Putative virulence-related genes in Vibrio anguillarum identified by random genome sequencing

The genome of Vibrio anguillarum strain H775-3 was partially determined by a random sequencing procedure. A total of 2,300 clones, 2,100 from a plasmid library and 200 from a cosmid library, were sequenced and subjected to homology search by the BLAST algorithm. The total length of the sequenced clones is 1.5 Mbp. The nucleotide sequences were classified into 17 broad functional categories. Forty putative virulence-related genes were identified, 36 of which are novel in V. anguillarum, including a repeat in toxin gene cluster, haemolysin genes, enterobactin gene, protease genes, lipopolysaccharide biosynthesis genes, capsule biosynthesis gene, flagellar genes and pilus genes.     

Detection and characterization of a rhabdovirus causing mortality in black bullhead catfish,Ameiurus melas

This study fully describes a severe disease outbreak occurred in 2016 in black bullhead catfish farmed in Italy. Affected fish showed nervous clinical signs as well as emaciations and haemorrhagic petechiae on the skin at the fin bases, abdomen and gills. Viral isolation in cell culture allowed the subsequent identification of a rhabdovirus, tentatively named ictalurid rhabdovirus (IcRV), through electron microscopy, immunofluorescence and whole genome sequencing (WGS). The newly isolated virus, together with 14 additional viral strains stored in our repository and detected during similar mortality episodes in the period 1993–2016, was phylogenetically analysed on the basis of the nucleoprotein and the glycoprotein nucleotide and amino acid sequences. The genetic distances among Italian IcRV strains were also estimated. Our results show that all the IcRV strains belong to the genus Sprivivirus and are closely related to the tench rhabdovirus (TenRV). Italian catfish production is constantly decreasing, mainly due to viral infections, which include the newly characterized IcRV. Data presented in this work will assist to investigate the molecular epidemiology and the diffusive dynamics of this virus and to develop adequate surveillance activities.     

脊尾白虾不同发育期mtDNA拷贝数变化特征分析

为了解脊尾白虾(Exopalaemon carinicauda)在不同发育期线粒体基因组(mtDNA)拷贝数的变化特征,本研究共采集其8个时期(受精卵期、溞状幼体Ⅰ期、溞状幼体Ⅱ期、溞状幼体Ⅲ期、溞状幼体Ⅳ期、溞状幼体Ⅴ期、仔虾期和成虾期)的DNA样品,利用TaqMan实时荧光定量PCR技术,对上述各发育期单个细胞中的mtDNA拷贝数进行了测定。检测结果显示,脊尾白虾受精卵期、溞状幼体Ⅰ期、溞状幼体Ⅱ期、溞状幼体Ⅲ期、溞状幼体Ⅳ期、溞状幼体Ⅴ期、仔虾期和成虾期的mtDNA拷贝数的均值分别为2366、2648、2644、2873、3559、9948、6452和8872。进一步统计分析结果显示,mtDNA拷贝数与发育时间存在正相关性,相关系数为0.83。研究表明,随着脊尾白虾不断生长,其单个细胞中mtDNA拷贝数总体呈上升趋势。     

斜带髭鲷线粒体DNA控制区序列的结构分析

采用PCR技术获得我国南海斜带髭鲷（Hapalogenys nitens）养殖及野生群体共50尾样品的mtDNA控制区全序列,长度范围788～790bp;测得序列与GenBank下载的其他鲈形目鱼类D-loop全序列利用CLUSTALX进行排序后,对控制区结构进行分析。识别了其终止结合序列区、中央保守区和保守序列区,指出了终止相关序列的主体是TACAT与其反向互补序列ATGTA以及一系列保守序列（CSB-F、CSB-E、CSB-D和CSB-1、CSB-2、CSB-3）,并给出了其一般形式;此外,基于斜带髭鲷D-Loop全长序列,利用贝叶斯法构建了分子系统进化树。结果显示,斜带髭鲷养殖群体与野生群体部分样品各自紧密聚成一小支,而在整棵进化树上,养殖样品与野生样品相互交错聚集在一起,可见本研究海区斜带髭鲷养殖群体与野生群体之间的遗传差异分化不显著。     

