Identification of a novel enterovirus E isolates HY12 from cattle with severe respiratory and enteric diseases.

In this study, a virus strain designated as HY12 was isolated from cattle with a disease of high morbidity and mortality in Jilin province. Biological and physiochemical properties showed that HY12 isolates is cytopathic with an extremely high infectivity. HY12 is resistant to treatment of organic solvent and acid, and unstable at 60°C for 1 h. Electron microscopy observation revealed the virus is an approximately 22-28 nm in diameter. The complete genome sequence of HY12 consists of 7416 nucleotides, with a typical picornavirus genome organization including a 5'-untranslated region (UTR), a large single ORF encoding a polyprotein of 2176 amino acids, and a 3'-UTR. Phylogenetic analysis clustered HY12 isolates to a new serotype/genotype within the clade of enterovirus E (formerly BEV-A). Alignment analysis revealed a unique insertion of 2 amino acid residues (NF) at the C-terminal of VP1 protein between aa 825 and 826, and several rare mutations in VP1 and VP4 of HY12 isolates in relation to known bovine enterovirus (BEV) strains. This is the first report of an enterovirus E in China, which is potentially associated with an outbreak in cattle with severe respiratory and enteric diseases

Body mass index and weight loss as risk factors for poor outcomes in patients with idiopathic pulmonary fibrosis: a systematic review and meta-analysis

AbstractObjective The association between nutritional status and prognosis of idiopathic pulmonary fibrosis (IPF) remains unclear. This systematic review and meta-analysis aimed to explore the effect of body mass index (BMI) and weight loss on the prognosis of IPF patients.Methods We accumulated studies on IPF, BMI, and weight loss from databases including PubMed, Embase, Web of science, Scopus, Ovid and Cochrane Library up to 4 August 2023. Using Cox proportional hazard regression model for subgroup analysis, hazard ratio (HR) and 95% confidence intervals (CI) for BMI in relation to mortality, acute exacerbation (AE), and hospitalization in IPF patients were calculated, and HR, odds ratio (OR), and 95% CI for weight loss corresponding to IPF patient mortality were assessed. Sensitivity analysis was peformed by eliminating every study one by one, and publication bias was judged by Egger’s test and trim-and-fill method.Results A total of 34 eligible studies involving 18,343 IPF patients were included in the meta-analysis. The pooled results by univariate Cox regression analysis showed that baseline BMI was a predictive factor for IPF mortality (HR = 0.93, 95%CI = [0.91, 0.94]). Furthermore, the results by the multivariable regression model indicated that baseline BMI was an independent risk factor for predicting IPF mortality (HR = 0.94, 95%CI = [0.91, 0.98]). Weight loss was identified as a risk factor for IPF mortality (HR = 2.74, 95% CI = [2.12, 3.54]; OR = 4.51, 95% CI = [1.72, 11.82]) and there was no predictive value of BMI for acute exacerbation (HR = 1.00, 95% CI= [0.93, 1.07]) or hospitalization (HR = 0.95, 95% CI = [0.89, 1.02]).Conclusion Low baseline BMI and weight loss in the course of IPF may indicate a high risk of mortality in patients with IPF, so it is meaningful to monitor and manage the nutritional status of IPF patients, and early intervention should be conducted for low BMI and weight loss

Partial physiochemical properties for HY12 strain.

<p>Partial physiochemical properties for HY12 strain.</p

Novel salamander amelogenin gene cDNA structure.

<p>Analysis of novel salamander amelogenin sequence revealed the full-length amelogenin cDNA <i>P</i><i>. cinereus</i>-L containing 7 exons including exon 1, 2, 2b, 3, 5, 6, and 7 (exon numbers is relative to published mammalian amelogenin exon numbers). Different from amelogenin genes published so far, a unique exon named exon 2b between exon 2 and exon 3 was detected. No corresponding sequence elements were detected resembling exon 4, suggesting that amelogenin exon 4 was skipped or deleted in <i>P</i><i>. cinereus</i>. Unlike a previously reported full-length of <i>P</i><i>. cinereus</i>-M isoform consisted of 6 exons, the novel splicing isoform of the <i>P</i><i>. cinereus</i>-S transcript contains 5 exons including exon 1, 2, 3, 5, and 7.</p

PCR amplification of potential amelogenin transcripts in <i>Plethodon</i><i>cinereus</i>.

<p>The cDNA was synthesized from total RNA isolated from tooth organs of <i>Plethodon</i><i>cinereus</i> and used to perform gradient PCR. PCR products amplified with different annealing temperatures were shown in lane 1(50°C), lane 2~3 (52°C, 54°C), lane 4 (56°C), and lane 5 (58°C), respectively. The arrow on the left showed the PCR products corresponding to AMEL-L, M and S (from top to bottom). Lane 6 is 100bp DNA plus ladder (Invitrogen).</p

Novel amelogenin gene splicing forms in <i>Plethodon</i><i>cinereus</i>.

