Deciphering the Significance of Platelet-Derived Chloride Ion Channel Gene (BEST3) Through Platelet-Related Subtypes Mining for Non-Small Cell Lung Cancer.

This study investigates platelet-related subtypes in non-small cell lung cancer (NSCLC) and seeks to identify genes associated with prognosis, focusing on the clinical significance of the chloride ion channel gene BEST3. We utilised sequencing and clinical data from GEO, TCGA and the Xena platform, building a risk model based on genetic features. TCGA and GSE37745 served as training cohorts, while GSE50081, GSE13213, GSE30129 and GSE42127 were validation cohorts.

Therapeutic Effect of Darkling Beetle () Hemolymph on Skin Thermal Injury in Mice Infected by .

Staphylococci are the most common pathogens isolated from skin infections in livestock or companion animals. Antibiotic therapy is the best treatment for infections, but local or systemic use of antimicrobials increases the risk of bacterial resistance. Insects are rich in antimicrobial peptides, which can reduce bacterial resistance and can be used to treat bacterial infections after skin burns.

Immunization with recombinant E-LTB fusion protein elicits protective immune responses against bovine viral diarrhea virus.

Bovine viral diarrhea virus (BVDV), a major infectious pathogen and is associated with major economic losses and significant impact on animal welfare worldwide. Here, recombinant E-LTB protein vaccine containing MF59 adjuvant was prepared and assessed using a mouse model. The recombinant plasmid (pET32a-E-LTB) was constructed and transformed into BL21 (DE3) cells to produce E-LTB protein.

[Comprehensive re-annotation of protein-coding genes for prokaryotic genomes by Z-curve and similarity-based methods].

The development of sequencing technology has generated huge genomic sequencing information and largely enriched public genetic resources. To analyze such big data, the algorithms and tools for comparison and annotation of genomes are updated continually, enabling genome annotation with higher accuracy various annotation tools. Many prokaryotic genomes in public database were sequenced and assembled more than a decade ago, and they contained multiple genes with unknown functions.

CasLocusAnno: a web-based server for annotating cas loci and their corresponding (sub)types.

In prokaryotes, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) systems constitute adaptive immune systems against mobile genetic elements (MGEs). Here, we introduce the Markov cluster algorithm (MCL) to Makarova et al.'s method in order to select a more reasonable profile.

Vgas: A Viral Genome Annotation System.

The in-depth study of viral genomes is of great help in many aspects, especially in the treatment of human diseases caused by viral infections. With the rapid accumulation of viral sequencing data, improved, or alternative gene-finding systems have become necessary to process and mine these data. In this article, we present Vgas, a system combining an method and a similarity-based method to automatically find viral genes and perform gene function annotation.

The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process.

Understanding how proteins evolve is important, and the order of amino acids being recruited into the genetic codons was found to be an important factor shaping the amino acid composition of proteins. The latest work about the last universal common ancestor (LUCA) makes it possible to determine the potential factors shaping amino acid compositions during evolution. Those LUCA genes/proteins from S2, which is one of the possible LUCA, were investigated.

Comprehensive exploration of the enzymes catalysing oxygen-involved reactions and COGs relevant to bacterial oxygen utilization.

To better understand the mechanisms of bacterial adaptation in oxygen environments, we explored the aerobic living-associated genes in bacteria by comparing Clusters of Orthologous Groups of proteins' (COGs) frequencies and gene expression analyses and 38 COGs were detected at significantly higher frequencies (p-value less than 1e-6) in aerobes than in anaerobes. Differential expression analyses between two conditions further narrowed the prediction to 27 aerobe-specific COGs. Then, we annotated the enzymes associated with these COGs.

Mutation Landscape of Base Substitutions, Duplications, and Deletions in the Representative Current Cholera Pandemic Strain.

Pandemic cholera is a major concern for public health because of its high mortality and morbidity. Mutation accumulation (MA) experiments were performed on a representative strain of the current cholera pandemic. Although the base-pair substitution mutation rates in Vibrio cholerae (1.

Amino acid compositions contribute to the proteins' evolution under the influence of their abundances and genomic GC content.

Inconsistent results on the association between evolutionary rates and amino acid composition of proteins have been reported in eukaryotes. However, there are few studies of how amino acid composition can influence evolutionary rates in bacteria. Thus, we constructed linear regression models between composition frequencies of amino acids and evolutionary rates for bacteria.

Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains.

Although more and more entangled participants of translation process were realized, how they cooperate and co-determine the final translation efficiency still lacks details. Here, we reasoned that the basic translation components, tRNAs and amino acids should be consistent to maximize the efficiency and minimize the cost. We firstly revealed that 310 out of 410 investigated genomes of three domains had significant co-adaptions between the tRNA gene copy numbers and amino acid compositions, indicating that maximum efficiency constitutes ubiquitous selection pressure on protein translation.

Genomic Complexity Places Less Restrictions on the Evolution of Young Coexpression Networks than Protein-Protein Interactions.

The differences in evolutionary patterns of young protein-protein interactions (PPIs) among distinct species have long been a puzzle. However, based on our genome-wide analysis of available integrated experimental data, we confirm that young genes preferentially integrate into ancestral PPI networks, and that this manner is consistent in all of six model organisms with widely different levels of phenotypic complexity. We demonstrate that the level of restrictions placed on the evolution of biological networks declines with a decrease of phenotypic complexity.

Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties.

Genomic islands are genomic fragments of alien origin in bacterial and archaeal genomes, usually involved in symbiosis or pathogenesis. In this work, we described Zisland Explorer, a novel tool to predict genomic islands based on the segmental cumulative GC profile. Zisland Explorer was designed with a novel strategy, as well as a combination of the homogeneity and heterogeneity of genomic sequences.

Gene re-annotation in genome of the extremophile Pyrobaculum aerophilum by using bioinformatics methods.

In this paper, we re-annotated the genome of Pyrobaculum aerophilum str. IM2, particularly for hypothetical ORFs. The annotation process includes three parts.