Host-Parasite Relationships of Hoplolaimus columbus on Cotton and Soybean

Hoplolaimus columbus suppressed growth and pod yield of soybean in greenhouse tests. Although populations of H. columbus decreased in short-term experiments, increases occurred in long-term studies. The nematode caused extensive damage to the cortical parenchyma and occasionally to the endodermal-vascular region of both cotton and soybean roots. The nematode frequently entered secondary root primordia. Roots of soybean parasitized by H. columbus at high inoculum levels were severely damaged. The relationship of populations of H. columbus and stunting of soybean and cotton is discussed.     

Host-Parasite Relationships of Meloidogyne trifoliophila Isolates from New Zealand

Root-infecting nematodes are commonly found on white clover in New Zealand pasture where they reduce yield, nitrogen fixation, and persistence. The dominant root-knot nematode on white clover in New Zealand is confirmed in this study as Meloidogyne trifoliophila by isozyme phenotype comparison with the type population from Tennessee. Results from a host differential test differed in the host ranges of M. trifoliophila and M. hapla from New Zealand locations, with M. trifoliophila failing to reproduce on the standard host plants of the test. The size and character of white clover root galls differ between species as M. trifoliophila galls are large, elongate, and smooth compared to the M. hapla galls, which are small, round, inconspicuous, and generally have adventitious, lateral roots. Culture and identification of root-knot nematode populations from sites in the North Island of New Zealand showed that M. trifoliophila is more widespread and abundant than M. hapla. Similar differential resistant and susceptible galling responses among half-sib families of white clover from a breeding program indicated that all M. trifoliophila populations tested were of the same pathotype. This resistant material was not effective in reducing reproduction of M. hapla. Meloidogyne trifoliophila did not develop to maturity on six grasses tested, but galls were formed on some species.     

Host-Parasite Relationships of Atalodera spp. (Heteroderidae)

Atalodera ucri, Wouts and Sher, 1971, and A. lonicerae, (Wouts, 1973) Luc et al., 1978, induce similar multinucleate syncytia in roots of golden bush and honeysuckle, respectively. The syncytium is initiated in the cortex; as it expands, it includes several partially delimited syncytial units and distorts vascular tissue. Outer walls of the syncytium are relatively smooth and thickest near the feeding site of the nematode; inner walls are interrupted by perforations which enlarge as syncytial units increase in size. The cytoplasm of the syncytium is granular and includes numerous plastids, mitochondria, vacuoles, Golgi, and a complex network of membranes. Nuclei are greatly enlarged and amoeboid in shape. Although more than one nucleus sometimes occur in a given syncytial unit, no mitotic activity was observed. Syncytia induced by species of Atalodera chiefly differ from those of Heterodera sensu lato by the absence of cell wall ingrowths; wall ingrowths increase solute transport and characterize transfer cells. In syncytia of Atalodera spp., a high incidence of pits and pit fields in walls adjacent to vasctdar elements suggests that in this case plasmodesmata provide the pathway for increased entry of sohttes. The formation of a syncytium by species of Atalodera and Heterodera sensu lato, but a single uninucleate giant cell by Sarisodera and Hylonema, indicates a pattern of host responses that may be useful, with other characters, for phylogenetic inference for Heteroderidae.     

