Ottowia cancrivicina sp. nov., isolated from human stomach.

A Gram-negative, facultative anaerobic, non-motile and rod-shaped bacterium, designated 10c7w1T, was isolated from a human gastrointestinal tract. Colonies on agar plates were small, circular, smooth and beige. The optimal growth conditions were determined to be 37 °C, pH 7.0-7.5 and 0 % (w/v) NaCl. Comparative analysis of complete 16S rRNA gene sequences revealed that strain 10c7w1T showed the highest sequence similarity of 95.8 % to Ottowia beijingensis MCCC 1A01410T, followed by Ottowia thiooxydans (95.2 %) JCM 11629T. The average amino acid identity values between 10c7w1T and O. beijingensis MCCC 1A01410T and O. thiooxydans JCM 11629T were above 60 % (71.4 and 69.5 %). The average nucleotide identity values between strain 10c7w1T and O. beijingensis MCCC 1A01410T and O. thiooxydans JCM 11629T were 76.9 and 72.5 %, respectively. The dominant fatty acids (≥10 %) were straight chain ones, with summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) and C16 : 00 being the most abundant. Q-8 was the only respiratory quinone. The major polar lipids of strain 10c7w1T were phosphatidylethanolamine, diphosphatidylglycerol and unknown lipids. The DNA G+C content of strain 10c7w1T was 63.6 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic data, strain 10c7w1T is considered to represent a novel species within the genus Ottowia, for which the name Ottowia cancrivicina sp. nov. is proposed. The type strain is 10c7w1T (=MCCC 1H01399T=KCTC 92200T).

Recombinant expression and immune function analysis of C-reactive protein (CRP) from Hexagrammos otakii.

C-reactive protein (CRP) belongs to the short-chain pentraxin family and functions as a soluble pattern recognition molecule (PRM) aiding in host defense against pathogens. In the present study, a CRP gene, designated HoCRP, was cloned from Hexagrammos otakii for the first time. The full length of the HoCRP cDNA sequence is 821 bp, which contains an open reading frame (ORF) of 675 bp encoding a 224 amino acid protein. The deduced protein is predicted to have a theoretical isoelectric point (pI) of 5.30 and a molecular weight of 25.4 kDa. The recombinant HoCRP protein (rHoCRP) was expressed in E. coli to further characterize the functions of HoCRP. Saccharide binding experiments demonstrated that rHoCRP exhibited a high affinity for various pathogen-associated molecular patterns (PAMPs). Furthermore, bacterial binding and agglutination assays indicated that rHoCRP had the capability to recognize a wide spectrum of microorganisms. These findings suggest that HoCRP functions not only as a PRM for binding PAMPs but also as an immune effector molecule. Considering the role CRP plays in the classical complement pathway, the interaction between rHoCRP and rHoC1q was assessed and proven by a Pull-down and Elisa assay, which implied that rHoCRP may be able to activate complement. In addition, phagocytosis enhancement by rHoCRP in the presence or absence of complement components was analysed by flow cytometry. The results showed that rHoCRP could synergistically enhance the phagocytosis of RAW264.7 cells with complement, providing further evidence of complement activation by rHoCRP through the opsonization of specific complement components. In summary, our findings suggest that rHoCRP may play a crucial role in host antibacterial defense by recognizing pathogens, activating the complement system, and enhancing macrophage function.

Molecular characterization and functional analysis of peroxiredoxin 1 (Prx1) from roughskin sculpin (Trachidermus fasciatus).

Peroxiredoxin1(Prx1), also known as natural killer enhancing factor A (NKEF-A), is a crucial antioxidant involving in various cellular activities and immune response against bacterial and viral infection in fish. In the present study, a full-length Prx1 cDNA sequence (TfPrx1) was firstly cloned from roughskin sculpin (Trachidermus fasciatus), which was composed of 1044 bp nucleotides encoding a peptide of 199 amino acids with a molecular weight of 22.35 kDa and a theoretical pI of 6.42, respectively. The predicted peptide was a typical 2-cys Prx containing two conserved characteristic motifs 43FYPLDFTFVCPTEI56 and 170GEVCPA175 with the two conserved peroxidatic and resolving cysteine residuals forming disulfide bond. Quantitative real-time PCR analysis showed that TfPrx1 was ubiquitously expressed in all tested tissues with the highest expression in the intestine. It could be significantly induced following LPS injection and heavy metal exposure. Recombinant TfPrx1 (rTfPrx1) displayed insulin disulfide reduction and ROS-scavenging activity in a concentration-dependent manner, and further exhibited DNA and cytoprotective effects under oxidative stress. These results suggested that TfPrx1 protein may play an important role in fish immune protection from oxidative damage.

MaxCLK: discovery of cancer driver genes via maximal clique and information entropy of modules.

