苹果EST中微卫星分析

利用MISA（microsatellite）软件分析了简单重复序列（simple sequence repeats,SSRs）在苹果EST中的分布频率与密度。结果表明,在263820条EST序列中,共获得160686条SSR序列,SSRs之间的距离约为0．79kb。其中,六碱基重复丰度最大,占57．2％,而单碱基、三碱基、二碱基、四碱基和五碱基重复丰度分别为14．5％,13．1％,10．1％,4．1％和1．0％。在单碱基、二碱基、三碱基和四碱基重复模体中,丰度最大的分别是A／T,AG,AAG和AAAG,而CG在编码区内丰度很低。用CAP3软件进行冗余分析表明,在这六种类型的重复模体中,冗余与非冗余的苹果EST之间没有显著差异,表明可从现有的ESTs数据中方便地获取有效的苹果微卫星标记。     

马铃薯X病毒完整基因组上微卫星分布

本文利用自编计算机程序提取并展示马铃薯X病毒完整基因组（NC_011620.1）上微卫星分布特性。借助MATLAB软件和借用最优完全子图算法,分析NCBI数据库中该基因组（NC_011620.1）微卫星分布特性。结果表明,计算出所有各种N-碱基组（N取1至6）在完整基因组序列上重复出现次数和出现位置,展示它们的分布规律（指数函数）,马铃薯X病毒完整基因组（NC_011620.1）上各种N-碱基组最大的重复出现次数随N按指数函数数减少;且呈现出重复出现次数由少到多排序,重复出现次数随序号增加;本文使用的方法,可以系统地应用到其它病毒完整基因组序列微卫星分布特性分析,从而为有效利用微卫星分布特性研究完整基因组的结构和功能、遗传和变异规律提供完整的数据支撑。     

牛、羊促卵泡素受体(FSHR)基因转录调控区的序列特征

测定了山羊、绵羊和牛的FSHR基因启动子区序列。比较发现序列长度存在差异，碱基变异率分别为3．14％、6．12％和6．72％。有2处较大的碱基插入／缺失突变。在检索出的转录调控元件（或潜在调控元件）中，3畜种在7个元件序列有碱基突变。与人和大鼠FSHR基因不同的是，在牛羊的FSHR基因启动子区检索出了TATA盒基元和多个类CAAT盒序列，且在山羊、绵羊和牛之间没有碱基差异。分析认为：（1）牛羊的FSHR基因启动子属TATA启动子型，而不是InR型。（2）尽管目前在绵羊的FSHR基因只发现1个转录起始点，但启动子区的序列特征表明牛羊可能存在第2转录起始点。（3）3畜种在转录调控元件的碱基变异和在不同位点的较大插入／缺失突变，可能影响基因的转录，从而造成双胎率的差异。因此，对牛羊FSHR基因转录启动和表达调控值得作进一步研究。     

杨树基因组中染色体基因丰度分化及EST序列对基因覆盖度的检测（英文）

高等植物基因组中,大部分序列为非表达序列,基因序列所占的比例很小,了解基因在基因组中的分布是研究基因组结构的一个重要方面。在美国能源部资助下,一个毛果杨无性系的基因组测序已经完成并对公众发布。杨树全基因组序列的完成,为我们了解林木基因组中基因的分布提供了一个特例。在本文中,我们利用泊松分析对杨树基因组中基因在各个染色体上的密度进行了检测,结果表明杨树基因组中各条染色体的基因含量存在显著差异。杨树全基因组测序项目揭示现代杨树基因组起源于一次古全基因组复制事件（称为杨柳科基因组复制）,所以杨树基因组不同染色体间存在很大的同源复制片段。但是我们的研究显示,杨树基因组中大多数高度同源的染色体上基因的密度与染色体间的同源性没有明显关系,这说明杨柳科全基因组复制事件后,各个高度同源染色体上的基因发生了流失,且基因流失的速率是不一样的。同时本文还对近九万条毛果杨EST序列进行了比对分析,结果显示这些EST序列覆盖的基因仅占杨树基因组中基因总数的16.8%左右。EST测序虽然是发现基因的一个重要手段,但小规模EST测序对基因的覆盖度很低,所以小规模EST测序的应用价值是有限的。     

