High Throughput Sequencing to Study the Effect of Chronic Renal Failure on the Diversity and Gene Function Prediction of Gut Microbiota in Dogs

This study aimed to investigate the effect of chronic renal failure(CRF) on the gut microbiota diversity and predict the gene function of the flora. A total of 30 2-year-old dogs were selected and randomly divided into the chronic renal failure model group (CRF, established by renal artery ligation), sham operation control group (Sham) and healthy control group (HCG). All animals were fed normally during the 56 days of test period. The serum creatinine (Scr), blood urea nitrogen (BUN) and urine protein / creatinine ratio (UP/C) were detected regularly during the experiment. The effects of chronic renal failure on the structure, diversity and function of gut microbiota were analyzed according to the result of bacterial 16S rDNA sequencing from fresh feces collected without contamination. The flora markers index (FMI) was constructed based on the principal component Logistic regression analysis of different microbiota in CRF group to predict the development of chronic renal failure. The results showed that: 1) The levels of Scr, BUN and UP/C in CRF group from the start of the 28th day of the experiment were significantly higher than those of HCG group and Sham group (P<0.05), and significantly higher than that of the first day of CRF group (P<0.05). 2) Compared with those before chronic renal failure (CRF group at day 0 and 28), HCG group and Sham group, the Chao 1 diversity and Shannon diversity of gut microbiota in CRF group at day 56 were significantly lower (P<0.05), while the relative abundance of Bacteroidetes, Proteobacteria and Actinobacteria significantly increased and the number of Firmicutes significantly decreased (P<0.05). 3) LEfSe analysis showed that 20 species were enriched in CRF group, mainly including Pseudomonas, Escherichia, Proteus and so on, and most of them had negative correlation with other intestinal bacteria. Functional prediction revealed that genes of those different species were mainly enriched in amino acid metabolism, sugar biosynthesis and metabolism and carbohydrate metabolism in CRF group. The area under ROC curve (AUC) of the FMI constructed with those species enriched was 0.788, which could be used as the intestinal microbial marker for CRF in dogs. In summary, chronic renal failure can reduce the diversity of intestinal microbiota, lead to the imbalance of bacterial structure and change of bacterial function. Moreover, the enriched gut microbiota in CRF group can be used as the intestinal microbial marker of CRF in dogs, and the best prediction effect can be obtained by FMI.     

Predictive equations of selenium accessibility of dry pet foods

The trace element selenium is essential to both dogs and cats. Dry diets are formulated with a large range of ingredients, which may vary in selenium concentration and accessibility. This paper reports equations to predict the average in vitro selenium accessibility from dry pet foods based on essential dietary nutrient concentrations, including crude protein, amino acids and crude fat. Predictive equations were made using stepwise linear regression for extruded and pelleted diets. The equations can be used to aid diet formulation to optimize selenium accessibility within the diet and to prevent selenium deficiency or toxicity.     

禽呼肠孤病毒C-98分离株S3基因的克隆及序列分析

参考GenBank中禽呼肠孤病毒S3基因序列设计一对引物,以禽呼肠孤病毒内蒙古分离株(C-98)基因组RNA为模板,应用RT-PCR方法获得病毒的S3基因,并克隆到pMD19-T载体后测序。应用计算机软件将所测定序列与参考毒株ARV 176、ARV S1133、ARV 138的S3基因序列进行比较,核苷酸同源性分别为99.8%,99.6%,87.7%,推导其氨基酸同源性分别为99.5%,98.9%,94.8%。应用PHD程序和DNAStar软件,对S3基因所编码的σB蛋白结构进行预测,结果表明,σB蛋白为结构紧密的球状蛋白分子。     

异源抗体对接方法预测流感病毒血凝素B细胞构象表位

为了对异源抗体对接方法预测流感病毒血凝素B细胞构象表位的可行性进行分析,本研究基于蛋白质相互作用界面的形状互补理论,使用异源抗体(来自于抗原抗体复合物1G9M、1RVF、1TPX、1NCA、1A2Y)的晶体结构同流感病毒血凝素(A/Aichi/2/68(H3N2))的晶体结构进行刚性分子对接,通过计算B细胞表位的预测表面和实际表面C-α原子之间的RSMD以及表位氨基酸的准确率,分析用异源抗体探测出血凝素B细胞表位的可能性。结果表明,不同的异源抗体均可结合到A/Aichi/2/68(H3N2)的已知B细胞表位,最佳的对接构象与原晶体结构重叠后表位残基C-α原子的均方根偏差均小于0.6埃,表位氨基酸预测的准确性大于60%,说明异源抗体对接方法可以尝试用于B细胞构象表位的预测。     

江苏省蚕桑综合利用模式分析

本文阐述了蚕桑综合利用是提高蚕桑产业经济效益的重要途径之一.江苏省是蚕桑生产大省,桑、蚕及其附属物和衍生物资源丰富,综合利用的潜能很大.文章结合江苏省蚕桑综合利用实际,分析蚕桑综合利用几种发展模式及经济效益.分析了当前江苏省蚕桑综合利用存在的主要问题,提出了蚕桑综合利用发展建议.     

