SERT might be able to mediate cocaine reward in the other's absence. To test this hypothesis, we examined double knockout mice with deletions of one or both copies of both the DAT and SERT genes. These mice display viability, weight gain, histologic features, neurochemical parameters, and baseline behavioral features that allow tests of cocaine influences. Mice with even a single wild-type DAT gene copy and no SERT copies retain cocaine reward/reinforcement, as measured by conditioned place-preference testing. However, mice with no DAT and either no or one SERT gene copy display no preference for places where they have previously received cocaine. The serotonin dependence of cocaine reward in DAT knockout mice is thus confirmed by the elimination of cocaine place preference in DAT/SERT double knockout mice. These results provide insights into the brain molecular targets necessary for cocaine reward in knockout mice that develop in their absence and suggest novel strategies for anticocaine medication development.

Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination.

The life history of Candida albicans presents an enigma: this species is thought to be exclusively asexual, yet strains show extensive phenotypic variation. To address the population genetics of C. albicans, we developed a genetic typing method for codominant single-locus markers by screening randomly amplified DNA for single-strand conformation polymorphisms. DNA fragments amplified by arbitrary primers were initially screened for single-strand conformation polymorphisms and later sequenced using locus-specific primers. A total of 12 single base mutations and insertions were detected from six out of eight PCR fragments. Patterns of sequence-level polymorphism observed for individual strains detected considerable heterozygosity at the DNA sequence level, supporting the view that most C. albicans strains are diploid. Population genetic analyses of 52 natural isolates from Duke University Medical Center provide evidence for both clonality and recombination in C. albicans. Evidence for clonality is supported by the presence of several overrepresented genotypes, as well as by deviation of genotypic frequencies from random (Hardy-Weinberg) expectations. However, tests for nonrandom association of alleles across loci reveal less evidence for linkage disequilibrium than expected for strictly clonal populations. Although C. albicans populations are primarily clonal, evidence for recombination suggests that sexual reproduction or some other form of genetic exchange occurs in this species.

QSAR e dinâmica molecular no estudo de sistemas biomoleculares: predição da atividade biológica de antagonistas do receptor sigma-1 e simulações de bicamadas lipídicas

Diferentes abordagens teóricas têm sido utilizadas em estudos de sistemas biomoleculares com o objetivo de contribuir com o tratamento de diversas doenças. Para a dor neuropática, por exemplo, o estudo de compostos que interagem com o receptor sigma-1 (Sig-1R) pode elucidar os principais fatores associados à atividade biológica dos mesmos. Nesse propósito, estudos de Relações Quantitativas Estrutura-Atividade (QSAR) utilizando os métodos de regressão por Mínimos Quadrados Parciais (PLS) e Rede Neural Artificial (ANN) foram aplicados a 64 antagonistas do Sig-1R pertencentes à classe de 1-arilpirazóis. Modelos PLS e ANN foram utilizados com o objetivo de descrever comportamentos lineares e não lineares, respectivamente, entre um conjunto de descritores e a atividade biológica dos compostos selecionados. O modelo PLS foi obtido com 51 compostos no conjunto treinamento e 13 compostos no conjunto teste (r² = 0,768, q² = 0,684 e r²teste = 0,785). Testes de leave-N-out, randomização da atividade biológica e detecção de outliers confirmaram a robustez e estabilidade dos modelos e mostraram que os mesmos não foram obtidos por correlações ao acaso. Modelos também foram gerados a partir da Rede Neural Artificial Perceptron de Multicamadas (MLP-ANN), sendo que a arquitetura 6-12-1, treinada com as funções de transferência tansig-tansig, apresentou a melhor resposta para a predição da atividade biológica dos compostos (r²treinamento = 0,891, r²validação = 0,852 e r²teste = 0,793). Outra abordagem foi utilizada para simular o ambiente de membranas sinápticas utilizando bicamadas lipídicas compostas por POPC, DOPE, POPS e colesterol. Os estudos de dinâmica molecular desenvolvidos mostraram que altas concentrações de colesterol induzem redução da área por lipídeo e difusão lateral e aumento na espessura da membrana e nos valores de parâmetro de ordem causados pelo ordenamento das cadeias acil dos fosfolipídeos. As bicamadas lipídicas obtidas podem ser usadas para simular interações entre lipídeos e pequenas moléculas ou proteínas contribuindo para as pesquisas associadas a doenças como Alzheimer e Parkinson. As abordagens usadas nessa tese são essenciais para o desenvolvimento de novas pesquisas em Química Medicinal Computacional.

