Genomic characteristics of natural recombinant infectious bronchitis viruses isolated in Korea / 대한수의학회지

Two infectious bronchitis virus (IBV) K046-12 and K047-12 strains were isolated and the nearly complete genomes of them were sequenced. Sequence comparisons showed that the K046-12 genome was most similar to Korean IBV strains, and the K047-12 genome was most similar to QX-like IBV strains. Phylogenetic analysis showed that nearly all K046-12 and most K046-12 genes were placed in the same cluster as Korean IBV isolates, but the S1 region was placed in the same cluster as Mass-type IBVs. For K047-12, nearly all K047-12 and most K047-12 genes were located in the same cluster as QX-like IBVs, but the M region was located in the same cluster as Korean IBV isolates with K047-12. Recombination analysis confirmed that K046-12 is a recombinant strain with the primary parental sequence derived from Korean IBVs and minor parental sequence derived from Mass-type IBV, and K047-12 is a recombinant strain with the major parental sequence derived from QX-IBV and minor parental sequence derived from Korean IBVs. This study showed that new IBV recombinants are constantly generated among various IBVs, including those used for vaccination. Therefore, genetic analysis of new virus isolates should be performed for effective infectious bronchitis control and appropriate vaccine development.

Molecular identification of cucumber mosaic virus in woad (Isatis tinctoria) with mosaic disease in Beijing / 中国中药杂志

To detect possible pathogenic virus(es) in woad (Isatis tinctoria) cultivated at Institute of Medicinal Plant Development in Beijing, reverse transcription(RT)-PCR was performed using total RNA of symptomatic woad leaves with primers for poty-, polero-, tobamovirus, broad bean wilt virus 2(BBWV2) and cucumber mosaic virus (CMV). A 657 bp fragment was amplified from symptomatic woad using CMV primers. Sequencing and BLAST analysis indicated that this fragment shared 99% nucleotide identity and 100% amino acid identity with CMV-Vi isolate. The isolate was named CMV-Isatis tinctorial (CMV-It). Phylogenetic analysis based on nucleotide sequences of CP genes showed that CMV-It clustered with CMV-K and belonged to subgroup I. To our knowledge, this is first identification of CMV in woad by RT-PCR and the CP gene was analyzed. This work provided data for research and control of woad mosaic disease.

Clinical features of sporadic cases with H7N9 avian influenza in Taizhou city of Zhejiang province and characteristics of viral gene / 中华临床感染病杂志

Objective To examine the clinical features of sporadic patients with H7N9 avian influenzain Taizhou city of Zhejiang province and to characterize its viral genes.Methods Fifteen patients with H7N9 influenza infection confirmed by Zhejiang Provincial Centre for Disease Control and Prevention during January 201 4 and January 201 5 were included in the study.The basic diseases,poultry exposure history,clinical manifestation,laboratory examination,imaging features,treatment and outcome and viral gene sequencing were analyzed retrospectively.Results The first clinical symptoms were fever and cough in all patients,acuterespiratory distress syndrome(ARDS)occurred in 1 3 patients,the average time from onset to antiviral therapy was (7 ±2)d.Among 1 5 patients,9 survived and 6 died,including 2 died of multiple organ failure (MOF).The phylogenetic tree showed that there was highly homologous in hemagglutinin (HA)and neuraminidase(NA)genes between human H7N9 virus strains and poultry reference strains.The result of genetic sequencing indicated that human H7N9 virus strains had mutations at 226 (Q226L)sites in HA protein.Conclusions ARDS is likely to occur in patients with H7N9 viral infection,and early antiviral treatment usually leads to a good prognosis.With the occurrence of adaptive mutation in avian influenza virus H7N9,spread from poultry to the human beings may take place.

Morphometric and molecular differentiation between quetzal subspecies of Pharomachrus mocinno (Trogoniformes: Trogonidae)

