Prediction of miRNA targets by learning from interaction sequences.

MicroRNAs (miRNAs) are involved in a diverse variety of biological processes through regulating the expression of target genes in the post-transcriptional level. So, it is of great importance to discover the targets of miRNAs in biological research. But, due to the short length of miRNAs and limited sequence complementarity to their gene targets in animals, it is challenging to develop algorithms to predict the targets of miRNA accurately.

Mig-14 may contribute to Salmonella enterica serovar Typhi resistance to polymyxin B by decreasing the permeability of the outer-membrane and promoting the formation of biofilm.

Mig-14 is essential for Salmonella enterica serovar Typhimurium (S. Typhimurium) resistance to antimicrobial peptides, including polymyxin B (PB). However, the molecular mechanism is as yet unknown.

Nucleotide-level Convolutional Neural Networks for Pre-miRNA Classification.

Due to the biogenesis difference, miRNAs can be divided into canonical microRNAs and mirtrons. Compared to canonical microRNAs, mirtrons are less conserved and hard to be identified. Except stringent annotations based on experiments, many in silico computational methods have be developed to classify miRNAs.

QsvR integrates into quorum sensing circuit to control Vibrio parahaemolyticus virulence.

Vibrio parahaemolyticus, the leading cause of seafood-associated gastroenteritis worldwide, requires the two type-III secretion systems (T3SS1 and T3SS2) and a thermostable direct hemolysin (encoded by tdh1 and tdh2) for full virulence. The tdh genes and the T3SS2 gene cluster constitute an 80 kb pathogenicity island known as Vp-PAI located on the chromosome II. Expression of T3SS1 and Vp-PAI is regulated in a quorum sensing (QS)-dependent manner but its detailed mechanisms remain unknown.

Identification and Characterization of a Antisense RNA of the Gene of Serovar Typhi.

Antisense RNAs from complementary strands of protein coding genes regulate the expression of genes involved in many cellular processes. Using deep sequencing analysis of the serovar Typhi ( Typhi) transcriptome, a novel antisense RNA encoded on the strand complementary to the gene was revealed. In this study, the molecular features of this antisense RNA were assessed using northern blotting and rapid amplification of cDNA ends.

A 3' UTR-derived non-coding RNA RibS increases expression of cfa and promotes biofilm formation of Salmonella enterica serovar Typhi.

Bacterial non-coding RNAs (ncRNAs) are widely studied and found to play important roles in regulating various cellular processes. Recently, many ncRNAs have been discovered to be transcribed or processed from 3' untranslated regions (3' UTRs). Here we reported a novel 3' UTR-derived ncRNA, RibS, which could influence biofilm formation of Salmonella enterica serovar Typhi (S.

Reciprocal Regulation of OmpR and Hfq and Their Regulatory Actions on the Vi Polysaccharide Capsular Antigen in Salmonella enterica Serovar Typhi.

Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of human typhoid fever. S.

The malS-5'UTR regulates hisG, a key gene in the histidine biosynthetic pathway in Salmonella enterica serovar Typhi.

Bacterial noncoding RNAs (ncRNA) regulate diverse cellular processes, including virulence and environmental fitness. The malS 5' untranslated region (named malS-5'UTR) was identified as a regulatory ncRNA that increases the invasive capacity of Salmonella enterica serovar Typhi. An IntaRNA search suggested base pairing between malS-5'UTR and hisG mRNA, a key gene in the histidine biosynthetic pathway.

Identification and Characterization of a Gene Located on the Linear Plasmid pBSSB1 as an Enhanced Gene of Growth and Motility in Serovar Typhi.

The linear plasmid pBSSB1 mediates the flagellar phase variation in H:z66 positive serovar Typhi ( Typhi). The gene named (. Typhi plasmid number 17 gene) is located on pBSSB1 and encodes the protein STP17.

RpoE promotes invasion and intracellular survival by regulating SPI-1 and SPI-2 in Salmonella enterica serovar Typhi.

Aim: To demonstrate the role of RpoE during the later stage of hyperosmotic stress in Salmonella.

Materials & Methods: Expressions of SPI-1 and SPI-2 under hyperosmotic stress for 120 min were investigated by a microarray, and the invasion and intracellular survival of wild-type and ΔrpoE strains were compared. The global differential expression of bacterial proteins between the wild-type and ΔrpoE strains was examined after 120 min of hyperosmotic stress.

The novel cis-encoded antisense RNA AsrC positively regulates the expression of rpoE-rseABC operon and thus enhances the motility of Salmonella enterica serovar typhi.

Bacterial non-coding RNAs are essential in many cellular processes, including response to environmental stress, and virulence. Deep sequencing analysis of the Salmonella enterica serovar typhi (S. typhi) transcriptome revealed a novel antisense RNA transcribed in cis on the strand complementary to rseC, an activator gene of sigma factor RpoE.

5'-UTR of malS increases the invasive capacity of Salmonella enterica serovar Typhi by influencing the expression of bax.

Aim: An RNA-seq analysis recently identified a 236-nucleotide transcript upstream from malS in Salmonella enterica serovar Typhi. Here, we investigated its molecular characteristics and function.

Materials & Methods: RACE and northern blotting were used to determine the molecular characteristics of the sequence, and mutagenesis, microarray, immunoblotting and an invasion assay were used to investigate the functions of the transcript.