Importância clínica do estudo molecular de alergénicos alimentares

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Concentrations and isotopic compositions of low molecular weight hydrocarbons in hydrothermal fluids from ODP Field, Middle Valley, northern Juan de Fuca Ridge

The presence of sedimentary organic matter blanketing midocean ridge crests has a potentially strong impact on metal transport in hydrothermal vent fluids. To constrain the role of organic matter in metal mobility during hydrothermal sediment alteration, we reacted organic-rich diatomaceous ooze from Guaymas Basin, Gulf of California, and organic-poor hemipelagic mud from Middle Valley, northern Juan de Fuca Ridge, with seawater and a Na-Ca-K-Cl fluid of seawater chlorinity, at 275° to 400°C, 350 to 500 bars, and initial fluid: sediment mass ratios ranging from 1.6 to 9.8. Reaction of these fluids with both sediment types released CO2 and high concentrations of ore-forming metals (Fe, Mn, Zn, Pb) to solution. Relatively low concentrations of Cu were observed in solution and likely reflect the reducing conditions that resulted from the presence of sedimentary organic matter. Both the concentrations of CO2 and dissolved metals were lower in fluids reacted with Middle Valley sediment compared with aqueous concentrations in fluids reacted with Guaymas Basin sediment. During alteration of both sediment types, metal concentrations varied strongly as a function of temperature, increasing by up to an order of magnitude over the 75°C range of each experiment. Major element fluid chemistry and observed alteration assemblages suggest that during hydrothermal alteration of organic-lean sediment from Middle Valley a feldspar-quartz-illite mineral assemblage buffered in situ pH. In contrast, data from the experimental alteration of organic-rich Guaymas Basin sediment suggest that a calcite-plagioclase-quartz assemblage regulated in situ pH. Fluid speciation calculations suggest that in situ pH during Guaymas Basin sediment alteration was lower than during alteration of Middle Valley sediment and accounts for the substantially greater metal mobility at a given temperature and pressure during the former experiment. Comparison of our results with the results of basalt alteration experiments indicate that except for Cu, hydrothermal sediment alteration results in equal or greater concentrations of ore-forming metals at a given temperature and pressure. Accordingly, the presence of ore-forming metals in fluids currently venting from sediment-covered hydrothermal systems at concentrations substantially lower than in fluids from bare-rock systems may reflect chemical reequilibration during subsurface cooling within the sediment pile.

On a resampling approach for tests on the number of clusters with mixture model-based clustering of tissue samples

We consider the problem of assessing the number of clusters in a limited number of tissue samples containing gene expressions for possibly several thousands of genes. It is proposed to use a normal mixture model-based approach to the clustering of the tissue samples. One advantage of this approach is that the question on the number of clusters in the data can be formulated in terms of a test on the smallest number of components in the mixture model compatible with the data. This test can be carried out on the basis of the likelihood ratio test statistic, using resampling to assess its null distribution. The effectiveness of this approach is demonstrated on simulated data and on some microarray datasets, as considered previously in the bioinformatics literature. (C) 2004 Elsevier Inc. All rights reserved.

Greenberger-Horne-Zeilinger-type and W-type entangled coherent states: Generation and Bell-type inequality tests without photon counting

We study Greenberger-Horne-Zeilinger-type (GHZ-type) and W-type three-mode entangled coherent states. Both types of entangled coherent states violate Mermin's version of the Bell inequality with threshold photon detection (i.e., without photon counting). Such an experiment can be performed using linear optics elements and threshold detectors with significant Bell violations for GHZ-type entangled coherent states. However, to demonstrate Bell-type inequality violations for W-type entangled coherent states, additional nonlinear interactions are needed. We also propose an optical scheme to generate W-type entangled coherent states in free-traveling optical fields. The required resources for the generation are a single-photon source, a coherent state source, beam splitters, phase shifters, photodetectors, and Kerr nonlinearities. Our scheme does not necessarily require strong Kerr nonlinear interactions; i.e., weak nonlinearities can be used for the generation of the W-type entangled coherent states. Furthermore, it is also robust against inefficiencies of the single-photon source and the photon detectors.

Molecular discrimination of taeniid cestodes :

DNA approaches are now being used routinely for accurate identification of Echinococcus and Taenia species, subspecies and strains, and in molecular epidemiological surveys of echinococcosis/taeniasis in different geographical settings and host assemblages. The publication of the complete sequences of the mitochondrial (int) genomes of E. granulosus, E. multilocularis, T solium and Asian Taenia, and the availability of mtDNA sequences for a number of other taeniid genotypes, has provided additional genetic information that can be used for more in depth phylogenetic and taxonomic studies of these parasites. This very rich sequence information has provided a solid molecular basis, along with a range of different biological, epidemiological, biochemical and other molecular-genetic criteria, for revising the taxonomy of the genus Echinococcus and for estimating the evolutionary time of divergence of the various taxa. Furthermore, the accumulating genetic data has allowed the development of PCR-based tests for unambiguous identification of Echinococcus eggs in the faeces of definitive hosts and in the environment. Molecular phylogenies derived from mtDNA sequence comparisons of geographically distributed samples of T solium provide molecular evidence for two genotypes, one being restricted to Asia, with the other occurring in Africa and America. Whether the two genetic forms of T solium differ in important phenotypic characteristics remains to be determined. As well, minor DNA sequence differences have been reported between isolates of T saginata and Asian Taenia. There has been considerable discussion over a number of years regarding the taxonomic position of Asian Taenia and whether it should be regarded as a genotype, strain, subspecies or sister species of T saginata. The available molecular genetic data do not support independent species status for Asian Taenia and T saginata. What is in agreement is that both taxa are closely related to each other but distantly related to T solium. This is important in public health terms as it predicts that cysticercosis in humans attributable to Asian Taenia does not occur, because cysticercosis is unknown in T saginata. (C) 2005 Elsevier Ireland Ltd. All rights reserved.