新关节炎动物模型的研究进展

文章主要论述了近年来新关节炎动物模型的发展概况,具体包括3个方面的内容:新型的转基因关节炎模型的种类及发病机理、免疫复合物关节炎模型的种类及发病机理和关节炎发生发展过程中涉及到的相关细胞因子的研究。     

Cloning and Bioinformatic Analysis of L1 Gene of BPV from Guizhou Province

In order to study and analyze L1 gene of bovine papillomavirus（BPV）in Guizhou province,the L1 gene of BPV-GZ01 strain was amplified,cloned and sequenced using bioinformatic softwares and methods,and the secondary structure,tertiary structure,B-cell preponderant epitope,conserved domains analysis, transmembrane domain and signal peptide of L1 gene were predicted.The results showed that the length of L1 gene was 1 494 bp,encoding 497 amino acids.The L1 gene of BPV-GZ01 strain shared an amino acid identities of 98.6%,99.4%,98.4%,94.4% and 91.3%,and a nucleotide identities of 99.1%,99.8%,99.4%,87.6% and 82.8% with those of BPV2,BPV2-SW01,BPV2-AKS01,BPV13 and BPV1 strains,respectively.The results of phylogenetic tree analysis indicated that there was a close relationship between BPV-GZ01 and BPV2-SW01 strains.The prediction of secondary structure of L1 protein indicated that the random coil,extended strand and alphahelix took a higher percentage.The L1 protein was supposed contain 6 potential antigen epitopes.And no transmembrane domains and no signal peptide were found.The tertiary structure of L1 protein was curved spiral structure.These results provided a theoretical basis for immunologic diagnosis and further research of nucleic acid vaccine of BPV.     

Genomic prediction for meat and carcass traits in Nellore cattle using a Markov blanket algorithm

This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner–Bratzler shear force (WBSF), respectively, from the Nellore Brazil Breeding Program. The animals have been genotyped using low-density SNP panel (30 k), and subsequently imputed for arrays with 777 k SNPs. Four Bayesian specifications of genomic regression models, namely Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression methods were compared in terms of prediction accuracy using a five folds cross-validation. Prediction accuracy for REA, BF and RF was all similar using the Bayesian Alphabet models, ranging from 0.75 to 0.95. For WBSF, the predictive ability was higher using Bayes B (0.47) than other methods (0.39 to 0.42). Although the prediction accuracies using Markov blanket of SNP markers were lower than those using all SNPs, for WBSF the relative gain was lower than 13%. With a subset of informative SNPs markers, identified using Markov blanket, probably, is possible to capture a large proportion of the genetic variance for WBSF. The development of low-density and customized arrays using Markov blanket might be cost-effective to perform a genomic selection for this trait, increasing the number of evaluated animals, improving the management decisions based on genomic information and applying genomic selection on a large scale.     

猫泛白细胞减少症病毒北京株NS1基因克隆与生物信息学分析

为分析猫泛白细胞减少症病毒（FPV）北京株（FPV-BJ 05株）NS1基因的分子特征及其编码蛋白的生物学功能,本研究对FPV-BJ 05株NS1基因进行PCR扩增、克隆及序列测定。应用生物信息学软件分析FPV-BJ 05株与GenBank上登录的11株FPV参考株NS1基因的同源性,并预测NS1蛋白理化性质、信号肽、跨膜结构、B细胞抗原表位、磷酸化位点、亚细胞定位及蛋白结构与功能、高级结构等。结果显示,NS1基因全长2 007 bp,编码668个氨基酸,且与其他FPV分离株NS1基因核苷酸序列同源性为98.8%~99.3%,氨基酸序列同源性为97.9%~98.8%。系统进化树分析结果显示,FPV-BJ 05株NS1蛋白与GenBank上登录的3株FPV参考株处于同一大分支,但由于氨基酸的突变导致其属于独立的一小分支。NS1蛋白既无信号肽也无跨膜结构域,属于非分泌型的疏水性蛋白。B细胞抗原表位预测结果显示,NS1蛋白柔韧性较好,抗原性及表面可及性较高,预测该蛋白含有13个优势抗原位点。修饰结构预测表明,NS1蛋白含有62个潜在磷酸化位点,27个O-糖基化位点和2个N-糖基化位点。亚细胞定位结果显示,NS1蛋白在细胞质和细胞核的概率较高,分别为69.6%和17.4%。NS1蛋白二级结构中α-螺旋、延伸链、无规则卷曲和β-转角分别占39.37%、15.42%、39.37%和5.84%。应用在线软件SWISS-Modle对NS1蛋白进行建模,预测其三级结构,结果发现NS1蛋白主要以α-螺旋为主。本试验结果将为北京地区FPV免疫诊断及核酸疫苗研究提供理论依据。     

“3S”技术在草地鼠虫害监测与预测中的应用

日益严重的草地鼠虫害,己成为引发草原退化、沙化、水土流失的重要因素之一,并威胁我国草地畜牧业的可持续发展。"3S"技术作为一种综合性技术手段,具有探测范围广、信息量大、成本低、受地面条件限制和人为因素影响小等特点,可实现对各种空间信息和环境信息的快速、机动、准确、可靠的收集、处理与更新。这一技术与地面调查资料的结合,不仅加快了对草地资源的宏观监测速度,而且能够快速、准确地反映草地鼠虫害的变化动态。结合鼠虫害发生的特点,重点概述了运用"3S"技术对草地鼠虫害进行监测的原理、方法及存在的问题,并分析了该领域未来的研究重点和"3S"技术的应用前景。