Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui,China

Fur seal feces-associated circular DNA virus(FSfa CV) is an unclassified circular replication-associated protein(Rep)-encoding single-stranded(CRESS) DNA virus that has been detected in mammals(fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province,China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfa CVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfa CV-CHN(Gen Bank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfa CV-as50 and the Japanese pig strain FSfa CVJPN1, respectively. It also clustered with the two previously identified FSfa CVs in a unique branch in the phylogenetic tree based on the open reading frame 2(ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses.Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4%(111/197) in Anhui Province. This is the first report of FSfa CVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.     

Modified McKeown Minimally Invasive Esophagectomy for Esophageal Cancer: A 5-Year Retrospective Study of 142 Patients in a Single Institution

Background

To achieve decreased invasiveness and lower morbidity, minimally invasive esophagectomy (MIE) was introduced in 1997 for localized esophageal cancer. The combined thoracoscopic-laparoscopic esophagectomy (left neck anastomosis, defined as the McKeown MIE procedure) has been performed since 2007 at our institution. From 2007 to 2011, our institution subsequently evolved as a high-volume MIE center in China. We aim to share our experience with MIE, and have evaluated the outcomes of 142 patients.

Methods

We retrospectively reviewed 142 consecutive patients who had presented with esophageal cancer undergoing McKeown MIE from July 2007 to December 2011. The procedure, surgical outcomes, disease-free and overall survival of these cases were assessed.

Results

The average total procedure time was 270.5±28.1 min. The median operation time for thoracoscopy was 81.5±14.6 min and for laparoscopy was 63.8±9.1 min. The average blood loss associated with thoracoscopy was 123.8±39.2 ml, and for laparoscopic procedures was 49.9±14.3 ml. The median number of lymph nodes retrieved was 22.8. The 30 day mortality rate was 0.7%. Major surgical complications occurred in 24.6% and major non-surgical complications occurred in 18.3% of these patients. The median DFS and OS were 36.0±2.6 months and 43.0±3.4 months respectively.

Conclusions

Surgical and oncological outcomes following McKeown MIE for esophageal cancer were acceptable and comparable with those of open-McKeown esophagectomy. The procedure was both feasible and safe – properties that can be consolidated by experience.     

野生矮牡丹高通量转录组测序分析

为探究野生稷山矮牡丹(Paeonia jishanensis)花青素等抗氧化活性物质生物合成的遗传基础,本文采用高通量测序技术Illumina NextSeqTM500对其幼嫩叶片、嫩茎和花芽混合池样本进行转录组测序分析。共获得39450个unigene,其中3563个unigene中有4106个SSR位点。在Swiss Prot数据库中注释到29420个unigene,其中11个与花青素生物合成过程相关,22个与类黄酮生物合成过程相关,15个与异黄酮生物合成过程相关;NR数据库中注释高达100%,有12个与类黄酮生物合成相关,7个与花青素生物合成相关;GO数据库中注释到24291个unigene,分为生物学过程、细胞组分及分子功能等三大类53个功能组,有21个unigene与黄酮、黄酮醇及异黄酮生物合成有关,4个unigene与花青素合成有关;eggNOG数据库中注释到38238个unigene,涉及植物生长发育过程绝大多数生命活动过程;KEGG数据库注释到5709个unigene,分别定位到6大类别42个代谢途径,其中25个unigene与花青素生物合成相关。研究表明,在稷山矮牡丹转录组序列中,共鉴定和发掘出多个涉及类黄酮化合物生物合成、花青素生物合成过程的相关基因序列及SSR位点,为下一步开展相关代谢合成途径研究奠定了基础。     

H1亚型猪流感病毒血凝素基因在昆虫细胞中的表达及其间接ELISA方法的初步建立

根据GenBank发表的H1亚型猪流感HA基因序列设计引物,扩增出HA基因片段.将其克隆到pFastBacGP67B杆状病毒载体上,筛选阳性重组转座载体pFastBacGP67B-H1,转化含有杆状病毒穿梭载体(bacmid)的DH10Bac感受态细胞,构建杆状病毒表达载体获得重组转座子(rBacmid-H1),在脂质体介导下转染sf9昆虫细胞,获得重组杆状病毒(rBV-H1),再感染细胞,收获目的蛋白.通过血凝试验、免疫印迹法、免疫组化分析表明该蛋白得到表达,且具有良好的生物学活性.利用表达的蛋白作为猪流感间接ELISA的抗原,初步建立H1亚型猪流感的间接ELISA检测方法,并对内蒙古、辽宁和黑龙江等地送检的93份猪血清进行了检测,阳性率为31.18%,为研制开发快速、准确、简便的H1亚型猪流感鉴别诊断试剂盒奠定基础.     

H3N2亚型猪流感病毒的拯救及HA与NA基因的替换

摘要：【目的】为研究流感病毒突破种间屏障分子机制,筛选流感基因工程疫苗株。【方法】本实验以猪流感病毒A/Swine/Henan/S4/01(H3N2)为亲本株,利用反向遗传学操作技术,采用RT-PCR技术对该病毒的8个基因片段分段进行扩增,通过与双向转录载体pHW2000连接, 重组质粒转染293T和MDCK共培养细胞,拯救出全部基因均来自于亲本株的猪流感病毒rgH3N2,并分别以人流感病毒A/ PR/8/34(H1N1)、禽流感病毒A/Duck/Nanchang /4-165/2000 (H4N6 )、马流感病毒A/Equine/Fuyun/2008/(H3N8)的HA和NA基因替换A/Swine/Henan/S4/01的相应基因,【结果】生物学实验结果表明rgH3N2在鸡胚半数感染量、组织培养半数感染量、稳定性试验等方面都与亲本株保持一致。rgH3N2经鸡胚多次传代后血凝价最高可达到1:256,接种MDCK细胞60 h后,血凝价可以达到1:64。基因替换后成功拯救出的重组病毒rgH1N1、rgH4N6和rgH3N8在鸡胚和细胞上均具有较高的增殖能力。【结论】病毒的成功拯救为流感病毒突破种间屏障分子机制,HA、NA基因在流感病毒跨种属传播中所扮演角色的研究和流感基因工程疫苗株的筛选奠定了基础。     