宁夏杂草稻的遗传多样性及其亲缘关系分析

以宁夏杂草稻、选育品种、地方品种共143份水稻种质为试验材料,进行主要农艺性状的的表型鉴定评价,并利用24对SSR引物进行不同类型水稻种质的遗传多样性比较、遗传相似性和聚类分析。表型评价表明,宁夏杂草稻表现为矮秆和早熟,表型变异范围较大;多数杂草稻种皮呈红色,颖壳呈秆黄色,均落粒。SSR标记分析结果,共检测到141个等位基因,每个位点等位基因数目变异在3~11个,平均为5.8333个;Nei's基因多样性指数变幅为0.2241~0.8065,平均为0.5219。杂草稻种质的等位基因数、有效等位基因数、Shannon指数均高于选育品种和地方品种。在不同来源杂草稻群体中,来自吴忠和永宁东河的杂草稻Nei's基因多样性指数最高,分别为0.4912和0.4814,而来自青铜峡的杂草稻Nei's基因多样性指数最低,为0.2802。相似性分析表明,杂草稻与地方品种高度相似,相似系数高达0.9585,而杂草稻与选育品种的相似性较低,其相似系数为0.4584;选育品种与地方品种的相似系数只有0.3560。聚类分析表明,参试材料分为3个类群,其中选育品种单独聚类于第Ⅰ类群,其遗传背景明显区别于杂草稻和地方品种;第Ⅱ类包括大部分杂草稻和地方品种,不同来源杂草稻及地方品种间分布比较均匀;第Ⅲ类是由小部分杂草稻和地方品种组成。宁夏杂草稻的分布没有明显的区域性,宁夏杂草稻与地方品种高度融合且遗传相似性很高。     

33份杂交稻亲本的SSR指纹图谱构建及遗传相似性分析

选用分布在12条染色体上84对SSR引物,对6个粳型和4个籼型核质互作雄性不育系、14个籼型和9个粳型父本,共33份杂交稻亲本材料进行遗传相似性分析,并建立SSR指纹图谱数据库.结果表明:在33份材料中能够扩增出多态性的引物有54对,占所用引物的64.3％;33 份材料间遗传相似系数变异范围为0.429～0.988,在遗传相似系数0,65处,33份材料被聚为籼、粳2个大类群;利用14对引物能将33份材料区分,引物RM264能将‘Ⅱ-32A'、‘协青早A'、‘冈46A’和‘K17A'4个籼型不育系与籼型恢复系区分开,引物RM432能区别5个粳型不育系与粳型可育品种,引物RM6、RM13、RM16、RM240、RM247和RM248均能鉴别籼、粳亚种.利用这6对引物的共显性标记可以鉴别籼粳亚种间杂交组合.     

高山被孢霉遗传操作系统的构建与应用

高山被孢霉是一种重要的产油丝状真菌,其油脂积累量高达细胞干重的50%,其中具有重要生理活性的多不饱和脂肪酸含量较高且种类丰富。近年来,针对高山被孢霉遗传操作系统建立的分子生物学研究进展迅速,这为进一步提高其多不饱和脂肪酸合成水平奠定了基础。对高山被孢霉遗传操作系统的最新应用进展进行了综述,包括高山被孢霉的转化方法、筛选标记的种类、各种方法的优缺点及遗传操作系统的应用。     

鸭茅种质资源遗传多样性的SRAP研究

利用SRAP(Sequence-related amplified polymorphism)标记对来自国内外的45份鸭茅（Dactylis glomerata L.）种质资源进行遗传多样性研究。21对引物扩增出438个条带,多态性条带为363条,多态性条带比率为82.08%,每对引物组合的多态性带数平均为17.29条。GS值范围在0.6248-0.9686间,平均GS值为0.7958,显示来源广泛的鸭茅种质资源间存在着丰富的遗传变异。聚类分析及主成分分析能将所有材料聚为4类,能较准确的反映材料的来源分布情况及供试材料的染色体倍性差异,表明鸭茅的遗传多样性与染色体倍性及地理分布密切相关。同时清楚的揭示出国产鸭茅品种遗传基础较为狭窄。本研究为育种和探讨鸭茅种质资源遗传变异奠定了较好的理论基础。     

大戟属植物亲缘关系的ISSR分析

利用ISSR标记对9种大戟属植物的亲缘关系进行了分析.结果表明:筛选出的24条ISSR引物共扩增251条带,其中多态性条带248条,多态率为98.8%.9种大戟属材料的遗传相似系数在0.51～0.69之间,平均为0.62.利用UPGMA法将9种大戟属植物分别聚为3个类群,第一类群包含地锦亚属与一品红亚属的5个种及大戟亚属的绿玉树,第二、第三类群分别包含大戟亚属中的3个种.ISSR标记获得的聚类结果与根据形态特征获得的分类结果有很大的差异.     