MOTIVATION: Cancer is caused by the accumulation of somatic mutations in multiple pathways, in which driver mutations are typically of the properties of high coverage and high exclusivity in patients. Identifying cancer driver genes has a pivotal role in understanding the mechanisms of oncogenesis and treatment. RESULTS: Here, we introduced MaxCLK, an algorithm for identifying cancer driver genes, which was developed by an integrated analysis of somatic mutation data and protein-protein interaction (PPI) networks and further improved by an information entropy index. Tested on pancancer and single cancers, MaxCLK outperformed other existing methods with higher accuracy. About pancancer, we predicted 154 driver genes and 787 driver modules. The analysis of co-occurrence and exclusivity between modules and pathways reveals the correlation of their combinations. Overall, our study has deepened the understanding of driver mechanism in PPI topology and found novel driver genes. AVAILABILITY AND IMPLEMENTATION: The source codes for MaxCLK are freely available at https://github.com/ShandongUniversityMasterMa/MaxCLK-main.

Downregulation of miR­7 and miR­153 is involved in Helicobacter pylori CagA induced gastric carcinogenesis and progression.

Helicobacter pylori (H. pylori) infection plays a pivotal role in the development of gastric cancer (GC). However, the association between aberrant microRNAs (miRNAs/miRs) expression and H. pylori­induced GC remains poorly understood. The present study reported that repeated infection of H. pylori caused the oncogenicity of GES­1 cells in BALB/c Nude mice. miRNA sequencing revealed that both miR­7 and miR­153 were significantly decreased in the cytotoxin­associated gene A (CagA) positive GC tissues and this was further confirmed in a chronic infection model of GES­1/HP cells. Further biological function experiments and in vivo experiments validated that miR­7 and miR­153 can promote apoptosis and autophagy, inhibit proliferation and inflammatory response in GES­1/HP cells. All the associations between miR­7/miR­153 and their potential targets were revealed via bioinformatics prediction and dual­luciferase reporter assay. Particularly, downregulation of both miR­7 and miR­153 obtained an improved sensitivity and specificity in diagnosing H. pylori (CagA+)­induced GC. The present study identified that the combination of miR­7 and miR­153 may be regarded as novel therapeutic targets in H. pylori CagA (+)­associated GC.

Helicobacter pylori and gastric microbiota homeostasis: progress and prospects.

Helicobacter pylori, a Gram-negative microaerobic bacteria belonging to the phylum Proteobacteria, can colonize in the stomach and duodenum, and cause a series of gastrointestinal diseases such as gastritis, gastric ulcer and even gastric cancer. At present, the high diversity of the microorganisms in the stomach has been confirmed with culture-independent methods; some researchers have also studied the stomach microbiota composition at different stages of H. pylori carcinogenesis. Here, we mainly review the possible role of H. pylori-mediated microbiota changes in the occurrence and development of gastric cancer to provide new ideas for preventing H. pylori infection and regulating microecological imbalance.

Sox9 Is Crucial for Mesenchymal Stem Cells to Enhance Cutaneous Wound Healing.

BACKGROUND AND OBJECTIVES: Human umbilical cord mesenchymal stem cells (HUC-MSCs) are promising candidates for cell-based therapy in regenerative medicine or other diseases due to their superior characteristics, including higher proliferation, faster self-renewal ability, lower immunogenicity, a noninvasive harvest procedure, easy expansion in vitro, and ethical access, compared with stem cells from other sources. METHODS AND RESULTS: In the present study, we knocked down the expression of SOX9 in HUC-MSCs by lentivirus interference and found that knockdown of SOX9 inhibited the proliferation and migration of HUC-MSCs and influenced the expression of cytokines (IL-6 and IL-8), growth factors (GM-CSF and VEGF) and stemness-related genes (OCT4 and SALL4). In addition, the repair effect of skin with burn injury in rats treated with HUC-MSCs transfected with sh-control was better than that rats treated with HUC-MSCs transfected with shSOX9 or PBS, and the accessory structures of the skin, including hair follicles and glands, were greater than those in the other groups. We found that knockdown of the expression of SOX9 obviously inhibited the expression of Ki67, CK14 and CK18. CONCLUSIONS: In conclusion, this study will provide a guide for modifying HUC-MSCs by bioengineering technology in the future.

Acute and chronic infection of H. pylori caused the difference in apoptosis of gastric epithelial cells.

