Integrated analysis of genetic,genomic and proteomic data

The rapid expansion of methods for measuring biological data ranging from DNA sequence variations to mRNA expression and protein abundance presents the opportunity to utilize multiple types of information jointly in the study of human health and disease. Organisms are complex systems that integrate inputs at myriad levels to arrive at an observable phenotype. Therefore, it is essential that questions concerning the etiology of phenotypes as complex as common human diseases take the systemic nature of biology into account, and integrate the information provided by each data type in a manner analogous to the operation of the body itself. While limited in scope, the initial forays into the joint analysis of multiple data types have yielded interesting results that would not have been reached had only one type of data been considered. These early successes, along with the aforementioned theoretical appeal of data integration, provide impetus for the development of methods for the parallel, high-throughput analysis of multiple data types. The idea that the integrated analysis of multiple data types will improve the identification of biomarkers of clinical endpoints, such as disease susceptibility, is presented as a working hypothesis.     

The Plasma Proteome: High Abundance versus Low Abundance

The field of proteomics is rapidly turning towards targeted mass spectrometry (MS) methods to quantify putative markers or known proteins of biological interest. Historically, the enzyme-linked immunosorbent assay (ELISA) has been used for targeted protein analysis, but, unfortunately, it is limited by the excessive time required for antibody preparation, as well as concerns over selectivity. Despite the ability of proteomics to deliver increasingly quantitative measurements, owing to limited sensitivity, the leads generated are in the microgram per milliliter range. This stands in stark contrast to ELISA, which is capable of quantifying proteins at low picogram per milliliter levels. To bridge this gap, targeted liquid chromatography (LC) tandem MS (MS/MS) analysis of tryptic peptide surrogates using selected reaction monitoring detection has emerged as a viable option for rapid quantification of target proteins. The precision of this approach has been enhanced by the use of stable isotope-labeled peptide internal standards to compensate for variation in recovery and the influence of differential matrix effects. Unfortunately, the complexity of proteinaceous matrices, such as plasma, limits the usefulness of this approach to quantification in the mid-nanogram per milliliter range (medium-abundance proteins). This article reviews the current status of LC/MS/MS using selected reaction monitoring for protein quantification, and specifically considers the use of a single antibody to achieve superior enrichment of either the protein target or the released tryptic peptide. Examples of immunoaffinity-assisted LC/MS/MS are reviewed that demonstrate quantitative analysis of low-abundance proteins (subnanogram per milliliter range). A strategy based on this technology is proposed for the expedited evaluation of novel protein biomarkers, which relies on the synergy created from the complementary nature of MS and ELISA.     

Modeling and analysis of soybean (Glycine max. L) Cu/Zn,Mn and Fe superoxide dismutases

Superoxide dismutase (SOD, EC 1.15.1.1) is an important metal-containing antioxidant enzyme that provides the first line of defense against toxic superoxide radicals by catalyzing their dismutation to oxygen and hydrogen peroxide. SOD is classified into four metalloprotein isoforms, namely, Cu/Zn SOD, Mn SOD, Ni SOD and Fe SOD. The structural models of soybean SOD isoforms have not yet been solved. In this study, we describe structural models for soybean Cu/Zn SOD, Mn SOD and Fe SOD and provide insights into the molecular function of this metal-binding enzyme in improving tolerance to oxidative stress in plants.     

鹰嘴豆种质资源对Ascochyta rabiei的抗性评价及遗传多态性分析

以25 个鹰嘴豆品系为试验材料,通过叶面喷雾的方式进行Ascochyta rabiei菌悬液室内外人工接种,评价不同鹰嘴豆种质资源的抗病性;同时利用RAPD方法进行基因型鉴定,采用NTSYSpc 2.10t软件对分子标记结果进行遗传相似性的统计分析并建立各品系间的亲缘关系聚类图,探讨不同鹰嘴豆品系对A.rabiei抗性与遗传多态性间的关系。通过室内和田间鹰嘴豆抗A.rabiei鉴定结果综合分析表明：在25个鹰嘴豆供试品系中,“系选 03”和“216”品系均表现出稳定抗性特性;北园春品系表现出稳定中抗特性。通过RAPD多态性引物对这25 个供试品系进行PCR扩增,共获得129 个扩增条带,其中多态性条带共有67 条,多态性比例达51.94%,遗传相似系数为0.3731-0.9254。结合抗病性和遗传多态性,经方差分析表明,本研究所采用的鹰嘴豆品系对A.rabiei的抗性强弱与其遗传相似性之间无显著相关性。     

