Common evolutionary origin of aquareoviruses and orthoreoviruses revealed by genome characterization of Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus (genus Aquareovirus, family Reoviridae)

Full-length and partial genome sequences of four members of the genus Aquareovirus, family Reoviridae (Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus) were characterized. Based on sequence comparison, the unclassified Grass carp reovirus was shown to be a member of the species Aquareovirus C The status of golden ide reovirus, another unclassified aquareovirus, was also examined. Sequence analysis showed that it did not belong to the species Aquareovirus A or C, but assessment of its relationship to the species Aquareovirus B, D, E and F was hampered by the absence of genetic data from these species. In agreement with previous reports of ultrastructural resemblance between aquareoviruses and orthoreoviruses, genetic analysis revealed homology in the genes of the two groups. This homology concerned eight of the 11 segments of the aquareovirus genome (amino acid identity 17-42%), and similar genetic organization was observed in two other segments. The conserved terminal sequences in the genomes of members of the two groups were also similar. These data are undoubtedly an indication of the common evolutionary origin of these viruses. This clear genetic relatedness between members of distinct genera is unique within the family Reoviridae. Such a genetic relationship is usually observed between members of a single genus. However, the current taxonomic classification of aquareoviruses and orthoreoviruses in two different genera is supported by a number of characteristics, including their distinct G+C contents, unequal numbers of genome segments, absence of an antigenic relationship, different cytopathic effects and specific econiches.

粗枝云杉( Picea asperata Mast.)天然群体的遗传变异

西南地区在我国的经济发展和生态环境建设中占重要地位，但也是我国生态环境最脆弱的地区之一，生态系统退化，生态功能减弱，严重制约着西南林业的可持续经营与发展。本项目采用DNA 分子标记SSR 研究不同生境条件下粗枝云杉群体的遗传变异及其时空分布格局，考察遗传变异与复杂的山地生态环境间的潜在联系，系统地揭示粗枝云杉天然群体与环境系统相互作用的生态适应与分子进化机制。粗枝云杉适应性强，生长迅速，在植树造林和工业用材方面占有重要地位，研究成果可为中国西南部亚高山天然林的可持续经营及退化生态系统的恢复与重建提供理论依据和科学指导。主要研究结果如下： 1. SSR 位点变异丰富，等位基因频率的分布格局多样。7 个SSR 标记全是多态位点，每位点的等位基因数变化范围为13~24，平均为19.9 个。SSR 位点的等位基因片段长度范围变化较大。73.1%的等位基因变异遵循逐步突变模型(SSM)而发生1 个重复基元的变化，22.3%和4.6%的变异分别按两阶段突变模型(TMP)发生1 个重复基元以上的变化和在SSR 位点侧翼区发生1 个碱基变化的插入-删除事件。 2. 粗枝云杉拥有中等偏高水平的遗传多样性和相对大的群体间遗传分化。通过分析代表10 个群体的250 个个体在7 个SSR位点的变化，调查了源自中国西南山区的粗枝云杉的微卫星变异。相当高的遗传多样性和强烈的群体分化发生在粗枝云杉中， 其群体平均Nei's 期望杂合度为0.707 ， 群体间遗传距离为0.121~0.224(FST)和0.100~0.537(RST)。然而，群体间遗传距离与地理距离之间无相关性，从而排除了简单的距离分离模式并暗示迁移不是影响粗枝云杉遗传变异格局的主要因素。事实上，使用私有等位基因估算的基因流数量非常低，仅等于0.753。等位基因置换检验(Allele permutation tests)揭示逐步突变及遗传漂变都对群体间分化有贡献。另外，在多数位点检测到显著的群体间遗传差异，这个结果说明自然选择，假设通过环境压力，是引起粗枝云杉微地理分化的主要因素之一。根据SSR基因型，250 个粗枝云杉个体的70%被正确地归类入其各自的来源群体，结果表明微卫星(SSR)对区分来自中国不同生态地理位点的粗枝云杉基因型是有效的。 3. 在SSR、RAPD 和AFLP 位点，显著的群体间遗传结构被发现的，但三种标记间遗传分化程度和群体遗传关系有差异。利用来自10 个群体的247 个个体，我们报告了关于样本粗枝云杉群体间遗传关系的总体看法。根据各自对评价遗传关系的信息能力和适用性，SSR、RAPD 和AFLP 标记被选用，三种技术非常有效地区别这些基因型。使用的SSR、RAPD 和AFLP 标记分别估计平均Dice 相似性系数。Mantel 检验产生显著但相对低的共表型适合度(RAPD = 0.63£AFLP = 0.60和SSR = 0.75)。比较三种标记系统，RAPD 和AFLP 共表型指数相对高地相关(r =0.59)，而RAPD 和SSR 及SSR 和AFLP 之间的相关系数分别是0.53 和0.35。所有系统树，包括不同标记资料结合获得的系统树，反映了多数群体依据它们的地理条件而成某种特定关系。结果暗示单个或结合标记系统能用来深入洞察粗枝云杉遗传研究，并且不同标记系统合并资料能提供更可靠的信息。 Southwestern region plays an important role in economic developmentand ecological construction in China. Yet, it is also one of the weak regionsof ecological environment in China with degraded ecosystem and imperfectfunction, which restricts the sustaining management and development ofsouthwestern forestry. The genetic variation and spatial distribution patternof P. asperata populations originating from different habitats wereinvestigated using SSR molecular markers in this study. The correlationsbetween genetic variation and ecological and environmental conditionswere detected, and the interaction between P. asperata populations andenvironmental system and the mechanism of ecological adaption -molecular evolution were revealed. Given the significant ecological andeconomic roles of the fast-growing and wide-adaptive species in reforestation and production of pulp wood and timber, the study couldprovide a strong theoretical evidence and scientific direction for thesustaining management of subalpine natural forest, and the afforestationand rehabilitation of degraded ecosystem. The results are as follows: 1. The genetic variation at SSR loci was abundant and the distributionof allelic frequencies was uneven. All seven loci were polymorphic, and thenumber of alleles per locus varied from 13 to 24 with a mean valueequaling 19.9. The allele sizes at SSR loci were found to vary widely.73.1% of allelic variation followed stepwise mutation model (SSM) whichresults increase or decrease by one repeat type, and 22.3% and 4.6% wereresulted from two-phase mutation model (TMP) with allele size varying bymore than one repeat type and from insertion-deletion events in theflanking regions at SSR loci with a single basepair changing, respectively. 2. P. asperata possessed a moderate to high level of genetic diversityand considerable genetic differentiation. Microsatellite variation of P.asperata. originating from the mountains of southwestern China wasinvestigated by analyzing variation at seven SSR loci in 250 individualsrepresenting ten populations. A fair degree of genetic diversity and strongpopulation subdivision occurred with the mean gene diversity (H) of 0.707,and genetic distances among populations varying between 0.121 and 0.224(FST) and between 0.100 and 0.537 (RST). However, inter-populationgenetic distances showed no correlation with geographic distances between the population sites. This ruled out a simple isolation by distance modeland suggested that migration does not have a great impact. In fact, theamount of gene flow, detected using private alleles, was very low, equalingonly 0.753. Allele permutation tests revealed that stepwise-like mutations,coupled with genetic drift, could contribute to population differentiation.Moreover, significant genetic differences between populations weredetected at most loci. The results indicate that natural selection, presumablythrough environmental stress, may be one of the main factors causingmicro-geographical differentiation in the genetic structure of P. asperata.Based on SSR genotypes, 70% of the 250 individuals were correctlyclassified into their sites of origin. This suggests that microsatellites (SSRs) are effective in distinguishing genotypes of P. asperata originating fromdiverse eco-geographical sites in China. 3. Using a set of 247 individuals from ten P. asperata populations wereport an overview on the genetic relationship among the sampled P.asperata populations. RAPD, AFLP and SSR were used in terms of theirinformativeness and applicability for evaluate relationship and all threetechniques discriminated the genotypes very effectively. Mean Dicesimilarities coefficient were estimated using RAPD, AFLP and SSR,respectively. The Mantel test resulted in a significant but relatively low fit(RAPD = 0.63, AFLP = 0.60 and SSR = 0.75) of cophenetic values.Comparing the three marker systems to each other, RAPD and AFLP cophenetic indices were highly correlated (r = 0.59), while correlationcoefficient between RAPD and SSR was r = 0.53 and between SSR andAFLP was r = 0.35. For all markers a relatively high similarity indendrogram topologies was obtained although some differences wereobserved. All the dendrograms, including that obtained by the combineduse of all the marker data, reflect some relationships for most of thepopulations according to their geographic conditions. The results indicatethat single or combined marker system could be used to insight into geneticstudy in P. asperata and the combined data of different marker systems canprovide more reliable information.