Helicobacter pylori (H. pylori) is one of the most important pathogenic bacteria associated with various gastrointestinal diseases. At present, its apoptotic or antiapoptotic mechanism on gastric epithelial cells remains unknown and needs further illustrated. In this study, acute infection model (H. pylori and GES-1 cells were co-cultured for 24 h at a multiplicity of infection MOI of 100:1) and chronic infection model (GES-1 cells were infected repeatedly every 24 h at a multiplicity of infection MOI of 100:1 for approximately 8 weeks) were established, respectively. the chronic H. pylori infected GES-1 cells underwent a typically morphological change and Western Blot results showed that there was slight decrease in expression of E-cadherin, and obvious increase in expression of Vimentin. Apoptosis of these two models were analyzed by flow cytometry compared with the control cells, meanwhile, apoptosis associated markers (Bcl-xL, Bcl-2, Bax, etc) were detected by Western blot, additional in clinical H. pylori-positive gastric cancer tissues. Results showed that compared with the control cells, acute infection of H. pylori significantly accelerated the apoptosis of GES-1, increased the expression of Bax and Cleaved caspase-3, down-regulated expression of Bcl-xL and Bcl-2. Moreover, an opposite result was found in chronic infection of model and clinical gastric cancer tissues, and enhanced expression of NF-κB p65. Taken together, these findings suggest that H. pylori infection plays differential effects on apoptosis of gastric epithelial cells.

The mitochondrial genome of the orange-striped green sea anemone Diadumene lineata (Actiniaria: Diadumenidae): the first complete sequence in the family Diadumenidae.

The complete mitogenome of the orange-striped green sea anemone (Diadumene lineata) has been sequenced and annotated for the first time. The total length of the mitogenome is 17,552 bp with an A+T content of 62.6%. Unlike typical metazoan mitogenome, this mitogenome include 14 protein-coding genes (13 energy pathway protein coding genes, and a heg gene), two tRNAs, two rRNAs, and 19 intergenic regions. The COX1 gene possesses a homing endonuclease gene. This circular genome contains two introns, one in ND5 and another in COX1.This sequence is the first sequenced complete mitogenome in Diadumenidae and provides fundamental data for exploring complicated evolutionary relationships in Actiniaria.

The mitochondrial genome of the toothed top shell snail Monodonta labio (Gastropoda: Trochidae): the first complete sequence in the subfamily monodontinae.

The mitochondrial genome (mitogenome) is a powerful tool that is extensively used in genomic and phylogenetic analysis. In this study, the complete mitogenome of the toothed top shell snail (Monodonta labio) has been sequenced and annotated for the first time. The complete circular genome is 16,440 bp in length including 13 protein-coding genes, 22 transfer RNA and two ribosomal RNA genes. All of the protein-coding genes use the standard initiation codon ATN and are terminated by the termination codons TAA and TAG. All of the tRNA genes have the typical clover leaf structure, with the exception of the tRNA-Asp, which lacks aTψC arm, and tRNA-Ser(AGN), which lacks a DHU arm. Relatively short intergenic spacers and overlaps are observed in this mitogenome. Our phylogenetic tree shows that M. labio is clustered together with other species within Trochidae. The complete mitogenome of M. labio provide essential DNA data for evolutionary and phylogenetic analysis of marine gastropods.

The diagnostic roles of neutrophil in bloodstream infections.

Bloodstream infections remain a leading cause of death worldwide, despite advances in critical care and understanding of the pathophysiology and treatment strategies. No specific biomarkers or therapy are available for these conditions. Neutrophils play a critical role in controlling infection and it is suggested that their migration and antimicrobial activity are impaired during sepsis which contribute to the dysregulation of immune responses. Recent studies further demonstrated that interruption or reversal of the impaired migration and antimicrobial function of neutrophils improves the outcome of sepsis in animal models. In this review, we provide an overview of the associated diagnostic biomarkers involved neutrophils in sepsis, and discuss the potential of neutrophils as a target to specifically predict the outcome of sepsis.

Complete mitochondrial genome of maritime striped squirrel Tamiops maritimus (Rodentia: Sciuridae).

The complete mitochondrial genome of the maritime striped squirrel (Tamiops maritimus) was first sequenced and characterized. The genome was 16 523 bp in length, and the composition and the arrangement of genes were analogous to other rodents. The sequence of T. maritimus was used to construct phylogenetic tree with additional mitochondrial genomes of seven sciurid species available on GenBank. Phylogenetic result indicated that T. maritimus has a close relationship with T. swinhoei. Our mitochondrial genome data may provide information for species identification, diversity evaluation, and other studies about this genus.

Complete mitochondrial genome of the mandarin vole Lasiopodomys mandarinus (Rodentia: Cricetidae).

The complete sequence of the mitochondrial genome of the mandarin vole (Lasiopodomys mandarinus) was completed and annotated in this study. The circular genome is 16,375 bp in length and contains the typical 37 genes that are arranged in the same order as that of the putative ancestor of vertebrate, 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. This study will provide genetic resource to clarify the taxonomic position of genus Lasiopodomys.