紫花苜蓿多元杂交后代优良株系筛选研究

通过对甘农3号、甘农5号和游客紫花苜蓿多元杂交后代选育的36个株系及其亲本的生长、产量、品质等相关指标的测定,采用灰色关联度理论,构造综合评价模型进行供试材料综合评价,筛选出速生12#、速生11#株系为最理想的优良株系,生长高度分别为105.44cm、105.42cm;生长速度分别为1.74cm/d、1.68cm/d;茎叶比分别为0.30、0.35;分枝数分别为23、17;鲜草产量分别为39.99 t/hm2、35.13 t/hm2;粗蛋白含量分别为19.95%、23.89%;相对饲用价值为153.15%、157.02%。多叶2#、速生5#、速生20#、速生21#等4个株系为较理想的优良株系。     

Evaluation of improved and local/landrace/sorghum varieties for covered kernel smut

Twelve varieties of improved and local (landrace) sorghum were tested under artificial inoculation conditions. Out of 12 sorghum varieties evaluated with covered kernel smut, notably local cultivar ‘Tetron’ was found to be highly resistant. Disease incidence and severity on the rest of the cultivars varied from 21 to 47% and 40 to 53% respectively. Differences among cultivars in yield loss were also observed. The highest yield loss (40%) was recorded on 97 MW 6129 (NVT-11 4) and for Tetron yield loss was nil. The effect of disease on germination was noticed but cannot be considered as conclusive due to moisture stress at the time of germination.     

Effect of cucumber mosaic virus infection on morphology,yield and phenolic contents of tomato

Ten tomato genotypes were screened for their resistance against cucumber mosaic virus (CMV) and its vector Myzus persicae under natural infection in field, using aphids M. persicae under net-house and mechanical inoculation under greenhouse. Large differences were observed among genotypes for infection percentage (IP) and severity index (SI) among the testing methods used. All genotypes showing tolerance to CMV in the field or through aphid inoculation, however, become susceptible and highly susceptible after mechanical inoculation. All the test genotypes also showed susceptibility to the aphid M. persicae population. Plants inoculated with CMV showed substantial decrease in yield and yield-contributing parameters which varied with cultivars that probably depended upon its genetic make up. All the test genotypes exhibited 0.97–30.19% decrease in plant height, 11.47–52.65% decrease in root length, 46.56–95.56% decrease in fresh plant weight, 65.78–92.84% decrease in root fresh weight, 19.97–87.65% decrease in the dry weight of plants, 75.63–95.43% decrease in dry root weight, 69.51–95.65% reduction in the number of fruits and 89.04–99.89% decrease in yield per plants. After 15 days of inoculation, the quantitative analysis using double beam spectrophotometer showed an increase in total phenolics in CMV-inoculated plants as compared to un-inoculated plants among genotypes. Similarly the thin layer chromatography (TLC) on silica gel G indicated that the number of phenolic compounds was increased in most of the inoculated genotypes while in others they were either decreased or remained same.     

Development and assessment of fusarium oxysporum-based mycoherbicide for control of Striga Hermonthica in sorghum

Abstract

Experiments were carried out from 2002 to 2003 to determine the most suitable form of fungal delivery for possible use by farmers in biological control of Striga hermonthica. Six mycoherbicides were developed, based on Fusarium oxysporum isolated from wilted S. hermonthica. In mycoherbicide formulation, rock phosphate powder, sorghum bran and gum arabic powder were used as carriers. Besides its role as a carrier, gum arabic powder was used as a sticker. There were three carriers with two formulations each, making six treatments altogether. Living propagule studies were based on colony, mycelium and conidium number of F. oxysporum. In greenhouse evaluation of mycoherbicides, each kg sorghum seed was coated with 10 g mycoherbicide before sowing. Carrier rock phosphate powder with gum arabic powder as a sticking agent was the most suitable form of its delivery for use by peasant farmers.     

Temperature response,pathogenicity, seed infection and mutant evaluation against Macrophomina phaseolina causing charcoal rot disease of sesame

Charcoal rot caused by Macrophomina phaseolina is a serious disease of sesame in Pakistan. M. phaseolina sesame isolate was subjected to growth rate test at 10, 15, 20, 25, 30, 35 and 40°C. The optimum temperature for fungal growth and microsclerotia production was found to be 30–35°C. Gray to black, radial fungal colonies with intermediate mycelial growth and jet black oval to round microsclerotia were observed at this optimum range. M. phaseolina was found to be pathogenic against all the 18 tested plant species and this pathogenicity proved its necrophytic behavior. Seed infection efficiency of M. phaseolina was 100% with significant reduction in seed index. For two consecutive years 21 mutants/varieties were screened in the field for their reactions to charcoal rot disease. During 2007 three mutants NS11704S1, NS11304S2 and NS26004 were ranked as resistant while others were moderately resistant to highly susceptible. During 2008 all mutants showed a susceptible to highly susceptible reaction with variable disease reactions. All over screening results revealed that four mutants viz, NS13P1, NS163-1, NS270P1 and NS26004 showed about 50% stand with consistent performance during both years under optimum disease conditions and can be used to manage the disease following the disease management strategies, however in the future improvement for high seed yield along with resistance is a prerequisite for sustainable high production.