A method of analyzing cultivar x location x year experiments: a new stability parameter

Summary Assessment of cultivar performance in a cultivar x location x year experiment is often difficult because of the presence of a location x year interaction. Our objective is to demonstrate a method on separation of environment effects (location x year) into predictable and unpredictabel components. The analysis consists of two parts: (1) a regression analysis based on location effects (averaged over years), assuming that the location means represent predictable environmental variation; and (2) the estimation of stability (denoted type 4) based on the years within location mean squares, assuming that years within location represent unpredictable environmental variation. From the regression analysis in (1), a breeder can determine the optimum range of locations in which a cultivar is well suited, and from (2) he can choose the most stable cultivars. The advantage of type 4 stability is that it is independent of the other cultivars included in the test and of the regression coefficient estimated for predictable variation. Three sets of published data are used to illustrate the analysis. Type 4 stability is compared with type 3 stability (deviation mean square from regression on environmental index) for genetic consistency. The analyses suggest that type 4 stability is consistent and is therefore a potential genetic parameter, but type 3 stability is not.Contribution No. I-806 from Engineering and Statistical Research Centre, Research Branch, Agriculture Canada, Ottawa, K1A OC6, Canada     

A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics

Human physiology is an ensemble of various biological processes spanning from intracellular molecular interactions to the whole body phenotypic response. Systems biology endures to decipher these multi-scale biological networks and bridge the link between genotype to phenotype. The structure and dynamic properties of these networks are responsible for controlling and deciding the phenotypic state of a cell. Several cells and various tissues coordinate together to generate an organ level response which further regulates the ultimate physiological state. The overall network embeds a hierarchical regulatory structure, which when unusually perturbed can lead to undesirable physiological state termed as disease. Here, we treat a disease diagnosis problem analogous to a fault diagnosis problem in engineering systems. Accordingly we review the application of engineering methodologies to address human diseases from systems biological perspective. The review highlights potential networks and modeling approaches used for analyzing human diseases. The application of such analysis is illustrated in the case of cancer and diabetes. We put forth a concept of cell-to-human framework comprising of five modules (data mining, networking, modeling, experimental and validation) for addressing human physiology and diseases based on a paradigm of system level analysis. The review overtly emphasizes on the importance of multi-scale biological networks and subsequent modeling and analysis for drug target identification and designing efficient therapies.     

用全基因组测序评价VNTR分型在泛耐药结核分枝杆菌传播中的应用

近年来,随着技术的进步、测序成本的降低,全基因组测序(whole-genome sequencing,WGS)技术开始应用于结核分枝杆菌传播的研究。本研究采用基于单核苷酸多态性(single nucleotide polymorphism,SNP)的分型方法评价多位点数目可变串联重复序列(variable-number tandem-repeat,VNTR)分型判断泛耐药结核分枝杆菌(extensively drug-resistant Mycobacterium tuberculosis,XDR-TB)传播及成簇特征的准确性。对2003-2009年重庆市肺科医院诊断的55例XDR-TB菌株分别进行9＋3个位点的VNTR分型和WGS分析,分别构建系统进化树,并比较两种方法判断成簇的一致性与差异。VNTR分型方法鉴定出45个基因型,其中39株为单一基因型,16株(29.1%)分别归入6个基因簇。规定菌株间差异不超过12个SNP即为成簇,WGS将20株(36.4%)分为5个簇。两种方法判断成簇的一致性为 63.6%。与WGS相比,VNTR分型的灵敏度为 40.0%,特异度为 77.1%。相比于WGS,VNTR分型特异度较高,但仅凭其结果可能会错误估计XDR-TB的传播性。因此,规定菌株间相差不超过12个SNP即有近期传播关系是否适用于XDR-TB,有待进一步研究。     

胡萝卜与烟草原生质体的低温保存

在较长的时间内,可保持正常生理状态与细胞活性的原生质体的制备及保存技术是进行空间细胞融合实验的前提条件。本研究以0.7ml/L的葡萄糖作渗透压,在6-8℃低温条件下经过72小时保存后,供试原生质体的存活率仍可达81%,并保持了其长壁与分裂的特性。 Abstract:Storage duration and acativity of isolated protoplasts are important problem for experiment on plant cell fusion in space.We have achieved preliminary success using glucose as osmotic reagent,The survival protopasts after 72 hour storage in 0.7mol/L glucose at 6~8℃ reached 81% and maintained a very high activity of division.     

Nonparametric estimation of age-at-onset distributions from censored kin-cohort data

We present a nonparametric estimator of genotype-specific age-at-onsetdistributions from kin-cohort data. Standard error calculationsare derived and the methodology is illustrated through an analysisof the influence of mutations of the Parkin gene on Parkinson'sdisease. Semiparametric efficiency considerations are brieflydiscussed.     

