Review on Applicability of Bioinformatics in Current Research and Database Management

A generation of new science has evolved with the development of bioinformatics and computational biology, which have molecular biology as an integrated part. In the past decade, technological advances have promoted a prominent development in expertise and knowledge in the molecular basis of phenotypes. In Bioinformatics, biological data is evaluated by computational science and processed in a more statistical and meaningful way. It includes the collection classification storage and evaluation of biochemical and organic statistics using computers in particular as implemented in molecular genetics and genomics. Computational Biology and Bioinformatics are emerging branches of science and include the use of techniques and concepts from informatics statistics, mathematics, chemistry, biochemistry, physics and linguistics. Therefore, bioinformatics and computational biology have sought to triumph over many challenges of which a few are listed in this overview. This evaluation intends to provide insight into numerous bioinformatics databases and their uses in the analysis of biological records exploring approaches emerging methodologies strategies tools that can provide scientific meaning to the information generated.

Polyphasic characterisation of Burkholderia cepaciacomplex species isolated from children with cystic fibrosis

Cystic fibrosis (CF) patients with Burkholderia cepacia complex (Bcc) pulmonary infections have high morbidity and mortality. The aim of this study was to compare different methods for identification of Bcc species isolated from paediatric CF patients. Oropharyngeal swabs from children with CF were used to obtain isolates of Bcc samples to evaluate six different tests for strain identification. Conventional (CPT) and automatised (APT) phenotypic tests, polymerase chain reaction (PCR)-recA, restriction fragment length polymorphism-recA, recAsequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) were applied. Bacterial isolates were also tested for antimicrobial susceptibility. PCR-recA analysis showed that 36 out of the 54 isolates were Bcc. Kappa index data indicated almost perfect agreement between CPT and APT, CPT and PCR-recA, and APT and PCR-recA to identify Bcc, and MALDI-TOF and recAsequencing to identify Bcc species. The recAsequencing data and the MALDI-TOF data agreed in 97.2% of the isolates. Based on recA sequencing, the most common species identified were Burkholderia cenocepacia IIIA (33.4%),Burkholderia vietnamiensis (30.6%), B. cenocepaciaIIIB (27.8%), Burkholderia multivorans (5.5%), and B. cepacia (2.7%). MALDI-TOF proved to be a useful tool for identification of Bcc species obtained from CF patients, although it was not able to identify B. cenocepacia subtypes.

Four New Species of Amanita in Inje County, Korea

Amanita (Agaricales, Basidiomycota) is one of the most well-known genera composed of poisonous mushrooms. This genus of almost 500 species is distributed worldwide. Approximately 240 macrofungi were collected through an ongoing survey of indigenous fungi of Mt. Jeombong in Inje County, Korea in 2014. Among these specimens, 25 were identified as members of Amanita using macroscopic features. Specimens were identified to the species level by microscopic features and molecular sequence analyses of the internal transcribed spacer and large subunit of nuclear ribosomal RNA. We molecularly identified 13 Amanita species, with seven species matching previously recorded species, four species (A. caesareoides, A. griseoturcosa, A. imazekii, and A. sepiacea) new to Korea, and two unknown species.

Filogenia de hongos roya (Uredinales) en la zona andina colombiana mediante el uso de secuencias del ADN ribosomal 28S

Phylogenetic analysis of rust fungi (Uredinales) from the Colombian Andean region using 28S ribosomal DNA sequences. Rust fungi (Uredinales, Basidiomycetes) are one of the most diverse and economically important plant-obligated parasites. Taxonomy of this group has been under revision during the last years using molecular techniques to define phylogenetic relationships. In this study we evaluated the phylogenetic affinities of a group of 40 rust fungi obtained from different plants in the Colombian Andean region using sequence analysis of the 28S ribosomal DNA, specifically D1/D2 domains. Comparisons were undertaken with sequences of rust fungi from around the world deposited in the GenBank database. An alignment of sequences was used to build a phylogenetic tree through Maximum parsimony analysis. Our results support the taxonomical validity of families Pucciniaceae, Phakopsoraceae, Phragmidiaceae, Pileolariaceae, Mikronegeriaceae, Coleosporiaceae and Cronartiaceae, while Pucciniosiraceae represents redundant taxa with Pucciniaceae. The analyses indicated that Uropyxidaceae, Raveneliaceae, Chaconiaceae and Pucciniastraceae correspond to poly-phyletic families. Melampsoraceae appear to be a basal taxon to the Uredinales. Information obtained in this study will be useful to incorporate a higher number of sequences from tropical rust fungi within global efforts to redefine the taxonomy of order Uredinales. Additionally, we propose to give priority to future phylogenetic studies of taxa: Gerwasia, Hemileia, Phragmidium, Prospodium, Puccinia and Uromyces, genera that include a high number of rust fungi from the tropics. Rev. Biol. Trop. 59 (2): 517-540. Epub 2011 June 01.

