人源H3N2亚型猪流感重组病毒的分离鉴定及全基因序列分析

本研究由疑似猪流感病料样品中分离一株病毒,通过HA、HI、电镜观察、生物学特性测定及全基因序列测定表明,分离病毒株为H3N2亚型人流感病毒和H1N1亚型古典猪流感病毒(SIV)的重组体,命名为A/Swine/Fujian/F2/07(H3N2).该分离株含有8个基因片段,共13 442 bp,与GenBank中登录的H3N2亚型人流感病毒、H1N1亚型古典SIV和H3N2亚型SIV进行比较分析显示:分离株的HA、NS、NA基因与H3N2亚型人流感病毒株的同源性分别为84.7 ％～98.1％、94.4 ％～99.5％和88.6 ％～97.6％;与H3N2亚型SIV的核苷酸同源性分别为87.7％～98.5％、82.5 ％～99.9％和87.6 ％～98.4％;M基因与H3N2亚型人流感病毒和SIV的同源性均在90.1％以下,而与H1N1亚型古典SIV的同源性在97.6％以上.基因型分析表明分离株的PB2、PBI、PA、HA、NP、NA和NS基因片段来源于1975年～1982年的人流感病毒,而M基因来源于H1N1亚型古典SIV,充分证明猪作为流感病毒“混合器”的作用.     

鹅细小病毒VP1-VP3非重叠区基因的克隆与序列分析

通过克隆鹅细小病毒(Goose parvovirus,GPV)分离株VP1-V3非重叠区基因,并对其进行序列分析,为鹅细小病毒感染与疫苗免疫的鉴别诊断奠定理论基础.进行鹅胚病毒增殖,收集尿囊液,提取基因组,参考发表的B株序列,设计合成一对引物,经PCR扩增,克隆VP1-VP3基因,筛选阳性克隆,对其进行序列测定及同源性分析.结果表明,克隆的基因片段为901 bp,VP1-VP3基因共594 bp,编码198个氨基酸;弱毒株之间亲缘关系很近,核苷酸同源性99.5％～100％,氨基酸同源性98.5％～100％;强毒株与B株亲缘关系较近,核苷酸同源性96.6％,氨基酸同源性97.5％;弱毒株与强毒株亲缘关系较远,核苷酸同源性92％～93％,氨基酸同源性96％～97.5％;弱毒株与B株亲缘关系最远,核苷酸同源性92.5％～93％,氨基酸同源性93.9％～95.5％.说明强毒株与弱毒株之间核苷酸序列存在差异.     

蒙古羊Hoxc8基因甲基化与胸椎数量的关系

为了研究蒙古羊Hoxc8基因的甲基化与胸椎数的关系,试验采用亚硫酸氢盐测序PCR方法进行检测。结果表明:蒙古羊的14枚胸椎个体(T14)占26.1%,7枚腰椎个体(L7)占69.5%,其中Hoxc8 exon-1含27个CpG。T13型个体的甲基化CpG分别为6,3,6;T14型个体的甲基化CpG分别为23,20,21。T13和T14的甲基化比例平均值分别为(18.500±0.064)%和(79.030±0.056)%(P=0.002)。T14蒙古羊Hoxc8 exon-1的甲基化功能区(120～142个碱基)的CpG胞嘧啶全部甲基化,而T13则相反。说明蒙古羊Hoxc8 exon-1甲基化CpG的密度和数量影响Hoxc8基因的表达,并且调控胸椎的发育。     

Genotypic and phenotypic characterization of lactic acid bacteria isolated from Italian ryegrass silage

Twenty-three lactic acid bacteria (LAB) isolated from three cultivars (Akiaoba, Nagahahikari and Tachiwase) of Italian ryegrass (Lolium multiflorum Lam.) silage were precisely characterized by a combination of phenotypic tests, genotypic 16S ribosomal DNA sequencing and rapid PCR-based analyses, focusing on their useful phenotypes for silage preparation as inoculants. We successfully identified both at the species and subspecies levels: phenotypically novel Lactococcus lactis subsp. lactis, Lactobacillus brevis, Lactobacillus coryniformis subsp. torquens, Lactobacillus curvatus, Lactobacillus plantarum subsp. plantarum, Lactobacillus sakei subsp. carnosus, Leuconostoc mesenteroides subsp. dextranicum and Pediococcus parvulus. This is the first report to elucidate the presence of Lactobacillus coryniformis ssp. torquens and Leuconostoc mesenteroides subsp. dextranicum in Italian ryegrass silages. Physiological and biochemical tests revealed that phenotypic characteristics are different among the different strains of the same species and subspecies, and that the isolates show unique and diverse phenotypes related to fermentation factors, such as available carbohydrates, optimal growth pH and temperature. These results suggest that, for various well-preserved silage preparations, the isolates may be useful in producing novel inoculants corresponding to their optimally climatic and ecological niches.     

鸡传染性支气管炎病毒SD060311株和GD080122(肾型)株的全基因组序列分析

通过对鸡传染性支气管炎病毒(IBV)分离株SD060311和GD080122(肾型)的基因组进行RT-PCR扩增和基因序列测定,结果表明其基因组大小分别为27 788 nt和27 407 nt,与已报道的IBV全基因组序列大小不完全一致,但基因组编码基因的顺序与已报道的IBV一致,均为5′cap-Replicase-S-3a-3b-3c-M-5a-5b-N-poly (A)3 ′.与已报道的IBV毒株和火鸡冠状病毒进行比较,绘制系统进化树,结果显示,SD060311和GD080122(肾型)分离株自成一支,与中国分离株BJ株和A2株的亲缘关系最近.本研究不仅丰富了冠状病毒的生物信息数据库,且为进一步研究IBV致病机理和变异机制等奠定了基础.     