基于SSR标记的草莓品种亲缘关系分析

摘要：用18对SSR引物对96份草莓栽培品种资源进行扩增。在18个SSR位点共获得184个条带,其中多态性条带为172个,多态性条带比率为93.5％,不同引物扩增的多态性条带数为6～19个,平均为9.56个。各位点PIC值在0.5726～0.8885之间,平均0.8057。NTSYS软件进行相似性系数计算,UPGMA法进行聚类分析结果显示,96份来源不同的草莓品种被混杂地聚在一起,草莓品种的亲缘关系与其来源并不存在明显的相关性,中国地方品种的聚类相对集中,中国地方品种与中国选育品种之间亲缘关系相对较远。欧美品种和日本品种的遗传基础要宽于中国选育品种和地方品种。     

一种花生快速遗传转化方法的建立与应用

遗传转化是植物基因工程的重要手段。快速、高效地将目的基因导入植物细胞, 并缩短获得转基因后代的时间是遗传转化的关键。花生(Arachis hypogaea)是我国重要的油料及经济作物。目前花生的遗传转化体系尚未完善, 制约着花生的基因功能解析和分子育种进程。该文建立了一套快速、稳定的花生遗传转化体系。通过将农杆菌注射于花生第2茎节的切面获得转化植株, 再将阳性植株进行移栽和回土, 采摘注射点以上的荚果进行后续鉴定与分析。结果表明, 利用该方法可获得40%以上的T₀代嵌合体植株, 约5个月可收获T₀代花生种子, 其中约有9%的T₁代花生植株为非嵌合体的杂合体。针对部分转基因植株结实少的问题, 进一步提出了将快速转化体系与传统组培方法相结合的优化方案。构建的快速转化方法对大蒜(Allium sativum)、马铃薯(Solanum tuberosum)和香雪兰(Freesia refracta)的遗传转化具有潜在应用价值, 对其它植物的遗传转化也有重要参考价值。     

一种新的分子遗传相似度计算方法

指出了Nei氏遗传相似度仅仅是用来描述两个二进制变量差异相似程度程度的一种距离系数或相似系数,与个体间亲缘程度没有必然联系。根据亲缘系数的定义,提出新的遗传相传相似计算公式即rA(x,y)=2N^2xy/NxNy或rA(x,y)=N^2/NxNy。并通过实例验证了该公式可用于判断个体间亲缘程度方面。     

一种新的分子遗传相似度计算方法

指出了Nei氏遗传相似度仅仅是用来描述两个二进制变量差异或相似程度的一种距离系数或相似系数,与个体间亲缘程度没有必然联系.根据亲缘系数的定义,提出新的遗传相似度计算公式即rA(x,y)=(2N2xy)/(NxNy)或rA(x,y)=(N2xy)/(NxNy).并通过实例验证了该公式可用于判断个体间亲缘程度方面。 Abstract:Nei's genetic similarity was only described as a kind of distance coefficient for binary system variables and it have not positive connection with the relationship between individuals.According to the definition of the relationship coefficient,a new formula which is about genetic similarity is put forward as following:rA(x,y)= It is verified by an example that this formula can be used to judge the relationship between individuals.     

甜高粱种质资源在新疆的多样性表现及聚类分析

采用多样性指数、变异系数和聚类分析等方法,对国内外72份甜高粱种质资源24个性状进行遗传多样性研究。结果表明,14个质量性状中粒色的遗传多样性指数最高为1.6333,幼苗色和结实形式的遗传多样性指数最低为0,平均为0.7460;10个数量性状中穗长、茎粗、锤度、单穗粒重、单株秆重、出汁率、千粒重、株高、穗重、生育期都存在较大的变异,变异系数幅度为7.85%～53.01%,各性状多样性指数均较大,平均2.0061;穗长的多样性指数最大,为2.1383,生育期多样性指数最小,为1.7331,表明新疆现有甜高粱资源拥有丰富的遗传多样性。聚类分析将72份资源划分为四大类。     