川西青杨组(Section Tacamahaca Spach)不同种的亲缘关系分析

青杨组（Section Tacamahaca Spach）杨树是我国重要的乡土经济树种，目前对其分子遗传变异和系统进化的研究还很少，尤其是在青杨组杨树遗传资源极为丰富的川西地区，杨树的分子进化及亲缘关系的研究极为缺乏，非常不利于该树种遗传资源的开发和利用。本研究从川西地区收集了青杨（Populus cathayana）、青海杨（P. prezewalskii）、滇杨（P. yunnanensis）、康定杨（P. kangdingensis）、西南杨（P. schneideri）、小叶杨（P.simonii）和三脉青杨（P. trinervis）这7 个青杨组树种的10 个群体，利用多种分子标记手段对其种间的亲缘关系进行比较，并结合形态和地史资料进行了全面的研究和评价，得到了如下的主要研究结果： 1. SSR 和ISSR 位点变异丰富。通过10 对引物对50 个杨树个体的DNA 样品进行了SSR 分析，所有位点展现了丰富的群体间和种间的多态性，多态位点率达到了100%，每位点的等位基因数变化范围为5 ~ 17，平均为11.9 个；通过11 条ISSR 随机引物对供试的混合DNA 样品进行分析，共检测到130 个标记，其中多态性标记为119 个，多态百分率为91.5%。研究认为，SSR 单个标记能展现高水平信息，而ISSR 单个引物能探测更多数量多态性。通过两个标记的遗传距离、聚类图和PCA 分析，表明：同一种内不同群体间的同源性最高；康定杨和西南杨有较近的亲缘关系；小叶杨和三脉青杨聚合在一起，显示了其相互较近的亲缘关系；滇杨与其它杨树种可能存在着较远的亲缘关系。 2. 采用4 对选择性引物对7 个青杨组杨树种10 个群体进行AFLP 分析，总共扩增出284 个位点，其中200 个位点显示出了多态性，多态位点百分比为70.4%，平均多态带为50 条。TE-AFLP 的分析总共扩增出192 个位点，其中139 个位点显示出了多态性，多态位点百分比为72.4%，平均多态带为34.7 条。比较的结果表明AFLP、TE-AFLP 的遗传信息含量比较接近，略小于ISSR，大约仅为SSR 的1/3；但这两个基于AFLP 的标记系统的信息探察能力也远大于ISSR 和SSR 标记系统。这两个分子标记的聚类结果，显示小叶杨、三脉青杨和滇杨三个种聚为一组，其中小叶杨与三脉青杨的亲缘关系更近；其它几个杨树种聚为一类，西南杨与青杨表现出较近的亲缘关系。 3. 所有7 对cpSSR 引物中，仅有4 个叶绿体位点在种间具有多态性，而在种内群体中并不具有多态性，共检测出13 个条带，组合成了4 种不同的单倍型；对于cpDNA的5 对引物，共检测出了73 条酶切片段，其中52 条是多态带，组合成了9 种不同的单倍型；而5 对mtDNA 通用引物未能检测出多态性的条带，表现出线粒体的保守性。叶绿体的聚类分析认为，小叶杨、三脉青杨和滇杨有较近的母性起源，且依次聚合；其余四种杨树聚为一类，并且康定杨与西南杨表现出最近的亲缘关系，并依次与青杨和青海杨聚合。 4. 根据本文的分子数据，结合形态和生境分布资料分析认为：青杨组杨树种内群体间的遗传变异程度是小于种间的遗传差异，显示了与传统分类一致的结果；三脉青杨和小叶杨有很近的亲缘关系，可能拥有相同的祖先类群；滇杨与小叶杨和三脉青杨之间具有一定的亲缘关系，特别是在其母性祖先的起源上有着一定的同源性；西南杨与青杨和康定杨均保持着较近的亲缘关系，且有可能是这两个种原始祖先杂交后所形成的。 Although western Sichuan is regarded as a natural distribution and variation center forthe Section Tacahamaca of the Populus species in China, little is currently known about themajority of poplar species occurring in this region. In the present study, molecular data wereutilized to determine the genetic relationships among Populus species in Section Tacamahacain western Sichuan including P. cathayana, P. prezewalskii, P. yunnanensis, P. kangdingensis,P. schneideri, P. simonii and P.trinervis. The results are as fellows: 1. The genetic variation at SSR and ISSR loci was abundant. All the 10 SSR loci werepolymorphic, and the number of alleles per locus varied from 5 to 17 with a mean valueequaling 11.9. Based on the 11 ISSR primers, 130 clear and reproducible DNA fragmentswere generated, of which 119 (91.5%) were polymorphic. Our results reveal that single SSRlocus can present more genetic information, while more polymorphic bands can be detectedby single ISSR primer. Moreover, the genetic distance, cluster and PCA analysisdemonstrated that: a close relationship among accessions of the same species and suggestedmonophyly in P. przewalskii and P. cathayana; P. schneideri is genetically highly similar to P.kangdingensis; P. trinervis and P. simonii have a close genetic affinity; P. yunnanensis isdistinct from the other species. 2. Genetic relationships of poplar species in Section Tacamahaca from western Sichuanwere evaluated by means of AFLP and TE-AFLP. For four AFLP primer combinations, atotal of 284 bands were obtained of which 200 (70.4%) were polymorphic with the average of50 polymorphic bands. For four TE-AFLP primer combinations, a total of 192 band wereobtained of which 139 (72.4%) were polymorphic with the average of 34.7 polymorphicbands. Our results indicate that the genetic information of AFLP is similar to that ofTE-AFLP, and little less than that of ISSR, but only about 1/3 of that of SSR. However, theability of information detection of the two AFLP-based markers is much higher than that ofISSR and SSR. In addition, the cluster analysis of AFLP, TE-AFLP and combined data revealthat: P. yunnanensis, P. trinervis and P. simonii clustered together, and P. trinervis and P.simonii showed more closed affinity; the other four poplar species clustered together, P.cathayana and P. schneideri showed more closed origin especially. 3. The cpSSR analysis for seven Populus species belonging to the Section Tacamahaca.Four out of the seven analyzed chloroplast loci were polymorphic, whereas none of the lociwere polymorphic across the accessions within a species. 13 bands and 4 different kinds ofhaplotypes were reduced. Based on 5 pairs of cpDNA primers, 73 fragments (52 polymorphic)and 9 kinds of haplotypes were produced. However, none of the polymorphic was detected bythe 5 mtDNA primer pairs, revealing conservation of mtDNA region. The cluster analysis ofcpDNA revealed that: similar maternal phylogeny among P. yunnanensis, P. trinervis and P.simonii; the other four species clustered together, P. schneideri and P. kangdingensis showedmore closed maternal lineage especially. 4. Our molecular data, morphological characters and nature habitat revealed that: sameto the traditional taxonomy assignment, genetic variation within a same Populus species islower than that among Populus species in Section Tacamahaca; P. yunnanensis may share itschloroplast ancestor with P. trinervis and P. simonii; moreover, sister genetic relationship of P.trinervis and P. simonii indicated their similar origin; P. schneideri clustered with P.kangdingensis and P. cathayana, respectively, and may have derived from an ancienthybridization event involving the ancestors of the two species.