禾本科植物微卫星序列的特征分析和比较

微卫星或简单序列重复（simple sequence repeats,SSRs）广泛存在于真核生物的基因组中,是目前最有用的分子标记之一。本研究首次利用全基因序列对4个禾本科植物种,包括二穗短柄草（Brachypodium distachyon）、水稻（Oryza sativa）、高粱（Sorghum bicolor）和玉米（Zea mays）的SSR的类型、丰度（数量）、相对丰度、频率、长度和偏好性等进行了分析和比较。结果表明,禾本科植物中SSR的丰度与基因组大小成正比,而相对丰度与基因组大小相关不显著;三核苷酸和六核苷酸基序类型比其它类型更为丰富;不同物种皆呈现出明显的基序偏好性。总的来讲,除个别例外,禾本科植物的基因组中更倾向于富含A/T的基序。本研究结果为研究禾本科植物的基因组进化和SSR标记的开发提供了有价值的信息。     

银杏EST序列中微卫星的分布特征

本文利用从NCBI下载的21590条银杏EST序列,分析了银杏（表达序列标签微卫星）EST-SSR在银杏EST序列的分布和比较了在不同长度EST序列中的SSR特性。在剔除冗余和低质量序列后,得到总长为5708.385kb的无冗余EST序列7961条,发现了405个EST序列（5.09%）含有475个SSR,长度400~1000bp的EST序列含SSR位点数为445个,占SSR总数的93.68%。二核苷酸和三核苷酸基元类型是银杏EST-SSR的主要类型,分别占SSR总数的73.89%和24.00%,最常见的SSR基元是：（AT）n、（AG）n、（AC）n、（AAG）n和（AAT）n。通过对银杏EST序列中SSR位点信息的发掘分析,为有针对性地设计EST-SSR引物,开发银杏EST-SSR分子标记奠定基础。     

杨树基因组AMT转运蛋白的生物信息学特性

本研究中，通过隐马尔科夫模型（HMM）和杨树蛋白质库搜索，共找到17个杨树铵转运体蛋白（PtAMTs）。利用生物信息学方法，我们对杨树家族17条AMT蛋白序列的系统发生和AMT基因组定位进行分析，然后对其氨基酸组成成分、理化性质以及二级结构进行预测和分析，同时还分析了杨树与拟南芥、水稻、番茄、百脉根和欧洲油菜的AMT基因家族之间的联系。二级结构预测结果发现不同成员间氨基酸数目、氨基酸序列间的疏水性存在一定的差异；仪一螺旋和无规则卷曲为主要二级结构组成部分。同源性比对分析表明，PtAMT基因家族主要分为2个亚家族，AMT1（11个成员）和AMT2（6个成员），基因结果分析表明AMT2亚家族成员不含内含子。杨树AMT蛋白的亚细胞定位分析表明PtAMT主要定位于膜结构上。电子表达图谱分析结果表明：只有XP002309151和XP002334025基因有对应的EST序列，并有相应的电子表达谱，并主要在花蕾表达。     

利用生物信息学方法进行基于表达序列标签的玉 米单核苷酸多态性标记的开发

针对简单重复序列（SSR）标记密度不足、单核苷酸多态性（SNP）标记开发一般只基于2种基因型的序列差异,用以检测其他基因型的材料时多态性不高,不能满足玉米基因精细定位需要的现状,本研究从公共数据库下载来自不同遗传背景的玉米表达序列标签（EST）,结合运用各种生物信息学软件,开发基于EST序列的高多态性SNP标记。通过对2018530条EST序列的比对分析,拼接发掘出遍布全基因组的80363个SNP位点。在SNP位点两侧保守序列上设计PCR引物,开发出12388 个SNP标记（www.sicau.edu.cn/web/yms/snp/snp.html）,包含34721个SNP位点。其中,6008个标记只含单一SNP位点,12762个位点的多态性信息含量（PIC）大于04,具有高度多态性。     