Comparison of Profile Similarity Measures for Genetic Interaction Networks

Analysis of genetic interaction networks often involves identifying genes with similar profiles, which is typically indicative of a common function. While several profile similarity measures have been applied in this context, they have never been systematically benchmarked. We compared a diverse set of correlation measures, including measures commonly used by the genetic interaction community as well as several other candidate measures, by assessing their utility in extracting functional information from genetic interaction data. We find that the dot product, one of the simplest vector operations, outperforms most other measures over a large range of gene pairs. More generally, linear similarity measures such as the dot product, Pearson correlation or cosine similarity perform better than set overlap measures such as Jaccard coefficient. Similarity measures that involve L₂-normalization of the profiles tend to perform better for the top-most similar pairs but perform less favorably when a larger set of gene pairs is considered or when the genetic interaction data is thresholded. Such measures are also less robust to the presence of noise and batch effects in the genetic interaction data. Overall, the dot product measure performs consistently among the best measures under a variety of different conditions and genetic interaction datasets.     

Integrative Analysis Reveals Relationships of Genetic and Epigenetic Alterations in Osteosarcoma

Background

Osteosarcomas are the most common non-haematological primary malignant tumours of bone, and all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies.

Principal Findings

The cell lines showed complex patterns of DNA copy number changes, where genomic copy number gains were significantly associated with gene-rich regions and losses with gene-poor regions. By integrating the datasets, 350 genes were identified as having two types of aberrations (gain/over-expression, hypo-methylation/over-expression, loss/under-expression or hyper-methylation/under-expression) using a recurrence threshold of 6/19 (>30%) cell lines. The genes showed in general alterations in either DNA copy number or DNA methylation, both within individual samples and across the sample panel. These 350 genes are involved in embryonic skeletal system development and morphogenesis, as well as remodelling of extracellular matrix. The aberrations of three selected genes, CXCL5, DLX5 and RUNX2, were validated in five cell lines and five tumour samples using PCR techniques. Several genes were hyper-methylated and under-expressed compared to normal osteoblasts, and expression could be reactivated by demethylation using 5-Aza-2′-deoxycytidine treatment for four genes tested; AKAP12, CXCL5, EFEMP1 and IL11RA. Globally, there was as expected a significant positive association between gain and over-expression, loss and under-expression as well as hyper-methylation and under-expression, but gain was also associated with hyper-methylation and under-expression, suggesting that hyper-methylation may oppose the effects of increased copy number for detrimental genes.

Conclusions

Integrative analysis of genome-wide genetic and epigenetic alterations identified dependencies and relationships between DNA copy number, DNA methylation and mRNA expression in osteosarcomas, contributing to better understanding of osteosarcoma biology.     

紫云英根瘤菌菌株107exo基因簇的遗传互补分析

紫云英根瘤菌菌株１０７经Ｔｎ５插入诱变,得到１２株胞外多糖缺陷型变种,以质粒ｐＭＮ２为载体,从其中７株ＥＰＳ－变种内分别构建了７个Ｒ－Ｐｒｉｍｅ质粒（ｅｘｏＲ＇）,大部分变种的ＥＰＳ－表型可被ｅｘｏＲ＇互补,恢复野生型表型（ＥＰＳ＋）。互补表明,１２株ＥＰＳ－变种可分为６个不同的互补群,其中５个在遗传上连锁。ｅｘｏＲ＇酶切分析,除ｅｘｏＲ＇－０２,ｅｘｏＲ＇－０４外,其余５只的外源片段均整合于ＰＭＮ２的两同向重复序列ＩＳ２１之间。     

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

The dramatic increase in heterogeneous types of biological data—in particular, the abundance of new protein sequences—requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity—GPCRs and kinases from humans, and the crotonase superfamily of enzymes—we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.