Resource brief: The National Non-Human Primate DNA Bank

A National Non-Human Primate (NHP) DNA bank has been established by the National Primate Research Centers and the National Center for Research Resources, NIH, providing a new resource for comparative genomic studies. The collection includes genomic DNA samples from macaques, chimpanzees, baboons, vervets, marmosets, sooty mangabeys and titi monkeys. The repository includes DNAs from 697 unrelated animals, suitable for comparing allele representation within and between species. Another 474 DNAs are derived from family-trios (dam, sire, off spring), and are useful for verifying the segregation of genetic variants. The National NHP DNA Bank includes specified holdings within each of the eight National Primate Research Centers, though detailed information on the entire collection is available through a common website.     

Large-scale profiling of microRNAs for The Cancer Genome Atlas

The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ∼11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute Genomics Cloud Pilots, such data resources will make intensive analysis of large-scale cancer genomics data widely accessible. To support such initiatives, and to enable comparison of TCGA microRNA data to data from other projects, we describe the process that we developed and used to generate the microRNA sequence data, from library construction through to submission of data to repositories. In the context of this process, we describe the computational pipeline that we used to characterize microRNA expression across large patient cohorts.     

Comparative Mouse Genomics Centers Consortium: the Mouse Genotype Database

The Comparative Mouse Genomics Centers Consortium (CMGCC) is a branch of the Environmental Genome Project sponsored by the National Institute of Environmental Health Sciences (NIEHS) focusing upon the identification of human single nucleotide polymorphisms (SNPs) that may confer disease susceptibility within the human population. The goal of the CMGCC (http://www.niehs.nih.gov/cmgcc/) is to make genetic mouse models for human SNPs within cell cycle control, DNA replication and DNA repair genes that may be associated with human pathologies. In order to facilitate information sharing and analysis within the consortium a set of informatics resources have been generated to support the mouse model development efforts. The primary entry point for information about the mouse models developed by the consortium is through the CMGCC Genotype Database (http://mrages.niehs.nih.gov/genotype/), which maintains both a consortium specific and public access display of the available and developing mouse models.     

IAEA/NUS Distance Learning Diploma Training Course for Tissue Bank Operators – Past, Present and Future

National University Hospital (NUH) Tissue Bank as the Regional Training Centre for Asia Pacific Region provided National University of Singapore (NUS) Diploma Course in Tissue Banking - a long distance diploma course since 1997. To date, five batches have participated - 94 tissue bank operators. Sixty-three tissue bank operators have convocated with NUS Diploma in Tissue Banking.From Regional Co-operative Agreement (RCA) Project, RAS 7/008 technology transfer was effected to Latin America and to Africa.A Memorandum of Understanding has been signed between International Atomic Energy Agency (IAEA) and NUS in July 2002 making Singapore the International Training Centre. An Internet NUS Diploma Course in Tissue Banking has been developed by IAEA and NUS. The first on-line diploma course will be launched in 2003.     

DNA 测序技术领域的相关政府投入分析

DNA测序技术是遗传工程的核心技术之一,发展快速和低成本的基因测序技术成为研究焦点。美国、欧盟等发达国家和地区大力支持DNA测序技术的创新研究,并投入了大量的科研经费。在美国,国家卫生研究院(NIH)下属的国家人类基因组研究院(NHGRI)、美国能源部(DOE)以及美国科学基金委(NSF)等机构是进行DNA测序技术相关项目经费分配的主要政府部门。DNA测序作为生命科学研究的关键技术也是欧盟框架计划资助的重要内容之一,其以多个欧洲国家间合作以及产学研合作的形式开展。中国在DNA测序技术领域也开展了一些研究。     

生命与健康大数据中心资源

生命与健康多组学数据是生命科学研究和生物医学技术发展的重要基础。然而,我国缺乏生物数据管理和共享平台,不但无法满足国内日益增长的生物医学及相关学科领域的研究发展需求,而且严重制约我国生物大数据整合共享与转化利用。鉴于此,中国科学院北京基因组研究所于2016年初成立生命与健康大数据中心(BIG Data Center, BIGD),围绕国家人口健康和重要战略生物资源,建立生物大数据管理平台和多组学数据资源体系。本文重点介绍BIGD的生命与健康大数据资源系统,主要包括组学原始数据归档库、基因组数据库、基因组变异数据库、基因表达数据库、甲基化数据库、生物信息工具库和生命科学维基知识库,提供生物大数据汇交、整合与共享服务,为促进我国生命科学数据管理、推动国家生物信息中心建设奠定重要基础。     