天祝白牦牛SRY基因克隆与原核表达

从天祝白牦牛的基因组DNA中扩增了SRY（Sex-determining Region on the Y Chromosome，SRY）基因编码区序列，将其克隆至pGEM-T easy载体并送至生物公司测序，天祝白牦牛SRY基因编码区长687 bp，编码229个氨基酸；对牦牛和奶牛的SRY基因编码区进行序列比对，发现存在2个碱基的变异，造成1个氨基酸的变异；将牦牛SRY基因编码区连接至pET-28a(+)载体，成功构建了表达载体pET-28a/SRY；把表达载体pET-28a/SRY转入大肠杆菌E.coli BL21（DE3）中，在合适的条件下诱导该大肠杆菌，SRY蛋白得到了大量表达；对表达产物进行了Western-blot检测，进一步确定牦牛SRY蛋白得到表达。     

斑点叉尾鮰趋化因子基因SCYA113内含子1的多态性分析

运用变性聚丙烯酰胺凝胶电泳和PCR产物测序技术检测斑点叉尾鮰CC趋化因子基因SCYA113 内含子1的序列长度和多态性。在3个群体的60个个体中,斑点叉尾鮰CC趋化SCYA113 内含子1存在15种单元型和8种长度类型,长度类型分别为A、B、C、D、E、F、G和H型。对这8种序列进行比对分析发现,斑点叉尾鮰SCYA113 内含子1长度为395~443 bp, 8种长度类型中A、G、T、C的平均百分比为30.01%、15.43%、38.37%、16.19%,而且G+C（31.62%）含量明显小于A+T（68.38%）含量,内含子1与外显子1和2的连接处存在真核基因中mRNA剪接的识别信号GT/AG;引起长度变化的主要原因是短串联重复序列（微卫星序列）TTC和TTA引起的;除了微卫星序列以外,共检测到6个突变位点,其中3个转换位点为118（C→T）,209（G→A）,250（T→C）,3个颠换位点为266（T→A）,289（G→T）,387（G→C）,核苷酸多样性指数(π)为0.004,平均核苷酸差异(K)为1.576;在变异水平上,3个群体表现出一定的遗传差异,84群体中检测到8种长度类型和14种基因型,97群体中检测到8种长度类型和10种基因型,04群体中6种长度类型和10种基因型（缺少A、B等位基因）。从3个群体60个个体拥有22种频率较低(0.017~0.150)的基因型可以看出,斑点叉尾鮰的遗传基因资源较为丰富。     

Diversity and antagonistic potential of Pseudomonas spp. associated to the rhizosphere of maize grown in a subtropical organic farm

Pseudomonas spp. are one of the most important bacteria inhabiting the rhizosphere of diverse crop plants and have been frequently reported as biological control agents (BCAs). In this work, the diversity and antagonistic potential of Pseudomonas spp. in the rhizosphere of maize cultivars Nitroflint and Nitrodent grown at an organic farm in Brazil was studied by means of culture-dependent and -independent methods, respectively. Sampling of rhizosphere soil took place at three different stages of plant development: 20, 40 and 106 days after sowing. A PCR-DGGE strategy was used to generate specific Pseudomonas spp. fingerprints of 16S rRNA genes amplified from total community rhizosphere DNA. Shifts in the relative abundance of dominant populations (i.e. PCR-DGGE ribotypes) along plant development were detected. A few PCR-DGGE ribotypes were shown to display cultivar-dependent relative abundance. No significant differences in diversity measures of DGGE fingerprints were observed for different maize cultivars and sampling times. The characterisation and assessment of the antagonistic potential of a group of 142 fluorescent Pseudomonas isolated from the rhizosphere of both maize cultivars were carried out. Isolates were phenotypically and genotypically characterised and screened for in vitro antagonism towards three phytopathogenic fungi and the phytopathogenic bacterium Ralstonia solanacearum. Anti-fungal activity was displayed by 13 fluorescent isolates while 40 isolates were antagonistic towards R. solanacearum. High genotypic and phenotypic diversity was estimated for antagonistic fluorescent Pseudomonas spp. PCR-DGGE ribotypes displayed by antagonists matched dominant ribotypes of Pseudomonas DGGE fingerprints, suggesting that antagonists may belong to major Pseudomonas populations in the maize rhizosphere. Antagonists differing in their genotypic and phenotypic characteristics shared the same DGGE electrophoretic mobility, indicating that an enormous genotypic and functional diversity might be hidden behind one single DGGE band. Cloning and sequencing was performed for a DGGE double-band which had no corresponding PCR-DGGE ribotypes among the antagonists. Sequences derived from this band were affiliated to Pseudomonas stutzeri and P. alcaligenes 16S rRNA gene sequences. As used in this study, the combination of culture-dependent and -independent methods has proven to be a powerful tool to relate functional and structural diversity of Pseudomonas spp. in the rhizosphere.     

