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.     

Techniques for Processing Eyes Implanted With a Retinal Prosthesis for Localized Histopathological Analysis

With the recent development of retinal prostheses, it is important to develop reliable techniques for assessing the safety of these devices in preclinical studies. However, the standard fixation, preparation, and automated histology procedures are not ideal. Here we describe new procedures for evaluating the health of the retina directly adjacent to an implant. Retinal prostheses feature electrode arrays in contact with eye tissue. Previous methods have not been able to spatially localize the ocular tissue adjacent to individual electrodes within the array. In addition, standard histological processing often results in gross artifactual detachment of the retinal layers when assessing implanted eyes. Consequently, it has been difficult to assess localized damage, if present, caused by implantation and stimulation of an implanted electrode array. Therefore, we developed a method for identifying and localizing the ocular tissue adjacent to implanted electrodes using a (color-coded) dye marking scheme, and we modified an eye fixation technique to minimize artifactual retinal detachment. This method also rendered the sclera translucent, enabling localization of individual electrodes and specific parts of an implant. Finally, we used a matched control to increase the power of the histopathological assessments. In summary, this method enables reliable and efficient discrimination and assessment of the retinal cytoarchitecture in an implanted eye.     

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。     

四株儿茶酚类铁载体高产菌株产消化酶活性及其益生特性

【背景】儿茶酚类铁载体对胃肠道菌群的生长代谢具有重要作用,研究儿茶酚类铁载体高产菌株的消化酶活性,挖掘其潜在益生特性具有重要意义。【目的】分析4株分离自健康成人粪样的儿茶酚类铁载体高产菌的产酶特性,通过分析菌株耐酸耐胆盐能力、粘附定殖能力、抗生素耐受性和急性毒性研究其益生特性。【方法】测定4株菌的蛋白酶、淀粉酶、脂肪酶、纤维素酶、植酸酶、乳糖酶和β-葡萄糖苷酶的酶活性。4株菌经人工模拟胃、肠液连续培养后分别计算其活菌数;分析4株菌的自凝集率、黏蛋白粘附率和表面疏水率;对小鼠连续7 d灌胃不同剂量的4株高产菌,观察并记录小鼠的一般体征,计算小鼠脏器指数,进行阳性细菌移位试验。【结果】在试验所测的7种消化酶中,E. coli Gut 07、E. coli Gut 12无蛋白酶和脂肪酶活性,B. cereus Gut 16无乳糖酶活性,E. coli Gut 20无蛋白酶活性,其余均具有。4株菌经人工模拟胃液培养6h后存活率均大于60%,转移到人工模拟肠液培养24 h后活菌数均大于初始菌落数;该4株菌具备在胃肠道中粘附定殖的能力,对大多数抗生素敏感,在浓度低于4.5×10~(11)CFU/m L、灌胃剂量为20m L/kg-bw时对小鼠无急性毒性,无阳性菌株移位现象。【结论】4株儿茶酚类铁载体高产菌株可作为潜在益生菌进行进一步的安全性和功能性研究。     

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.