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Staphylococcus aureus biofilm is a common bio-contaminant source that leads to food cross-contamination and foodborne disease outbreaks. Hence, there is a need for searching novel antibiofilm agents with potential anti-virulence properties to control S. aureus contamination and infections in food systems. In this study, the antibiofilm effects of lactobionic acid (LBA) against S. aureus and its influence on virulence were explored. The minimum inhibition concentration of LBA on S. aureus was 8 mg/mL. Viable count and crystal violet assays revealed that LBA inhibited and inactivated S. aureus biofilms. Microscopic observations further confirmed the antibiofilm activity of LBA on S. aureus that disrupted the biofilm architecture and inactivated the viable cells in biofilms. Moreover, LBA decreased the release of extracellular DNA (eDNA) and extracellular polysaccharide (EPS) in S. aureus biofilms. LBA suppressed biofilm formation by intervening metabolic activity and reduced virulence secretion by repressing the hemolytic activity of S. aureus. Furthermore, LBA altered the expressions of biofilm- and virulence-related genes in S. aureus, further confirming that LBA suppressed biofilm formation and reduced the virulence secretion of S. aureus. The results suggest that LBA might be useful in preventing and controlling biofilm formation and the virulence of S. aureus to ensure food safety. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus biofilms are a serious problem in the food industry. Wall teichoic acid (WTA) is crucial in S. aureus biofilm formation. Overexpression of the WTA-hydrolyzing enzyme glycerophosphoryl diester phosphodiesterase (GlpQ), induced by lactobionic acid (LBA), may be related to biofilm formation. We investigated the relationship between the regulation on GlpQ degradation of WTA by LBA and S. aureus biofilm formation. LBA minimum inhibitory concentration for S. aureus was 12.5 mg/mL. Crystal violet staining revealed the LBA-mediated inhibition of S. aureus adhesion and biofilm formation. RT-qPCR revealed the repressed expression of adhesion-related genes by LBA. Scanning electron microscopy revealed the obvious disruption of S. aureus surface structure, confirming the repression of S. aureus adhesion and biofilm formation by LBA. Native-PAGE results suggested that the WTA content of S. aureus was reduced under the inhibition of LBA. Additionally, LBA induced the overexpression of glpQ. Combined with our previous work, these results suggest that glpQ is induced in S. aureus to function in WTA degradation with the addition of LBA, resulting in decreased WTA content and subsequent reduction of adhesion and biofilm formation. The findings provide new insight into the degradation mechanism of S. aureus WTA and indicate the potential of LBA as an anti-biofilm agent. [ABSTRACT FROM AUTHOR]

Flurochloridone (FLC) is a widely used herbicide in developing countries. Although the testes are a target organ for FLC in rats, the adverse effects of FLC on testes have not been fully elucidated. To clarify them, we performed RNA-seq analysis using the testes of FLC-treated rats from our previous subchronic toxicity tests. Unilateral testes of three male rats from solvent control groupand three FLC-treated groups (3 mg/kg, 31.25 mg/kg and 125 mg/kg) were used for RNA extraction. A poly A selection protocol coupled with an Illumina TruSeq RNA-Seq library protocol was used to construct RNA-Seq libraries. Principal component analysis (PCA), differentially expressed gene (DEG) analysis, and hierarchical clustering analysis (HCA) were conducted using R. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to understand the biological characteristics of the DEGs using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The results indicated that many up-regulated DEGs were enriched in pathways associated with testicular injury, such as mitogen-activated protein kinase (MAPK) signaling, lysosome and focal adhesion. Many down-regulated DEGs were enriched in pathways associated with testicular reproduction function, such as sexual reproduction, spermatogenesis and germ cell development. Moreover, we confirmed the oral no-observed-adverse-effect level (NOAEL) of 3 mg/kg in subchronic toxicity test, because the overall testicular gene expression in 3 mg/kg FLC-treated group was similar to that of the solvent control group. In 31.25 mg/kg and 125 mg/kg groups, DEGs revealed that testicular injury was related to oxidative stress. [ABSTRACT FROM AUTHOR]