青藏高原栽培青稞遗传多样性研究

青稞，是我国藏区居民对裸大麦的称谓，它不仅是藏民的主要食粮、燃料和牲畜饲料，而且也是啤酒、医药和保健品生产的原料；青稞不仅为藏区人民的健康和经济发展做出了很大的贡献，而且对人类健康和社会经济的可持续发展都有重要的意义。青藏高原是我国及世界上青稞分布和种植面积最大的地区，资源极其丰富。虽然从经典遗传直到分子标记对我国大麦遗传多样性都有研究，但研究手段、数量仍然不够深入，对我国大麦资源遗传多样性研究的信息非常有限，不能很好地满足大麦遗传研究和育种应用的需要，尤其是对西藏栽培大麦的遗传多样性的研究还只是刚刚开始，关于栽培青稞多态性的研究报道很少。本研究采用SSR标记和蛋白质电泳两类技术，从SSR标记位点、单体醇溶蛋白、B组醇溶蛋白和淀粉粒结合蛋白（SGP）等四个方面对我国青藏高原栽培青稞的遗传多样性进行了综合评价。 SSR标记具有基因组分布广泛、数量丰富、多态性高、容易检测、共显性、结果稳定可靠、实验重现性好、操作简单、经济、易于高通量分析等许多优点，被认为是用于遗传多样性、品种鉴定、物种的系统发育、亲缘关系及起源等研究的非常有效的分子标记。本研究采用SSR标记分析了64份青藏高原栽培青稞的遗传多样性，同时评估SSR标记在我国大麦育种和品种鉴定中的应用潜力。选择了30个已知作图位点SSR标记，其中25个标记与重要性状的控制位点连锁紧密。选择的30个SSR标记，5个未得到很好的扩增产物，3个无多态性。22个多态性SSR标记位点中，每位点检测出等位基因2~15个，共检测出等位基因132个，平均每位点6.0 个。各多态位点检测出基因型为2~11种，位点HVM33的基因型最多。各多态位点的多态信息指数为0.16~0.91, 平均为0.65。根据PIC值选择了13个SSR标记用于我国青藏高原栽培青稞基因型鉴定，这些标记的PIC值为0.6以上。结合PIC值和基因型差异，选择了8个多态信息含量高的SSR标记，构建了高效指纹图谱，此图谱能把64份材料完全区分。 贮藏蛋白电泳分析是研究相关编码蛋白基因多态性的非常有效的方法。大麦单体蛋白与小麦醇溶蛋白相对应，具有丰富的多态性，可用于大麦遗传多样性、品种鉴定和群体进化等研究。本研究通过A-PAGE电泳技术研究了84份青藏高原栽培青稞的单体醇溶蛋白多态性。大麦单体醇溶蛋白图谱与小麦醇溶蛋白电泳图谱类似，所分离的蛋白清晰地分为ω－，γ－，β－和α－四个部分。青藏高原栽培青稞单体醇溶蛋白具有丰富的多态性，84份青稞材料中存在43条不同的蛋白带，75种组合带谱；其中67种为单一材料所独有，另8种则分别包含了2-3份材料。每份材料中拥有醇溶蛋白带为6－16条，含有6-10条单体醇溶蛋白带材料较多。西藏和四川材料群体单体醇溶蛋白多态性不同，具有区域特异性。西藏材料中发现了40条不同蛋白带，3条特异带，46 种蛋白组合；四川材料中出现了40种不同蛋白带，26种条带组合, 3条特异带。基于单体蛋白多态性的聚类与材料的来源有一定的相关性。A-PAGE单体蛋白具有丰富的多态性，可作为遗传研究和品种鉴定的标记。 大麦醇溶蛋白（hordein）是大麦籽粒的主要贮藏蛋白，与大麦的营养品质和加工品质密切相关，而且具有丰富的多态性，广泛用于品种鉴定、种质筛选、遗传多样性和亲缘关系研究。B组醇溶蛋白是主要的醇溶蛋白组份，约占总醇溶蛋白的80%，而且具有丰富的多态性。本研究采用SDS-PAGE分析了72份青藏高原栽培青稞B组醇溶蛋白的遗传多样性。青藏高原栽培青稞B组醇溶蛋白具有丰富的多态性，72份青稞材料中存在15种蛋白带，30种组合带谱，其中15种为单一材料所独有，另15种则分别包含了2-10份材料。每份材料中B组醇溶蛋白条带数为4-8条，含5、6条的材料较常见。不同来源的群体材料间B组醇溶蛋白组成存在差异，西藏青稞含有26种蛋白组合带谱，其中有19种特异带谱；四川群体中共发现11种蛋白组合带型，其中有4种特有带谱。两群体中都存在稀有条带。聚类分析将材料分成三组，材料聚类与材料来源地没有明显的相关性。 淀粉粒蛋白（Starch granule proteins, SGPs）是一类与淀粉粒结合的微量蛋白，一些淀粉粒蛋白具有淀粉生化合成中主要的酶蛋白功能，其变异会影响淀粉含量和特性，从而影响淀粉的应用。关于我国大麦淀粉粒组成研究还未见报道。本实验首次开创了我国大麦淀粉粒结合蛋白的研究工作。采用SDS-PAGE电泳技术研究了青藏高原栽培青稞的SGP组成，并分析了不同SGP组合间淀粉含量的差异，初步探索了所分离的SGP蛋白与淀粉合成的关系。66份青稞材料中分离了10种主要的SGP，其表观分子量为40-100KD，低于60KD的SGP带有7条，共有16种组合带谱；各SGP蛋白和组合带谱出现的频率存在差异，青藏高原青稞的SGP组成存在多态性。西藏青稞和四川青稞的SGP组成有很大差异，SGP组成具有地域差异性，西藏青稞含有12种蛋白组合带谱，其中有9种特异带谱；四川群体中共发现7种蛋白组合带型，其中有4种特有带谱；两群体中仅有3种共同的蛋白组合带谱。SGP蛋白特性将66份青稞分为三组, 即Ⅰ、Ⅱ、Ⅲ，材料聚类与材料来源具有一定的相关性。不同组合带谱材料间淀粉含量差异显著性检验结果显示，不同带谱间材料的总淀粉含量、直链淀粉含量和支链淀粉含量有差异，带谱2（SGP1+3+7+9+10）和8（SGP1+2+4+6+8）的总淀粉含量及支链淀粉含量显著大于组合带谱3（SGP1+3+7+10）的总淀粉含量。组合带谱7（SGP1+2+6+8）的直链淀粉含量显著低于带谱11（SGP1+5+8）的直链淀粉。带谱SGP2、3、4、5、6、7、8、9、10可能参与淀粉合成，SGP9可能与高支链淀粉的合成相关。 SSR标记位点、单体醇溶蛋白、B组醇溶蛋白、淀粉结合蛋白等四个方面的研究结果表明青藏高原SSR标记多态性、单体醇溶蛋白多态性、B组醇溶蛋白多态性和SGP多态性都非常丰富，与青藏高原是栽培青稞的多样性分布中心的观点一致。 青藏高原栽培青稞的SSR标记、单体醇溶蛋白、B组醇溶蛋白和SGP多态性表现出很大差异。SSR标记覆盖了整个基因组，多态性非常高。单体蛋白、B组醇溶蛋白、SGP蛋白是育种中非常关注的性状，他们只是代表基因组中的某一区域或位点，多态性相对较低。但单体蛋白多态性很高，84份材料中检测出43条不同蛋白带，75种不同的组合带谱。SSR标记技术和单体蛋白技术都是遗传多样性研究的有力工具，但单体蛋白技术不仅多态性高，而且经济、操作简便，是种质鉴定的理想方法。 对不同标记的多态性材料数据进行聚类，聚类图能为我们提供各材料间的遗传相似信息，为材料选择提供参考。但材料聚类与材料来源的地理区域的相关性表现不一致。SSR聚类和B组醇溶蛋白聚类与材料的来源地无相关性，而单体醇溶蛋白和SGP聚类与材料来源地有一定相关性，即西藏群体和四川群体分别有集中类群，这可能是人为选择的附加效应。 不同来源的群体材料的遗传多样性不同，具有区域特异稀有基因，加强不同地区间资源的交换和配合使用，有利于增加群体遗传多样性和新品种培育。 青藏高原栽培青稞的麦芽浸提性状、淀粉性状、病虫及裸粒等重要农艺性状控制位点存在丰富的变异，遗传基础宽广，可能蕴藏着多种不同的等位基因，是研究重要性状遗传特性、基因资源挖掘和遗传育种的宝贵资源库。 Hulless barley, due to its favorable attributes such as high feed value, good human nutrition，rich dietary fiber and ease processing, attracts people,s attention . Hulless barley plays a very important role in Tibetan life, used as essential food crop, main animal feed and important fuel. In addition to tsampa (roasted barley flour), a main food for Tibetan, hulless barley is also made into cake, soup, porridge, recent naked barley liquor and cornmeal. Qinghai-Tibet Plateau is one of a few areas which plant naked barley widely in the world and also has a long growing history. Genetic diversity of the cultivated hulless barley in this region , however, has not been documented. The study of genetic diversity existing within this population is of particular interest in germplasm identification, preservation, and new cultivar development. This study analyzed the genetic diversity of the cultivated naked barley from Qinghai-Tibet plateau through the study of SSR marker loci and monomeric prolamins, B-horden and starch granule proteins. SSRs are present abundantly in genomes of higher organisms and have become a popular marker system in plant studies. SSRs offer a number of advantages, such as the high level of polymorphisms, locus specificity, co-dominance, reproducibility, ease of use through PCRand random distribution throughout the genome. In barley, several hundred SSRs have been developed and genetically mapped and can therefore be selected from specific genomic regions. The genetic diversity of 64 cultivated naked barley from Tibet and Sichuan was studied with 30 SSRs of known map location.Among the selected SSR markers, PCR products of 5 SSR markers were not obtained and 3 SSR marker loci were monomeric. A total of 132 alleles were identified at 22 polyomeric SSR loci. The number of alleles per locus ranged from 2 to 15, with an average of 6.0. The polymorphism information content values for the SSRs ranged from 0.08 to 0.94, with an average of 0.65. 