Primers used in this study.

*<p>Primers used for sequencing.</p

Different HCV Genotype Distributions of HIV-Infected Individuals in Henan and Guangxi, China

<div><h3>Background</h3><p>Due to shared transmission routes, hepatitis C virus (HCV) infection is highly prevalent among people infected with human immunodeficiency virus (HIV). Highly active antiretroviral therapy (HAART) is associated with hepatotoxicity, leading to the negative effects on patients with HIV/HCV co-infection. In order to provide valuable information for HCV management in this particular population, we investigated the HCV genotypes in HIV-infected individuals from Henan and Guangxi, the two provinces with the most HIV-infected cases in China.</p> <h3>Methods</h3><p>Individuals, who acquired HIV infection through various risk routes, were recruited from Henan and Guangxi. Test of antibodies against HCV (anti-HCV) was conducted, and detection of HCV RNA was performed by PCR amplification. HCV subtypes were determined by direct sequencing of amplicons, followed by phylogenetic analysis.</p> <h3>Results</h3><p>We recruited a total of 1,112 HIV-infected people in this present study. Anti-HCV was detected from 218 (50.1%) patients from Henan and 81 (12.0%) patients from Guangxi, respectively. The highest prevalence of HIV/HCV co-infection was observed from FBDs (former blood donors) (87.2%) in Henan and IDUs (intravenous drug users) (81.8%) in Guangxi, respectively. The seroprevalence rate of HCV among people with sexual contact was significantly higher in Henan than in Guangxi (18.7% vs. 3.5%, <em>P</em><0.05). The positive rate of HCV RNA in Henan and Guangxi was 30.6% (133/435) and 11.2% (76/677), respectively. Moreover, we found that 20 anti-HCV negative samples were HCV positive by PCR amplification. HCV subtype 1b (52.7%) was predominant in Henan, followed by subtype 2a (41.9%). The most frequently detected subtypes in Guangxi were 6a (35.6%) and 3b (32.9%).</p> <h3>Conclusion</h3><p>The HCV genotype distributions were different in HIV-infected people from Henan and Guangxi. HIV/HCV co-infection was not only linked to the transmission routes, but also associated with the geographic position.</p> </div

MPT for the HCV NS5B region sequence obtained from HIV/HCV co-infected patients in Henan and Guangxi.

<p>The sequences correspond to nucleotides 8,343-9,226 in HCV H77 genome (NC_004102). This dataset included sequences from 242 HCV specimens. The dataset had an aligned length of 884 characters in the dataset, of which, 318 characters are constant, 45 are variable and parsimony-uninformative, and 521 are parsimony-informative. Maximum Parsimony analysis yielded 88 equally parsimonious trees (TL  = 2073, CI  = 0.314, RI  = 0.774, RC  = 0.287, HI  = 0.686). Parsimony bootstrap proportions higher than 70% were indicated along branches. The sequences determined in this study are indicated by the following signs: sequences from Henan (♦), sequences from Guangxi (◊). Reference sequences used to classify HCV genotypes are displayed in bold with the following format: Ref/subtype/country code/accession number.</p

MPT for the HCV NS5B region sequence obtained from HIV/HCV co-infected patients in Guangxi.

<p>The sequences correspond to nucleotides 8343-9226 in HCV H77 genome (NC_004102). This dataset included sequences from 116 HCV specimens. The dataset had an aligned length of 884 characters in the dataset, of which, 331 characters are constant, 46 are variable and parsimony-uninformative, and 507 are parsimony-informative. Maximum Parsimony analysis yielded 100 equally parsimonious trees (TL  = 3012, CI  = 0.233, RI  = 0.678, RC  = 0.282, HI  = 0.767). Parsimony bootstrap proportions higher than 70% were indicated along branches. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050343#pone-0050343-g001" target="_blank">Figure 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050343#pone-0050343-g002" target="_blank">Figure 2</a> for reference sequences naming details and signing scheme.</p

Population characteristics of the study cohort and the seroprevalence rate of HCV among HIV-infected people from various risk groups in Henan and Guangxi.

<p>Population characteristics of the study cohort and the seroprevalence rate of HCV among HIV-infected people from various risk groups in Henan and Guangxi.</p

Preclinical Evaluation of the Novel Monoclonal Antibody H6-11 for Prostate Cancer Imaging

The biological properties of the novel monoclonal antibody (mAb) H6-11 and its potential utility for oncological imaging studies were evaluated using <i>in vitro</i> and <i>in vivo</i> assays. Immunoreactivity of H6-11 to the human prostate cancer PC-3 cell line and solid tumor xenografts was initially demonstrated using immunofluorescence staining; the specificity of H6-11 for prostate cancer was further evaluated using a commercial array of human prostate cancer and normal tissue samples (<i>n</i> = 49) in which H6-11 detected 95% of prostate adenocarcinomas. The <i>K</i>_d value of 61.7 ± 30 nM was determined using ¹²⁵I-labeled H6-11. Glycosylation analysis suggested the antigenic epitope of the glycan is an O-linked β-<i>N</i>-acetylglucoside (<i>O</i>-GlcNAc) group. Imaging studies of PC-3 tumor-bearing mice were performed using both optical imaging with NIR fluorescent dye-labeled H6-11 and microPET imaging with ⁸⁹Zr-labeled H6-11. These <i>in vivo</i> studies revealed that the labeled probes accumulated in PC-3 tumors 48–72 h postinjection, although significant retention in liver was also observed. By 120 h postinjection, the tumors were still evident, although the liver showed significant clearance. These studies suggest that the mAb H6-11 may be a useful tool to detect prostate cancer <i>in vitro</i> and <i>in vivo</i>

MPT for the HCV NS5B region sequence obtained from HIV/HCV co-infected patients in Henan.