趋化因子CX3CL1与冠心病合并2型糖尿病发病的相关关系

目的:探讨趋化因子CX3CL1与冠心病合并2型糖尿病发病的相关关系。方法:采用病例-对照的研究方法,收集冠心病合并2型糖尿病患者400例,收集对照组400例,利用免疫组化检测冠心病合并2型糖尿病患者颈外动脉旋切术后斑块组织中CX3CL1表达水平,分别检测上述2组不同人群血清中的CX3CL1表达水平,同时采用直接测序方法检测CX3CL1基因rs170364位点基因型及等位基因的分布频率在对照组和冠心病合并2型糖尿病人群的分布差异。结果:冠心病合并2型糖尿病患者颈外动脉斑块组织中CX3CL1表达明显增高,冠心病合并2型糖尿病患者血清中CX3CL1的表达水平明显高于对照人群中CX3CL1的表达。CX3CL1基因rs170364单核苷酸多态位点的三种基因型分布频率(GG型,GT型和TT型)在冠心病合并2型糖尿病患者的分布频率为42.7%,40.0%和17.2%,在对照组分布频率为50.2%,39.6%和10.2%,CX3CL1基因rs170364位点T等位基因是冠心病合并2型糖尿病发病的一个独立危险因素(P0.05)。Logistic回归校正性别、年龄、体重指数、吸烟、高血压、高脂血症等冠心病合并2型糖尿病的易患因素后,CX3CL1基因rs170364 T等位基因仍是冠心病合并2型糖尿病发病的一个独立的危险因素。结论:CX3CL1在冠心病合并2型糖尿病的患者血清和颈外动脉动脉血管组织中表达明显增高,CX3CL1基因rs170364T等位基因可能是冠心病合并2型糖尿病患者发病的独立危险因素。     

黑龙江地区400例乙型肝炎病毒基因分型与耐药突变研究

目的:运用基因芯片技术分析黑龙江地区乙型肝炎病毒(HBV)基因型分布特征及基因耐药变异情况。方法:随机选择2012年11月至2015年11月本医院乙型肝炎患者血清样本400例,应用PCR-反向点杂交的基因芯片技术对样本血清中HBV基因型及常见4类抗病毒药物耐药相关的多个位点进行检测,并进行数据分析。结果:400例样本中基因型分布以C型为主占83.25%(333例),B型7.25%(29例)、D型0.25%(1例)及混合基因型2.75%(11例);耐药突变位点检出188例,总耐药率为45.19%,其中突变位点236T(4.61%)提示阿德福韦酯单项耐药,耐药率为5.82%(10例),与拉米夫定耐药相关的为126例,突变位点以rt204I和(rt180M+rt240V)为主,显著高于其他抗病毒类药物,耐药风险较高。结论:黑龙江地区乙型肝炎基因分型以C为主,B型和其它混合型较少,且更容易对拉米夫定产生耐药。     

Genotypes Analyses of Ten Genes Related to Eating Quality of Twenty-three Fragrant Rice Cultivars by Molecular Marker

Fragrance is a very important quality traits of rice, fragrant rice research has been an important research issue in rice research fields in nowadays. In our study, using the detection method of molecular markers, genotypes of the 10 genes (Wx, SSII 3, SBE3, AGPiso, SSIII 2, AGPlar, PUL, SSI, ISA, SSIV 2) associated rice eating quality were analyzed in the 23 fragrant rice cultivars. The result indicated that the “2845”rice cultivar possesses the best combination of genotypes related to the highest eating quality, and the next best rice cultivars were “Songxiangzaojing”, ”Suhuxiangjing”, “B1”, “Wuyun2645”, “Tongyunjing”, “Yinxiang28”, “Xiangjing49②”, “99983”, “Wxiang99075”, “07-08”, “Yunjingyou15”, “29185”, “Nanhai318”. Other 9 rice cultivars (“Dahuaxiangjing”, “Wuxiang14”, “Xiangjing”, “Della”, “Dalixiang”, “Taiguoxiangdao”, “Cxiang517”, “Xiangdao No1”, “Zhongxiang No1”) obtain some of bad genotypes which may have adverse effect on rice eating quality. This study was helpful to establish an overall understanding of the genotypes of these ten eating quality related genes in the 23 tested fragrant rice cultivars, and provides the important genotype information in selecting and cultivating new fragrant rice with good eating quality in future via molecular markers assisted selection method.     

建鲤ODC1基因型与增重的相关性分析

构建了建鲤（Cyprinus carpio var. jian）鸟氨酸脱羧酶（Ornithine decarboxylase,ODC）jlODC1a基因上6个和jlODC1b基因上4个SNP位点的PCR-RFLP方法,检测了这10个位点在12个家系约900尾建鲤选育群体中的基因型,各位点的基因型频率存在差异,最小等位基因频率（MAF）为0.140.48。各位点不同基因型与增重相关分析结果,其中7个SNPs与建鲤增重显性相关的位点,ODC1s基因上与雌鱼增重相关的SNP位点（7个）较雄鱼（4个）多。标记富集结果表明富集与建鲤增重相关的优势基因型的SNP个数越多的个体增重速度越快SNP个数越多的个体增重速度越快,富集4个的平均增重显著快于富集03的个体增重,且比0标记的快约14%,这反映出生长为数量性状。进一步对所检测位点进行双倍型分析,结果显示具有四个优势基因型且全部杂合优势基因型的4567（XXXXXXACCTCTCT）组的增重最快,比0优势基因型的增重快达26.6%,可以考虑用于今后的快增长建鲤的选育计划中。此外,双倍型分析结果还表明,不同位点之间可能存在或颉抗或协同的互作,如1和4之间存在拮抗关系,因此在今后的选育计划中,在考虑标记富集的情况下还应考虑标记之间的关系。宜在选择互为协同作用优势基因型的前提下,富集尽可能多的SNP标记。