The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group

Computational resources associating diseases with genotypes, phenotypes and exposures

The causes of a disease and its therapies are not only related to genotypes, but also associated with other factors, including phenotypes, environmental exposures, drugs and chemical molecules. Distinguishing disease-related factors from many neutral factors is critical as well as difficult. Over the past two decades, bioinformaticians have developed many computational resources to integrate the omics data and discover associations among these factors. However, researchers and clinicians are experiencing difficulties in choosing appropriate resources from hundreds of relevant databases and software tools. Here, in order to assist the researchers and clinicians, we systematically review the public computational resources of human diseases related to genotypes, phenotypes, environment factors, drugs and chemical exposures. We briefly describe the development history of these computational resources, followed by the details of the relevant databases and software tools. We finally conclude with a discussion of current challenges and future opportunities as well as prospects on this topic.

The role of genetic background in susceptibility to chemical warfare nerve agents across rodent and non-human primate models

Genetics likely play a role in various responses to nerve agent exposure, as genetic background plays an important role in behavioral, neurological, and physiological responses to environmental stimuli. Mouse strains or selected lines can be used to identify susceptibility based on background genetic features to nerve agent exposure. Additional genetic techniques can then be used to identify mechanisms underlying resistance and sensitivity, with the ultimate goal of developing more effective and targeted therapies. Here, we discuss the available literature on strain and selected line differences in cholinesterase activity levels and response to nerve agent-induced toxicity and seizures. We also discuss the available cholinesterase and toxicity literature across different non-human primate species. The available data suggest that robust genetic differences exist in cholinesterase activity, nerve agent-induced toxicity, and chemical-induced seizures. Available cholinesterase data suggest that acetylcholinesterase activity differs across strains, but are limited by the paucity of carboxylesterase data in strains and selected lines. Toxicity and seizures, two outcomes of nerve agent exposure, have not been fully evaluated for genetic differences, and thus further studies are required to understand baseline strain and selected line differences.

Clinical Chemistry Reference Intervals for C57BL/6J, C57BL/6N, and C3HeB/FeJ Mice (Mus musculus)

Although various mouse inbred strains are widely used to investigate disease mechanisms and to establish new therapeutic strategies, sex-specific reference intervals for laboratory diagnostic analytes that are generated from large numbers of animals have been unavailable. In this retrospective study, we screened data from more than 12,000 mice phenotyped in the German Mouse Clinic from January 2006 through June 2014 and selected animals with the genetic background of C57BL/6J, C57BL/6N, or C3HeB/FeJ. In addition, we distinguished between the C57BL/6NTac substrain and C57BL/6N mice received from other vendors. The corresponding data sets of electrolytes (sodium, potassium, calcium, chloride, inorganic phosphate), lipids (cholesterol, triglyceride), and enzyme activities (ALT, AST, ALP, α-amylase) and urea, albumin, and total protein levels were analyzed. Significant effects of age and sex on these analytes were identified, and strain- or substrain- and sex-specific reference intervals for 90- to 135-d-old mice were calculated. In addition, we include an overview of the literature that reports clinical chemistry values for wild-type mice of different strains. Our results support researchers interpreting clinical chemistry values from various mouse mutants and corresponding wild-type controls based on the examined strains and substrains.

Beyond captions: linking figures with abstract sentences in biomedical articles

Although figures in scientific articles have high information content and concisely communicate many key research findings, they are currently under utilized by literature search and retrieval systems. Many systems ignore figures, and those that do not typically only consider caption text. This study describes and evaluates a fully automated approach for associating figures in the body of a biomedical article with sentences in its abstract. We use supervised methods to learn probabilistic language models, hidden Markov models, and conditional random fields for predicting associations between abstract sentences and figures. Three kinds of evidence are used: text in abstract sentences and figures, relative positions of sentences and figures, and the patterns of sentence/figure associations across an article. Each information source is shown to have predictive value, and models that use all kinds of evidence are more accurate than models that do not. Our most accurate method has an -score of 69% on a cross-validation experiment, is competitive with the accuracy of human experts, has significantly better predictive accuracy than state-of-the-art methods and enables users to access figures associated with an abstract sentence with an average of 1.82 fewer mouse clicks. A user evaluation shows that human users find our system beneficial. The system is available at http://FigureItOut.askHERMES.org.

Suggestive linkage to chromosome 1q for bone mineral apparent density in Brazilian sister adolescents

OBJECTIVE

To investigate linkage to chromosome 1q and 11q region for lumbar spine, femoral neck and total body BMD and volumetric BMD in Brazilian sister adolescents aged 10-20-year-old and 57 mothers.