Riemerella anatipestifer is one of the most important bacterial pathogen of ducks and causes a contagious septicemia. R. anatipestifer infection causes serositis syndromes similar to other bacterial infections in ducks, including infection by Escherichia coli, Salmonella enterica and Pasteurella multocida. Clinically differentiating R. anatipestifer infections from other bacterial pathogen infections is usually difficult. In this study, MAb 1G2F10, a monoclonal antibody against R. anatipestifer GroEL, was used to develop a colloidal gold immunochromatographic strip. Colloidal gold particles were prepared by chemical synthesis to an average diameter of 20±5.26 nm by transmission electron microscope imaging. MAb 1G2F10 was conjugated to colloidal gold particles and the formation of antibody-colloidal gold conjugates was monitored by UV/Vis spectroscopy. Immunochromatographic strips were assembled in regular sequence through different accessories sticked on PVC plate. Strips specifically detected R. anatipestifer within 10 min, but did not detect E. coli, S. enterica and P. multocida. The detection limit for R. anatipestifer was 1×106 colony forming units, which was 500 times higher than a conventional agglutination test. Accuracy was 100% match to multiplex PCR. Assay stability and reproducibility were excellent after storage at 4°C for 6 months. The immunochromatographic strips prepared in this study offer a specific, sensitive, and rapid detection method for R. anatipestifer, which is of great importance for the prevention and control of R. anatipestifer infections. [ABSTRACT FROM AUTHOR]

Riemerella anatipestifer is reported worldwide as a cause of septicemic and exudative diseases of domestic ducks. In this study, we identified a mutant strain RA2640 by Tn4351 transposon mutagenesis, in which the AS87_04050 gene was inactivated by insertion of the transposon. Southern blot analysis indicated that only one insertion was found in the genome of the mutant strain RA2640. SDS-PAGE followed by silver staining showed that the lipopolysaccharide (LPS) pattern of mutant strain RA2640 was different from its wild-type strain Yb2, suggesting the LPS was defected. In addition, the phenotype of the mutant strain RA2640 was changed to rough-type, evident by altered colony morphology, autoaggregation ability and crystal violet staining characteristics. Bacterial LPS is a key factor in virulence as well as in both innate and acquired host responses to infection. The rough-type mutant strain RA2640 showed higher sensitivity to antibiotics, disinfectants and normal duck serum, and higher capability of adherence and invasion to Vero cells, compared to its wild-type strain Yb2. Moreover, the mutant strain RA2640 lost the agglutination ability of its wild-type strain Yb2 to R. anatipestifer serotype 2 positive sera, suggesting that the O-antigen is defected. Animal experiments indicated that the virulence of the mutant strain RA2640 was attenuated by more than 100,000-fold, compared to its wild-type strain Yb2. These results suggested that the AS87_04050 gene in R. anatipestifer is associated with the LPS biosynthesis and bacterial pathogenicity. [ABSTRACT FROM AUTHOR]

Highlights: [•] A static and dynamic model is presented for a producing CBM field in Qinshui Basin, China. [•] Dynamic model is history matched using the 16-month field data of 43 CBM wells. [•] A new purpose-build economic model is presented. [•] Well spacing for CBM production is optimised based on an integrated techno-economic approach. [•] Feasibility of ECBM for various injection gas compositions, injection timing, gas price and carbon credits is studied. [Copyright &y& Elsevier]

