牛源流行性出血病病毒(EHDV)血清10型毒株在我国的分离鉴定

我国存在多种血清型流行性出血热病毒(Epizootic haemorrhagic disease virus,EHDV)的流行,但尚未有关于EHDV-10型毒株的分离报道。为了解云南省EHDV的流行情况,2012～2015年,本研究在云南省设立江城、师宗、芒市三个监控点,定期采集监控动物血液,接种幼仓鼠肾细胞(Baby hamster kidney cell,BHK-21)进行病毒分离;通过PCR检测、血清中和试验、琼脂糖凝胶电泳和电镜观察等方法对分离病毒进行鉴定;对分离毒株的Seg-2/VP2与Seg-3/VP3基因节段进行克隆、测序与序列分析。2013年在云南省师宗县的哨兵牛上分离出一株EHDV毒株(YNSZ-V277-2013),病毒可引起BHK-21细胞出现圆缩、裂解的细胞病变(Cytopathic effect,CPE);电镜下病毒粒子呈球形,无囊膜,表面有大量纤维突,直径在70～80nm之间;病毒基因组dsRNA的琼脂糖凝胶电泳显示分离毒株与其他血清型EHDV一致,呈现"3-3-3"的电泳带型;序列分析显示YNSZ-V277-2013毒株的Seg-2/VP2与Seg-3/VP3序列与日本EHDV-10型毒株(ON-4/N/98)相似度最高,分别为97.5%/98.5%与98.1%/99.8%,证实分离毒株为EHDV-10型;系统发育分析显示YNSZ-V277-2013毒株的Seg-2与日本EHDV-10型毒株(ON-4/N/98)的亲缘关系最近,Seg-3与分离至日本和澳大利亚的EHDV毒株同属Eastern型。本研究首次报道了EHDV-10型毒株在我国的分离以及分离毒株的Seg-2与Seg-3基因序列特征,为进一步开展中国EHDV-10型的流行病学调查与致病性研究提供了基础。     

实时荧光定量PCR及RT-PCR与常规PCR及RT-PCR检测对虾病毒效果的比较

常规PCR及RT-PCR已用于对虾DNA及RNA病毒检测,但存在费时、灵敏度较低、不能定量等问题。建立了TaqMan实时荧光定量PCR及RT-PCR方法,分别用于检测白斑综合症病毒(WSSV)、传染性皮下及造血组织坏死病毒(IHHNV)及桃拉综合征病毒(TSV)、黄头病毒(YHV)4种对虾病毒。与常规PCR及RT-PCR比较,所建立的TaqMan实时荧光定量PCR及RT-PCR检测上述4种对虾病毒不仅有很高的特异性,检测灵敏度也提高了10～100倍,同时还具有快速、简便、不污染环境、重复性好、实时定量等优点,可明显提高对虾病毒检验检疫工作质量及效率。     

Simple sequence repeat genetic linkage maps of A-genome diploid cotton (Gossypium arboreum)

This study introduces the construction of the first intraspacific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat (SSR) markers using 189 F2 plants derived from the cross of two Asiatic parents were detected using 6 092 pairs of SSR primers. Two-hundred and sixty-eight pairs of SSR pdmers with better polymorphisms were picked out to analyze the F2 population. In total, 320 polymorphic bands were generated and used to construct a linkage map with JoinMap3.0. Two-hundred and sixty-seven loci, Including three phenotypic traits were mapped at a logarithms of odds ratio (LOD) ≥ 3.0 on 13 linkage groups. The total length of the map was 2 508.71 cM, and the average distance between adjacent markers was 9.40 cM. Chromosome assignments were according to the association of linkages with our backbone tetraploid specific map using the 89 similar SSR loci. Comparisons among the 13 suites of orthologous linkage groups revealed that the A-genome chromosomes are largely collinear with the At and Dt sub-genome chromosomes. Chromosomes associated with inversions suggested that allopolyploidization was accompanied by homologous chromosomal rearrangement. The inter-chromosomal duplicated loci supply molecular evidence that the A-genome diploid Asiatic cotton is paleopolyploid.     

海南岛番木瓜和扶桑上粉虱传双生病毒的检测及序列分析

粉虱传双生病毒(Whitefly-transmitted geminivirus,WTGV)是一类广泛发生在热带、亚热带地区植物上的具有孪生颗粒形态的单链DNA病毒,在分类上属双生病毒科(Geminiviridae)的菜豆金色花叶病毒属(Begomovirus),该属的大多数病毒都由2个组分(DNA-A和DNA-B)组成,为两条闭合环状ssDNA分子,长度相似,每条为2.5-2.8kb,少数病毒为单组分,仅有DNA-A组分[1].我国自1983年报道发现双生病毒以来,在云南、广西、广东和海南等省区的已相继发现多种双生病毒[2～6],表明这类病毒在我国的危害有蔓延和加重的趋势.本文对从海南番木瓜(Carica papaya)和扶桑(Hibiscus rosa-sinensis)上采集到的表现典型双生病毒症状的样品进行了分子检测,并对序列进行了分析.     