Quantitative real-time PCR effectively detects and quantifies colonization of sclerotia of Sclerotinia sclerotiorum by Trichoderma spp.

Some members of the fungal genus Trichoderma are able to colonize and destroy sclerotia, the thick-walled resting structures of the soilborne plant pathogenic fungus Sclerotinia sclerotiorum, thus providing a potential means of biological disease control. However, current methods to detect and quantify colonization of sclerotia are labor-intensive, and generally qualitative rather than quantitative in nature. Our objective was to develop quantitative real-time PCR (polymerase chain reaction) methods to detect and measure colonization of sclerotia by Trichoderma spp. Specific PCR primer/probe sets were developed for Trichoderma spp. and for S. sclerotiorum. A total of 180 ITS1 (internal transcribed spacer) and ITS2 sequences from different species in the genus Trichoderma were aligned, and consensus sequences were determined. Six candidate primer sets were based on conserved regions of the consensus sequence, and the specificity of each nucleotide sequence was examined using BLAST (Basic Local Alignment Search Tool; NCBI) software. Each candidate primer set was tested on genomic DNA of T. harzianum strain ThzID1-M3, as well as six different Trichoderma isolates from soil, and on genomic DNA of S. sclerotiorum. The optimum primer/probe set selected, TGP4, successfully amplified genomic DNA of all Trichoderma isolates tested, and showed high precision and reproducibility over a linear range of eight orders of magnitude, from 85 ng to 8.5 fg of T. harzianum genomic DNA. TGP4 did not amplify S. sclerotiorum DNA. A specific PCR primer/probe set (TMSCL2) was developed for S. sclerotiorum, based on the calmodulin gene sequence. TMSCL2 did not amplify Trichoderma DNA. Quantitative real-time PCR with the primers then was evaluated in experiments to test differential effects of two soil moisture levels (−50 kPa, −1000 kPa matric potential) on biocontrol of S. sclerotiorum by indigenous Trichoderma spp. Periodically over 40 days, Trichoderma and S. sclerotiorum DNA in sclerotia were quantified by PCR with appropriate primers. Over 90% of the sclerotia were colonized by indigenous Trichoderma spp. at −1000 kPa, over the 40-day period, compared to only 60% at −50 kPa. In addition to determining incidence of colonization, the PCR method allowed measurement of the extent of sclerotial colonization, which also was significantly greater in the drier soil. Quantitative real-time PCR with the TGP4 primer/probe set provides a sensitive detection and measurement tool to evaluate colonization of sclerotia by Trichoderma spp.     