METHODS

We evaluated 161 sister pairs (n=329) aged 10-20 years old and 57 of their mothers in this study. Physical traits and lifestyle factors were collected as covariates for lumbar spine (LS), femoral neck (FN) and total body (TB) BMD and bone mineral apparent density (BMAD). We selected nine microsatellite markers in chromosome 1q region (spanning nearly 33cM) and eight in chromosome 11q region (spanning nearly 34cM) to perform linkage analysis.

RESULTS

The highest LOD score values obtained from our data were in sister pairs LS BMAD analysis. Their values were: 1.32 (P<0.006), 2.61 (P<0.0002) and 2.44 (P<0.0004) in D1S218, D1S2640 and D1S2623 markers, respectively. No significant LOD score was found with LS and FN BMD/BMAD in chromosome 11q region. Only TB BMD showed significant linkage higher than 1.0 for chromosome 11q region in the markers D11S4191 and D11S937.

DISCUSSION/CONCLUSIONS

Our results provided suggestive linkage for LS BMAD at D1S2640 marker in adolescent sister pairs and suggest a possible candidate gene (LHX4) related to adolescent LS BMAD in this region. These results reinforce chromosome 1q21-23 as a candidate region to harbor one or more bone formation/maintenance gene. In the other hand, it did not repeat for chromosome 11q12-13 in our population.

The cytoplasmic domain of MUC1 induces hyperplasia in the mammary gland and correlates with nuclear accumulation of β-catenin

MUC1 is an oncoprotein that is overexpressed in up to 90% of breast carcinomas. A previous in vitro study by our group demonstrated that the cytoplasmic domain of MUC1 (MUC1-CD), the minimal functional unit of MUC1, contributes to the malignant phenotype in cells by binding directly to β-catenin and protecting β-catenin from GSK3β-induced degradation. To understand the in vivo role of MUC1-CD in breast development, we generated a MUC1-CD transgenic mouse model under the control of the MMTV promoter in a C57BL/6J background, which is more resistant to breast tumor. We show that the expression of MUC1-CD in luminal epithelial cells of the mammary gland induced a hyperplasia phenotype characterized by the development of hyper-branching and extensive lobuloalveoli in transgenic mice. In addition to this hyperplasia, there was a marked increase in cellular proliferation in the mouse mammary gland. We further show that MUC1-CD induces nuclear localization of β-catenin, which is associated with a significant increase of β-catenin activity, as shown by the elevated expression of cyclin D1 and c-Myc in MMTV-MUC1-CD mice. Consistent with this finding, we observed that overexpression of MUC1-C is associated with β-catenin nuclear localization in tumor tissues and increased expression of Cyclin D1 and c-Myc in breast carcinoma specimens. Collectively, our data indicate a critical role for MUC1-CD in the development of mammary gland preneoplasia and tumorigenesis, suggesting MUC1-CD as a potential target for the diagnosis and chemoprevention of human breast cancer.

Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception

BACKGROUND

Human immunodeficiency virus type one (HIV-1) is the major pathogen that causes the acquired immune deficiency syndrome (AIDS). With the availability of large-scale protein-protein interaction (PPI) measurements, comparative network analysis can provide a promising way to study the host-virus interactions and their functional significance in the pathogenesis of AIDS. Until now, there have been a large number of HIV studies based on various animal models. In this paper, we present a novel framework for studying the host-HIV interactions through comparative network analysis across different species.

RESULTS

Based on the proposed framework, we test our hypothesis that HIV-1 attacks essential biological pathways that are conserved across species. We selected the Homo sapiens and Mus musculus PPI networks with the largest coverage among the PPI networks that are available from public databases. By using a local network alignment algorithm based on hidden Markov models (HMMs), we first identified the pathways that are conserved in both networks. Next, we analyzed the HIV-1 susceptibility of these pathways, in comparison with random pathways in the human PPI network. Our analysis shows that the conserved pathways have a significantly higher probability of being intercepted by HIV-1. Furthermore, Gene Ontology (GO) enrichment analysis shows that most of the enriched GO terms are related to signal transduction, which has been conjectured to be one of the major mechanisms targeted by HIV-1 for the takeover of the host cell.

