Molecular characterization and geographical distribution of Zika virus worldwide from 1947 to 2022.

Objectives: We conducted molecular characterization, demonstrated the geographical distribution of Zika virus (ZIKV) circulating worldwide from 1947 to 2022 and explored the potential genetic recombination site in the Thailand ZIKV genomes.

Methods: We constructed phylogenetic trees based on ZIKV coding sequences (CDS) and determined the geographical distribution of the representative viruses by genetic relationship and timeline. We determined genetic recombination among ZIKV and between ZIKV and other flaviviruses using similarity plot and bootscan analyzes, together with the phylogeny encompassing the CDS and eight subgenomic regions.

Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids.

Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR-single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids.

Phylogenetic analysis of two new complete genomes of the hepatitis E virus (HEV) genotype 3 from Thailand.

Hepatitis E virus (HEV) is a causative agent of acute viral hepatitis globally. Evolutionary phylogeny classifies the HEV into eight genotypes that correlate with the viral transmission. Only four genotypes have been proven to be responsible for transmission in humans.

Dysregulation of microRNA in cholangiocarcinoma identified through a meta-analysis of microRNA profiling.

Background: In the past decades, the potential of microRNA (miRNA) in cancer diagnostics and prognostics has gained a lot of interests. In this study, a meta-analysis was conducted upon the pooled miRNA microarray data of cholangiocarcinoma (CCA).

Aim: To identify differentially expressed (DE) miRNAs and perform functional analyses in order to gain insights to understanding miRNA-target interactions involved in tumorigenesis pathways of CCA.

An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data.

Whole-genome sequencing (WGS) data allow for an inference of Mycobacterium tuberculosis (Mtb) clusters by using a pairwise genetic distance of ≤12 single nucleotide polymorphisms (SNPs) as a threshold. However, a problem of discrepancies in numbers of SNPs and genetic distance measurement is a great concern when combining WGS data from different next generation sequencing (NGS) platforms. We performed SNP variant calling on WGS data of 9 multidrug-resistant (MDR-TB), 3 extensively drug-resistant tuberculosis (XDR-TB) and a standard M.

Characterization of Flagellotropic, Chi-Like Phages Isolated from Thai Poultry Farms.

Despite a wealth of knowledge on phages worldwide, little is known about poultry-associated phages from Thailand. Here, we isolated 108 phages from Thai poultry farms that infect serovar Typhimurium. Phages STm101 and STm118 were identified as temperate phages.

Infection of multiple strains among tuberculosis/human immunodeficiency virus co-infected patients: A molecular study in Myanmar.

Background: Appearance of Mycobacterium tuberculosis (MTB) in the sputum of a tuberculosis (TB)/human immunodeficiency virus (HIV) co-infected patient under treatment may indicate either failure or new infection. This study aims to evaluate whether TB treatment failure among TB/HIV co-infected patients is a real failure.

Methods: A prospective cohort study was conducted among 566 TB/HIV co-infected patients who started TB treatment in 12 townships in the upper Myanmar.

Transcriptomic analysis of male and female Schistosoma mekongi adult worms.

Background: Schistosoma mekongi is one of five major causative agents of human schistosomiasis and is endemic to communities along the Mekong River in southern Lao People's Democratic Republic (Laos) and northern Cambodia. Sporadic cases of schistosomiasis have been reported in travelers and immigrants who have visited endemic areas. Schistosoma mekongi biology and molecular biology is poorly understood, and few S.

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates.

Tuberculosis presents a global health challenge. Mycobacterium tuberculosis is divided into several lineages, each with a different geographical distribution. M.

Molecular Phylogenetics: Concepts for a Newcomer.

Molecular phylogenetics is the study of evolutionary relationships among organisms using molecular sequence data. The aim of this review is to introduce the important terminology and general concepts of tree reconstruction to biologists who lack a strong background in the field of molecular evolution. Some modern phylogenetic programs are easy to use because of their user-friendly interfaces, but understanding the phylogenetic algorithms and substitution models, which are based on advanced statistics, is still important for the analysis and interpretation without a guide.

Evolution of protein indels in plants, animals and fungi.

Background: Insertions/deletions (indels) in protein sequences are useful as drug targets, protein structure predictors, species diagnostics and evolutionary markers. However there is limited understanding of indel evolutionary patterns. We sought to characterize indel patterns focusing first on the major groups of multicellular eukaryotes.

SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments.

Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences.

Distribution and sequence analysis of virulence associated genes in Vibrio cholerae O1, O139 and non-O1/non-O139 isolates from Thailand.

Virulence-associated genes of Vibrio cholerae including O1, O139 and non-O1/non-O139 from an outbreak in Songkhla Province and sporadic cases occurred in Thailand during 1993 - 2002 were investigated. One hundred eighty-five V. cholerae strains were examined for the presence of virulence-associated genes including ctxA, tcpA, zot, toxR, toxS, toxT, and ace by polymerase chain reaction.