Relationships between soil penetration resistance and soif nematode burden in barley on Prince Edward Island

Fifty sloping fields of barley with different short-term cropping histories across Prince Edward Island were examined for variations in root-zone depth and the severity of soil parasitic nematodes as part of a wider study of relationships between cropping sequence, topographic position, soil physical conditions and crop performance. Root lesion nematode (Pratylenchus penetrans) density in the roots was significantly greater (13%) at foot slopes than at top slopes, and stunt nematode (Tylenchorhynchus spp.) was significantly greater (8%) at top slopes where the soil was drier. The density of stunt nematodes and root lesion nematodes in the soil was significantly greater (>15%) under miscellaneous cereals-barley sequences than under potato-barley or hay-barley, attributable to level of carryover. Root lesion nematode density in the roots was significantly greater (12%) under hay-barley than either of the other two sequences. This nematode also showed a strong tendency to increase in number with increasing root-zone depth, and may be explained on the basis that increased root-zone depth provides increased host root mass (substrate). Stunt nematodes, on the other hand, increased with decreasing root-zone depth and may be explained by the known propensity of these organisms for drier, shallower soil conditions.     

Relationships between soil penetration resistance and soif nematode burden in barley on Prince Edward Island

Fifty sloping fields of barley with different short-term cropping histories across Prince Edward Island were examined for variations in root-zone depth and the severity of soil parasitic nematodes as part of a wider study of relationships between cropping sequence, topographic position, soil physical conditions and crop performance. Root lesion nematode (Pratylenchus penetrans) density in the roots was significantly greater (13%) at foot slopes than at top slopes, and stunt nematode (Tylenchorhynchus spp.) was significantly greater (8%) at top slopes where the soil was drier. The density of stunt nematodes and root lesion nematodes in the soil was significantly greater (>15%) under miscellaneous cereals-barley sequences than under potato-barley or hay-barley, attributable to level of carryover. Root lesion nematode density in the roots was significantly greater (12%) under hay-barley than either of the other two sequences. This nematode also showed a strong tendency to increase in number with increasing root-zone depth, and may be explained on the basis that increased root-zone depth provides increased host root mass (substrate). Stunt nematodes, on the other hand, increased with decreasing root-zone depth and may be explained by the known propensity of these organisms for drier, shallower soil conditions.     

A forage grass and legume plant collecting expedition in Portugal

The Plant Genetic Resources Unit of the Institute of Grassland and Environmental Research, U.K., and the Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Portugal, carried out a joint plant collecting expedition in Portugal in May 1995. Seven regions of Portugal were explored from the north to the south. A diverse range of habitats was sampled covering different altitudes, management systems and ecological conditions, where semi-natural grassland and wild unmanaged grassland was found. Vegetative samples of forage grass and legume populations were collected wherever possible. Seed samples were collected in the absence of live plants and from farmers' stores. Detailed collection site data was recorded at every site. 113 populations of Lolium spp., Festuca spp., Agrostis spp., Dactylis spp. and Briza spp. and 53 populations of Trifolium spp., Medicago spp. and Lupinus spp. were collected from 115 sites. It was possible to find traditional agricultural systems throughout Portugal but they are changing in response to European Union farming policies. For example, Lolium multiflorum Lam. is still intercropped with maize, although seed production of this crop on the farm is no longer permissible and, therefore, local land races are being replaced by commercial varieties. These changes to traditional agricultural systems are contributing to a major loss of genetic diversity.     

Molecular distinction among mulberry (Morus spp.) species and varieties cultivated in the Democratic People’s Republic of Korea

Mulberry (Morus spp.) is a cross-pollinating and highly hybridized plant of which productivity are greatly varied in different varieties. Accurate distinction among mulberry varieties and understanding of phylogenetic relationship among them would be crucial for the development of sericulture. We have analysed molecular distinction among four mulberry species and varieties cultivated in DPR Korea by using nuclear ribosomal internal transcribed spacer (ITS) sequences and inter simple sequence repeat (ISSR) markers. ITS sequences doesn’t represent a remarkable interspecific distinction among four mulberry species used in our study, suggesting that it could not be employed to identify them. ISSR analysis using 16 random primers generated 158 different markers ranging from 100 to 4000 bp in size. The results showed the inter-specific genetic variation (55.34%) was slightly higher than intra-specific genetic variation (44.66%), with comparatively low average number of migrants per generation (Nm) among populations (0.3886). Using ISSR primers selected in this study, in the future, the suitable breeding strategy might be established in raising of elite mulberry varieties on the basis of interspecific hybridization.