CONCLUSIONS

This proof-of-concept study clearly shows that the comparative analysis of PPI networks across different species can provide important insights into the host-HIV interactions and the detailed mechanisms of HIV-1. We expect that comparative multiple network analysis of various species that have different levels of susceptibility to similar lentiviruses may provide a very effective framework for generating novel, and experimentally verifiable hypotheses on the mechanisms of HIV-1. We believe that the proposed framework has the potential to expedite the elucidation of the important mechanisms of HIV-1, and ultimately, the discovery of novel anti-HIV drugs.

An ontology-based comparative anatomy information system

INTRODUCTION

This paper describes the design, implementation, and potential use of a comparative anatomy information system (CAIS) for querying on similarities and differences between homologous anatomical structures across species, the knowledge base it operates upon, the method it uses for determining the answers to the queries, and the user interface it employs to present the results. The relevant informatics contributions of our work include (1) the development and application of the structural difference method, a formalism for symbolically representing anatomical similarities and differences across species; (2) the design of the structure of a mapping between the anatomical models of two different species and its application to information about specific structures in humans, mice, and rats; and (3) the design of the internal syntax and semantics of the query language. These contributions provide the foundation for the development of a working system that allows users to submit queries about the similarities and differences between mouse, rat, and human anatomy; delivers result sets that describe those similarities and differences in symbolic terms; and serves as a prototype for the extension of the knowledge base to any number of species. Additionally, we expanded the domain knowledge by identifying medically relevant structural questions for the human, the mouse, and the rat, and made an initial foray into the validation of the application and its content by means of user questionnaires, software testing, and other feedback.

METHODS

The anatomical structures of the species to be compared, as well as the mappings between species, are modeled on templates from the Foundational Model of Anatomy knowledge base, and compared using graph-matching techniques. A graphical user interface allows users to issue queries that retrieve information concerning similarities and differences between structures in the species being examined. Queries from diverse information sources, including domain experts, peer-reviewed articles, and reference books, have been used to test the system and to illustrate its potential use in comparative anatomy studies.

RESULTS

157 test queries were submitted to the CAIS system, and all of them were correctly answered. The interface was evaluated in terms of clarity and ease of use. This testing determined that the application works well, and is fairly intuitive to use, but users want to see more clarification of the meaning of the different types of possible queries. Some of the interface issues will naturally be resolved as we refine our conceptual model to deal with partial and complex homologies in the content.

CONCLUSIONS

The CAIS system and its associated methods are expected to be useful to biologists and translational medicine researchers. Possible applications range from supporting theoretical work in clarifying and modeling ontogenetic, physiological, pathological, and evolutionary transformations, to concrete techniques for improving the analysis of genotype-phenotype relationships among various animal models in support of a wide array of clinical and scientific initiatives.

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner.

Genetic segregation of spontaneous erosive arthritis and generalized autoimmune disease in the BXD2 recombinant inbred strain of mice

The BXD2 strain of mice is one of approximately 80 BXD recombinant inbred (RI) mouse strains derived from an intercross between C57BL/6J (B6) and DBA/2J (D2) strains. We have discovered that adult BXD2 mice spontaneously develop generalized autoimmune disease, including glomerulonephritis (GN), increased serum titres of rheumatoid factor (RF) and anti-DNA antibody, and a spontaneous erosive arthritis characterized by mononuclear cell infiltration, synovial hyperplasia, and bone and cartilage erosion. The features of lupus and arthritis developed by the BXD2 mice segregate in F2 mice generated by crossing BXD2 mice with the parental B6 and D2 strains. Genetic linkage analysis of the serum levels of anti-DNA and RF by using the BXD RI strains shows that the serum titers of anti-DNA and RF were influenced by a genetic locus on mouse chromosome (Chr) 2 near the marker D2Mit412 (78 cm, 163 Mb) and on Chr 4 near D4Mit146 (53.6 cm, 109 Mb), respectively. Both loci are close to the B-cell hyperactivity, lupus or GN susceptibility loci that have been identified previously. The results of our study suggest that the BXD2 strain of mice is a novel model for complex autoimmune disease that will be useful in identifying the mechanisms critical for the immunopathogenesis and genetic segregation of lupus and erosive arthritis.

Current approaches for deciphering the molecular basis of combined anterior pituitary hormone deficiency in humans

This review focuses on the general strategies currently used to decipher the molecular bases of combined pituitary hormone deficiency (CPHD) of genetic origin. By summarizing illustrative approaches that turned out to be successful for identifying an increasing number of genes involved in CPHD in the human, this article consider predictable obstacles specific to the investigation of these rare and heterogeneous conditions, while underlining the previously unsuspected roles of several of these genes during the development of extrapituitary structures.