A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni

To provide a novel resource for analysis of the genome of Biomphalaria glabrata, members of the international Biomphalaria glabrata Genome Initiative (http://biology.unm.edu/biomphalaria-genome.html), working with the Arizona Genomics Institute (AGI) and supported by the National Human Genome Research Institute (NHGRI), produced a high quality bacterial artificial chromosome (BAC) library. The BB02 strain B. glabrata, a field isolate (Belo Horizonte, Minas Gerais, Brasil) that is susceptible to several strains of Schistosoma mansoni, was selfed for two generations to reduce haplotype diversity in the offspring. High molecular weight DNA was isolated from ovotestes of 40 snails, partially digested with HindIII, and ligated into pAGIBAC1 vector. The resulting B. glabrata BAC library (BG_BBa) consists of 61824 clones (136.3 kb average insert size) and provides 9.05 x coverage of the 931 Mb genome. Probing with single/low copy number genes from B. glabrata and fingerprinting of selected BAC clones indicated that the BAC library sufficiently represents the gene complement. BAC end sequence data (514 reads, 299860 nt) indicated that the genome of B. glabrata contains ~ 63% AT, and disclosed several novel genes, transposable elements, and groups of high frequency sequence elements. This BG_BBa BAC library, available from AGI at cost to the research community, gains in relevance because BB02 strain B. glabrata is targeted whole genome sequencing by NHGRI.     

The Rare Disease Bank of Japan: establishment,current status and future challenges

Research on rare diseases cannot be performed without appropriate samples from patients with such diseases. Due to the limited number of such patients, securing biosamples of sufficient quality for extensive research is a challenge and represents an important barrier to the advancement of research on rare diseases. To tackle this problem, the Rare Disease Bank (RDB) was established in 2009 at the National Institute of Biomedical Innovation (NIBIO; currently, the National Institutes of Biomedical Innovation, Health and Nutrition in Japan). Since then, the RDB has focused on three objectives: (1) emphasizing the importance of collecting biosamples from patients with rare diseases, together with appropriate clinical information, from various medical facilities nationwide; (2) maintaining strict high-quality sample management standards; and (3) sharing biosamples with research scientists across Japan for the advancement of research on rare diseases. As of August 2017, the bank has collected 4147 biosamples from patients with rare diseases, including DNA, serum, plasma, and cell samples from various university hospitals and other medical institutions across the country, and provided various research institutions with 13,686 biosample aliquots from 2850 cases. In addition, the management committee has successfully established a bank system that provides high-quality biosamples together with the results of human leukocyte antigen analysis. It is anticipated that the RDB, through the collection and sharing of biosamples with the medical research community, will enhance the understanding, prevention, and treatment of rare diseases in Japan and the world at large.     

Native supercoiling of DNA: The effects of DNA gyrase and ω protein in E. coli

Molecular Genetics and Genomics - This study deals with the effects of a temperature-sensitive (ts) mutation at the gene encoding the DNA gyrase B subunit (gyrB ts) and a deletion of the top gene...     

Endonuclease α from Saccharomyces cerevisiae shows increased activity on ultraviolet irradiated native DNA

Molecular Genetics and Genomics - Endonuclease α isolated from the nucleus of the yeast Saccharomyces cerevisiae is a DNA endonuclease which has been shown to act preferentially on denatured...     

Construction of a fused operon consisting of the recA and kan (Kanamycin resistance) genes and regulation of its expression by the lexA gene

Molecular Genetics and Genomics - The kanamycin resistance gene (kan) of transposon Tn5 was cloned into a derivative of plasmid pBR322. A DNA fragment containing the promoter-operator region of the...     

MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms

MonkeySNP is a web-based resource created by the Genetic Resource and Informatics Program at the Oregon National Primate Research Center to facilitate access to non-human primate (NHP) single nucleotide polymorphisms (SNP) data. MonkeySNP is a mirror of the NCBI dbSNP database and contains additional NHP subpopulation genotype data and visual genotype displays to support SNP review and selection. AVAILABILITY: http://monkeysnp.ohsu.edu/snp/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Weigle reactivation of diploid M13 phage

Molecular Genetics and Genomics - The limited ability of ultraviolet (UV)-irradiated E. coli cells to W-reactivate UV-irradiated, single-stranded DNA phages fd and M13 was investigated. The...     

Oral Session Abstracts

For more than two decades Genomics has grown as a discipline separately from Genetics. During this period the HGP was completed, other species were analyzed and the technology dramatically incremented. Methods for nucleic acids analysis now include the NexGen sequencing technologies for analysis of whole genomes and new DNA capture methods that allow sequencing of every human exon in a single sample. As a consequence, we are beginning to accrue the raw sequence of the whole genomes of multiple individuals and cell types. These methods are also being directed at finding specific disease alleles, and to characterize the full spectrum of variation in human populations as well as to study cancer. In combination these technologies provide unprecedented opportunity to study fundamental questions in biology. At long last the two disciplines of Genetics and Genomics are coming back together.     

