Isolation and characterization of a human heart cDNA encoding a new member of the small heat shock protein family — HSPL27

AbstractA novel cDNA clone was isolated from a human adult heart cDNA library. This cDNA clone is similar to the small heat shock protein (smhsp) in both DNA and amino acid sequences, especially in the conserved region. Sequence analysis has shown that the putative novel smhsp, named 27 kDa heat-shock-protein-like protein (HSPL27) is a protein of 241 amino acids with a deduced molecular mass of 26.7 kDa and a deduced pI of 8.0. We have expressed the HSPL27 in E. coli and the expressed protein was found to be present in the soluble fraction of the bacterial cell lysate. Chromosomal mapping data shows that the HSPL27 gene is located at human chromosome 5q11.2

A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation

Background: Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes. Findings. Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ∼90% of 100 assemblies with 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%. Conclusions: A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks. © 2012 Jiang et al; BioMed Central Ltd.published_or_final_versio

The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens

© 2014 The Authors. Published by Elsevier Inc. Background A sequenced house dust mite (HDM) genome would advance our understanding of HDM allergens, a common cause of human allergies. Objective We sought to produce an annotated Dermatophagoides farinae draft genome and develop a combined genomic-transcriptomic-proteomic approach for elucidation of HDM allergens. Methods A D farinae draft genome and transcriptome were assembled with high-throughput sequencing, accommodating microbiome sequences. The allergen gene structures were validated by means of Sanger sequencing. The mite's microbiome composition was determined, and the predominant genus was validated immunohistochemically. The allergenicity of a ubiquinol-cytochrome c reductase binding protein homologue was evaluated with immunoblotting, immunosorbent assays, and skin prick tests. Results The full gene structures of 20 canonical allergens and 7 noncanonical allergen homologues were produced. A novel major allergen, ubiquinol-cytochrome c reductase binding protein-like protein, was found and designated Der f 24. All 40 sera samples from patients with mite allergy had IgE antibodies against rDer f 24. Of 10 patients tested, 5 had positive skin reactions. The predominant bacterial genus among 100 identified species was Enterobacter (63.4%). An intron was found in the 13.8-kDa D farinae bacteriolytic enzyme gene, indicating that it is of HDM origin. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a phototransduction pathway in D farinae, as well as thiamine and amino acid synthesis pathways, which is suggestive of an endosymbiotic relationship between D farinae and its microbiome. Conclusion An HDM genome draft produced from genomic, transcriptomic, and proteomic experiments revealed allergen genes and a diverse endosymbiotic microbiome, providing a tool for further identification and characterization of HDM allergens and development of diagnostics and immunotherapeutic vaccines.Link_to_subscribed_fulltex

Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus

Background: Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinical isolates of V. parahaemolyticus are currently available, but the genome dynamics across the species and virulence potential of environmental strains on a genome-scale have not been described before. Results: Here we present genome sequences of four V. parahaemolyticus clinical strains from stool samples of patients and five environmental strains in Hong Kong. Phylogenomics analysis based on single nucleotide polymorphisms revealed a clear distinction between the clinical and environmental isolates. A new gene cluster belonging to the biofilm associated proteins of V. parahaemolyticus was found in clincial strains. In addition, a novel small genomic island frequently found among clinical isolates was reported. A few environmental strains were found harboring virulence genes and prophage elements, indicating their virulence potential. A unique biphenyl degradation pathway was also reported. A database for V. parahaemolyticus (http://kwanlab.bio.cuhk.edu.hk/vp webcite) was constructed here as a platform to access and analyze genome sequences and annotations of the bacterium. Conclusions: We have performed a comparative genomics analysis of clinical and environmental strains of V. parahaemolyticus. Our analyses could facilitate understanding of the phylogenetic diversity and niche adaptation of this bacterium.

A "developmental hourglass" in fungi

<p>#PdTT Version 1.0 (January 2015)<br>#This program develops algorithms for Phylostratigraphy, dN/dS ratio, Transcriptome age index (TAI) and Transcriptome divergence index (TDI) analysis.</p> <p>#Please cite:<br>#Cheng X, Hui JHL, Lee YY, Law PTW, Kwan HS. 2015. A "developmental hourglass" in fungi. <em>Mol Biol Evol.</em> 32(6):1556-66. doi: 10.1093/molbev/msv047</p> <p>Please read carefully the following before running the programs:<br>README_TAI.txt for phylostratigraphy analysis and transcriptome age index (TAI) calculation, and<br>README_TDI.txt for dN/dS ratio analysis and transcriptome divergence index (TDI) calculation.</p> <p>The algorithms are implemented in Perl. Please make sure that Perl (https://www.perl.org/) is properly installed on your computer.</p> <p>All source codes are included in this fileset. You can modify some of the codes to suit the purpose of your study.</p

Sputum Microbiota in Tuberculosis as Revealed by 16S rRNA Pyrosequencing

<div><h3>Background</h3><p>Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen <em>Mycobacterium tuberculosis</em>. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease.</p> <h3>Methodology/Principal Findings</h3><p>Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. <em>Firmicutes</em>, <em>Proteobacteria</em>, <em>Bacteroidetes</em>, <em>Actinobacteria</em>, and <em>Fusobacteria</em> were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. <em>Proteobacteria</em> and <em>Bacteroidetes</em> were more represented in the TB samples and <em>Firmicutes</em> was more predominant in the controls. Sixteen major bacterial genera were recovered. <em>Streptococcus</em>, <em>Neisseria</em> and <em>Prevotella</em> were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. <em>Actinomyces</em>, <em>Fusobacterium</em>, <em>Leptotrichia</em>, <em>Prevotella</em>, <em>Streptococcus</em>, and <em>Veillonella</em> were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera <em>Mogibacterium</em>, <em>Moryella</em> and <em>Oribacterium</em> were enriched statistically in the TB samples, while a genus belonging to the unclassified <em>Lactobacillales</em> was enriched in the controls. The diversity of microbiota was similar in the TB and control samples.</p> <h3>Conclusions/Significance</h3><p>The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.</p> </div

List of genera and species significantly different between TB and control groups.

∧<p>OTUs clustered at 97% similarity.</p>#<p>Using RDP classifier, down to the genus level.</p>*<p>Against the NCBI 16S rRNA database.</p