The resplendent Quetzal (Pharomachrus mocinno) is an endemic Mesoamerican bird species of conservation concern. Within this species, the subspecies P. m. costaricensis and P. m. mocinno, have been recognized by apparent morphometric differences; however, presently there is no sufficient data for confirmation. We analyzed eight morphometric attributes of the body from 41 quetzals: body length, tarsus and cord wing, as well as the length, wide and depth of the bill, body weight; and in the case of the males, the length of the long upper-tail cover feathers. We used multivariate analyses to discriminate morphometric differences between subspecies and contrasted each morphometric attribute between and within subspecies with paired non-parametric Wilcoxon test. In order to review the intraspecific taxonomic status of this bird, we added phylogenetic analysis, and genetic divergence and differentiation based on nucleotide variations in four sequences of mtDNA. The nucleotide variation was estimated in control region, subunit NDH6, and tRNA Glu and tRNA Phe in 26 quetzals from eight localities distributed in five countries. We estimated the genetic divergence and differentiation between subspecies according to a mutation-drift equilibrium model. We obtained the best mutation nucleotide model following the procedure implemented in model test program. We constructed the phylogenetic relationships between subspecies by maximum parsimony and maximum likelihood using PAUP, as well as with Bayesian statistics. The multivariate analyses showed two different morphometric groups, and individuals clustered according to the subspecies that they belong. The paired comparisons between subspecies showed strong differences in most of the attributes analyzed. Along the four mtDNA sequences, we identified 32 nucleotide positions that have a particular nucleotide according to the quetzals subspecies. The genetic divergence and the differentiation was strong and markedly showed two groups within P. mocinno that corresponded to the quetzals subspecies. The model selected for our data was TVM+G. The three phylogenetic methods here used recovered two clear monophyletic clades corresponding to each subspecies, and evidenced a significant and true partition of P. mocinno species into two different genetic, morphometric and ecologic groups. Additionally, according to our calculations, the gene flow between subspecies is interrupted at least from three million years ago. Thus we propose that P. mocinno be divided in two independent species: P. mocinno (Northern species, from Mexico to Nicaragua) and in P. costaricensis (Southern species, Costa Rica and Panama). This new taxonomic classification of the quetzal subspecies allows us to get well conservation achievements because the evaluation about the kind and magnitude of the threats could be more precise. Rev. Biol. Trop. 58 (1): 357-371. Epub 2010 March 01.

El Quetzal (Pharomachrus mocinno) es un ave endémica mesoamericana de interés en conservación. Dentro de esta especie, se reconocen a las subespecies P. m. costaricensis y P. m. mocinno por aparentes diferencias morfométricas, sin embargo, hasta el momento no hay datos suficientes que las confirmen. En este estudio, analizamos ocho rasgos morfométricos de 41 quetzales: la longitud del cuerpo, del tarso y de la cuerda alar, así como la longitud, el ancho y la profundidad del pico, el peso corporal, y en el caso de los machos, la longitud de las plumas cobertoras supracaudales. Usamos análisis multivariados para discriminar diferencias morfométricas entre las subespecies. Comparamos cada rasgo morfométrico dentro y entre las subespecies a partir de comparaciones pareadas con el análisis no-paramétrico de Wilcoxon. Realizamos análisis filogenéticos, y de diferenciación y divergencia genéticas fundamentados en las variaciones nucleotídicas de cuatro secuencias de ADNm con la finalidad de revisar el estatus taxonómico de esta ave. La variación nucleotídica fue estimada en la región control, la subunidad NDH6 y los tRNA Glu y tRNA Phe en 26 quetzales de ocho localidades de cinco países. Estimamos la divergencia y la diferenciación genética entre subespecies con base en el modelo de equilibrio mutación-deriva. Obtuvimos el mejor modelo de mutación nucleotídica siguiendo el procedimiento implementado en el programa Model test. Construimos las relaciones filogenéticas entre las subespecies con máxima parsimonia y máxima verosimilitud usando PAUP, así con estadística Bayesiana. Los análisis multivariados discriminaron dos grupos morfométricos, y los individuos se agruparon de acuerdo con la subespecie a la que pertenecen. Las comparaciones pareadas entre las subespecies mostraron fuertes diferencias en la mayoría de los rasgos analizados. En las cuatro secuencias de ADNmt identificamos 32 posiciones nucleotídicas que tienen un nucleótido particular de acuerdo con la subespecie de quetzal. La divergencia genética y la diferenciación fueron marcadas y mostraron dos grupos dentro de P. mocinno que correspondieron a las subespecies de quetzales. El modelo seleccionado para nuestros datos fue el TVM+G. Los tres métodos filogenéticos usados recuperaron dos clados monofiléticos robustos correspondiendo a cada una de las subespecies. Consideramos que nuestros resultados muestran una significativa y real división de P. mocinno en dos grupos genéticos, morfométricos y ecológicos. Además de acuerdo con nuestras estimaciones, el flujo génico está interrumpido entre las subespecies desde al menos hace tres millones de años. Por ello, proponemos que P. mocinno sea dividido en dos especies independientes: P. mocinno (especie norteña, desde México hasta Nicaragua) y P. costaricensis (especie sureña, Costa Rica y Panamá). Esta nueva clasificación de las subespecies de quetzal permitirá mejores logros en su conservación, dado que la evaluación de la clase y magnitud de las amenazas serán más precisas.

