中医寒体与热体特征性基因筛选的研究

目的:用基因芯片技术筛选出寒体与热体的特征性基因,进一步研究寒体与热体的产生机制。方法:通过测量大鼠两后脚掌掌心温度,将其分为寒体组、热体组和常体组,分别取各组大鼠的肝脏和下丘脑组织,抽提总RNA来进行逆转录,标记后与大鼠全基因组芯片杂交,分析3组基因表达谱的差异情况。结果:筛选出寒体组和热体组表达差异基因31条,其中表达上调的基因26条,表达下调的基因5条,其中特征性基因2条。结论:寒体和热体在基因水平上存在显著差异,并存在特征性基因,故为临床上通过药物或食物调节特异性基因来改善体质提供了实验依据。

试论中药材特征性基因研究

本文就研究中药材的特征性基因，建立我国特有的“中药材特征性基因”库，以及在保护中药材种质资源，实现中药现代化质量控制等问题进行了论述，并提出评价道地药材，利用基因工程技术进行活性成份的大规模生产，对于扩大中药新资源方面均有重要意义。

3种保虫宿主日本血吸虫特征性差异表达基因的筛选与验证

目的筛选日本血吸虫3种重要保虫宿主来源虫体的特征性差异表达基因,寻找可以用于鉴别这3种宿主来源虫体的遗传标记。方法日本血吸虫尾蚴人工感染黄牛、水牛和山羊,收集感染后49 d成虫,分别抽提RNA,逆转录成cD NA,体外转录为cRNA并进行片段化;采用定制的血吸虫芯片分别进行杂交,筛选每种宿主来源虫体的特征性差异表达基因。采用实时定量PCR法对所筛选差异表达基因的表达水平做进一步测定,验证芯片数据的结果,并对这些特征性差异表达基因进行验证。结果通过芯片杂交,分析筛选获得实验黄牛组来源虫体特征性差异表达基因3个,水牛组来源虫体4个,山羊组来源虫体7个。其中黄牛组2个、水牛组3个、山羊组5个特征性差异表达基因在另一批次3种宿主来源虫体的重复试验中得到验证。结论芯片杂交筛选出10个3种宿主来源虫体的特征性差异表达基因,这些基因可能可以作为这3种不同宿主来源虫体的遗传标记。

Cloning, Characterization and Chromosome Localization of Two Powdery Mildew Resistance-Related Gene Sequences from Wheat

Reverse_transcription Polymerase Chain Reaction (RT_PCR) was performed using cDNAs as templates from wheat_ Haynaldia villosa 6VS/6AL translocation line and 'Yangmai 5' induced with fungus Erysiphe graminis , and degenerate primers designed based on the conserved amino acid sequences of known plant disease_resistance genes. The cDNA sequences encoding cyclophilin_like and H +_ATPase_like genes were first isolated and characterized in wheat. The putative amino acid sequences of the two clones showed that they were highly homologous to those of cyclophilin proteins and H +_ATPases isolated from other plants. Thus they were designated as Ta_Cyp and Ta_MAH . The obvious expression differences could be observed between wheat_ H. villosa 6VS/6AL translocation line and susceptible wheat cultivar 'Yangmai 5', implying that the two genes may be related with the resistance of wheat_ H. villosa 6VS/6AL translocation line to disease. Southern blot indicated that the wheat genome contained 2-3 copies of Ta_Cyp gene and one copy of the Ta_MAH gene. Chinese Spring nulli_tetrasomic line analysis located the Ta_Cyp homologous genes on wheat chromosome 6A, 6B and 6D. Southern blot using Ta_Cyp clone as a probe showed that the polymorphic bands existed among the H. villosa , amphiploid of Triticum durum _ H. villosa , wheat_ H. villosa 6VS/6AL translocation line and 'Yangmai 5', suggesting that Ta_Cyp homologies exist in wheat genome as well as on the short arm of chromosome 6V in H. villosa .

Study on the sex-related AFLP marker of the Yangtze finless porpoise

The sex-related molecular marker of the Yangtze finless porpoise was screened using Amplified Fragment Length Polymorphism (AFLP) technique combined with the bulked segregant analysis. Totally 36 AFLP primer combinations were used to detect the genome DNA bulks of the female and male porpoises, and one sex-related AFLP marker was finally obtained. The marker can be applied to sex identification, and provides a base for further cloning of sex-related genes and analyzing of Y chromosome haplotypes of the Yangtze finless porpoise.

Rapeseed Breeding for Quality Character in Hunan Province

Eight single-low or double-low rapeseed cultivars were bred from 1980 to 2000 in Hunan Province. In this paper, characters and breeding method of these cultivars are introduced.