13 SSR markers with the PIC value >0.6 have been selected for discrimination of Qinghai-Tibet naked barley genotypews. A finger Print map was developed through 7 SSR markers with the high PIC value. It could be used as an efficient tool for gene discovery and identification of gernplasm. Hordeins, the main storage proteins of the barley seed, are composed of momomeric and polymeric prolamins and divided into -A, B, C and D groups in order of decreasing electrophoretic mobility. Hordeins show high inter-genotypic variation and have been extensively used as markers for cultivar identification and analyzing the genetic diversity. This study analyzed the genetic diversity of B-hordein in 72 naked barley from Qinqhai-Tibet Plateau. Extensive diversity was observed. A total of 15 different bands and 30 distinct patterns were found. Jaccard's coefficient of similarity was calculated, and the accessions were divided into three　main groups by cluster analysis using UPGMA. Differentiation among the populations from different collecting regions based on the polymorphism of B-hordein was investigated. Monomeric prolamins show high inter-genotypic variation and have been used as molecular markers for cultivar identification, analyzing the genetic diversity in collections and investigating the evolution processes and structure of populations However, the cultivated hulless accessions from Qinghai-Tibet Pateau in China have never been examined with respect to monomeric prolamins. This study analyzed the genetic diversity of monomeric prolamins (protein fraction corresponding to wheat gliadins) using the Acid -PAGE technique in eighty-four cultivated hulless barley from Qinqhai-Tibet Plateau in China. Extensive diversity was observed. A total of 43 different bands were found, of which 21 different bands were in the region of ω group, 8 in the region of γ, 8 in the region of β, and 6 in the region of α group. Among the 86 accessions, 75 distinct patterns were identified. The number of bands ranged from 6 to 16, depending on the variety. Jaccard’s coefficient of similarity was calculated, and the lines were grouped by cluster analysis using UPGMA. A dendrogram was obtained from the analysis of the groups and five main clusters were identified. No relationship between the distribution in the dendrogram and growth habits and origins of the cultivars could be detected. Starch is the major constituent of the cereal endosperm, comprising approximately 65% of the dry weight of the mature wheat grain. The starch formed in all organs of plants is packaged into starch granules, which vary widely between species and cultivars in size and shape. Wheat endosperm starch granules contain about corresponding to the main biosynthase of starch. This report firstly dealed with intraspecific variation of the major SGPs in cultivated naked barley from Qinghai-Tibet plateau. A total of 10 major SGPs were observed in the range of 40KD-100KD and 16 types of patterns were found. Based on the variation of SGPs, accessions studied were classified into 3 groups. A geographical cline of electrophoregram was observed. In addition, significance test of the difference of starch content among groups and types of patterns were done, and the results indicated those SGPs could be related to the content of starch. Diagram obtained through cluster analysis exhibited a structuration of diversity and genetic relationship among cultivated hulless accessions. In breeding program, parents with genetically distant relationship for hybridization will increase genetic diversity of progenies. In conclusion, cultivated naked barley from Qinghai-Tibet Plateau in China presents a high variability with respect to monomeric prolamins，SSR markers , B- hordeins and SGPs. The result of this study supports Qinghai-Tibet Plateau is the center of cultivated hulless barley and the cultivated naked barley is considered to be a gene pool with large diversity and could be applied to breeding for cereal.