Identification and characterization of a cis antisense RNA of the parC gene encoding DNA topoisomerase IV of Salmonella enterica serovar Typhi.

Bacterial cis-encoded antisense RNAs are transcribed from the opposite strand of protein coding genes, and their regulatory roles adapt cells to changing environmental conditions. By deep sequencing of the transcriptome of Salmonella enterica serovar Typhi, an antisense RNA that is encoded in cis to the parC gene was found. parC encodes the subunit A component of topoisomerase IV, a class of enzymes that relax both positively and negatively supercoiled DNA and are also required for segregation of daughter chromosomes in bacteria.

Design of a comprehensive biochemistry and molecular biology experiment: phase variation caused by recombinational regulation of bacterial gene expression.

Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about Salmonella enterica serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation, antibody agglutination test, and PCR analysis.

Mig-14 plays an important role in influencing gene expression of Salmonella enterica serovar Typhi, which contributes to cell invasion under hyperosmotic conditions.

mig-14 is a horizontally acquired host-induced virulence gene in Salmonella enterica serovar Typhi. The molecular function of mig-14 is still unknown; sequence analysis showed that mig-14 shared homology with the helix-loop-helix motif of the AraC family of transcriptional regulatory proteins. In our previous microarray-based studies, mig-14 was upregulated at the early stage of high osmotic stress, indicating a potential role under this condition.

Identification and characterization of a cis-encoded antisense RNA associated with the replication process of Salmonella enterica serovar Typhi.

Antisense RNAs that originate from the complementary strand of protein coding genes are involved in the regulation of gene expression in all domains of life. In bacteria, some of these antisense RNAs are transcriptional noise while others play a vital role to adapt the cell to changing environmental conditions. By deep sequencing analysis of transcriptome of Salmonella enterica serovar Typhi, a partial RNA sequence encoded in-cis to the dnaA gene was revealed.

OmpR may regulate the putative YehU/YehT two-component system in Salmonella enterica serovar Typhi under hypotonic growth condition.

Decreased expression (twofold) of a putative yehUTS operon of which yehUT encodes a putative YehU/YehT two-component system in the ompR mutant from Salmonella enterica serovar Typhi (S. Typhi) GIFU10007 under hypotonic growth condition was observed by qRT-PCR. Purified recombinant protein OmpR(His6) of GIFU10007 was shown to bind the upstream region of the yehU gene by the gel-shift assay.

Molecular characterization of a functional type VI secretion system in Salmonella enterica serovar Typhi.

The type VI secretion system (T6SS) of Salmonella enterica serovar Typhi (S. typhi) is associated with Salmonella pathogenicity island 6 (SPI-6). Though the T6SS gene cluster is intact in S.

Coregulation of gene expression by sigma factors RpoE and RpoS in Salmonella enterica serovar Typhi during hyperosmotic stress.

Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, a food-borne disease that is prevalent worldwide, most particularly in developing countries. RNA polymerase sigma factors RpoE (σ(E)) and RpoS (σ(S)) govern transcription initiation of two sets of genes in Escherichia and Salmonella.

RpoE may promote flagellar gene expression in Salmonella enterica serovar typhi under hyperosmotic stress.

Salmonella enterica serovar Typhi z66 positive strain contains a fljBA-like operon on a linear plasmid. The operon contains the gene fljB:z66 which encodes the z66 antigen. RpoE is a sigma factor σ(E) that initiates transcription of a series of genes in Escherichia and Salmonella under environmental stresses.

Expression of FLJB:Z66 on a Linear Plasmid of Salmonella Enterica Serovar Typhi is Dependent on FLIA and FLHDC and Regulated By OMPR.

Salmonella enterica serovar Typhi z66-positive strains have two different flagellin genes, fliC:d/j and fljB:z66, located on the chromosome and on a linear plasmid, respectively. To investigate the mechanism underlying the expressional regulation of fljB:z66, gene deletion mutants of the regulators FliA, FlhDC, and OmpR were constructed in this study. The expression levels of fliC and fljB:z66 were analyzed by qRT-PCR in the wild-type strain and mutants at high and low osmolarity.

Expression of tviA is transiently repressed by Hfq in Salmonella enterica serovar Typhi at hyperosmotic stress.

The putative global post-transcriptional regulator gene hfq was deleted in Salmonella enterica serovar Typhi (Salmonella typhi). Genomic DNA microarray assay and quantitative real time PCR were used to estimate the level of gene expression. The expression of tviA, the gene required for expression of the Vi capsular antigen, was increased in the hfq mutant at 30 min of an up-shift osmotic stress but was not at sustained high or low osmolarity, compared to the wild type strain.

Global transcriptional response of Salmonella enterica serovar Typhi to anti-z66 antiserum.

Recent studies have shown that flagella may modulate physiological processes by sensing environmental changes in temperature and moisture. When the z66(+) strain of Salmonella enterica serovar Typhi (S. Typhi) was exposed to an antiserum against the z66 flagellar antigen, the fljBA operon was deleted from a linear plasmid, leading to the unidirectional flagellar phase variation from FljB to FliC.

Identification of a fljA gene on a linear plasmid as the repressor gene of fliC in Salmonella enterica serovar Typhi.

Salmonella enterica serovar Typhi z66-positive strain contains an fljBA-like operon on a linear plasmid and the fliC gene on the chromosome encoding d or j antigen. The fljB-like gene has been identified as the gene encoding z66 antigen. To investigate the function of the fljA-like gene in S.