Invasion and spreading of Cabomba caroliniana revealed by RAPD markers

Applying randomly amplified polymorphic DNA (RAPD), the genetic variation of Cabomba caro- liniana Gray (cabomba or fanwort), a new alien plant in China, was analyzed in this paper. Total 143 bands, in- cluding 47 polymorphic bands, were amplified from 23 primers in 20 samples. The sampling distance was large, but its genetic diversity was low. The main results were that: (1) Cabomba, which grew and dispersed mainly in fragment, was an abundant and dominant species in freshwater, and its main dispersal mechanism was vegetative reproduction. (2) Cabomba was originally introduced into China as an aquarium submerged plant. Somehow, those discarded cabomba became invasive species in the areas of Hangzhou, Shanghai, and Meicheng, and other places. (3) Although the level of genetic diversity in cabomba was low, their rapid dispersion and propagation could seriously harm to local aquatic community. Therefore, specific measure should be used to control cabomba from uncontrolled spreading and damage to local vegetation communities.

Molecular characterization of cyanobacterial diversity in Lake Gregory, Sri Lanka

Eutrophication or the process of nutrient enrichment of stagnant waters due to excessive use of fertilizer is becoming a critical issue worldwide. Lake Gregory, an artificial lake situated in Nuwara Eliya, Sri Lanka was once a very attractive landscape feature and recreational area attracting a large number of visitors. Rapid urbanization in surrounding areas and the consequent intensification of agricultural and industrial activities led to eutrophication and siltation in the lake. Present study was conducted to detect cyanobacterial diversity and their ability to produce hepatotoxic microcystins using polymerase chain reaction (PCR)-based techniques. Twenty five water samples (surface and bottom) were collected from the lake and total nitrogen and total carbon were estimated. Cyanobacterial cultures were grown in appropriate media and microscopic observations were used to determine the morphological diversity of cyanobacteria isolated from different sites. Genomic DNA was isolated and purified from cyanobacteria using Boom's method. DNA samples were analyzed by PCR with oligonucleotide primers for 16S rRNA gene and mcyA gene of the operon that encodes a microcystin synthetase. The 16S rRNA gene sequences revealed the presences of cyanobacteria belong to Synechococcus sp., Microcystis aeruginosa, Calothrix sp., Leptolyngbya sp., Limnothrix sp., order Oscillatoriales and order Chroococcales. The sequences obtained from this study were deposited in the database under the accession numbers (GenBank: GU368104-GU368116). PCR amplification of mcyA primers indicated the potential for toxin formation of isolated M. aeruginosa from Lake Gregory. This preliminary study shows that the Lake Gregory is under the potential risk of cyanobacterial toxicity. Clearly more work is needed to extend this finding and clarify if other cyanobacterial isolates have genetic potential to produce microcystin since this lake is utilized for recreational activities.

Characterization of a Chinese KCNQ1 mutation （R259H） that shortens repolarization and causes short QT syndrome 2

Objectives To evaluate the association between a KCNQ 1 mutation, R259H, and short QT syndrome （SQTS） and to explore the elec- trophysiological mechanisms underlying their association. Methods We performed genetic screening of SQTS genes in 25 probands and their family members （63 patients）. We used direct sequencing to screen the exons and intron-exon boundaries of candidate genes that en- code ion channels which contribute to the repolarization of the ventricular action potential, including KCNQI, KCNH2, KCNE1, KCNE2, KCNJ2, CACNAlc, CACNB2b and CACNA2D1. In one of the 25 SQTS probands screened, we discovered a KCNQ1 mutation, R259H. We cloned R259H and transiently expressed it in HEK-293 cells; then, currents were recorded using whole cell patch clamp techniques. Results R259H-KCNQ 1 showed significantly increased current density, which was approximately 3-fold larger than that of wild type （WT） after a depolarizing pulse at 1 s. The steady state voltage dependence of the activation and inactivation did not show significant differences between the WT and R259H mutation （P 〉 0.05）, whereas the time constant of deactivation was markedly prolonged in the mutant compared with the WT in terms of the test potentials, which indicated that the deactivation of R259H was markedly slower than that of the WT. These results suggested that the R259H mutation can effectively increase the slowly activated delayed rectifier potassium current （Irs） in phase 3 of the cardiac action potential, which may be an infrequent cause of QT interval shortening. Conclusions R259H is a gain-of-function muta- tion of the KCNQ1 channel that is responsible for SQTS2. This is the first time that the R259H mutation was detected in Chinese people.

