Identification and genetic diversity analysis of Memecylon species using ISSR, RAPD and Gene-Based DNA barcoding tools

Background: Memecylon species are commonly used in Indian ethnomedical practices. The accurate identification is vital to enhance the drug's efficacy and biosafety. In the present study, PCR based techniques like RAPD, ISSR and DNA barcoding regions, such as 5s, psbA-trnH, rpoC1, ndh and atpF-atpH, were used to authenticate and analyze the diversity of five Memecylon species collected from Western Ghats of India. Results: Phylogenetic analysis clearly distinguished Memecylon malabaricum from Memecylon wightii and Memecylon umbellatum from Memecylon edule and clades formed are in accordance with morphological keys. In the RAPD and ISSR analyses, 27 accessions representing five Memecylon species were distinctly separated into three different clades. M. malabaricum and M. wightii grouped together and M. umbellatum, M. edule and Memecylon talbotianum grouped in the same clade with high Jaccard dissimilarity coefficient and bootstrap support between each node, indicating that these grouped species are phylogenetically similar. Conclusion: Data from the present study reveals that chloroplast psbA-trnH region could be used as a potential candidate region for identifying Memecylon species, and ISSR marker system could be used for estimating genetic diversity since it has high percent polymorphism compared to RAPD marker.

Molecular identification of the species of Biomphalaria snails in Shenzhen reservoir based on 16S rDNA sequences / 中华地方病学杂志

Objective To identify the species of Biomphalaria snails collected in Shenzhen reservoir,based on the mitochondrial 16S rDNA sequences.Methods The 16S rDNA fragments were amplified by PCR from the genome DNA of Biomphalaria snails,and inserted in plasmid pMD-18T for sequencing.The sequence of 16S rDNA fragment and its phylogenetic relationships with those of other species of Biomphalaria snails were analyzed with BLAST and MEGA4 software.Results The amplified 16S rDNA fragment of the Biomphalaria snails was about 466 bp in length.As aligned with the corresponding sequences of the related Biomphalaria species,the identity of nucleotides was 99％ with 1 isolate of Biomphaltria straminea (B.straminea),98％ with 3 isolates of B.kuhniana,95％ with 1 isolate of B.intermedia,and 94％ with 1 isolate of B.edisoni.Based on the 16S rDNA sequence,the results of phylogenetic analysis with neighbor-joining (NJ) and unweighted pair-group method with arithmetic means (UPGMA) indicated that the snails had close genetic relationships with the B.straminea isolate (Genbank accession NO.AY030213.1) Conclusion The Biomphalaria snails collected in Shenzhen reservoir could be classified as B.straminea based on the characteristics of 16S rDNA sequence.

Whole genome sequence analysis of an emerging Japanese encephalitis virus (genotype Ⅴ) strain isolated in mainland China / 中华微生物学和免疫学杂志

Abstract] Objective To analyze the molecular characteristics of the full-length genome of a new-ly isolated genotypeⅤJapanese encephalitis virus (JEV) strain (XZ0934) in China and the first genotypeⅤJEV strain ( Muar) isolated in Malaya 60 years ago.Methods Several softwares including ClustalX 2.0.9, DNAStar 7.1, Bioedit 7.2.5 and MEGA6.06 were used to conduct sequence alignments and phylo-genetic analysis.Results The full-length genomes of XZ0934 strain (isolated in Tibet, China in 2009) and Muar strain (isolated in Malaya in 1952) were composed of 10 983 and 10 988 nucleotides, respective-ly.The XZ0934 strain was highly similar with the Muar strain showing the homology of 90.6%in nucleotide (nt) and 98.3%in amino acid (aa).The open reading frame (ORF) of the two genotype Ⅴ JEV strains encoded 3433 aa while the ORF of other four genotypes (Ⅰ-Ⅳ) (10 299 nt) encoded 3432 aa.Compared with JEV strains of other genotypes, a serine were inserted into the NS4A gene of JEV strains genotype Ⅴand 10-14 nucleotides were inserted into the downstream of the ORF stop codon in 3′-untranslated region. Phylogenetic analysis of E sequences of all JEV strains genotypedⅠ-Ⅴrevealed that in the cluster of geno-typeⅤ, XZ0934 and 10-1827 ( isolated from mosquitoes in South Korea, 2010) stains formed a branch and were divergent from that of Muar strain indicating that there were molecular genetic differences among geno-typeⅤJEV strains after a 60 years hiatus.Conclusion The two genotypeⅤJEV strains showed high lev-els of identity in nucleotide sequences and amino acid sequences with serine insertion in the NS4A gene. However, there were molecular genetic differences between genotypeⅤJEV strains isolated after a 60 years hiatus.