油气、微生物与砂岩型铀矿形成关系研究——以东胜铀矿床和钱家店铀矿床为例

Sandstone-type uranium deposits are frequently found close to oil fields or uraniferous sandstones contain bitumen or petroleum. However, few evidence has been presented to indicate the association of uranium mineralization with petroleum oxidation. Thus, Dongsheng uranium deposit in Ordos Basin and Qianjiadian deposit in Kailu Basin are taken for examples to solve the puzzle. Integration data from sedimentary petrology, mineralogy, race elements geochemistry, isotope geochemistry and organic geochemistry, the uranium and petroleum sources, and diagenetic paragenesis of the host sandstone are analyzed, and then the genetic relationship between microbes, petroleum and uranium deposits are discussed. The observation under microscope shows that the host sandstone samples from Middle Jurassic Zhiluo Formation in the Dongsheng deposit contained different kinds of metamorphic rock fragments, which should have been derived form outcrops north to this basin. The LREE/HREE ratios of gneiss and amphibolite sampled from outcrops were close to the highest and the lowest LREE/HREE ratios of the sandstones with well-compared chondrite-normalized REE patterns, respectively. So these results consistently indicated that parent rocks of sandstones were mainly contributed from these two kinds of metamorphic rocks. There was very high Th/U ratio for granite gneiss, which was a mainly potential U resource. Hydrocarbon inclusions and adsorbed hydrocarbons are observed under fluorescence microscope in the host sandstone of Dongsheng uranium deposit, suggesting that the sandstones may have been utilized as oil migration pathways. Based on biomarker parameters, it is indicated that the inclusion oils and adsorbed hydrocarbons were marginally mature to mature, and were derived from humic-sapropel type organic matter under poor reducing freshwater to semi-saline environment. The features are similar to those of organic matter extracted from Triassic sandstone and source rock, but are different from that of cretaceous sandstone. Thus, it can be concluded that the inclusion oils and adsorbed hydrocarbons were mainly derived from Triassic lacustrine facies source rock. Observation results under Scanning Electron Microscopy and Electron Microprobe with Energy Spectrum Analysis show that, in Dongsheng area, the main uranium ore mineral is coffinite. The coffinite is intimately intergrown or coexists with pyrite and calcite, thus, the solution during mineralization stage is inferred to be alkaline. The alkaline environment is not favored for uranium to be pre-concentrated by absorption, and then be reduced abiogenetically. δ34S of pyrite and δ13C of calcite indicate that pyrite was formed by bacterial sulfate reduction (BSR) and part of the carbon of calcite has been dirived from oxidation of petroleum, respectively. Additionally, petroleum is found biodegraded. All the lines of evidence consistently indicate that petroleum was involved in uranium mineralization. Coffinite with microbe-like structures is found in the high U sandstone samples and is composed of nanoparticles, indicating the coffinite is biogenic. The conclusion are also supportted by laboratory experiment studies, which have shown that SRB are capable of utilizing U(VI) as the preferred electron acceptor for respiration and reduce U(VI) to U(IV) directly, coupled the oxidaton of organic matter and sulfate reduction. Based on the research results mentioned above, in the Dongsheng area, coffinite is likely to have formed by mixing of brine containing petroleum derived from Triassic with uranium-bearing meteoric water from outcrops north to Ordos Basin. SRB utilize hydrocarbon as carbon source, and directly reduce U(VI) resulting in precipitation of coffinite. The product of metabolism, H2S and CO2, was precipitated as pyrite and calcite during mineralization stage. Petroleum in fluid inclusions and adsorbed type in host sandstone from Lower Cretaceous Yaojia Formation in Qianjiadian uranium deposit, Kailu Basin, are derived from Jurassic Jiufotang Formation in this basin and the uranium mineral consists mainly of pitchblende. The δ34S and δ13C values of pyrite and calcite during mineralization stage indicate SRB have likely degraded petroleum, which is similar to that of Dongsheng deposit. The alkaline environment as indicated by the diagenetic mineral assemblage calcite, Fe dolomite, pyrite and pitchblende deposit suggests that U ore in the Qiangjiajiadian has a similar origin, i.e., direct reduction by SRB. However, less part of pitchblende is intergrown with kaolinite, suggesting the solution during mineralization stage is acidic. The environment is favorable for U(VI) to be adsorded on quartz or other mineral, and then reduced by H2S produced by SRB. Thus, it can be concluded that U(VI) reduction with petroleum oxidation by SRB and other microbes is an important ore-forming mechanism in petroleum-related sandstone-type uranium deposits. The finding is significant in that it provides a theoretical basis for exploration of both uranium and petroleumr.

乍得西南部中新生代火山作用与盆地演化

Located in the Central and West African, Chad, which is not well geological explored, is characterized by Mesozoic- Cenozoic intra-continental rift basins. The boreholes exposed that, during Mesozoic-Cenozoic times, volcanic activities were intense in these basins, but study on volcanic rocks is very weak, especially on those embedded in rift basins, and so far systematic and detailed work has still no carried out. Based on the project of China National Oil and Gas Exploration and Development Corporation, “The analysis of reservoir condition and the evaluation of exploration targets of seven basins in block H in Chad”, and the cooperative project between Institute of Geology and Geophysics, CAS and CNPC International (Chad) Co. Ltd., “Chronology and geochemistry studies on Mesozoic-Cenozoic volcanic rocks from southwestern Chad Basins”, systematic geochronology, geochemistry and Sr-Nd-Pb isotopic geochemistry studies on volcanic rocks from southwestern Chad basins have been done in the thesis for the first time. Detailed geochronological study using whole-rock K-Ar and Ar-Ar methods shows the mainly eruption ages of these volcanic rocks are Late Cretaceous- Paleogene. Volcanic rocks in the well Nere-1 and Figuier-1 from Doba basin are products of the Late Cretaceous which majority of the K-Ar (Ar-Ar) ages fall in the interval 95-75 Ma, whereas volcanic rocks in the well Ronier-1 from Bongor Basin and the Well Acacia-1 from Lake Chad Basin formed in the Paleogene which the ages concentrated in 66-52Ma. Two main periods of volcanic activity can be recognized in the study area, namely, the Late Cretaceous period and the Paleogene period. Volcanic activities have a general trend of south to north migration, but this may be only a local expression, and farther future studies should be carried on. Petrology study exhibits these volcanic rocks from southwestern Chad basins are mainly tholeiitic basalt. Major- and trace elements as well as Sr-Nd-Pb isotopic geochemistry studies show that the late Cretaceous and the Paleogene basalts have a definitely genetic relationship, and magmas which the basalts in southwestern Chad basins derived from were produced by fractional crystallization of olivine and clinopyroxene and had not do suffered from crustal contamination. These basalts are prominently enriched light rare earth elements (LREE), large-ion lithophile elements (LILE) and high field strength elements (HFSE) and depleted compatible elements. They have positive Ba, Pb, Sr, Nb, Ta, Zr, Hf anomalies and negative Th, U, P,Y anomalies. It is possible that the basalts from southwestern Chad basins mainly formed by mixing of depleted mantle (DM) and enriched mantle (EMⅡ) sources. The late Cretaceous basalts have higher (87Sr/86Sr)i ratios than the Paleogene basalts’, whereas have lower (143Nd/144Nd)i ratios than the latter, showing a significant temporal evolution. The mantle sources of the Late Cretaceous basalts may have more enriched mantle(EMⅡ) compositions, whereas those of the Paleogene basalts are relatively more asthenospheric mantle (DM) components. The mantle components with temporal change observed in basalts from Chad basins were probably correlated with the asthenospheric mantle upwelling and lithospheric thinning in Central and Western Africa since Mesozoic. Mesozoic- Cenozoic Volcanism in Chad basins probably is a product of intra- plate extensional stress regime, corresponded to the tectonic setting of the whole West and Central African during Cretaceous. Volcanism is closely correlated with rifting. As time passed from early period to late, the basaltic magma of Chad basins, characterized with shallower genetic depth, higher density and smaller viscosity, probably indicates the gradual strengthening evolution of the rifting. In the initial rife stage, volcanic activities are absent in the study area. Volcanic activities are basiccally corresponded with the strong extensional period of Chad basins, and the eruption of basalts was slightly lagged behind the extensional period. In the post-rift stage (30-0Ma), these basins shifted to the thermal sag phase, volcanic activities in the study area significantly decreased and then terminated.

