Biomedical subjects

Genomics

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PubMed2006

Acquisition of genome information from single-celled unculturable organisms (radiolaria) by exploiting genome profiling (GP).

BACKGROUND: There is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians. Even worse, such organisms are often very difficult to collect. Sequence analysis of 18S rDNA has been carried out, but obtaining the data has been difficult and it has provided a rather limited amount of genome information. In this paper, we have developed a method which provides a sufficient amount of data from an unculturable organism. The effectiveness of this method was demonstrated by applying it to the provisional classification of a set of unculturable organisms (radiolarians). RESULTS: Dendrogram was drawn regarding the single-celled unculturable species based on the similarity score termed PaSS, offering a consistent result with the conventional taxonomy of them built up based on phenotypes. This fact has shown that genome profiling-based technology developed here can obtain genome information being sufficient for identifying and classifying species from a single-celled organism. CONCLUSION: Since this method is so simple, general, and yet powerful, it can be applied to various organisms and cells, especially single-celled, uncluturable ones, for their genome analysis.

Animals↗

PubMed2006

The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella.

BACKGROUND: Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all lineages. RESULTS: For the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames (ORFs), with a mean number of 726 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains. CONCLUSION: These results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships.

DNA, Bacterial↗

PubMed2007

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists.

BACKGROUND: The Ashbya Genome Database (AGD) 3.0 is an innovative cross-species genome and transcriptome browser based on release 40 of the Ensembl developer environment. DESCRIPTION: AGD 3.0 provides information on 4726 protein-encoding loci and 293 non-coding RNA genes present in the genome of the filamentous fungus Ashbya gossypii. A synteny viewer depicts the chromosomal location and orientation of orthologous genes in the budding yeast Saccharomyces cerevisiae. Genome-wide expression profiling data obtained with high-density oligonucleotide microarrays (GeneChips) are available for nearly all currently annotated protein-coding loci in A. gossypii and S. cerevisiae. CONCLUSION: AGD 3.0 hence provides yeast- and genome biologists with comprehensive report pages including reliable DNA annotation, Gene Ontology terms associated with S. cerevisiae orthologues and RNA expression data as well as numerous links to external sources of information. The database is accessible at http://agd.vital-it.ch/.

Databases, Genetic↗

PubMed1994

Analysis of products of the Escherichia coli genomic genes and regulation of their expressions: an applicable procedure for genomic analysis of other microorganisms.

A partial library of the Escherichia coli genomic genes has been constructed, in which each clone has part of a genomic gene fused in frame with the lacZ gene in addition to its promoter and operator. DNA of randomly selected clones was sequenced, and the resultant deduced N-terminal amino acid sequences showed that 17 out of 26 genes analyzed encode unknown proteins. Genomic locations of the cloned genes and their expressional regulations under the aerobic and anaerobic conditions were also analyzed. These results suggest that this library is useful for the global analysis of the E. coli genomic genes and that this strategy may be applicable to the genomic analysis of other microorganisms.

Bacterial Proteins↗

PubMed2000

An automated system for genome analysis to support microbial whole-genome shotgun sequencing.

We developed a semi-automated genome analysis system called GAMBLER in order to support the current whole-genome sequencing project focusing on alkaliphilic Bacillus halodurans C-125. GAMBLER was designed to reduce the human intervention required and to reduce the complications in annotating thousands of ORFs in the microbial genome. GAMBLER automates three major routines: analyzing assembly results provided by genome assembler software, assigning ORFs, and homology searching. GAMBLER is equipped with an interface for convenience of annotation. All processes and options are manipulatable through a WWW browser that enables scientists to share their genome analysis results without choosing computer platforms.

Automation↗

PubMed2004

Genomic background predicts the fate of duplicated genes: evidence from the yeast genome.

Gene duplication with subsequent divergence plays a central role in the acquisition of genes with novel function and complexity during the course of evolution. With reduced functional constraints or through positive selection, these duplicated genes may experience accelerated evolution. Under the model of subfunctionalization, loss of subfunctions leads to complementary acceleration at sites with two copies, and the difference in average rate between the sequences may not be obvious. On the other hand, the classical model of neofunctionalization predicts that the evolutionary rate in one of the two duplicates is accelerated. However, the classical model does not tell which of the duplicates experiences the acceleration in evolutionary rate. Here, we present evidence from the Saccharomyces cerevisiae genome that a duplicate located in a genomic region with a low-recombination rate is likely to evolve faster than a duplicate in an area of high recombination. This observation is consistent with population genetics theory that predicts that purifying selection is less effective in genomic regions of low recombination (Hill-Robertson effect). Together with previous studies, our results suggest the genomic background (e.g., local recombination rate) as a potential force to drive the divergence between nontandemly duplicated genes. This implies the importance of structure and complexity of genomes in the diversification of organisms via gene duplications.

Evolution, Molecular↗

PubMedDate not supplied

Parasite genome projects and the Trypanosoma cruzi genome initiative.

Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given.

Animals↗

PubMed1997

Visual Genome Explorer: a comparative visual interface to genome data.

In response to the deluge of genome data, we are developing Visual Genome Explorer, an interactive graphical interface to genome data. Given is a description of the prototype program, which introduces the concept of visual comparative genomics for complete bacterial genomes.

