极大节旋藻(Arthrospira maxima)生物钟基因kaiC的克隆及分析

以kaiC基因簇部分已知序列为引物设计位点,采用PCR反应池法从节旋藻基因组fosmid文库中筛选到kaiC基因克隆,通过步移测序获得了kaiC基因全长序列。kaiC基因编码区长1554bo,基因GC碱基含量平均为41．76％,密码子第三位明显偏向于U。在基因上游385bp范围内发现一个可能的启动子序列和一些基因调控元件。KaiC蛋白分析发现了Walker A、DXXG、不完整的Walker B等重要模体和具有催化作用的功能位点。Southem杂交的结果证明kaiC基因在极大节旋藻中为单拷贝。极大节旋藻kaiC基因的特殊结构特征为研究kai基因簇的进化提供了重要的启示。     

Consideration of the BDNF gene in relation to two phenotypes: Hoarding and obesity.

The gene coding for the brain derived neurotrophic factor (BDNF) has emerged as an interesting candidate for multiple brain and brain disorder-related phenomena. The primary aim of the present investigation was to consider the relationship between the BDNF Val66Met variant and two phenotypes: compulsive hoarding as a symptom dimension of obsessive–compulsive disorder (OCD), and body mass index (BMI). We examined the BDNF gene in a large (N = 301) clinical sample of probands with OCD. Participants were classified as hoarding or nonhoarding using a strict, multimeasure grouping approach. Results revealed that the Val/Val genotype was linked with hoarding classification and more severe hoarding behaviors, as well as greater BMI levels. Hoarding status was also associated with greater BMI scores, with individuals in the hoarding group being far more likely to be classified as obese compared with the nonhoarding group. Our findings may provide a distinct avenue through which hoarding and BMI could be linked. These findings are suggestive of a complex gene, body weight, and psychopathology relationship wherein a primitive, survival “thrifty gene” strategy may be conserved and represented in a subgroup of humans manifesting severe hoarding symptoms. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

蛋白质功能预测方法研究进展

蛋白质功能预测是后基因组时代生物信息学的研究热点之一。利用计算方法预测蛋白质的功能,可以弥补传统生物实验方法周期长、效率低和成本高等方面不足。首先介绍蛋白质功能预测的研究背景,并从计算角度定义蛋白质功能预测问题;然后,对蛋白质功能预测方法的研究现状进行分析与总结,最后指出已有方法中存在的不足及未来的研究方向。     

The polymerase chain reaction: Applications for the detection of foodborne pathogens

Faster methods for the detection of foodborne microbial pathogens are needed. The polymerase chain reaction (PCR) can amplify specific segments of DNA and is used to detect and identify bacterial genes responsible for causing diseases in humans. The major features and requirements for the PCR are described along with a number of important variations. A considerable number of PCR‐based assays have been developed, but they have been applied most often to clinical and environmental samples and more rarely for the detection of foodborne microorganisms. Much of the difficulty in implementing PCR for the analysis of food samples lies in the problems encountered during the preparation of template DNAs from food matrices; a variety of approaches and considerations are examined. PCR methods developed for the detection and identification of particular bacteria, viruses, and parasites found in foods are described and discussed, and the major features of these reactions are summarized.     

基于遗传算法的基因微阵列数据聚类

微阵列基因数据用以挖掘特定的生物信息,聚类分析对于研究基因功能和基因调控机制有重要意义.结合改进的遗传算法对基因微阵列数据进行聚类分析,并且通过实验与K均值聚类进行比较.仿真实验表明,该算法可以有效改进基因微阵列数据的聚类准确率.     

Newly identified mutations at the CSN1S1 gene in Ethiopian goats affect casein content and coagulation properties of their milk