Los hongos roya (Uredinales, Basidiomycetes) representan uno de los grupos de fitoparásitos más diversos y con mayor importancia económica agrícola mundial. Su taxonomía se ha basado en el estudio de caracteres morfológicos, que resulta en muchos casos en la formación de taxones polifiléticos. Sin embargo, en los últimos años se han tratado de incorporar herramientas moleculares que conduzcan a la generación de sistemas de clasificación basados en afinidades evolutivas. Este trabajo pretendió aumentar la base del conocimiento sobre la uredobiota tropical, mediante el estudio de características morfológicas y filogenéticas de un grupo de royas de los Andes de Colombia. Para esto se secuenció parte de la región 28S del ADNr y se realizó un análisis de agrupamiento mediante Máxima parsimonia. Los resultados confirmaron la validez de las familias Pucciniaceae, Phakopsoraceae, Phragmidiaceae, Pileolariaceae, Mikronegeriaceae, Coleosporiaceae y Cronartiaceae, mientras que Pucciniosiraceae es un taxón redundante con Pucciniaceae. Por su parte, Uropyxidaceae, Raveneliaceae, Chaconiaceae y Pucciniastraceae se muestran como familias polifiléticas. Aparentemente Melampsoraceae se presenta como un taxón basal al grupo. La información que se deriva de este estudio se espera sea incorporada en los estudios mundiales que buscan redefinir el sistema taxonómico de los hongos roya.

Sequence analyses of the Cps2J gene in 9 strains of Streptococcus suis serotype2 isolated in Zhejiang province / 中国人兽共患病学报

To explore the molecular characteristics of Streptococcus suis serotype 2(ss2) isolated in Zhejiang province by deciding the variation loci and its variation frequency of Cps2J gene.The total DNA of 9 strains of ss2 isolated in Zhejiang province were extracted and amplifed by PCR. Then,the Cps2J fragments were cloned into plasmid carrier and completely sequenced after purification.Finally,the sequence results of all 9 ss2 isolates were compared with those obtained by other studies around the world.It was found that the open reading fragments of Cps2J in 9 SS2 isolates encoding 333 amino acids were 999 bp in length.Comparisons of this region among ss2 isolates revealed a similarity of between 98.8% and 99.9%, while the homology to ss1 strains varied between 56.8% and 57.0%.Our study shows the sequences of complete Cps2J segment are fairly stable and all these 9 ss2 strains of different sources possibly have the same evolutionary origin.

Population densities and genetic diversity of actinomycetes associated to the rhizosphere of Theobroma cacao / Densidades populacionais e diversidade genética de actinomicetos associados a rizosfera de Theobroma cacao

In spite of the acknowledged importance of growth-promoting bacteria, only a reduced number of studies were conducted with these microorganisms on Theobroma cacao. The objectives of this work were to study the population densities and genetic diversity of actinomycetes associated with the rhizosphere of cacao as a first step in their application in plant growth promotion and biological control. The populations densities of actinomycetes in soil and cacao roots were similar, with mean values of 1,0 x 10(6) CFU/g and 9,6 x 10(5) CFU/g, respectively. All isolates selected and used in this study were identified through sequencing analyses of a fragment of the rpoB gene that encodes the [beta]-subunit of the RNA polymerase as species of the genus Streptomyces. In vitro cellulolytic, xilanolytic and chitinolytic activity, indolacetic acid production and phosphate solubilization activities were observed in most of the isolates tested. The data obtained in this study demonstrate that actinomycetes account for a higher percentage of the total population of culturable bacteria in soil than on cacao roots. Additionally, actinomycetes from the cacao rhizosphere are genetically diverse and have potential applications as agents of growth promotion.

Apesar da reconhecida importância das bactérias promotoras de crescimento, apenas um reduzido número de estudos foi conduzido com este grupo de microrganismos na cultura do cacaueiro. Os objetivos deste trabalho foram o estudo da densidade populacional e da diversidade genética de actinomicetos associados à rizosfera do cacaueiro como o primeiro passo para sua utilização na promoção de crescimento de mudas desta cultura e no controle biológico de doenças. As densidades populacionais de actinomicetos em amostras de solo e de raízes de cacaueiro foram semelhantes, com valores médios de 1,0 x 10(6) UFC/g e de 9,6 x 10(5) UFC/g, respectivamente. Todos os isolados selecionados para este estudo foram identificados através de análises de seqüências de um fragmento do gene rpoB, que codifica a beta-subunidade da RNA polimerase, como pertencentes ao gênero Streptomyces. Dentre os isolados testados, constatou-se in vitro, a produção de celulase, xilanase, quitinase, ácido indolacético e a capacidade de solubilização de fosfato. Os dados obtidos demonstram que os actinomicetos representam uma maior proporção da população total de bactérias cultiváveis em solo do que em raízes. Adicionalmente, os actinomicetos da rizosfera do cacaueiro são geneticamente diversos e apresentam potencial para atuarem como agentes de promoção de crescimento.

Cloning and sequencing of the VL and VH genes from the anti-hCD154 McAb hybridoma cell line / 中国病理生理杂志

AIM:To obtain the light chain region(VL) and heavy chain region(VH) genes from the hybridoma cell line and analyse their sequence for construction of the engineering antibody against hCD154. METHODS: In this research ,total RNA was extracted from the hybridoma cell line 7E8, which secretes McAb against hCD154, and subjected to reverse transcription. The VL gene and VH gene were amplified by PCR, cloned into puc18 vector and sequenced by Sanger's dideoxymediated chain-termination method. RESULTS: The VL cDNA of 7E8 McAb consists of 341 bp encoding 113 amino acid residues. Compared with mouse Ig database, the VL region is in accord with the characterization of DNA sequence present in the mouse Ig Vk region , it belong to mouse V?2 light chain. The VH cDNA of 7E8 McAb consists of 354 bp encoding 118 amino acid residues. Compared with mouse Ig database, the VH region is in accord with the characterization of DNA sequence present in the mouse Ig VH region. CONCLUSION: The DNA squence analysis showed that the cloned genes code the light and heavy chain variable region of mouse respectively.