Construção de uma biblioteca de módulos para utilização na composição de workflows para filogenia / Construction of a library of modules for use in the composition of workflows for phylogeny

Com o advento da era pós-genômica, ocorreu uma explosão de informações onde inúmeras descobertas geraram grande quantidade de dados biológicos, que para serem analisados, necessitavam da cooperação de várias áreas de conhecimento. Inicialmente, as atividades de análises destes dados são suportadas por programas que constituem um fluxo de trabalho, baseado em scripts, que normalmente são executados por linha de comando, obrigando os seus usuários a terem domínio de algoritmos e lógica de programação. Tais scripts auxiliam muito na entrada, processamento e resultado final da análise, mas ainda apresentam dificuldades em interferir, coletar e armazenar dados ao longo de sua execução. Além disso, dependendo da especificidade do script, o seu uso pode ser muito complexo, em função da dificuldade da implementação, manutenção e reuso. Também, neste tipo de ambiente, o registro de execução das atividades do fluxo, da origem dos dados utilizados e das transformações aplicadas aos dados, geralmente, não são mantidos. Para tanto, tem havido o crescente uso de workflows científicos na execução e condução de experimentos científicos. Os workflows científicos pressupõem a resolução de problemas científicos através das técnicas de composição do fluxo de atividades, onde os passos normalmente são compostos por programas de bioinformática que recebem, processam e geram um conjunto de dados que podem ser repassados aos demais passos do workflow. Toda a estrutura de desenvolvimento e execução desses workflows é apoiada por sistemas específicos, conhecidos como Sistemas de Gerenciamento de Workflows Científicos (SGWfC), que possuem seus próprios mecanismos de gerência e linguagem. Considerando as vantagens de uso dos SGWfC no cenário da Bioinformática, este trabalho apresenta o workflow científico para reconstrução filogenética denominado PHYLO...

With the advent of post-genomic era, there was an explosion of information where many discoveries have generated large amounts of biological data, which, to be analyzed, needed the cooperation of various fields of knowledge. Initially, the to industrial activities of analysis of these data are supported by programs that constitute the workflow, based on scripts, that normally run from command line, forcing users to algorithms and programming logic. Such scripts help much the input, processing and outcome of the analysis, but still present difficulties for usersto interfere, collect and store data throughout their implementation. Also, according to the specific use of the script, it can be very complex, depending on the difficultyof implementation, maintenance and reuse. Also, in this type of environment, the registration of the execution of the activities of the flow, the source of data use d and the transformations applied to the data are generally not retained. For these, there has been the growing use of scientific workflows for the implementation and execution of scientific experiments. Scientific workflows assume scientificproblems solving through techniques of composition of the flow of activities, where the steps are usually composed of bioinformatics programs that receive, process and generate a data set that can be passed on to other steps of the workflow. The structure of development and implementation of these workflows is supported by specific systems, known as Scientific Workflows Management Systems (SGWfC), which have their own management mechanisms and language. Considering theadvantages of using the scenario SWfMS in the scientific bioinformatics, this work presents the scientific workflow PHYLO for phylogenetic reconstruction...

Evolutionary insights into duffy gene in mammalian taxa with comparative genetic analysis.

Background & objectives: Evolutionary analyses of genes conserved across taxa are keys to understand the complexity of gene and genome variation. Since malaria is a highly infectious human disease and its susceptibility in human is genetically controlled, characterization and evolutionary analyses of such genes are of prime importance to understand genetic mechanisms of disease susceptibility. In the present study we have characterized and performed comparative genomic analyses of the human Duffy gene responsible for malaria pathogenesis in nine different mammalian taxa. Methods: DNA sequences of human duffy gene were downloaded from public domain and have been characterized in detail and compared with eight other different mammalian taxa (Pan troglodytes, Macaca mulatta, Pongo pygmaeus, Rattus norvegicus, Mus musculus, Monodelphis domestica, Bos taurus and Canis familiaris). Comparative and evolutionary analyses were performed using statistical software and tools. Results: We observed that the genetic architecture of this gene was entirely different across all the nine taxa and a close similarity between Homo sapiens and Pan troglodytes (chimpanzee) was evident for several aspects of this gene. Comparisons on several aspects, such as ratio of coding and non-coding regions, total gene length number and size of introns and difference of number of nucleotides in human and chimpanzees have revealed interesting features. Phylogenetic inferences based on the Duffy gene among nine different taxa were found to be different than other genes previously studied. Interpretation & conclusion: Most remarkably, human and chimpanzee were only 0.75% different in this gene. The results were discussed on the similarities between human and chimpanzee and gain of introns in human-chimpanzee clade with an inference on the role of evolutionary forces (mainly natural selection) in maintaining such variations across closely-related mammalian taxa.

Alignment and phylogenetic analysis of type II DNA topoisomerases.

DNA topoisomerases have been evolved to solve the topological problems of DNA during replication, transcription, recombination and segregation. Discovery of several new enzymes and their characterization has necessitated this compilation. This analysis shows the distinct evolutionary relatedness of type II DNA topoisomerases. A striking feature is the absence of a contiguous stretch of about 160 amino acids in one of the subunits of prokaryotic type II enzymes, which might have important implications to their structure and function.