Identification and characterization of a gene with base substitutions associated with the absorptive hypercalciuria phenotype and low spinal bone density

Absorptive hypercalciuria (AH) is a kidney stone-forming condition frequently complicated by bone loss. Previously, we mapped the locus for an inherited form of AH to chromosome 1q23.3-q24. We have sequenced a putative gene (subsequently shown by others to be homologous with the rat soluble adenylate cyclase gene) in this region in 12 unrelated Caucasian AH patients. Eighteen base substitutions were identified in the soluble adenylate cyclase human homolog gene. All sequence variations were further evaluated in 3-68 additional unrelated AH patients and 19-132 normal subjects, and 1 additional base substitution was identified. Six of the identified sequence variations occurred with increased frequency in the AH population and tracked with the AH phenotype in AH families. Calculated odds ratios showed that the occurrence of any 4 of these individual base substitutions was associated with a 2.2- to 3.5-fold increase in estimated risk for AH (P < 0.02). In addition, 1 or more base changes was associated with a lower L2-L4 vertebral bone density. Sequence analysis of 3 other genes within the AH linkage interval showed no difference in the distribution of sequence variations between AH and normal populations. This is the first description of a specific gene defect associated with AH.

Identification of transcripts expressed under functional differentiation in primary culture of cerebral cortical neurons

In this study, we utilized primary cultures of cerebral cortical neurons and RNA arbitrarily primed polymerase chain reaction (RAP-PCR) to identify differentially expressed transcripts in neurons of different culture ages. Eleven cDNA fragments with high sequence similarity to known genes and Expressed Sequence Tags (ESTs) were cloned. From the National Center for Biotechnology Information (NCBI) sequence database, two clones were shown to be identical to known sequences, Mus musculus HP1-BP74 protein mRNA and Mus musculus KRAB-containing zinc finger protein, both were up-regulated. These genes have never before been shown to be involved in neuronal functional maturation. Among the remaining clones, clone 8-14 (239 bp) was very similar to Rattus norvegicus rS-Rex-b mRNA, which was further confirmed by sequencing its shortest isoform (1.5 kb) obtained by computer cloning. This study has identified eleven potential genes and transcripts, which might be involved in the development and differentiation of GABAergic neurons in culture.

Confirmation and fine mapping of chromosomal regions influencing peak bone mass in mice

Bone mineral density (BMD) is determined by both environmental influences and polygenic inheritance. The extreme difficulty of dissecting out environmental factors from genetic ones in humans has motivated the investigation of animal models. Previously, we used quantitative trait locus (QTL) analysis to examine peak BMD in 24 recombinant inbred (RI) mouse strains, derived from a cross between C57BL/6 (B6) and DBA/2 (D2) progenitors (RI-BXD). The distribution of BMD values among these strains indicated strong genetic influences and a number of chromosomal sites linked to BMD were identified provisionally. Using three additional independent mapping populations derived from the same progenitors, we have confirmed loci on chromosomes 1, 2, and 4, and 11 that contain genes that influence peak BMD. Using a novel fine-mapping approach (RI segregation testing [RIST]), we have substantially narrowed two of the BMD-related chromosomal regions and in the process eliminated a number of candidate genes. The homologous regions in the human genome for each of these murine QTLs have been identified in recent human genetic studies. In light of this, we believe that findings in mice should aid in the identification of specific candidate genes for study in humans.

A mouse genetic locus with death clock and life clock features

A senility syndrome, with weight loss and priapism, occurs in CBAT6/T6 mice, an exceptionally long-lived strain. Instead of dying at the expected time, these mice get senile weight loss and priapism and go on living. We have postulated that a mutant death clock kills the wrong neurons. Crosses with the NZW and C57BL/6 strains show causation by a single genetic locus (Priap1), with a pronounced gene dosage effect on timing. We report here that various cancers were the cause of death in 31 of 32 NZW mice, compared to only five of 22 CBAT6/T6 mice, a highly significant difference (P<0.001). The longevity of (CBAT6/T6xNZW)F1 hybrids, and the segregation of longevity with priapism and senile weight loss in (CBAT6/T6xNZW) F2 hybrids, indicates that Priap1, or a linked gene, inhibits the cancers that usually shorten the lives of NZW mice. If a timer gene is involved, the cancer resistance action could be because the locus impedes the normal mid-life regression of anti-cancer defence. The priapism suggests loss of the medullary reticular formation neurons which normally inhibit male spinal sexual reflexes. In this region of the medulla there are also the respiratory and cardiac control centres, where apoptotic neuron destruction by the wild-type locus could govern maximal life-span. The CBAT6/T6 locus may be a mutant life-stage control clock. Its discovery could be the revelation of a new, major class of aetiology of disease.