     

Occurrence and characterization of nitrogen-fixing Azospirilla in some soils of Egypt

The occurrence and characterization of N₂-fixing azospirilla in some Egyptian soils has been investigated. Seven soils, representing a wide range in texture and properties were selected from different localities in Egypt. The highest nitrogenase activity reported for soil samples under investigation were related to numbers of N₂-fixing microorganisms (Azotobacter spp., Azospirillum spp., and Clostridium spp.). Seven strains of azospirilla were isolated and purified. Based on morphological characteristics, three types of cell morphology were distinguished. Cultural and physiological characteristics as well as nitrogenase activity of representative isolates in presence of different concentrations of NaCl were determined. According to the physiological properties studied, all isolates were classified as members of Azospirillum brasilense.     

低温复合发酵剂对冬季牛粪堆肥微生物多样性的影响

在-20℃下进行冬季牛粪堆肥,研究其温度、可培养微生物数量及细菌种群多样性的变化。堆肥处理的第6 d进入高温期并持续10 d,最高温度67.4℃;对照温度始终在-11～-13℃。处理的可培养细菌、放线菌、真菌数量分别高于对照0.018～1.368、0.040～0.966、-0.778～0.547个数量级;微生物总的变化趋势是细菌最多,放线菌次之,真菌最少。处理不同时期细菌DGGE图谱有着明显的差异性,对照不同时期图谱无明显差异;UPGAMA聚类分析,处理的相似性在0.54～0.70,对照的在0.95～0.98。处理的优势菌:初期为Clostridium ther-mopalmarium、Psychrobacter spp,升温期为Psychrobacter spp,高温期为Hydrogenobacter hydrogenophilus、Clostridiumspp、Psychrobacter spp、Saccharococcus thermophilus等,降温期为Clostridium thermolacticum、Psychrobacter spp;对照的各个时期优势菌相同,为Clostridium spp、Pseudomonas spp、Psychrobacter spp等;整个堆肥过程中Psychrobacterspp为处理和对照的共同优势菌。     

Gingers of Manipur: diversity and potentials as bioresources

The gingers are well-known for their medicinal and economic significance and occur chiefly in the tropical regions of the world mainly in the Indo-Malaysian area of Asia. From Manipur in northeast India, 33 species under 9 genera have been collected from different parts of the State. Collected specimens were planted in the Experimental Field of the Department of Life Sciences, Manipur University. The morphological details of the various species were worked out. The characteristic features of the specimen, their traditional uses, anti-oxidant compounds present and biological activities are described. The identified genera are Alpinia (3 spp.), Amomum (5 spp.), Boesenbergia (1 sp.), Curcuma (10 spp.), Elettaria (1 sp.), Hedychium (7 spp. and 1 variety), Kaempferia (2 spp.), Roscoea (1 sp.) and Zingiber (3 spp.). Of these, 26 species have been used variously as food (15), traditional medicine (21) and ornamental plants (9) by the ethnic people in their culture. Ten species have been identified to possess various bioactive molecules.     

几种生物质热解特性及动力学的对比

该文对芒属、芦苇、狼尾草进行常压热重分析,同时与稻草相比较,试验结果表明：草类生物质热解过程可以分为4个阶段,干燥失水、过渡阶段、快速热解、炭化阶段。在290℃附近存在一个肩峰,失重都集中在187～400℃,挥发分综合释放指数芒属＞稻草＞狼尾草＞芦苇,活化能芒属＞稻草＞狼尾草＞芦苇,固体剩余物芒属＞狼尾草＞稻草＞芦苇,所以总体上看芒属的热解稳定性相对较差,芦苇的热解稳定性较好,同时采用二级反应动力学模型由Coats-Redfern法求的相应得活化能和频率因子。