Very high casein content and good coagulation properties previously observed in some Ethiopian goat breeds led to investigating the α_s1-casein (CSN1S1) gene in these breeds. Selected regions of the CSN1S1 gene were sequenced in 115 goats from 5 breeds (2 indigenous: Arsi-Bale and Somali, 1 exotic: Boer, and 2 crossbreeds: Boer × Arsi-Bale and Boer × Somali). The DNA analysis resulted in 35 new mutations: 3 in exons, 3 in the 5′ untranslated region (UTR), and 29 in the introns. The mutations in exons that resulted in an amino acid shift were then picked to evaluate their influence on individual casein content (α_s1-, α_s2-, β-, and κ-CN), micellar size, and coagulation properties in the milk from the 5 goat breeds. A mutation at nucleotide 10657 (exon 10) involved a transversion: CAG→CCG, resulting in an amino acid exchange Gln₇₇→Pro_77. This mutation was associated with the indigenous breeds only. Two new mutations, at nucleotide 6072 (exon 4) and 12165 (exon 12), revealed synonymous transitions: GTC→GTT in Val₁₅ and AGA→AGG in Arg₁₀₀ of the mature protein. Transitions G→A and C→T at nucleotides 1374 and 1866, respectively, occurred in the 5′ UTR, whereas the third mutation involved a transversion T→G at nucleotide location 1592. The goats were grouped into homozygote new (CC), homozygote reference (AA), and heterozygote (CA) based on the nucleotide that involved the transversion. The content of α_s1-CN (15.32 g/kg) in milk samples of goats homozygous (CC) for this newly identified mutation, Gln₇₇→Pro₇₇ was significantly higher than in milks of heterozygous (CA; 9.05 g/kg) and reference (AA; 7.61 g/kg) genotype animals. The α_s2-, β-, and κ-CN contents showed a similar pattern. Milk from goats with a homozygous new mutation had significantly lower micellar size. Milk from both homozygote and heterozygote new-mutation goats had significantly shorter coagulation rate and stronger gel than the reference genotype. Except the transversion, the sequence corresponded to allele A and presumably derived from it. Therefore, this allele is denoted by A₃. All goats from the reference genotype (AA) were homozygous for the allele at nucleotide position 1374 and 1866, whereas all mutations in the 5′ UTR existed in a heterozygous form in both heterozygous (CA) and the new mutation (CC) genotype. The newly identified mutation (CC) detected in some of the goat breeds is, therefore, important in selection for genetic improvement and high-quality milk for the emerging goat cheese-producing industries. The finding will also benefit farmers raising these goat breeds due to the increased selling price of goats. Further studies should investigate the effect of this amino acid exchange on the secondary and tertiary structure of the α_s1-CN molecule and on the susceptibility of peptide hydrolysis by digestive enzymes.     

Genomic analyses and biological validation of candidate genes for rectal temperature as an indicator of heat stress in Holstein cattle

Heat stress is a major cause of welfare issues and economic losses to the worldwide dairy cattle industry. Genetic selection for heat tolerance has a great potential to positively affect the dairy industry, as the gains are permanent and cumulative over generations. Rectal temperature (RT) is hypothesized to be a good indicator trait of heat tolerance. Therefore, this study investigated the genetic architecture of RT by estimating genetic parameters, performing genome-wide association studies, and biologically validating potential candidate genes identified to be related to RT in Holstein cattle. A total of 33,013 RT records from 7,598 cows were used in this study. In addition, 1,114 cows were genotyped using the Illumina 150K Bovine BeadChip (Illumina, San Diego, CA). Rectal temperature measurements taken in the morning (AMRT) and in the afternoon (PMRT) are moderately heritable traits, with estimates of 0.09 ± 0.02 and 0.04 ± 0.01, respectively. These 2 traits are also highly genetically correlated (r = 0.90 ± 0.08). A total of 10 SNPs (located on BTA3, BTA4, BTA8, BTA13, BTA14, and BTA29) were found to be significantly associated with AMRT and PMRT. Subsequently, gene expression analyses were performed to validate the key functional genes identified (SPAG17, FAM107B, TSNARE1, RALYL, and PHRF1). This was done through in vitro exposure of peripheral blood mononuclear cells (PBMC) to different temperatures (37°C, 39°C, and 42°C). The relative mRNA expression of 2 genes, FAM107B and PHRF1, significantly changed between the control and heat stressed PBMC. In summary, RT is heritable, and enough genetic variability exists to enable genetic improvement of heat tolerance in Holstein cattle. Important genomic regions were identified and biologically validated; FAM107B and PHRF1 are the main candidate genes identified to influence heat stress response in dairy cattle.     

Analysis of a change in bacterial community in different environments with addition of chitin or chitosan

The temporal changes of a bacterial community in soil with chitin or chitosan added were analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) targeting the 16S rRNA gene using total DNAs prepared from the community. Band patterns of PCR-DGGE confirmed that 31 species become predominant after the addition of chitin or chitosan. The determination of the nucleotide sequences of the bands of the 31 species indicated that 20 species belonged to the division Proteobacteria, and that the genus Cellvibrio was apparently predominant among them (7/20). The 16S rRNA sequences of the 16 deduced species (16/31) showed less than 98% similarities to those of previously identified bacteria, indicating that the species were derived from unidentified bacteria. The total community DNAs extracted from bacterial cells adsorbed on the surface of flakes of chitin and chitosan placed in a river, a moat, or soil were subjected to PCR-DGGE to examine the extent of diversity of chitinolytic bacteria among different environments. The predominant species significantly differed between the chitin and chitosan placed in the river and moat, but not so much between those placed in the soil. The large difference between the diversities of the three bacterial communities indicated that a wide variety of bacteria including unidentified ones are involved in the degradation of chitin and chitosan in the above-mentioned natural environments.     

Two-stage Nested PCR Effectiveness for Direct Detection of Vibrio vulnificus in Natural Samples

The nested primers designed to amplify a 222-base pair portion of the hemolysin gene, vvhA, were specific for all V. vulnificus strains tested. The nested PCR amplification, coupled with direct extraction of template DNA, revealed improved sensitivity sufficient for detection of 1 to 10 CFU V. vulnificus in 1 mL of seafood homogenates, and eliminated the need for enrichment culturing. Thereby, the nested PCR method achieved a broader applicability, making it effective for extensive use in identification of the pathogen in natural samples such as raw seafoods, seawater and sediments.