The genetics of rheumatoid arthritis and the need for animal models to find and understand the underlying genes

The causes of rheumatoid arthritis (RA) are largely unknown. However, RA is most probably a multifactorial disease with contributions from genetic and environmental factors. Searches for genes that influence RA have been conducted in both human and experimental model materials. Both types of study have confirmed the polygenic inheritance of the disease. It has become clear that the features of RA complicate the human genetic studies. Animal models are therefore valuable tools for identifying genes and determining their pathogenic role in the disease. This is probably the fastest route towards unravelling the pathogenesisis of RA and developing new therapies.

The Mouse Genome Database (MGD): integration nexus for the laboratory mouse

The Mouse Genome Database (MGD) is the community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology and disease (http://www.informatics.jax.org). MGD provides standard nomenclature and consensus map positions for mouse genes and genetic markers; it provides a curated set of mammalian homology records, user-defined chromosomal maps, experimental data sets and the definitive mouse 'gene to sequence' reference set for the research community. The integration and standardization of these data sets facilitates the transition between mouse DNA sequence, gene and phenotype annotations. A recent focus on allele and phenotype representations enhances the ability of MGD to organize and present data for exploring the relationship between genotype and phenotype. This link between the genome and the biology of the mouse is especially important as phenotype information grows from large mutagenesis projects and genotype information grows from large-scale sequencing projects.

Towards an understanding of the genetics of human male infertility: lessons from flies

It has been argued that about 4-5% of male adults suffer from infertility due to a genetic causation. From studies in the fruitfly Drosophila, there is evidence that up to 1500 recessive genes contribute to male fertility in that species. Here we suggest that the control of human male fertility is of at least comparable genetic complexity. However, because of small family size, conventional positional cloning methods for identifying human genes will have little impact on the dissection of male infertility. A critical selection of well-defined infertility phenotypes in model organisms, combined with identification of the genes involved and their orthologues in man, might reveal the genes that contribute to human male infertility.

Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos

We have adapted the whole-mount in situ hybridization technique to perform high-throughput gene expression analysis in mouse embryos. A large-scale screen for genes showing specific expression patterns in the mid-gestation embryo was carried out, and a large number of genes controlling development were isolated. From 35760 clones of a 9.5 d.p.c. cDNA library, a total of 5348 cDNAs, enriched for rare transcripts, were selected and analyzed by whole-mount in situ hybridization. Four hundred and twenty-eight clones revealed specific expression patterns in the 9.5 d.p.c. embryo. Of 361 tag-sequenced clones, 198 (55%) represent 154 known mouse genes. Thirty-nine (25%) of the known genes are involved in transcriptional regulation and 33 (21%) in inter- or intracellular signaling. A large number of these genes have been shown to play an important role in embryogenesis. Furthermore, 24 (16%) of the known genes are implicated in human disorders and three others altered in classical mouse mutations. Similar proportions of regulators of embryonic development and candidates for human disorders or mouse mutations are expected among the 163 new mouse genes isolated. Thus, high-throughput gene expression analysis is suitable for isolating regulators of embryonic development on a large-scale, and in the long term, for determining the molecular anatomy of the mouse embryo. This knowledge will provide a basis for the systematic investigation of pattern formation, tissue differentiation and organogenesis in mammals.

Capitalizing on large-scale mouse mutagenesis screens

Variation is the crux of genetics. Mutagenesis screens in organisms from bacteria to fish have provided a battery of mutants that define protein functions within complex pathways. Large-scale mutation isolation has been carried out in Caenorhabditis elegans, Drosophila melanogaster and zebrafish, and has been recently reported in the mouse in two screens that have generated many new, clinically relevant mutations to reveal the power of phenotype-driven screens in a mammal.