<p>(A) Alignment analysis of the full-length salamander amelogenin gene cDNA sequence of <i>P</i><i>. cinereus</i>-M with the novel salamander amelogenin cDNA sequence <i>P</i><i>. cinereus</i>-L, and <i>P</i><i>. cinereus</i>-S. The full-length of <i>P</i><i>. cinereus</i>-M transcript is 812 bp, while the <i>P</i><i>. cinereus</i>-L and <i>P</i><i>. cinereus</i>-S transcripts are 851 bp and 416 bp, respectively. In relation to <i>P</i><i>. cinereus</i>-M, the <i>P</i><i>. cinereus</i>-L contains an additional 39 bp located between nucleotide 136 and 137, and <i>P</i><i>. cinereus</i>-S is short of 396 nucleotides between nucleotides 230 and 629. The 5’-untranslated region contains 82 nucleotides upstream of the translation start codon ATG. The 3’-untranslated region contains 181 nucleotides downstream stop codon TAA. (B) Sequence analysis of the deduced amino acid sequence of <i>P</i><i>. cinereus</i>-M, <i>P</i><i>. cinereus</i>-L, and <i>P</i><i>. cinereus</i>-S. In relation to <i>P</i>.<i>cinereus</i>-182 encoded by <i>P</i><i>. cinereus</i>-M, the <i>P</i>.<i>cinereus</i>-195 encoded by <i>P</i><i>. cinereus</i>-L contains an additional 13 amino acid residues located between amino acid residue 18 and 19. <i>P</i>.<i>cinereus</i>-50 was short of 123 amino acid residues between AA 49 and 181.</p

Effect of exon 2b sequence on the amelogenin protein structures.

<p>(A) Hydrophilicity-plot analysis using the Kyte and Doolittle algorithm. Hydrophilicity-plots of <i>P</i>.<i>cinereus</i>-182, <i>P</i>.<i>cinereus</i>-195 and mouse (D31768.1) were generated and compared. In relation to <i>P</i>.<i>cinereus</i>-182 and mouse amelogenin, the region underlined with a black line (middle panel) is the exon 2b sequence, which was hydrophilic. (B) Exon 2b has no significant effect on the secondary structure of P.cinereus-195 predicted by Psipred. Similar to that of mouse amelogenin (AA 4~12), one potential helical region for <i>P</i>.<i>cinereus</i>-182 (AA 4~11) and <i>P</i>.<i>cinereus</i>-195 (AA 4~11) was revealed by Psipred prediction. (C) Exon 2b sequence effects on the tertiary structures of <i>P</i>.<i>cinereus</i>-195. <i>P</i>.<i>cinereus</i>-182 and <i>P</i>.<i>cinereus</i>-195 were used as query sequence for homology detection and structure prediction by HMM-HMM comparison using HHpred. A bar graph summarizes the positions and color-coded significances of the database matches with the probability. A tabular hit lists probabilities, E-values, scores, and match regions in queries and templates.</p

Recombination revealed in the HY12 strain.

<p>Neighbor-joining trees of the structural proteins VP1-VP4, and the non-structural protein 3D of 15 enteroviruses were compared. When amino acid sequences for VP1, VP3, and VP4 were used to generate phylogenetic tree, similar patterns were observed as those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097730#pone-0097730-g003" target="_blank">Fig 3B, 3D, and 3E</a>, indicating a interserotype recombination for the HY12 strain. Like the observation in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097730#pone-0097730-g003" target="_blank">Fig 3A, F and G</a>, the HY12 was clustered closely to K2577, SL305, PS 42 and PS 83 strains, an indication of complex interserotypic and intraserotypic recombination in the evolution for HY12. The positions of HY12 were highlighted with a triangle.</p

Outsplicing of exon 6 in <i>P</i>.<i>cinereus</i>-50 has dramatic effects on secondary and tertiary structure.

<p>(A–B) <b>Outsplicing</b> of exon 6 dramatically affects amelogenin secondary structure of <i>P</i>.<i>cinereus</i>-50 predicted by Psipred in relation to <i>P</i>.<i>cinereus</i>-182. One potential helical region was observed in <i>P</i>.<i>cinereus</i>-182 (AA 4-11), while two potential helical regions were revealed for <i>P</i>.<i>cinereus</i>-50 (AA 3~15, 38~48) in addition to a beta-strand region (AA 28~35) as revealed by Psipred prediction. (C–D) Exon 6 outsplicing affects the tertiary structure of <i>P</i>.<i>cinereus</i>-50. <i>P</i>.<i>cinereus</i>-182 and P.cinereus-50 were used as query sequence for homology detection and structure prediction by HMM-HMM comparison using HHpred. A bar graph summarizes the positions and color-coded significances of the database matches with the probability.</p

Primers used for amplifying the complete genome sequence for HY12.

<p>S stands for sense; AS refers to antisense.</p