胶东蓬家夼式金矿床矿床成因模型与找矿模型研究

The dynamic environments of mineralization in Mesozoic Jiaodong gold mine concentrated area can be devided into two types, compressive environment which related to intracontinental collision and extensional environment which related to intracontinental volcanic rift. The altered rock type (Jiaojia type) and quartz vein type (Linglong type) which related to the former one, were discovered for several years, and became the main types of gold deposits in recent years. A new type gold deposit, syn-detachment altered tectonic breccia type gold deposit, such as Pengjiakuang gold deposit and Songjiagou gold deposit has been discovered on the northeastern margin of Jiaolai Basin. In this paper, the new type of gold deposit has been studied in detail. The study area is located at the northeastern boundaries of Jiaolai Basin, and between the Taocun-Jimo Fault and Wji-Haiyang Fault, in the eastern part of the Jiaodong Block. Pengjiakuang gold deposit and Songjiagou gold deposit occur in a arc-shape detachment fault zone between conglomerate of Lower Cretaceous Laiyang Formation and metamorphic complex of Lower Proterozoic Jingshan Group. Regional geological studies show that Kunyuanshan and Queshan granite intrusions and Qingshanian volcanism were formed in different period of lithospheric thinning of East China in Mesozoic. Granite intrusions were formed in compressive environment, while Qingshanian volcanism were formed in extensional environment. They are all related to the detachment of Sulu Orogenic Belt and the sinistral motion of Tanlu Fault. The Pengjiakuang detachment systems which were formed in the the sinistral motion of Tanlu Fault are the important ore-controlling and ore-containing structure. The Pengjiakuang type gold deposit, controlled by detachment structure, was formed before Yanshanian volcanic period concerning with mixture of meteoric water and magmatic water found in fluid inclusions of gold ores. The minerogenetic epoch has been proposed in 90～120Ma. the host rocks have been extensively subjected to pyritization, silicification, sericitization and carbonatization. Individual ore-body has maximum length of 800m, oblique extension of 500～700m and gold grade of 1～43 * 10~(-6). Native gold is disseminated in silicified, phyllic or carbonatized tectonic breccia. Sulfur, carbon and lead isotope studies on gold ores and wall rocks show that the sulfur come from the metamorphic complex of Lower Proterozoic Jingshan Group, carbon comes from the marble in Jingshan Group, while a part of lead comes from the mantle. The mineralizing fluid is rich in Na~+ and Cl~-, but relatively impoverished in K~+ and F~-. According to the date from hydrogen and oxygen isotopic compositions (δ~(18)OH_2O = 0.59%～4.03%, δDH_2O = -89.5%～97.9%), the conclusion can be reached that the mineralizing fluid of Pengjiakuang gold deposit was a kind of mixed hydrothermal solution which was mainly composed of meteoric water and magmatic water. A genetical model has been formulated. Some apparent anomaly features which show low in the central part and high in the both sides corresponding to the gold-bearing structure, were sum up after analying a vast amount of date by prospecting the orebodies using gamma-ray spectrometer, electrogeochemical parameter technique, controlled source audio magnetic telluric (CSAMT) and shallow surface thermometry in Pengjiakuang gold deposit. The location forecasting problem of buried orebodies has been solved according to these features, and the successful rate is very high in well-drilling. The structural geological-geophysical-geochemical prospecting model has been formulated on the base of the study of geological, geophysical and geochemical characteristics of Pengjiakuang type gold deposit, and the optimum combinational process of geophysical and geochemical prospecting techniques has been summed up. A comparative study shows that the Pengjiakuang type gold deposit, the syn-detachment altered tectonic breccia type gold deposit, is different from Jiaojia type gold deposits and Linglong type gold deposits, in Jiaodong Block. In general, if formed under an extensional tectonic condition and located at detachment fault zone along the margin of Mesozoic Jiaolai basin, and the gold mineralization has also close genetic relationship with alkaline magamtism. Being a new type of gold deposit in Jiaodong gold mine concentrated area, it could be potential to explore in the same regions which processed the same ore-forming geological conditions and mineralization informations.

东营凹陷下第三系岩性油气藏形成条件与预测

The Dongying depression, located in the northern part of the jiyang Sag in the Buohaiwan Basin, comprises one of the major oil-producing bases of the Shengli oil-field. The prediction and exploration of subtle or litho1ogical oil traps in the oil-field has become the major confronted target. This is also one of the frontier study areas in the highly-explored oil-bearing basins in East China and abroad. Based on the integrated analysis of the geological, seismic and logging data and the theories of sequence stratigraphy, tectono-stratigraphy and petroleum system, the paper has attempted to document the characteristics of the sequence stratigraphic and structural frameworks of the low Tertiary, the syndepositional faults and their control on deposition, and then to investigate the forming conditions and distribution of the tithological oil traps in the depression. The study has set up a set of analysis methods, which can be used to effectively analysis the sequence stratigraphy of inland basins and predict the distribution of sandstone reservoirs in the basins. The major achievements of the study are as follows: 1. The low Tertiary can be divided into 4 second-order sequences and 13 third-order sequences, and the systems tracts in the third-order sequences have been also identified based on the examination and correction of well logging data and seismic profiles. At the same time, the parasequences and their stacking pattern in the deltaic systems of the third member of the Shahejie Formation have been recognized in the key study area. It has been documented that the genetic relation of different order sequences to tectonic, climatic and sediment supply changes. The study suggested that the formation of the second-order sequences was related to multiple rifting, while the activity of the syndepositional faults controlled the stacking pattern of parasequences of the axial deltaic system in the depression. 2. A number of depositional facies have been recognized in the low Tertiary on the basis of seismic facies and well logging analysis. They include alluvial fan, fan delta or braided delta, axial delta, lowstand fan, lacustrine and gravity flow deposits. The lacustrine lowstand fan deposits are firstly recognized in the depression, and their facies architecture and distribution have been investigated. The study has shown that the lowstand fan deposits are the important sandstone reservoirs as lithological oil traps in the depression. 3. The mapping of depositional systems within sequences has revealed the time and special distrbution of depositional systems developed in the basin. It is pointed out that major elastic systems comprise the northern marginal depositional systems consisting of alluvial fan, fan delta and offshore lowstand fan deposits, the southern gentle slope elastic deposits composed of shallow lacustrine, braided delta and lowstand fan deposits and the axial deltaic systems including those from eastern and western ends of the depression. 4. The genetic relationship between the syndepositional faults and the distribution of sandstones has been studied in the paper, upper on the analysis of structural framework and syndepositional fault systems in the depression. The concept of structural slope-break has been firstly introduced into the study and the role of syndepositional faults controlling the development of sequence architecture and distribution of sandstones along the hinged and faulted margins have been widely investigated. It is suggested that structural styles of the structural slope-break controlled the distribution of lowstand fan deposits and formed a favorable zone for the formation of lithological or structure-lithological oil traps in the basin. 5. The paper has made a deep investigation into the forming condition and processes of the lithological traps in the depression, based the analysis of composition of reservoir, seal and resource rocks. It is pointed out that there were two major oil pool-forming periods, namely the end of the Dongying and Guangtao periods, and the later one is the most important. 6. The study has finally predicted a number of favorable targets for exploration of lithologieal traps in the depression. Most of them have been drilled and made great succeed with new discovered thousands tons of raw oil reserves.