The murine DSCR1-like (Down syndrome candidate region 1) gene family: conserved synteny with the human orthologous genes

A recently recognized gene family, conserved from yeast to humans, includes Down syndrome candidate region 1 gene (DSCR1), Adapt78 (recognized as the hamster ortholog of the DSCR1 isoform 4), ZAKI-4 (renamed DSCR1-like 1, DSCR1L1) and DSCR1L2 (a novel gene on human chromosome 1), along with yeast and C. elegans single members (Strippoli P., Lenzi L., Petrini M., Carinci P., Zannotti M., 2000. A new gene family including DSCR1 (Down Syndrome Candidate Region 1) and ZAKI-4: characterization from yeast to human and identification of DSCR1-like 2, a novel human member. Genomics 64, 252-263). The proposed family labels were a putative single-strand nucleic acid binding domain similar to the RNA recognition motif, and a unique, highly-conserved serine-proline motif. We have used a bioinformatics-driven molecular biology approach to characterize the murine members of DSCR1-like gene family. Systematic expressed-sequence-tags (EST) database search and reverse-transcription polymerase chain rection (RT-PCR) product sequencing allowed identification of the murine DSCR1, DSCR1L1 and DSCR1L2. The sequences of the respective protein products are of 198, 197 and 241 amino acids, respectively, and are very similar to the corresponding human proteins. The very broad expression pattern of the murine DSCR1 genes is similar to that of the human genes. Using a radiation hybrid panel, we mapped the murine DSCR1-like family members. The murine DSCR1 ortholog is located on the chromosome 16, in a region corresponding to that on human chromosome 21 just upstream of the Down syndrome candidate region. DSCR1L1 and DSCR1L2 murine genes are also located in chromosomal segments of chromosome 17 and 4, respectively, exactly corresponding to those containing the respective human homologs on chromosomes 6 and 1. Description of the mouse orthologs for DSCR1-like genes will allow knockout mice to be obtained for specific family members.

Murine Bv8 gene maps near a synteny breakpoint of mouse chromosome 6 and human 3p21

The genomic structure of the murine Bv8 gene was determined in 129/SvJ mouse, and the chromosomal localization was identified. Bv8 has first been characterized from skin secretion of the yellow-bellied toad, Bombina variegata. When injected into rat brain, this polypetide causes hyperalgesia. The murine Bv8 gene was shown to consist of four exons and was localized on chromosome 6 between the microsatellite markers D6Mit66 and D6Mit36 near the gene mem1, whereas the human counterpart was assigned to the non-syntenic region 3p21.1. Furthermore, the primary Bv8 transcript appeared to be alternatively spliced. The first variant contained all four exons yielding a product with a stretch highly enriched in basic amino acids in its central part. This domain is absent in the peptides from frog as well as in a splice variant expressed in mouse testis. A third variant gives rise to a truncated polypeptide.

Future opportunities for life science programs in space

Most space-related life science programs are expensive and time-consuming, requiring international cooperation and resources with trans-disciplinary expertise. A comprehensive future program in "life sciences in space" needs, therefore, well-defined research goals and strategies as well as a sound ground-based program. The first half of this review will describe four key aspects such as the environment in space, previous accomplishments in space (primarily focusing on amphibian embryogenesis), available resources, and recent advances in bioinformatics and biotechnology, whose clear understanding is imperative for defining future directions. The second half of this review will focus on a broad range of interdisciplinary research opportunities currently supported by the National Aeronautics and Space Administration (NASA), National Institute of Health (NIH), and National Science Foundation (NSF). By listing numerous research topics such as alterations in a diffusion-limited metabolic process, bone loss and skeletal muscle weakness of astronauts, behavioral and cognitive ability in space, life in extreme environment, etc., we will attempt to suggest future opportunities.

Linkage analysis of systemic lupus erythematosus induced in diabetes-prone nonobese diabetic mice by Mycobacterium bovis

Systemic lupus erythematosus induced by Mycobacterium bovis in diabetes-prone nonobese diabetic mice was mapped in a backcross to the BALB/c strain. The subphenotypes-hemolytic anemia, antinuclear autoantibodies, and glomerular immune complex deposition-did not cosegregate, and linkage analysis for each trait was performed independently. Hemolytic anemia mapped to two loci: Bah1 at the MHC on chromosome 17 and Bah2 on distal chromosome 16. Antinuclear autoantibodies mapped to three loci: Bana1 at the MHC on chromosome 17, Bana2 on chromosome 10, and Bana3 on distal chromosome 1. Glomerular immune complex deposition did not show significant linkage to any genomic region. Mapping of autoantibodies (Coombs' or antinuclear autoantibodies) identified two loci: Babs1 at the MHC and Babs2 on distal chromosome 1. It has previously been reported that genes conferring susceptibility to different autoimmune diseases map nonrandomly to defined regions of the genome. One possible explanation for this clustering is that some alleles at loci within these regions confer susceptibility to multiple autoimmune diseases-the "common gene" hypothesis. With the exception of the H2, this study failed to provide direct support for the common gene hypothesis, because the loci identified as conferring susceptibility to systemic lupus erythematosus did not colocalize with those previously implicated in diabetes. However, three of the four regions identified had been previously implicated in other autoimmune diseases.