Salmonella enterica serovar Enteritidis (S. Enteritidis) presents an excellent capacity to survive in egg white, which is a hostile environment for bacterial growth. To reveal its survival mechanism, this study focuses on the specific gene SEN1393, which has been found to exist only in the genomic sequence of S. Enteritidis. The survival capacity of the deletion mutant strain ΔSEN1393 was proven to be significantly reduced after incubation in egg white. RNA sequencing and RT-qPCR results demonstrate that the expression levels of 19 genes were up-regulated, while the expression levels of 9 genes were down-regulated in egg white. These genes were classified into 6 groups based on their functional categories, namely the sulfate assimilation pathway, arginine biosynthesis, the tricarboxylic acid cycle, the fimbrial protein, the transport and chelation of metal ion, and others (sctT , rhs , and pspG). The strain ΔSEN1393 was deduced to damage Fe S cluster enzymes and increase the sulfate and iron requirements, and to reduce bacterial motility and copper homeostasis. Via InterProScan analysis, the gene SEN1393 was speculated to encode a TerB-like and/or DjlA-like protein, and therefore, together with cysJ , possibly reduced the oxidative toxicities resulting from oxyanions such as tellurite, and/or improved CysPUWA conformation to restrain the uptake of the toxic oxyanions. In summary, the gene SEN1393 enabled the higher survival of S. Enteritidis in egg white as compared to other pathogens by regulating the sulfate assimilation pathway. • The gene SEN1393 was speculated to encode a TerB-like and/or DjlA-like protein. • The strain ΔSEN1393 was deduced to damage Fe S cluster enzymes. • SEN1393, together with cysJ , possibly reduced the oxyanion toxicities. • SEN1393 possibly improved CysPUWA conformation to restrain the oxyanion uptake. • SEN1393 could significantly increase the survival of S. Enteritidis in egg white. [ABSTRACT FROM AUTHOR]

The homeoprotein Msx1 plays a critical role in embryonic patterning, particularly to maintain myogenic progenitor cell fate. However, the mechanisms underlying Msx1-mediated inhibition of myogenesis remain largely unknown. Here, we show that Msx1 cooperates with the protein kinase C-related kinase 1 (Pkn1), a member of the protein kinase C-related kinase family, to prevent the terminal differentiation of myogenic precursor cells. In mouse C2C12 cells, Pkn1 knockout partly impaired Msx1-mediated inhibition of myogenic differentiation, indicating a role for Pkn1 in this process. Furthermore, we found that Pkn1 was required for Msx1 enrichment at the promoter of Myf5, a myogenic regulatory gene. In Pkn1 knockout cells, this reduced Msx1 enrichment at the Myf5 promoter coincided with attenuated repression of Myf5 transcription. Together with our observation that Msx1 and Pkn1 were associated in a protein complex, these findings strongly suggest that Msx1 cooperates with Pkn1 to down-regulate Myf5 and, therefore, prevent the differentiation of myogenic precursor cells. Collectively, our data provide key insights into the mechanisms underlying Msx1 function in the prevention of myogenic differentiation. • Msx1 cooperates with Pkn1 to prevent the differentiation of myogenic precursor cells. • Msx1 cooperates with Pkn1 to promote cell proliferation. • Pkn1 cooperates with Msx1 to inhibit Myf5 expression. • Pkn1 drives Msx1 localisation to the nuclear periphery. [ABSTRACT FROM AUTHOR]

Summary We comprehensively analyzed clinical, genomic, and transcriptomic data of a cohort of 465 primary triple-negative breast cancer (TNBC). PIK3CA mutations and copy-number gains of chromosome 22q11 were more frequent in our Chinese cohort than in The Cancer Genome Atlas. We classified TNBCs into four transcriptome-based subtypes: (1) luminal androgen receptor (LAR), (2) immunomodulatory, (3) basal-like immune-suppressed, and (4) mesenchymal-like. Putative therapeutic targets or biomarkers were identified among each subtype. Importantly, the LAR subtype showed more ERBB2 somatic mutations, infrequent mutational signature 3 and frequent CDKN2A loss. The comprehensive profile of TNBCs provided here will serve as a reference to further advance the understanding and precision treatment of TNBC. Graphical Abstract Highlights • We build the genomic and transcriptomic landscape of 465 primary TNBCs • Chinese TNBC cases demonstrate more PIK3CA mutations and LAR subtype • Transcriptomic data classify TNBCs into four subtypes • Multi-omics profiling identifies potential targets within specific TNBC subtypes Jiang et al. characterize primary Chinese triple-negative breast cancer (TNBC) and classify it into four subtypes. They find that these TNBCs have more frequent PIK3CA mutations and chromosome 22q11 copy-number gains than non-Asian TNBCs and that the LAR subtype has more ERBB2 somatic mutations and CDKN2A loss. [ABSTRACT FROM AUTHOR]

RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples that are generally considered less useful byproducts during the processes of plasma and serum separation, respectively. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis. We performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns, detection of differentially expressed genes, and immunological characterizations, suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis. Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research., Supplementary Information: The online version contains supplementary material available at 10.1007/s43657-023-00121-1., Competing Interests: Conflict of InterestThe authors declare no competing financial interests. ZC and RZ are the editorial operation team members of Phenomics, and they were not involved in reviewing this paper., (© The Author(s) 2023.)

Background: Drug metabolizing enzymes and transporters (DMETs) play crucial roles in drug absorption and disposition. Species differences in the interaction of compounds with DMETs may contribute to the accuracy of animal models in predicting human responses in clinical studies. Thus it is important to clarify the expression heterogeneity of DMETs between human and rat, that is commonly used as a model for evaluating drug efficacy and drug safety., Methods: We compared the expression patterns of DMETs based on a rat RNA-seq dataset and the human Genotype-Tissue Expression (GTEx) datasets. A relatively high correlation of expression of DMETs between rat and human was observed in most organs, while a lower correlation was detected in the liver and kidney; however, a greater number of genes were variably expressed in the latter two organs. We characterized the basal expression traits of DMETs in rat in terms of organ, sex, and developmental differences., Results: Co-expressed modules across organs of DMETs were identified to include potential functionally- related genes. Interestingly, most of these modules showed liver- and/or kidney-specific expression. Moreover, we identified DMETs modules that were highly correlated to sex or developmental stages. Finally, we created networks containing sex and/or developmentally-related drugs and diseases with their related DMETs to display the clinical significance of sexually dimorphic and/or developmentally- specific DMET genes., Conclusion: Our study provides a deeper understanding of species differences in not only DMETs but specific susceptibility to adverse drug reactions (ADRs)., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.)

Riemerella anatipestifer is a well-described pathogenic bacterium, which is reported worldwide as the cause of epizootic infectious polyserositis of waterfowl and other avian species. Here, we present the complete genome sequence of R. anatipestifer strain CH3, the serotype 1 prevalent in China., (Copyright © 2015 Wang et al.)

Mitogen-activated protein kinase 1 (MAPK1) acts as an integration point for multiple biochemical signals, and is involved in a wide variety of biological processes such as cell proliferation and differentiation, transcription regulation, and development. Mitogen-activated protein kinase 1 plays an important role in inducing cell death in bacterial infections. In this study, the duck MAPK1 gene was cloned for the first time from the Cherry Valley duck. Sequence analysis showed that duck MAPK1 cDNA is 1,557 bp long, with an open reading frame of 1,107 bp. It encodes 368 amino acids, with 85.4, 84.5, and 97.3% homology with the human, mouse, and chicken MAPK1 gene, respectively. Furthermore, a SYBR Green quantitative real-time PCR assay was developed to detect duck MAPK1 expression. Following Riemerella anatipestifer infection by virulent strain Yb2, MAPK1 mRNA level increased more than 200-fold in the duck spleens, suggesting that increased duck MAPK1 expression can be used as an indicator of bacterial infection. Our results provide ground work to warrant further studies of the duck MAPK1 gene in bacterial pathogenesis., (© 2014 Poultry Science Association Inc.)