Endotoxin receptor CD14 gene variants and histological features in chronic HCV infection

AIM:To analyze the correlation between CD14 rs2569190/C-159T single nucleotide polymorphism (SNP) and disease progression in chronic hepatitis C.METHODS: Liver biopsy specimens from a total of 137 and 349 patients with chronic hepatitis C were separately evaluated with respect to necroinflammatory activity (grading) and architectural changes (staging). In one group, further histological lesions characteristic for hepatitis C, hepatitis C virus subtypes, and biochemical parameters of liver disease were also investigated. Samples of genomic DNA were genotyped for the respective SNP by 5'-nuclease assays using fluorescent dye-labeled allele-specif ic probes.RESULTS: Genotype distribution did not deviate from the Hardy-Weinberg equilibrium. In the first group, patients homozygous for the variant allele T were found to be younger than C allele carriers (39.6±12.5 vs 45.7±11.5, P=0.008). Among the histological lesions studied, portal lymphoid aggregates were more frequently observed among TT homozygotes than among C carriers (21/37 vs 32/100, P=0.008). The presence of portal lymphoid aggregates was closely correlated with hepatic inflammation (P=0.003) and with bile duct damage (P<0.001). The degree of fibrosis, in contrast, was not found to be related to the CD14 gene C-159T polymorphism.CONCLUSION: The data suggest a possible relationship between CD14 C-159T polymorphism and the formation of portal lymphoid aggregates, but not liver fibrosis progression in chronic hepatitis C.

中医寒体与热体基因差异性表达的RT-PCR分析

目的:用基因芯片技术筛选出寒体与热体的特征性基因,并对基因差异性表达进行RT-PCR分析。方法:通过测量大鼠两后脚掌掌心温度,将其分为寒体组、热体组和常体组,取各组大鼠的肝脏组织,抽提总RNA来进行逆转录,标记后与大鼠全基因组芯片杂交,分析3组基因表达谱的差异情况,并用RT-PCR技术对其中部分表达差异基因的表达水平变化进行验证。结果:基因Atp6n l、Ins2、AChE、Txnrd1在热体组和寒体组中的表达存在差异,且具有统计学意义(P<0.05)。结论:寒体和热体在基因水平和基因表达水平上存在显著差异,可为临床通过药物或食物调节特异性基因表达水平来改善体质提供了前提条件。

Performance Analysis of Parallel Eigensolvers of Two Libraries on BlueGene/P

Many applications in computational science and engineering require the computation of eigenvalues and vectors of dense symmetric or Hermitian matrices. For example, in DFT （density functional theory） calculations on modern supercomputers 10% to 30% of the eigenvalues and eigenvectors of huge dense matrices have to be calculated. Therefore, performance and parallel scaling of the used eigensolvers is of upmost interest. In this article different routines of the linear algebra packages ScaLAPACK and Elemental for parallel solution of the symmetric eigenvalue problem are compared concerning their performance on the BlueGene/P supercomputer. Parameters for performance optimization are adjusted for the different data distribution methods used in the two libraries. It is found that for all test cases the new library Elemental which uses a two-dimensional element by element distribution of the matrices to the processors shows better performance than the old ScaLAPACK library which uses a block-cyclic distribution.

Predicting potential cancer genes by integrating network properties,sequence features and functional annotations

The discovery of novel cancer genes is one of the main goals in cancer research.Bioinformatics methods can be used to accelerate cancer gene discovery,which may help in the understanding of cancer and the development of drug targets.In this paper,we describe a classifier to predict potential cancer genes that we have developed by integrating multiple biological evidence,including protein-protein interaction network properties,and sequence and functional features.We detected 55 features that were significantly different between cancer genes and non-cancer genes.Fourteen cancer-associated features were chosen to train the classifier.Four machine learning methods,logistic regression,support vector machines(SVMs),BayesNet and decision tree,were explored in the classifier models to distinguish cancer genes from non-cancer genes.The prediction power of the different models was evaluated by 5-fold cross-validation.The area under the receiver operating characteristic curve for logistic regression,SVM,Baysnet and J48 tree models was 0.834,0.740,0.800 and 0.782,respectively.Finally,the logistic regression classifier with multiple biological features was applied to the genes in the Entrez database,and 1976 cancer gene candidates were identified.We found that the integrated prediction model performed much better than the models based on the individual biological evidence,and the network and functional features had stronger powers than the sequence features in predicting cancer genes.

Sex differences in the expression of GH/IGF axis genes underlie sexual size dimorphism in the yellow catfish(Pelteobagrus fulvidraco)

Dear Editors,Sexual dimorphism is the systematic difference in size,shape,color,physiology,and behavior,between male and female individuals of the same species（Mei and Gui,2015）.Some studies have indicated that the traits of sexual dimorphism in vertebrates are the consequences of sex-biased gene expression and are controlled by multiple critical genes during growth and development（Williams and Carroll,2009）.However,the exact molecular mechanism underlying sexual dimorphism remains unclear.