Selective mapping: a strategy for optimizing the construction of high-density linkage maps

Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps.

Primary structure of mouse and rat nephrin cDNA and structure and expression of the mouse gene

Nephrin is a central component of the glomerular podocyte slit diaphragm and is essential for the normal renal filtration process. This study describes the complete structure of the mouse nephrin gene, which was shown to be homologous to the human gene, the major difference being 30 exons in the mouse gene as opposed to 29 in human. The complete primary structure of mouse and rat nephrins was also determined. The sequence identity between the mouse and rat proteins was shown to be 93%, while both rodent proteins have only about 83% sequence identity with human nephrin. The availability of the three mammalian sequences is significant for the interpretation of sequence variants and mutations in the nephrin gene in patients with congenital nephrotic syndrome. In situ hybridization analyses of whole mouse embryos and tissues revealed high expression of nephrin in kidney glomeruli and, surprisingly, an intense and highly restricted expression in a set of cells in hindbrain and spinal cord. No expression was observed elsewhere. This expression pattern may explain occasionally occurring neural symptoms caused by inactivating mutations in the nephrin gene in patients with congenital nephrotic syndrome.

Characterization of JDP genes, an evolutionarily conserved J domain-only protein family, from human and moths

We characterized evolutionarily conserved J domain containing protein (JDP) genes from human, Bombyx mori, and Manduca sexta. Each of the JDP proteins contains a J domain at its N-terminus and a highly conserved C-terminal domain. Southern blot analysis revealed that the human JDP1 gene is present as a single copy in the human genome. Expression was higher in brain, heart, and testis than in kidney or stomach. Human JDP1 was mapped in silico to chromosome 10q21.1, which exhibits a conserved synteny with the central region of mouse chromosome 10. Drosophila jdp is located at 99F4-99F11 on the right arm of the third chromosome.

Integrating functional genomic information into the Saccharomyces genome database

The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the 'locus page' and directs users to the detailed information they seek. SGD is endeavoring to integrate the existing information about yeast genes with the large volume of data generated by functional analyses that are beginning to appear in the literature and on web sites. New features will include searches of systematic analyses and Gene Summary Paragraphs that succinctly review the literature for each gene. In addition to current information, such as gene product and phenotype descriptions, the new locus page will also describe a gene product's cellular process, function and localization using a controlled vocabulary developed in collaboration with two other model organism databases. We describe these developments in SGD through the newly reorganized locus page. The SGD is accessible via the WWW at http://genome-www.stanford.edu/Saccharomyces/

The eukaryotic promoter database (EPD)

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. WWW-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria, and to navigate to related databases exploiting different cross-references. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch

TRANSFAC: an integrated system for gene expression regulation

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group

The Mouse Genome Database (MGD) is a comprehensive public database of mouse genomic, genetic and phenotypic information (http://www. informatics.jax.org). This community database provides information about genes, serves as a mapping resource of the mouse genome, details mammalian orthologs, integrates experimental data, represents standardized mouse nomenclature for genes and alleles, incorporates links to other genomic resources such as sequence data, and includes a variety of additional information about the laboratory mouse. MGD scientists and annotators work cooperatively with the research community to provide an integrated, consensus view of the mouse genome while also providing experimental data including data conflicting with the consensus representation. Recent improvements focus on the representation of phenotypic information and the enhancement of gene and allele descriptions.

Website review: The Jackson Laboratory Mouse Genome Informatics Site: version 2.3.2

Site authors: Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine. Project PI: Janan Eppig. All screen views from the website are reproduced with the kind permission of Janan Eppig.

Genealogies of mouse inbred strains

The mouse is a prime organism of choice for modelling human disease. Over 450 inbred strains of mice have been described, providing a wealth of different genotypes and phenotypes for genetic and other studies. As new strains are generated and others become extinct, it is useful to review periodically what strains are available and how they are related to each other, particularly in the light of available DNA polymorphism data from microsatellite and other markers. We describe the origins and relationships of inbred mouse strains, 90 years after the generation of the first inbred strain. Given the large collection of inbred strains available, and that published information on these strains is incomplete, we propose that all genealogical and genetic data on inbred strains be submitted to a common electronic database to ensure this valuable information resource is preserved and used efficiently.