河北寿王坟铜矿成矿定年及同位素地球化学特征

Samples from carbonate wall-rocks, skarn, ore of skarn type, later calcite vein, and ore of porphyry type in Shouwangfen copper deposit district were collected. Systematic study was carried out on carbon, oxygen, rubidium, strontium and sulfur isotope compositions of carbonates and sulfides in these samples. The first Isochron dating by the Rb-Sr isotopes in chalcopyrite of ore sub-sample was done as well. The following conclusions were obtained. The age (113.6±4.3Ma), obtained by Rb-Sr isotope isochron dating of chalcopyrite and pyrite from sub-sample of skarn ores, probably represents the true mineralization age of skarn ores. That demonstrates the genetic relationship between granodiorite in Shouwangfen complex and skarn copper ores. On the other hand, the Rb-Sr isochron age (73±15Ma) of chalcopyrite from porphyry ores is a little incredible because of bad synthesizing evaluation. But combined with other age data of igneous rocks, it implies the possibility of hydrothermal mineralization in connection with magma activity during the fourth period of Yanshanian in Hebei Province, even in the whole northern edge of Huabei continental block. Together from structure analysis of sulfide sub-samples, from pretreating preccedure of Rb-Sr isotope isochron and its' valuating, we found out that Rb-Sr isotope isochron of sulfide sub-samples is influenced by the crystal structure of sulfides. That is, sulfide ores with very big crystals are not suitable for sub-sample isochron. Carbon, oxygen, sulfur and strontium compositions, of different minerals in these two kinds of ores, imply that the ore-forming hydrothermal fluids were probably derived from magma deep under the crust. The calcite ~(87)Sr/~(86)Sr ratios from the porphyry are consistent to the initial 87Sr/86Sr ratio of the Rb-Sr isochron of chalcopyrite and pyrite in the skarn ore, indicating that these two kinds of ores have the same source characteristic, although the porphyry deposit was formed probably 40 million years later than the skarn one according to our dating results. Skarn and skarn ores are usually considered as interaction product between carbonate wall-rocks and magmatic fluids, but the carbon of the sedimentary carbonate seems not involved in the skarn ores. Considering the connection of magmatic processes and hydrothermal ore formation in the Shouwangfen district, particularly, the spatial distribution of skarn-type and porphyry-type ores, it is possible that the Shouwangfen ore district corresponds to a hydrothermal ore-forming system, which was promoted by high-intruding magmatic rocks. Systematic stable isotopic research can help to reveal the upper part of this hydrothermal ore-forming system, which mainly related to heated and circulating meteoric water, and the lower part principally related to ascending magmatic fluids. Both skarn and porphyry ore-bodies are formed by up-intruding magmatic fluids (even more deep mantle-derived fluids).

Significant correlation in linkage signals from genome-wide scans of schizophrenia and schizotypy

Prior family and adoption studies have suggested a genetic relationship between schizophrenia and schizotypy. However, this has never been verified using linkage methods. We therefore attempted to test for a correlation in linkage signals from genome-wide scans of schizophrenia and schizotypy. The Irish study of high-density schizophrenia families comprises 270 families with at least two members with schizophrenia or poor-outcome schizoaffective disorder (n = 637). Non-psychotic relatives were assessed using the structured interview for schizotypy (n = 746). A 10-cM multipoint, non-parametric, autosomal genomewide scan of schizophrenia was performed in Merlin. A scan of a quantitative trait comprising ratings of DSM-III-R criteria for schizotypal personality disorder in non-psychotic relatives was also performed. Schizotypy logarithm of the odds (LOD) scores were regressed onto schizophrenia LOD scores at all loci, with adjustment for spatial autocorrelation. To assess empirical significance, this was also carried out using 1000 null scans of schizotypy. The number of jointly linked loci in the real data was compared to distribution of jointly linked loci in the null scans. No markers were suggestively linked to schizotypy based on strict Lander Kruglyak criteria. Schizotypy LODs predicted schizophrenia LODs above chance expectation genome wide (empirical P = 0.04). Two and four loci yielded nonparametric LOD (NPLs) > 1.0 and > 0.75, respectively, for both schizophrenia and schizotypy (genome-wide empirical P = 0.04 and 0.02, respectively). These results suggest that at least a subset of schizophrenia susceptibility genes also affects schizotypy in non-psychotic relatives. Power may therefore be increased in molecular genetic studies of schizophrenia if they incorporate measures of schizotypy in non-psychotic relatives.

Post-mortem examination of a wild muntjac from Northern Ireland.

1. Deer are of major concern with regards to impacts on biodiversity, forestry and agriculture as well as human health. The invasive Reeves’ muntjac deer Muntiacus reevesi, native to Asia but established in Great Britain, has recently appeared in the wild in Ireland.

2. The first verified record in the wild in Northern Ireland was confirmed during June 2009 as a result of a road traffic accident near Newtownards, Co. Down. The second record was a culled animal shot in the grounds of Mount Stewart, Co. Down during June 2011.

3. The current report aimed to perform a detailed investigation of the most recently obtained animal to establish a) its age, b) its genetic relationship with the first animal and c) the threat it might pose in terms of carrying endo- or ecto-parasites or other micro-pathogens, principally viruses and bacteria.

4. Analysis of its dentition suggested the culled animal was 56 weeks old (range 55-57 weeks).

5. Genetic analysis indicated that there was no possibility of a father-son relationship with the buck killed in 2009. There was a 6.25% probability of both individuals being full-sibs and a 25% probability of a half-sib relationship.

6. The deer was free from all the major pathogens. Most significantly, a novel species of Gammaherpesvirus was detected most closely matching type 2 ruminant rhadinovirus (Gammaherpesvirinae) from mule deer. Further sequencing is required to provide a definitive classification. There is no evidence suggesting this virus is pathogenic but its detection is nonetheless of concern.