Non-parametric change-point method for differential gene expression detection

Background

We proposed a non-parametric method, named Non-Parametric Change Point Statistic (NPCPS for short), by using a single equation for detecting differential gene expression (DGE) in microarray data. NPCPS is based on the change point theory to provide effective DGE detecting ability.

Methodology

NPCPS used the data distribution of the normal samples as input, and detects DGE in the cancer samples by locating the change point of gene expression profile. An estimate of the change point position generated by NPCPS enables the identification of the samples containing DGE. Monte Carlo simulation and ROC study were applied to examine the detecting accuracy of NPCPS, and the experiment on real microarray data of breast cancer was carried out to compare NPCPS with other methods.

Conclusions

Simulation study indicated that NPCPS was more effective for detecting DGE in cancer subset compared with five parametric methods and one non-parametric method. When there were more than 8 cancer samples containing DGE, the type I error of NPCPS was below 0.01. Experiment results showed both good accuracy and reliability of NPCPS. Out of the 30 top genes ranked by using NPCPS, 16 genes were reported as relevant to cancer. Correlations between the detecting result of NPCPS and the compared methods were less than 0.05, while between the other methods the values were from 0.20 to 0.84. This indicates that NPCPS is working on different features and thus provides DGE identification from a distinct perspective comparing with the other mean or median based methods.     

Adverse Events of Pirfenidone for the Treatment of Pulmonary Fibrosis: A Meta-Analysis of Randomized Controlled Trials

Background

Pirfenidone (PFD) is a novel antifibrotic agent approved for patients with pulmonary fibrosis. However, there are concerns regarding toxicity of the drug. In this meta-analysis, we analyzed the adverse events (AEs) of PFD for the treatment of pulmonary fibrosis.

Methods

We performed a systematic search of PubMed, Embase, ClinicalTrials.gov, and Cochrane Central Register of Controlled Trials for trials published between January 1999 and October 2011. Data extracted from literature were analyzed with Review manager 5.0.24.

Results

The results of six randomized controlled trials (1073 participants) revealed that the number of individuals who discontinued PFD therapy was significantly higher than patients receiving placebo. The PFD group had a significantly higher rate of gastrointestinal (nausea, dyspepsia, diarrhea, and anorexia), neurological (dizziness and fatigue), and dermatological (photosensitivity and rash) AEs compared to the placebo group.

Conclusions

PFD used for the treatment of pulmonary fibrosis is not so safe or well-tolerated. Notably, gastrointestinal, neurological and dermatological adverse effects were more common in patients receiving PFD therapy, and therefore appropriate precaution is needed.     

文峪河上游河岸带不同植被类型土壤nirS反硝化菌群结构及功能

以文峪河上游河岸带不同演替阶段的8种植被类型五花草甸(WH)、沙棘林(HR)、柳树林(SS)、山杨林(PC)、山杨白桦林(PQ)、山杨白桦落叶松林(PQL)、落叶松云杉林(LP)和云杉林(PM)土壤为研究对象,采用高通量测序技术测定nirS反硝化细菌群落组成及相对丰度,乙炔抑制法测定反硝化酶活性(DEA)。对其土壤理化性质及反硝化细菌群落组成及相对丰度进行方差分析,采用冗余分析(RDA)和Spearman相关性分析不同植被类型及土层反硝化细菌群落结构及功能及土壤理化因子的关联性。结果表明:1)不同植被类型及土层土壤理化因子存在显著差异,柳树林(SS)0—15 cm土层硝态氮(NO~+_3-N)含量显著高于其他植被类型各土层;2)土壤反硝化菌群多样性指数在五花草甸(WH)、山杨白桦林(PQ)和云杉林(PM)中较其他植被类型高;3)沙棘林(HR)及柳树林(SS)反硝化酶活性(DEA)显著高于其他植被类型;4)不同植被类型反硝化优势菌群分布存在显著差异及特异性,如浮霉菌门(Planctomycetes)仅在落叶松云杉混交林(LP)和云杉林(PM)植被类型15—30 cm土层中分布;5)土壤pH、土壤有机碳(SOC)、土壤铵态氮(NH~+_4-N)和硝态氮(NO~+_3-N)等是影响土壤反硝化细菌群落结构及组成的重要因子,其中土壤铵态氮和硝态氮含量变化是导致土壤反硝化菌群多样性和反硝化酶活性差异的关键因子。本研究揭示了文峪河上游河岸带不同植被类型土壤反硝化细菌群落结构及功能的变化和分布特征,为进一步研究该区域河岸带氮素循环及水体污染防治提供重要参考依据。     

Complete genomic sequence of duck flavivirus from china

We report here the complete genomic sequence of the Chinese duck flavivirus TA strain. This work is the first to document the complete genomic sequence of this previously unknown duck flavivirus strain. The sequence will help further relevant epidemiological studies and extend our general knowledge of flaviviruses.