Future vision of the GDB human genome database

In 1973, scientists assembled at the first Human Gene Mapping Workshop to discuss the 64 human genes mapped at that time. In 1989, the GDB Human Genome Database was created to store information on 1, 700 mapped human genes. Ten years later, as the human genome project closes in on the release of the complete DNA sequence holding as many as 100,000 human genes, GDB is evolving to continue to meet the needs of the scientific community. Well known as a resource for data which has been stringently reviewed as part of the curation process, GDB prepares to continue to provide a compilation of the human genome including maps, map objects, polymorphisms, and mutations. As more sites across the Internet are established to share biological information, it becomes increasingly burdensome for the scientist to collect data from all sources of a particular domain. In an attempt to reduce this burden, GDB continues to load data from large genome centres and accept submissions from researchers around the world. Moreover, GDB looks to provide a mechanism to link gene-related information to the human reference sequence. In doing this, GDB plans to establish federated linkages with "boutique" databases around the world that could contain enormous amounts of valuable information about specific genes or chromosomes.

The breast cancer gene database: a collaborative information resource

The Breast Cancer Gene Database (BCGD) is a compendium of molecular genetic data relating to genes involved in breast cancer, and which is freely available via the World Wide Web. The data in BCGD is extracted from the published biomedical research literature and stored as a collection of 'Facts', which in turn are collected into topical categories organized by gene. This organization facilitates quick searches and rapid retrievals of specific data such as gene characteristics, functions and role in oncogenesis, and is an important factor allowing for continuous updates. BCGD can be searched either by gene name or keyword. Data is deposited and retrieved from the database through a set of interactive Web forms, making it both platform-independent and universally accessible in facilitating worldwide collaborative authoring of the database. Data in BCGD is linked to other on-line resources such as Entrez, GeneCards and On-Line Mendelian Inheritance in Man. BCGD is located at http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html.

The promise of comparative genomics in mammals

Dense genetic maps of human, mouse, and rat genomes that are based on coding genes and on microsatellite and single-nucleotide polymorphism markers have been complemented by precise gene homolog alignment with moderate-resolution maps of livestock, companion animals, and additional mammal species. Comparative genetic assessment expands the utility of these maps in gene discovery, in functional genomics, and in tracking the evolutionary forces that sculpted the genome organization of modern mammalian species.

Once-weekly resistance exercise improves muscle strength and neuromuscular performance in older adults

OBJECTIVE

To determine the effect of frequency of resistive training on gain in muscle strength and neuromuscular performance in healthy older adults.

DESIGN

A randomized controlled trial with subjects assigned either to high-intensity resistance training 1 (EX1), 2 (EX2), or 3 (EX3) days per week for 24 weeks or to a control group (CO).

SETTING

An exercise facility at an academic medical center.

SUBJECTS

Forty-six community-dwelling healthy men (n = 29) and women (n = 17) aged 65 to 79 years.

INTERVENTION

Progressive resistance training consisting of three sets of eight exercises targeting major muscle groups of the upper and lower body, at 80% of one-repetition maximum (1-RM) for eight repetitions, either 1, 2, or 3 days per week.

MEASURES

Dynamic muscle strength (1-RM) using isotonic equipment every 4 weeks, bone mineral density and body composition by dual energy X-ray absorptiometry (DXA), and neuromuscular performance by timed chair rise and 6-meter backward tandem walk.

RESULTS

For each of the eight exercises, muscle strength increased in the exercise groups relative to CO (P < .01), with no difference among EX1, EX2 and EX3 groups at any measurement interval. Percent change averaged 3.9 +/- 2.4 (CO), 37.0 +/- 15.2 (EX1), 41.9 +/- 18.2 (EX2), and 39.7 +/- 9.8 (EX3). The time to rise successfully from the chair 5 times decreased significantly (P < .01) at 24 weeks, whereas improvement in the 6-meter backward tandem walk approached significance (P = .10) in the three exercise groups compared with CO. Changes in chair rise ability were correlated to percent changes in quadriceps strength (r = -0.40, P < .01) and lean mass (r = -0.40, P < .01).

CONCLUSIONS

A program of once or twice weekly resistance exercise achieves muscle strength gains similar to 3 days per week training in older adults and is associated with improved neuromuscular performance. Such improvement could potentially reduce the risk of falls and fracture in older adults.