苦荞和甜荞查尔酮合成酶基因的克隆及序列比较

以苦荞品种‘西农9920’和甜荞品种‘西农9976’为材料,根据其它植物查尔酮合成酶(chalcone synthase,CHS)基因DNA序列的保守区域设计的一对简并引物,进行PCR扩增,从2种荞麦基因组中克隆出了长度均为860 bp的CHS基因片段,对其进行回收、克隆,挑选阳性克隆测序;序列分析表明这2个片段含有CHS基因的N端和C端的结构域,分别为苦荞和甜荞的CHS基因片段,命名为FtCHS和FeCHS。对获得的2种荞麦CHS基因的DNA序列进行比较分析,发现两者间存在多达43处单碱基多态性,这些单碱基多态性可能是苦荞和甜荞种子中类黄酮含量差异的重要原因之一。苦荞和甜荞CHS与其它植物CHS的氨基酸序列的进化分析表明,其与同为蓼科的掌叶大黄和石竹科的满天星的同源性较近。     

Comparison of object manipulation among 74 species of non-human primates

Seventy-four primates species (24 genera of six families) were presented with a nylon rope and a wooden cube, and their subsequent manipulations were recorded in detail. Five hundreds and six manipulation patterns were distinguished on the basis of the actions performed, body-parts used and relations to other objects. Inter-specific comparisons revealed three groups: (1) lemurs, marmosets, spider monkeys and leaf-eaters; (2) Old World monkeys except leaf-eaters; and (3) cebus monkeys and apes. The first group had the smallest repertoire of manipulations, in which only a few types of actions and body-parts were involved. The second and third groups had more varied modes of manipulation. Actions such as Roll, Rub and Slide, and use of fingers characterized these groups. Except for the lesser ape, their manipulations were frequently related with other objects. Moreover, actions such as Drape, Drop, Strike, Swing and Throw were typical of the third group. The factors producing such inter-specific differences in manipulations and the relations to tool use are discussed.     

Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes

Hox genes are key regulators of anterior-posterior axis patterning and have a major role in hindbrain development. The zebrafish Hox4 paralogs have strong overlapping activities in hindbrain rhombomeres 7 and 8, in the spinal cord and in the pharyngeal arches. With the aim to predict enhancers that act on the hoxa4a, hoxb4a, hoxc4a and hoxd4a genes, we used sequence conservation around the Hox4 genes to analyze all fish:human conserved non-coding sequences by reporter assays in stable zebrafish transgenesis. Thirty-four elements were functionally tested in GFP reporter gene constructs and more than 100 F1 lines were analyzed to establish a correlation between sequence conservation and cis-regulatory function, constituting a catalog of Hox4 CNEs. Sixteen tissue-specific enhancers could be identified. Multiple alignments of the CNEs revealed paralogous cis-regulatory sequences, however, the CNE sequence similarities were found not to correlate with tissue specificity. To identify ancestral enhancers that direct Hox4 gene activity, genome sequence alignments of mammals, teleosts, horn shark and the cephalochordate amphioxus, which is the most basal extant chordate possessing a single prototypical Hox cluster, were performed. Three elements were identified and two of them exhibited regulatory activity in transgenic zebrafish, however revealing no specificity. Our data show that the approach to identify cis-regulatory sequences by genome sequence alignments and subsequent testing in zebrafish transgenesis can be used to define enhancers within the Hox clusters and that these have significantly diverged in their function during evolution.     

黄唇鱼(Bahaba flavolabiata)的全基因组测序和基因组特征研究

黄唇鱼(Bahaba flavolabiata)为国家二级重点保护野生动物、IUCN(世界自然保护联盟)红色名录的极度濒危物种(CR)。基于其样本数量极其有限,全基因组研究可以提供大量与重要性状相关的功能基因和分子标记,从而揭示其重要生命现象的遗传机制。采用二代测序技术于2018年5月完成了黄唇鱼基因组精细图的测序,分析结果表明,测序得到约202 Gb的高质量数据,总测序深度约为317×;组装得到的基因组大小为637.43 Mb,Contig N50约为88 Kb,Scaffold N50约为4.65 Mb;重复序列约142.72 Mb,占比22.39%,预测得到23743个基因、920个t RNA、85个rRNA、176个假基因;98.46%的基因可以注释到NR、GO等数据库中;有67个基因家族是黄唇鱼所特有的。本研究从单碱基错误率、核心基因完整性及二代Reads比对分析3个方面对黄唇鱼基因组精细图的组装结果进行了评估,结果显示所组装的基因区的完整性较好。黄唇鱼基因组序列图谱的绘制完成,对于黄唇鱼自然资源的保护和种质资源挖掘具有极其重要的科学意义。     

Characterization of robust optimization for VMAT plan for liver cancer

PurposeWe investigated the feasibility of robust optimization for volumetric modulated arc therapy (VMAT) stereotactic body radiation therapy (SBRT) for liver cancer in comparison with planning target volume (PTV)-based optimized plans. Treatment plan quality, robustness, complexity, and accuracy of dose delivery were assessed.MethodsTen liver cancer patients were selected for this study. PTV-based optimized plans with an 8-mm PTV margin and robust optimized plans with an 8-mm setup uncertainty were generated. Plan perturbed doses were evaluated using a setup error of 8 mm in all directions from the isocenter. The dosimetric comparison parameters were clinical target volume (CTV) doses (D_98%, D_50%, and D_2%), liver doses, and monitor unit (MU). Plan complexity was evaluated using the modulation complexity score for VMAT (MCSv).ResultsThere was no significant difference between the two optimizations with respect to CTV doses and MUs. Robust optimized plans had a higher liver dose than did PTV-based optimized plans. Plan perturbed dose evaluations showed that doses to the CTV for the robust optimized plans had small variations. Robust optimized plans were less complex than PTV-based optimized plans. Robust optimized plans had statistically significant fewer leaf position errors than did PTV-based optimized plans.ConclusionsComparison of treatment plan quality, robustness, and plan complexity of both optimizations showed that robust optimization could be feasibile for VMAT of liver cancer.