牦牛基因组和转录组研究进展

为了解牦牛基因组和转录组研究现状,以"牦牛、基因组、转录组和高通量测序"为关键词,对2012—2018年的研究进展进行文献检索。研究发现:在牦牛基因组研究方面,已有研究对牦牛基因组进行了首次测序和重测序分析,构建了基因组"草图"和变异图谱,比较了家、野牦牛及与其他物种间全基因组水平上的异同,阐释了牦牛高原适应的遗传学机制,探究了牦牛的驯化和群体历史发展动态,初步揭示了牦牛与普通牛种间杂交渐渗状况,并对部分性状(如角、多肋性状)进行了全基因组关联分析和遗传机理揭示;在牦牛转录组研究方面,已有研究对牦牛睾丸、卵巢、心脏等多个组织器官及不同发育阶段的卵母细胞和胚胎细胞进行了转录组分析,发掘出一批潜在的与牦牛经济性状及一些生物学变化相关的差异表达基因。为推动牦牛分子育种进程,应进一步利用高通量测序技术获得牦牛大数据,继续完善牦牛全基因组结构。     

转录组测序研究兰州百合抗冻关键基因及途径

【目的】百合 (Lilium) 是国家卫生部首批公布的药食同源植物,也是著名的观赏植物。低温冻害严 重影响植物的产量和分布,探究兰州百合对零下低温胁迫应答的分子机制。【方法】采用高通量 Illumina Hiseq 测序平台对兰州百合的 20℃常温对照与 -4℃寒冷处理 (D) 进行测序,并对测序数据进行分析研究。【结果】处 理 24 h 后检测到 24 465 个差异表达的基因,筛选后获得 4 143 个表达量上升的基因和 4 415 个表达量下降的基因, 占差异表达基因总数的 10.27%。【结论】经富集分析认为,与蛋白激酶、蛋白磷酸酶、碳代谢以及 ABA 等相关 的基因可作为研究兰州百合零下低温响应机制的主要研究对象。qRT-PCR 分析表明,随机选出的 10 个差异性 表达基因的表达趋势与高通量测序结果相一致。此外,吲哚 -3- 甘油磷酸合成酶、蛋白磷酸酶、已糖激酶、钙 结合蛋白、叶绿素 a/b 结合蛋白等基因可作为与兰州百合寒冷响应相关的应答候选基因,为揭示兰州百合抗冻分 子机制奠定了基础。     

绿肥配施减量化肥对土壤固氮菌群落的影响

为了探讨绿肥配施减量化肥对土壤固氮菌的影响,以开展八年的紫云英配施减量化肥的长期定位试验站为平台,选取不施肥(CK)、单施化肥(NPK)、紫云英配施80%化肥(MF80)、紫云英配施60%化肥(MF60)和紫云英配施40%化肥(MF40)共5个处理,于水稻分蘖期采集土样,采用荧光定量PCR和Illumina Miseq高通量测序技术,分析了不同施肥制度下土壤固氮菌nif H基因丰度和多样性的变化规律。结果表明:与单施化肥相比,翻压紫云英的减量施肥处理水稻产量与其无显著差异,从化肥用量和产量综合考虑,MF60处理是一种适宜的施肥制度。翻压绿肥处理土壤全氮明显增加;碱解氮含量(除MF60处理)与NPK处理无显著差异。翻压紫云英配施减量化肥的施肥处理(除MF40处理)土壤固氮菌丰度明显高于NPK处理,且固氮菌丰度与土壤碱解氮、硝态氮和p H呈显著正相关。翻压紫云英后土壤固氮菌Shannon指数明显低于NPK处理,各施肥处理间OTU指数差异不明显。各施肥处理的土壤固氮菌均以变形菌门为绝对优势菌门,翻压紫云英的减量施肥处理变形菌门丰度显著低于单施化肥处理。主坐标分析表明,翻压紫云英配施减量化肥的3个施肥处理与CK、NPK处理的土壤固氮菌的群落结构差异较明显。研究表明,紫云英配施减量化肥有利于提升土壤肥力和固氮菌的数量,紫云英的施用和化肥用量都是影响土壤固氮菌群落结构的重要因素。     

Comparative study of the intestinal microbial community of wild and cultured kaluga sturgeon,Huso dauricus

The kaluga, Huso dauricus (Georgi 1775), is a large‐sized semi‐anadromous sturgeon native to the Amur River basin. Gut microbes play an important role in the growth and development of fish. Because wild samples of this species are difficult to obtain, very few studies have analysed the microbial community of the kaluga gut. Here, we used high‐throughput sequencing to determine differences in the intestinal microbial communities of wild and cultured kaluga, to lay the foundation for development of micro‐ecological preparations that might ultimately assist with conserving wild kaluga by benefitting sturgeon aquaculture. Two 2‐year‐old (wild) fish collected from the Heilongjiang River basin were size‐ and age‐matched with two 2‐year‐old (cultured) fish obtained from a breeding base in Yunnan Province, for molecular analysis of gut samples. In total, 483,008 16S rRNA sequences were obtained. The intestinal microbial diversity was greater in the wild kaluga than in the cultured fish. The dominant phyla in the gut community of wild kaluga were Proteobacteria (47.9%), Fusobacteria (30.5%) and Firmicutes (8.85%), whereas samples from the cultured kaluga were dominated by Fusobacteria (78%). This result may be attributed to differences in environmental conditions, particularly water quality and temperature, as well as diet between the wild and cultured animals. The findings provide basic data to assist further research and the development of feed as a part of artificial breeding technology.