<p>The sequences correspond to nucleotides 8343-9226 in HCV H77 genome (NC_004102). This dataset included sequences from 159 HCV specimens. The dataset had an aligned length of 884 characters in the dataset, of which, 335 characters are constant, 43 are variable and parsimony-uninformative, and 506 are parsimony-informative. Maximum Parsimony analysis yielded 88 equally parsimonious trees (TL  = 1945, CI  = 0.276, RI  = 0.859, RC  = 0.237, HI  = 0.724). Parsimony bootstrap proportions higher than 70% were indicated along branches. The HIV transmission route for each patient is listed opposite each sequence: FBDs (•); transfusion exposure (○), sexual contact (★), IDUs (☆), perinatal exposure (▴), unknown infection route (▪). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050343#pone-0050343-g001" target="_blank">Figure 1</a> for reference sequences naming details.</p

Data_Sheet_2_A body map of super-enhancers and their function in pig.PDF

IntroductionSuper-enhancers (SEs) are clusters of enhancers that act synergistically to drive the high-level expression of genes involved in cell identity and function. Although SEs have been extensively investigated in humans and mice, they have not been well characterized in pigs.MethodsHere, we identified 42,380 SEs in 14 pig tissues using chromatin immunoprecipitation sequencing, and statistics of its overall situation, studied the composition and characteristics of SE, and explored the influence of SEs characteristics on gene expression.ResultsWe observed that approximately 40% of normal enhancers (NEs) form SEs. Compared to NEs, we found that SEs were more likely to be enriched with an activated enhancer and show activated functions. Interestingly, SEs showed X chromosome depletion and short interspersed nuclear element enrichment, implying that SEs play an important role in sex traits and repeat evolution. Additionally, SE-associated genes exhibited higher expression levels and stronger conservation than NE-associated genes. However, genes with the largest SEs had higher expression levels than those with the smallest SEs, indicating that SE size may influence gene expression. Moreover, we observed a negative correlation between SE gene distance and gene expression, indicating that the proximity of SEs can affect gene activity. Gene ontology enrichment and motif analysis revealed that SEs have strong tissue-specific activity. For example, the CORO2B gene with a brain-specific SE shows strong brain-specific expression, and the phenylalanine hydroxylase gene with liver-specific SEs shows strong liver-specific expression.DiscussionIn this study, we illustrated a body map of SEs and explored their functions in pigs, providing information on the composition and tissue-specific patterns of SEs. This study can serve as a valuable resource of gene regulatory and comparative analyses to the scientific community and provides a theoretical reference for genetic control mechanisms of important traits in pigs.</p

PCR reaction used in this study.

<p>PCR reaction used in this study.</p

Data_Sheet_3_A body map of super-enhancers and their function in pig.PDF

IntroductionSuper-enhancers (SEs) are clusters of enhancers that act synergistically to drive the high-level expression of genes involved in cell identity and function. Although SEs have been extensively investigated in humans and mice, they have not been well characterized in pigs.MethodsHere, we identified 42,380 SEs in 14 pig tissues using chromatin immunoprecipitation sequencing, and statistics of its overall situation, studied the composition and characteristics of SE, and explored the influence of SEs characteristics on gene expression.ResultsWe observed that approximately 40% of normal enhancers (NEs) form SEs. Compared to NEs, we found that SEs were more likely to be enriched with an activated enhancer and show activated functions. Interestingly, SEs showed X chromosome depletion and short interspersed nuclear element enrichment, implying that SEs play an important role in sex traits and repeat evolution. Additionally, SE-associated genes exhibited higher expression levels and stronger conservation than NE-associated genes. However, genes with the largest SEs had higher expression levels than those with the smallest SEs, indicating that SE size may influence gene expression. Moreover, we observed a negative correlation between SE gene distance and gene expression, indicating that the proximity of SEs can affect gene activity. Gene ontology enrichment and motif analysis revealed that SEs have strong tissue-specific activity. For example, the CORO2B gene with a brain-specific SE shows strong brain-specific expression, and the phenylalanine hydroxylase gene with liver-specific SEs shows strong liver-specific expression.DiscussionIn this study, we illustrated a body map of SEs and explored their functions in pigs, providing information on the composition and tissue-specific patterns of SEs. This study can serve as a valuable resource of gene regulatory and comparative analyses to the scientific community and provides a theoretical reference for genetic control mechanisms of important traits in pigs.</p