On the Lab. II building site

425 special CDSs in PCN033 (XLSX 29 kb

Additional file 1: Table S1. of Isolation and full-genome sequencing of Seneca Valley virus in piglets from China, 2016

List of primers used in the study. (DOCX 19 kb

A Transcriptome Map of <i>Actinobacillus pleuropneumoniae</i> at Single-Nucleotide Resolution Using Deep RNA-Seq

<div><p><i>Actinobacillus pleuropneumoniae</i> is the pathogen of porcine contagious pleuropneumoniae, a highly contagious respiratory disease of swine. Although the genome of <i>A</i>. <i>pleuropneumoniae</i> was sequenced several years ago, limited information is available on the genome-wide transcriptional analysis to accurately annotate the gene structures and regulatory elements. High-throughput RNA sequencing (RNA-seq) has been applied to study the transcriptional landscape of bacteria, which can efficiently and accurately identify gene expression regions and unknown transcriptional units, especially small non-coding RNAs (sRNAs), UTRs and regulatory regions. The aim of this study is to comprehensively analyze the transcriptome of <i>A</i>. <i>pleuropneumoniae</i> by RNA-seq in order to improve the existing genome annotation and promote our understanding of <i>A</i>. <i>pleuropneumoniae</i> gene structures and RNA-based regulation. In this study, we utilized RNA-seq to construct a single nucleotide resolution transcriptome map of <i>A</i>. <i>pleuropneumoniae</i>. More than 3.8 million high-quality reads (average length ~90 bp) from a cDNA library were generated and aligned to the reference genome. We identified 32 open reading frames encoding novel proteins that were mis-annotated in the previous genome annotations. The start sites for 35 genes based on the current genome annotation were corrected. Furthermore, 51 sRNAs in the <i>A</i>. <i>pleuropneumoniae</i> genome were discovered, of which 40 sRNAs were never reported in previous studies. The transcriptome map also enabled visualization of 5'- and 3'-UTR regions, in which contained 11 sRNAs. In addition, 351 operons covering 1230 genes throughout the whole genome were identified. The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures). The transcriptional units described in this study provide a foundation for future studies concerning the gene functions and the transcriptional regulatory architectures of this pathogen.</p></div

Additional file 1 of TGFβ1-induced hedgehog signaling suppresses the immune response of brain microvascular endothelial cells elicited by meningitic Escherichia coli

Additional file 1

Prevalence Study and Genetic Typing of Bovine Viral Diarrhea Virus (BVDV) in Four Bovine Species in China

<div><p>To determine the nationwide status of persistent BVDV infection in different bovine species in China and compare different test methods, a total of 1379 serum samples from clinical healthy dairy cattle, beef cattle, yaks (<i>Bos grunniens</i>), and water buffalo (<i>Bubalus bubalis</i>) were collected in eight provinces of China from 2010 to 2013. The samples were analyzed using commercial antibody (Ab) and antigen (Ag) detection kits, and RT-PCR based on the 5’-UTR and Npro gene sequencing. Results showed that the overall positive rates for BVDV Ab, Ag and RT-PCR detection were 58.09% (801/1379), 1.39% (14/1010), and 22.64% (146/645), respectively, while the individual positive rates varied among regions, species, and farms. The average Ab-positive rates for dairy cattle, beef cattle, yaks, and water buffalo were 89.49% (298/333), 63.27% (248/392), 45.38% (236/520), and 14.18% (19/134), respectively, while the Ag-positive rates were 0.00% (0/116), 0.77% (3/392), 0.82% (3/368), and 5.97% (8/134), respectively, and the nucleic acid-positive rates detected by RT-PCR were 32.06% (42/131), 13.00% (26/200), 28.89% (52/180), and 19.40% (26/134), respectively. In addition, the RT-PCR products were sequenced and 124 5’-UTR sequences were obtained. Phylogenetic analysis of the 5’-UTR sequences indicated that all of the 124 BVDV-positive samples were BVDV-1 and subtyped into either BVDV-1b (33.06%), BVDV-1m (49.19%), or a new cluster, designated as BVDV-1u (17.74%). Phylogenetic analysis based on Npro sequences confirmed this novel subtype. In conclusion, this study revealed the prevalence of BVDV-1 in bovine species in China and the dominant subtypes. The high proportion of bovines with detectable viral nucleic acids in the sera, even in the presence of high Ab levels, revealed a serious threat to bovine health.</p></div

Correction made to the start site of a gene.

<p>Visualization of the single-nucleotide resolution transcriptome map shows the transcription of upstream of the gene ‘‘APJL_1947”. The predicted and actual start codons within the ORF are marked.</p

Geographical distribution of serum samples.

<p>Geographical distribution of serum samples.</p

Interaction of the JEV NS5 protein with identified cellular proteins.

<p>293T cells were transfected with expression plasmids encoding Flag-NS5 and Hsp70-Myc (A), eEF-1α-Myc (B) or Ran-Myc (C). Cell extracts were prepared at 36 h post-transfection and used for co-immunprecipitation (co-IP) with Flag-specific antibody. The immunoprecipitates as well as in the cell extracts were subjected to immunoblotting (IB) with anti-Flag and anti-Myc antibodies, respectively. An empty vector was used as a negative control.</p

Comparisons between BVDV Ab and nucleic acid detection by RT-PCR.

<p>Comparisons between BVDV Ab and nucleic acid detection by RT-PCR.</p

<i>hp0197</i> controls CcpA activity by HPr-Ser-46P.

<p>The purified FLAG-tagged HPr from the log-phase WT or Δ<i>hp0197</i> bacteria were compared to evaluate the binding of CcpA to its target site (<i>cre</i>) by EMSA. The HPr from the stable-phase WT strain served as a control. Significant more DNA (indicated by *) with CcpA and HPr from Log-phase WT migrated slower than DNA with CcpA and HPr from Δhp0197 or from the stable-phase WT strain, indicating that HPr from log-phase WT could enhance the binding of CcpA to <i>cre</i> and the HPr from log-phase Δ<i>hp0197</i>could not enhance the ability significantly.</p