The mitochondrial genome of Murina huttoni rubella (Chiroptera: Vespertilionidae) from China.

Murina huttoni rubella is a common Murina species in China, with a medium forearm length and reddish brown hairs. In this study, based on a male M. h. rubella individual from Jiangxi, China, its complete mitochondrial genome was sequenced and analyzed. The genome is 16,707 bp in length, including 22 tRNA genes, two rRNA genes, 13 protein-coding genes and a control region. The composition and arrangement of genes are similar to other bats. Phylogenetic trees that covered all released complete mitochondrial genome of bats were constructed using Bayesian Inference and maximum likelihood methods. Both phylogenetic results showed that M. h. rubella and M. ussuriensis have closer phylogenetic relationship. The complete mtDNA genome sequence of M. h. rubella would provide valuable information for solving taxonomic and phylogenetic problem in future.

The nearly complete mitochondrial genome of Chinese pygmy dormouse Typhlomys cinereus (Rodentia: Platacanthomyidae).

In this study, we report the nearly complete mitochondrial genome of a Chinese pygmy dormouse Typhlomys cinereus (Rodentia: Platacanthomyidae). The 15,011 bp genome is consisted of 13 protein-coding genes, 16S rRNA, 21 tRNAs, partial 12S rRNA and control region. A phylogenetic tree was built using 12 protein-coding genes of 19 species from Dipodoidea and Muroidea. Our result shows that T. cinereus represents the earliest split within Muroidea. The genome would contribute to further study of phylogeny in Muroidea and Rodentia.

Complete mitochondrial genome of Perny's long-nosed squirrel Dremomys pernyi (Rodentia: Sciuridae).

The complete mitochondrial genome of Perny's long-nosed squirrel (Dremomys pernyi) was firstly sequenced and characterized. The genome was 16,573 bp in length, and its composition and arrangement of genes were analogous to other rodents. The sequences of 13 protein-coding genes were used to construct phylogenetic tree for D. pernyi and other 13 sciurid species available on GenBank. To date, this is the first species whose complete mitochondrial genome sequence was sequenced in genus Dremomys. Our results will provide information for further molecular studies.

Analysis of complete mitochondrial genome and its application to phylogeny of Caryomys inez (Rodentia: Cricetidae: Arvicolinae).

In this study, the complete mitochondrial genome of Inez's red-backed vole Caryomys inez was sequenced and analyzed as the first species in genus Caryomys. The complete mitochondrial genome of C. inez is 16,354 bp in length and shows a typical vertebrate pattern with 13 PCGs, 22 tRNAs, 2 rRNAs and 2 non-coding regions. To gain a clear phylogenetic position of C. inez, a ML phylogenetic tree was constructed based on 12 PCGs on H-strand from 23 rodent species except for ND6 gene which is on L-strand. As a result, C. inez is clustered with genera Eothenomys and Myodes, showing their close phylogenetic relationships. The present study may facilitate further investigation of the taxonomic studies and phylogenetic analyses of the genus Caryomys.

Complete mitochondrial genome of the greater bandicoot rat Bandicota indica (Rodentia: Muridae).

The complete mitochondrial genome of the greater bandicoot rat (Bandicota indica) was first sequenced and characterized. The genome was 16 326 bp in length, the composition and arrangement of its genes were analogous to other rodents. To confirm the phylogenetic position of B. indica, the mitochondrial nucleotide sequence data of other 20 Rodentia species were used to construct phylogenetic tree by maximum likelihood. Phylogenetic analysis demonstrated that genera Bandicota and Rattus were sister taxa, and B. indica was closer to the genus Rattus than to genera Niviventer and Leopoldamys. The mitochondrial genome of B. indica presented in this study can provide useful information for species delimitation, taxonomic and phylogenetic analyses as well as other studies of the species.

Molecular evidence revealed Lepus hainanus and L. peguensis have a conspecific relationship.

Accurate species delimitation in Lepus was often hindered by highly conserved morphology and frequent introgression. In this study, we used rigorous molecular species delimitation methods to evaluate the taxonomic status of Hainan hare (Lepus hainanus) which has been traditionally identified as a distinct species, or a subspecies of Burmese hare (L. peguensis). The genetic distance and phylogenetic network support L. hainanus and L. peguensis are conspecific. However, the phylogenetic species concept and Bayesian species delimitation analysis based on combined mtDNA supported they are different species. The discordance between different methods can be explained by different species criterion. By taking into account our conflict results, we hold the opinion that adoption of the phylogenetic species concept and Bayesian species delimitation analysis would increase the risk of taxonomic inflation of island biota or otherwise spatially isolated population. Conservatively, we suggest that L. hainanus and L. peguensis are conspecific based on the results of our genetic divergence and phylogenetic network exclusively.