Detecção molecular e análise filogenética do gene H de amostras do vírus da cinomose canina em circulação no município de Campinas, São Paulo / Molecular detection and phylogenetic analysis of the gene H from canine distemper virus isolates circulating at the municipality of Campinas, São Paulo

O vírus da cinomose canina (CDV), um Morbillivirus da família Paramyxoviridae, é o agente etiológico de doença neurológica e sistêmica em cães. O diagnóstico laboratorial da infecção requer o isolamento viral ou detecção do material genético do vírus em secreções ou tecidos de cães com suspeita clínica da doença. A diversidade genética entre os isolados de CDV pode ser aferida pelo sequenciamento efilogenia molecular do gene que codifica a hemaglutinina viral (gene H), havendo atualmente um especial interesse em comparar as amostras circulantes a campo com o genogrupo América-1, que abrange as cepas presentes nas vacinas disponíveis no mercado. No presente estudo, foi realizada a detecção molecular do gene H de CDV a partir de amostras biológicas colhidas ante- e post- -mortem de 15 cães com sinais clínicos sugestivos de cinomose na região metropolitana de Campinas, São Paulo. Dez dos 15 cães analisados tiveram ao menos um órgão positivo na detecção molecular e os amplicons obtidos foram submetidos ao sequenciamento nucleotídico seguido de análise filogenética molecular. De forma semelhante ao que já foi reportado para estudo analisando a diversidade do gene H em outros países, a reconstrução filogenética obtida para as amostras de casos de cinomose da região de Campinas demonstrou as mesmas foram agrupadas junto a amostras norte-americanas, europeias e japonesas recentes, em um grupo genético distinto do grupo de amostras clássicas de CDV, nomeado America-1, o qual engloba as estirpes vacinais Snyder Hill, Onderstepoort e Lederle.

Canine distemper virus (CDV), a Morbillivirus of the family Paramyxoviridae, is the etiological agent of neurological and systemic disease in dogs. The laboratory diagnosis of infection requires viral isolation or detection of genetic material of the virus in secretions or tissues of dogs with clinical suspicion of the disease. The genetic diversity among isolates of CDV can be assessed by sequencing and phylogenetic analysis of the gene that encodes the viral hemagglutinin (H gene), and there is currently a special interest in comparing the strains currently circulating in the field with the genogroup America-1, which comprises strains present in vaccines available in the market. In this study, the molecular detection of CDV gene H was performed from biological samples harvested ante-and post-mortem from 15 dogs with clinical signs suggestive of canine distemper in the metropolitan region of Campinas, São Paulo. Ten of the 15 dogs examined had at least one positive organ under molecular detection and the obtained amplicons were sequenced and further analyzed by molecular phylogenetic analysis. Similarly to what has already been reported on previous studies regarding the diversity of the gene H in other countries, the phylogenetic reconstruction obtained for the samples of cases of distemper from Campinas region showed they were grouped with the North American, European and Japanese newly described samples, a genetic group distinguished from classical samples of CDV, named America-1, which encompasses the vaccine strains Snyder Hill, Onderstepoort and Lederle.

Detecção molecular e análise filogenética de vírus respiratório sincicial bovino (BRSV) em swabs e tecido pulmonar de bovinos adultos / Molecular detection and phylogenetic analysis of bovine respiratory syncytial virus (BRSV) in swabs and lung tissues of adult cattle

Bovine respiratory syncytial viruses virus (BRSV) is one of the etiologic agents of pneumonia in young cattle. Few studies have been made aiming detection of the virus in samples collected from adult animals, especially those asymptomatic bovines. However, it is assumed that infections in these groups may occur mostly asymptomatic and this would be an important mechanism for maintaining of BRSV in herds. In this study, the goal was to conduct an analysis of the occurrence of asymptomatic infections by BRSV in lung samples (n=68) and nasal swabs (209) taken from adult animals collected in abattoirs from Southern and Southeastern Brazil respectively, to detect via polymerase chain reaction the occurrence of infected animals in populations of adult cattle. The samples that resulted positive (6) on RT-PCR were subsequently subjected to cutting with restriction enzymes and sequencing for genetic characterization (2 samples). All samples belongs to subgroup B of BRSV, which is reported as the one circulating in Brazil. The results obtained demonstrate that BRSV may be present in samples taken from adult animals, which is in agreement the hypothesis that infections in adults run in a sub-clinical way that may be of importance as a maintenance mechanism of the virus in bovine herds.

O vírus respiratório sincicial bovino (BRSV) é rebanhos. No presente estudo, o objetivo foi realizar uma um dos agentes etiológicos de pneumonias em bovinos jo-análise da prevalência de infecções assintomáticas pelo vens. Poucos estudos foram realizados visando à detecção BRSV em pulmões (n=68) e swabs nasais (209) coletados do agente em amostras coletadas de animais adultos, e em de bovinos adultos coletadas em frigoríficos da região Sul especial de bovinos assintomáticos. No entanto, presume-e Sudeste respectivamente, no sentido de detectar por in-se que as infecções ocorridas nestes grupos possam ocor-termédio de reação da polimerase em cadeia qual a taxa rer em sua maioria de forma assintomática e este seria de animais infectados em populações de animais adultos um mecanismo importante para manutenção do BRSV nos onde não ocorram sinais clínicos da infecção. As amostras positivas à RT-PCR (6) foram posteriormente submetidas ao corte com enzimas de restrição (REA) e sequenciamento para caracterização genética do gene F (2 das amostras). Todas as amostras se enquadram no subgrupo B de BRSV, o grupo circulante no Brasil conforme estudos anteriores. Os resultados obtidos demonstram que o BRSV pode estar presente em amostras obtidas de animais sadios, reforçando a hipótese de que infecções subclínicasfazem parte do mecanismo de manutenção do vírus nos rebanhos.