Ecology,physiology and genetics of a phycodnavirus infecting the noxious bloom-forming raphidophyte <Emphasis Type="Italic">Heterosigma akashiwo</Emphasis>

Abstract:   Heterosigma akashiwo virus (HaV) is a large icosahedral virus (∼0.2 μm) harboring a double-stranded DNA (dsDNA) genome (∼294 kbp). The virus is the only member of the genus Raphidovirus in the family Phycodnaviridae. Since its first discovery, a number of ecologic, physiologic and genetic studies about HaV have been conducted; especially, the relationship between H. akashiwo and HaV in nature was studied and viral infection is now regarded as a significant factor influencing the dynamics and termination of H. akashiwo blooms. HaV infection has considerable impacts on H. akashiwo populations in both aspects of fluctuation in biomass (quantity) and changes in clonal composition (quality). Partial sequencing of the HaV genome revealed that a number of genes showed considerable similarity to those of other protist-infecting viruses; still, the phylogenetic position of HaV suggested a number of enigmas in host–virus coevolution. Here are summarized the ecology, physiology and genetics of HaV especially from the viewpoint of the host–virus relationship.     

鱼类弹状病毒分子生物学研究动态

鱼类弹状病毒(Fish rhabdovirus)是一类引起鱼及其他水生动物致死性和流行性病害的重要病毒病原。对鱼类弹状病毒基因组的结构和功能研究,是深入探讨这类病毒感染和致病机理、研制病毒疫苗及诊断试剂的理论基础。本文就鱼类弹状病毒的基因组结构,包括N基因、P基因、M基因、G基因、NV基因、L基因及编码的相应蛋白、3′前导区和5′拖尾区、基因连接区等的组成及功能的研究进展作一综述,旨为抗病毒疫苗的研制及建立准确高效的检测方法提供借鉴。     

装配式地下粮仓钢板-混凝土组合仓壁轴压受力性能分析

为了研究装配式地下粮仓钢板-混凝土组合仓壁的轴压力学性能,该研究在仓壁试件轴压试验的基础上,对仓壁试件进行非线性有限元分析,模拟试件加载的全过程,进一步分析试件及其组件在加载过程中的受力性能及工作机理,并对钢板强度、混凝土强度、距厚比等不同的参数影响规律进行了分析.结果表明:有限元模拟结果与试验结果吻合较好,在最大试验...     

大白菜InDels标记开发及其在剩余杂合体鉴定中的应用

大白菜(Brassica rapa ssp.pekinensis)参考基因组序列的公布及测序成本的降低为大规模开发插入/缺失(Insertion/Deletion,InDel)标记提供了可能.本研究以性状差异明显的大白菜自交系He102与06-247为亲本,开展了全基因组重测序、标记开发和验证工作.二者测序深度分别为10×和8×,经筛选共获得330 218个InDels差异位点,出现频率为1.2个/kb,其中有11 238个差异位点位于编码区,包括5 184个差异基因,每个基因平均包含2.2个差异位点.分别以He102与06-247测序数据中筛选出的多态性InDels位点为参照,从10条染色体上随机选择933个位点进行了PCR扩增及电泳检测验证.结果表明,测序深度对假阳性率有直接影响,以测序较深的材料中筛选到的差异位点为参照,其验证结果的假阳性率亦较高,反之则较低.本研究中以He102与06-247为参照选择InDels位点验证的平均假阳性率分别是51.9％和22.5％.从933个位点中共筛选出593个在亲本之间实际表现为多态性的位点,这些差异位点中有375个位于编码区,是潜在的功能性标记.利用上述差异位点,检测了He102与06-247衍生的F7代重组自交系群体,明确了F7代各株系在593个位点的纯/杂合状态,为利用剩余杂合株系精细解析和精准定位大白菜耐抽薹、抗病毒、抗干烧心等重要农艺性状奠定了基础.