Vitamin B12 transport inEscherichia coli K12 does not require thebtuE gene of thebtuCED operon

Molecular Genetics and Genomics - Transport of vitamin B12 across the cytoplamic membrane ofEscherichia coli requires the products ofbtuC andbtuD, two genes in thebtuCED operon. The role ofbtuE,...     

Diploma Training for Technologists in Tissue Banking

There is a great demand for a formal training programme for tissue bank technologists not only for the Asia Pacific Region but also for technologists in other regions including Latin America and Africa. To meet this need, National University Hospital (NUH) Tissue Bank was established as the International Atomic Energy Agency (IAEA)/National University of Singapore (NUS) Regional Training Centre for training tissue bank operators in the Asia Pacific Region (Regional co-operative Agreement, RCA) in November 1997. The training centre conducts a one-year distance learning Diploma in Tissue Banking offered by the NUS. The syllabus for the Diploma Course included the multi-media IAEA curriculum on tissue banking. The first Diploma Course has been successfully completed in October 1998. Twelve students convocated, 4 with Distinction, 5 with Credit and 3 with Pass. Sixteen candidates from the Asia Pacific Region registered for the Second Diploma Course in April 1999. This second batch will be due to sit for their Diploma Examination in April 2000. With the increasing popularity of this Diploma Course, the third batch of students which will be registered in April 2000, will include technologists not only from Asia Pacific Region but also from other regions including Africa.     

Nutritional composition of the diet of the western gorilla (Gorilla gorilla): Interspecific variation in diet quality

To meet nutritional needs, primates adjust their diets in response to local habitat differences, though whether these dietary modifications translate to changes in dietary nutrient intake is unknown. A previous study of two populations of the mountain gorilla (MG: Gorilla beringei) found no evidence for intraspecific variation in the nutrient composition of their diets, despite ecological and dietary differences between sites. One potential explanation is that nutritional variability in primate diets requires greater ecological divergence than what was captured between MG sites, underpinning environmental differences in the nutrient quality of plant foods. To test whether Gorilla exhibits interspecific variation in dietary composition and nutrient intake, we studied the composition and macronutrients of the western gorilla (WG: Gorilla gorilla) staple diets and compared them with published data from the two MG populations. We recorded feeding time and food intake of four adult female WGs from one habituated group over a period of 11 months (December 2004–October 2005) at the Mondika Research Center, Republic of Congo, allowing for assessment of seasonal patterns of nutrient intake. Staple diets of WGs and MGs diverged in their dietary and macronutrient composition. Compared to MGs, the staple diet of WGs (by intake) contained higher proportions of fruit (43%) and leaf (12%) and a lower proportion of herb (39%), resulting in a higher intake of total nonstructural carbohydrate and fiber and a lower intake of crude protein. Staple gorilla fruits and herbs differed in nutrient quality between sites. Gorillas exhibit nutritional flexibility that reflects ecological variation in the nutrient quality of plant foods. Since dietary quality typically affects rates of growth and reproduction in primates, our results suggest that interspecific differences in nutrient intake and food quality may shape differences in gorilla nutrient balancing and female life history strategies.     

Issues concerning ethical conduct and genetic mapping raised at Montreal meeting

Ethical concerns about the Human Genome Diversity Project were discussed in Montreal last year during the 1st International Conference on DNA Sampling and Banking. This article, the second in a 2-part series, looks at the potential for misuse and commercialization of DNA samples and discusses some of the ethical concerns surrounding genetic mapping.     

Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14

The data provided to the Genetic Analysis Workshop 14 (GAW 14) was the result of a collaboration among several different groups, catalyzed by Elizabeth Pugh from The Center for Inherited Disease Research (CIDR) and the organizers of GAW 14, Jean MacCluer and Laura Almasy. The DNA, phenotypic characterization, and microsatellite genomic survey were provided by the Collaborative Study on the Genetics of Alcoholism (COGA), a nine-site national collaboration funded by the National Institute of Alcohol and Alcoholism (NIAAA) and the National Institute of Drug Abuse (NIDA) with the overarching goal of identifying and characterizing genes that affect the susceptibility to develop alcohol dependence and related phenotypes. CIDR, Affymetrix, and Illumina provided single-nucleotide polymorphism genotyping of a large subset of the COGA subjects. This article briefly describes the dataset that was provided.     

Expression and stability of Escherichia coli F-prime factors in Proteus mirabilis

Molecular Genetics and Genomics - The expression and stability of Escherichia coli F-primes in Proteus mirabilis is examined. It is possible to consecutively introduce, and stably maintain, the DNA...