Multi-species SIR models from a dynamical Bayesian perspective

Multi-species compartment epidemic models, such as the multi-species susceptible–infectious–recovered (SIR) model, are extensions of the classic SIR models, which are used to explore the transient dynamics of pathogens that infect multiple hosts in a large population. In this article, we propose a dynamical Bayesian hierarchical SIR (HSIR) model, to capture the stochastic or random nature of an epidemic process in a multi-species SIR (with recovered becoming susceptible again) dynamical setting, under hidden mass balance constraints. We call this a Bayesian hierarchical multi-species SIR (MSIR_B) model. Different from a classic multi-species SIR model (which we call MSIR_C), our approach imposes mass balance on the underlying true counts rather than, improperly, on the noisy observations. Moreover, the MSIR_B model can capture the discrete nature of, as well as uncertainties in, the epidemic process.     

Length-weight relationships of four fish species from the Yalong River,China

Parameters of the length-weight relationship (LWR) were estimated for four fish species [Beaufortia szechuanensis (Fang, 1930), Claea dabryi (Sauvage, 1874), Percocypris pingi (Tchang, 1930), and Yunnanilus sichuanensis Ding, 1995] from the Yalong River. Samples were collected seasonally from June 2018 to July 2019, using various fishing gears [set nets (mesh: 1.5 × 2.0 cm), hook, drift gill nets (three mesh sizes: 1.0; 2.0; 3.0 cm) and electro fishing]. Two new maximum standard length were recorded for C. dabryi and P. pingi.     

A risk signature-based on metastasis-associated genes to predict survival of patients with osteosarcoma

Osteosarcoma (OS) is the most common primary solid malignant bone tumor, and its metastasis is a prominent cause of high mortality in patients. In this study, a prognosis risk signature was constructed based on metastasis-associated genes. Four microarrays datasets with clinical information were downloaded from Gene Expression Omnibus, and 256 metastasis-associated genes were identified by limma package. Further, a protein-protein interaction network was constructed, and survival analysis was performed using data from the Therapeutically Applicable Research to Generate Effective Treatments data matrix, identifying 19 genes correlated with prognosis. Six genes were selected by the least absolute shrinkage and selection operator regression for multivariate cox analysis. Finally, a three-gene (MYC, CPE, and LY86) risk signature was constructed, and datasets GSE21257 and GSE16091 were used to validate the prediction efficiency of the signature. The survival times of low- and high-risk groups were significantly different in the training set and validation set. Additionally, gene set enrichment analysis revealed that the genes in the signature may affect the cell cycle, gap junctions, and interleukin-6 production. Therefore, the three-gene survival risk signature could potentially predict the prognosis of patients with OS. Further, proteins encoded by CPE and LY86 may provide novel insights into the prediction of OS prognosis and therapeutic targets.     

microRNA-95 knockdown inhibits epithelial–mesenchymal transition and cancer stem cell phenotype in gastric cancer cells through MAPK pathway by upregulating DUSP5

This study investigated the role of microRNA-95 (miR-95) in gastric cancer (GC) and to elucidate the underlying mechanism. Initially, bioinformatic prediction was used to predict the differentially expressed genes and related miRNAs in GC. miR-95 and DUSP5 expression was altered in GC cell line (MGC803) to evaluate their respective effects on the epithelial–mesenchymal transition (EMT) process, cellular processes (cell proliferation, migration, invasion, cell cycle, and apoptosis), cancer stem cell (CSC) phenotype, as well as tumor growth ability. It was further predicted in bioinformatic prediction and verified in GC tissue and cell line experiments that miR-95 was highly expressed in GC. miR-95 negatively regulated DUSP5, which resulted in the MAPK pathway activation. Inhibited miR-95 or overexpressed DUSP5 was observed to inhibit the levels of CSC markers (CD133, CD44, ALDH1, and Lgr5), highlighting the inhibitory role in the CSC phenotype. More important, evidence was obtained demonstrating that miR-95 knockdown or DUSP5 upregulation exerted an inhibitory effect on the EMT process, cellular processes, and tumor growth. Together these results, miR-95 knockdown inhibited GC development via DUSP5-dependent MAPK pathway.     

Pseudomonas oryzae sp. nov. isolated from a paddy soil in South China

A Gram-staining-negative, rod-shaped and motile with several polar flagellums bacterium, designated WM-3^T, was isolated from a rice paddy soil in South China. Growth occurred with 0–3.0 % (w/v) NaCl (optimum 2.0 %), at pH 5.5–9.0 (optimum pH 7.0) and at 25–42 °C (optimum 30–37 °C) in liquid Reasoner’s 2A medium. Analysis of the 16S rRNA gene and gyrB gene sequences revealed that strain WM-3^T was most closely related to the type strains of the species Pseudomonas linyingensis and Pseudomonas sagittaria. Its sequence similarities with P. linyingensis CGMCC 1.10701^T and P. sagittaria JCM 18195^T were 97.4 and 97.3 %, respectively, for 16S rRNA gene, and were 94.1 and 94.2 %, respectively, for gyrB gene. DNA–DNA hybridization between strain WM-3^T and these two type strains showed relatedness of 35.6 and 30.9 %, respectively. G+C content of genomic DNA was 69.4 mol%. The whole-cell fatty acids mainly consisted of C_16:0 (30.0 %), C_16:1 ω6c and/or C_16:1 ω7c (19.3 %) and C_18:1 ω6c and/or C_18:1 ω7c (16.3 %). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain WM-3^T belongs to genus Pseudomonas but represents a novel species, for which the name Pseudomonas oryzae sp. nov. is proposed. The type strain is WM-3^T (=KCTC 32247^T =CGMCC 1.12417^T).     

The N Termini of a-Subunit Isoforms Are Involved in Signaling between Vacuolar H+-ATPase (V-ATPase) and Cytohesin-2

Previously, we reported an acidification-dependent interaction of the endosomal vacuolar H⁺-ATPase (V-ATPase) with cytohesin-2, a GDP/GTP exchange factor (GEF), suggesting that it functions as a pH-sensing receptor. Here, we have studied the molecular mechanism of signaling between the V-ATPase, cytohesin-2, and Arf GTP-binding proteins. We found that part of the N-terminal cytosolic tail of the V-ATPase a2-subunit (a2N), corresponding to its first 17 amino acids (a2N(1–17)), potently modulates the enzymatic GDP/GTP exchange activity of cytohesin-2. Moreover, this peptide strongly inhibits GEF activity via direct interaction with the Sec7 domain of cytohesin-2. The structure of a2N(1–17) and its amino acids Phe⁵, Met¹⁰, and Gln¹⁴ involved in interaction with Sec7 domain were determined by NMR spectroscopy analysis. In silico docking experiments revealed that part of the V-ATPase formed by its a2N(1–17) epitope competes with the switch 2 region of Arf1 and Arf6 for binding to the Sec7 domain of cytohesin-2. The amino acid sequence alignment and GEF activity studies also uncovered the conserved character of signaling between all four (a1–a4) a-subunit isoforms of mammalian V-ATPase and cytohesin-2. Moreover, the conserved character of this phenomenon was also confirmed in experiments showing binding of mammalian cytohesin-2 to the intact yeast V-ATPase holo-complex. Thus, here we have uncovered an evolutionarily conserved function of the V-ATPase as a novel cytohesin-signaling receptor.