7. During late 2009 (after the first animal was recovered) and early 2010, there were a number of sightings of muntjac within the vicinity of Mount Stewart. Our results indicate that the animal shot in June 2011 could not have been this same animal, as the shot animal must have been born in spring 2010. Moreover, genetic analysis indicates that the two recovered individuals were highly unlikely to share the same mother and father, suggesting they were the offspring of a minimum of three breeding adults (two fathers and one mother or two mothers and one father). This brings the total number of known individuals to 5 including the two offspring. The location of the breeding adults is unknown and may be either in captivity with subsequent escapees, or deliberate releases, or be free living in the wild. However, a further sighting during early 2012 may suggest a wild origin.

Detection of a novel porcine boca-like virus in the background of porcine circovirus type 2 induced postweaning multisystemic wasting syndrome

Porcine circovirus type 2 (PCV-2) has been found to be the causative agent of postweaning multisystemic wasting syndrome (PMWS). However, PCV-2 is a ubiquitous virus in the swine population and a majority of pigs infected with PCV-2 do not develop the disease. Different factors such as age, maintenance, the genetics of PCV-2, other pathogens, etc. have been suggested to contribute to the development of PMWS. However, so far no proven connection between any of these factors and the disease development has been found. In this study we explored the possible presence of other so far unknown DNA containing infectious agents in lymph nodes collected from Swedish pigs with confirmed PMWS through random amplification and high-throughput sequencing. Although the vast majority of the amplified genetic sequences belonged to PCV-2, we also found genome sequences of Torque Teno virus (TTV) and of a novel parvovirus. The detection of TTV was expected since like PCV-2, TTV has been found to have high prevalence in pigs around the world. We were able to amplify a longer region of the parvovirus genome, consisting of the entire NP1 and partial VP1/2. By comparative analysis of the nucleotide sequences and phylogenetic studies we propose that this is a novel porcine parvovirus, with genetic relationship to bocaviruses.

Molecular tools in the diagnostic and epidemiology of infections caused by members of Mycobacterium avium Complex

Mycobacterium avium Complex (MAC) comprises microorganisms that affect a wide range of animals including humans. The most relevant are Mycobacterium avium subspecies hominissuis (Mah) with a high impact on public health affecting mainly immunocompromised individuals and Mycobacterium avium subspecies paratuberculosis (Map) causing paratuberculosis in animals with a high economic impact worldwide. In this work, we characterized 28 human and 67 porcine Mah isolates and evaluated the relationship among them by Multiple-Locus Variable number tandem repeat Analysis (MLVA). We concluded that Mah population presented a high genetic diversity and no correlations were inferred based on geographical origin, host or biological sample. For the first time in Portugal Map strains, from asymptomatic bovine faecal samples were isolated highlighting the need of more reliable and rapid diagnostic methods for Map direct detection. Therefore, we developed an IS900 nested real time PCR with high sensitivity and specificity associated with optimized DNA extraction methodologies for faecal and milk samples. We detected 83% of 155 faecal samples from goats, cattle and sheep, and 26% of 98 milk samples from cattle, positive for Map IS900 nested real time PCR. A novel SNPs (single nucleotide polymorphisms) assay to Map characterization based on a Whole Genome Sequencing analysis was developed to elucidate the genetic relationship between strains. Based on sequential detection of 14 SNPs and on a decision tree we were able to differentiate 14 phylogenetic groups with a higher discriminatory power compared to other typing methods. A pigmented Map strain was isolated and characterized evidencing for the first time to our knowledge the existence of pigmented Type C strains. With this work, we intended to improve the ante mortem direct molecular detection of Map, to conscientiously aware for the existence of Map animal infections widespread in Portugal and to contribute to the improvement of Map and Mah epidemiological studies.

Biofilm Forming Multi Drug Resistant Staphylococcus spp. Among Patients with Conjunctivitis

Biofilm forming multidrug resistant Staphylococcus spp. are major reservoirs for transmission of ophthalmic infections. They were isolated from ocular patients suffering from conjunctivitis. In this study we analyzed biofilm forming ability, antibiotic resistance profile of the Staphylococcus spp. isolated from clinical ocular patients, and their phylogenetic relationship with other community MRSA. Sixty Staphylococcus spp. strains isolated from clinical subjects were evaluated for their ability to form biofilm and express biofilm encoding ica gene. Among them 93% were slime producers and 87% were slime positive. Staphylococcus aureus and S. epidermidis were dominant strains among the isolates obtained from ocular patients. The strains also exhibited a differential biofilm formation quantitatively. Antibiotic susceptibility of the strains tested with Penicillin G, Ciprofloxacin, Ofloxacin, Methicillin, Amikacin, and Gentamicin indicated that they were resistant to more than one antibiotic. The amplicon of ica gene of strong biofilm producing S. aureus strains, obtained by polymerase chain reaction, was sequenced and their close genetic relationship with community acquired MRSA was analyzed based on phylogenetic tree. Our results indicate that they are genetically close to other community acquired MRSA

Petrology and geochemistry of the banded iron formation in the Eastern Sierras Pampeanas of San Luis (Argentina): Implications for the evolution of the Nogoli Metamorphic Complex

The metamorphosed banded iron formation from the Nogoli Metamorphic Complex of western Sierra de San Luis, Eastern Sierras Pampeanas of Argentina (Nogoli area, 32 degrees 55`S-66 degrees 15`W) is classified as an oxide facies iron formation of Algoma Type, with a tectonic setting possibly associated with an island arc or back arc, on the basis of field mapping, mineral and textural arrangements and whole rock geochemical features. The origin of banded iron formation is mainly related to chemical precipitation of hydrogenous sediments from seawater in oceanic environments. The primary chemical precipitate is a result of solutions that represent mixtures of seawater and hydrothermal fluids, with significant dilution by maficultramafic volcanic and siliciclastic materials. Multi-stage T(DM) model ages of 1670, 1854 and 1939 Ma and positive, mantle-like xi Nd((1502)) values of +3.8, +1.5 and +0.5 from the banded iron formation are around the range of those mafic to ultramafic meta-volcanic rocks of Nogoli Metamorphic Complex, which are between 1679 and 1765 Ma and +2.64 and +3.68, respectively. This Sm and Nd isotopic connection suggests a close genetic relationship between ferruginous and mafic-ultramafic meta-volcanic rocks, as part of the same island arc or back arc setting. A previous Sm-Nd whole rock isochron of similar to 1.5 Ga performed on mafic-ultramafic meta-volcanic rocks led to the interpretation that chemical sedimentation as old as Mesoproterozoic is possible for the banded iron formation. A clockwise P-T path can be inferred for the regional metamorphic evolution of the banded iron formation, with three distinctive trajectories: (1) Relict prograde M(1)-M(3) segment with gradual P and T increase from greenschist facies at M(1) to amphibolite facies at M(3). (2) Peak P-T conditions at high amphibolite-low granulite facies during M(4). (3) Retrograde counterpart of M(4), that returns from amphibolite facies and stabilizes at greenschist facies during M(5). Each trajectory may be regarded as produced by different tectonic events related to the Pampean? (1) and the Famatinian (2 and 3) orogenies, during the Early to Middle Paleozoic. The Nogoli Metamorphic Complex is interpreted as part of a greenstone belt within the large Meso- to Neoproterozoic Pampean Terrane of the Eastern Sierras Pampeanas of Argentina. (C) 2009 Elsevier Ltd. All rights reserved.