Computer Communication Networks↗

PubMed2002

Integrating cancer genomics and proteomics in the post-genome era.

The dawn of the post-genome era is leading to extraordinary opportunities in biomedicine. Our group has embarked on a major effort to integrate genomics, transcriptomics and proteomics for the profiling of tumor tissues, an approach we refer to as operomics. Our major goals are the molecular classification of tumors and the identification of markers for the early detection of cancer. Molecular analyses of tumors rely on microdissected tissues, which are simultaneously investigated for genomic, transcriptomic and proteomic changes. Genomic alterations in tumor cells being investigated include deletions, amplifications and methylation changes across the entire genome as well as point mutations in specific genes. Expression analysis at the RNA level is being undertaken using oligonucleotide and cDNA based microarrays. An important aspect of our approach is the large-scale identification and quantitative analysis of tumor proteins in whole cell lysates as well as in protein compartments. Protein separation strategies include two-dimensional polyacrylamide gel electrophoresis and liquid chromatography. Specific protein subsets, of interest include membrane proteins, secreted proteins and antigenic proteins as sources of biomarkers for early detection of cancer. Our current approach is illustrated with findings stemming from our studies of human gliomas.

Brain Neoplasms↗

PubMed2002

Structural genomics: bridging functional genomics and structure-based drug design.

Considerable advances in structural genomics have been witnessed in the last year. Several pilot studies have begun to report their initial results, and new centers have been funded to join the endeavor. The legacies of the genome sequencing efforts, namely high-throughput molecular biology and whole-organism genome sequences, have been integrated as front-end modules for structural genomics pipelines. Impressive advances have been made in NMR spectroscopy and X-ray crystallography. New methods in structural bioinformatics and computational chemistry have been published that provide the means to exploit the wealth of new information in drug discovery. Not surprisingly, the biopharmaceutical industry has been quick to recognize the benefits of these new developments and has begun to adopt them. This article reviews recent results from structural genomics initiatives and the potential applications of new information and technologies in the drug discovery process.

Drug Design↗

PubMed2004

[A method for preparation of genomic DNA from Grifola frondosa and construction of a genomic library].

Grifola frondosa, is a valuable medicinal fungus. High quality total genomic DNA is difficult to prepare due to its high polysaccharide content. A method for the preparation of Grifola frondosa total genomic DNA and construction of Grifola frondosa, genomic library is described. Genomic DNA prepared by this method is digested by Sau3A I restriction enzyme. Constructed genomic library give a titer of 2 x 10(5) transformants/50mg , with a average insert size of 14kb. This has paved way for the cloning of other Grifola frondosa genes and molecular biology studies.

DNA, Fungal↗

PubMed2004

[Detection of the introgression of genome elements of the Aegilops cylindrica host. into the Triticum aestivum L. genome by ISSR and SSR analysis].

To reveal sites of the donor genome in wheat crossed with Aegilops cylindrica, which acquired conferred resistance to fungal diseases, a comparative analysis of introgressive and parental forms was conducted. Two systems of PCR analysis, ISSR and SSR-PCR, were employed. Upon use of 7 ISSR primers in genotypes of 30 individual plants BC1 F9 belonging to lines 5/55-91 and 5/20-91, 19 ISSR loci were revealed and assigned to introgressive fragments of Aegilops cylindrica genome in Triticum aestivum. The 40 pairs of SSR primers allowed the detection of seven introgressive alleles; three of these alleles were located on common wheat chromosomes in the B genome, while four alleles, in the D genome. Based on data of microsatellite analysis, it was assumed that the telomeric region of the long arm of common wheat chromosome 6A also changed. ISSR and SSR methods were shown to be effective for detecting variability caused by introgression of foreign genetic material into the genome of common wheat.

Alleles↗

PubMed2005

Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations.

BRCA1 or BRCA2 germline mutations cause approximately 30% of breast cancers within high-risk families. This represents 5% of total breast cancer incidence. Although BRCA1 and BRCA2 are both implicated in DNA repair and genome stability, it is unknown whether BRCA1 and BRCA2 are associated with similar or distinct diseases. In a previous study we reported that BRCA1-related breast carcinomas show a distinct genomic profile as determined by comparative genomic hybridization (CGH). We now hypothesize that, if functionally equivalent, mutations in BRCA1 and BRCA2 would result in similar genomic profiles in tumors. Here we report the chromosomal gains and losses as measured by CGH in 25 BRCA2-associated breast tumors and compared them with our existing 36 BRCA1 and 30 control profiles. We compared all chromosomal regions and determined the regions of differential gain or loss between tumor classes and controls. BRCA2 and control tumors have very similar genomic profiles. As a consequence, and in contrast to BRCA1-associated tumors, CGH profiles from BRCA2-associated tumors could not be distinguished from control tumors using the classification methodology as we have developed before. The largest number of significant differences existed between BRCA1 and controls, followed by BRCA1 compared with BRCA2, suggesting different tumor development pathways for BRCA1 and BRCA2.

Breast Neoplasms↗

PubMed1996

Toward genome-wide scanning of gene expression: a functional aspect of the Genome Project.

The progress of world-wide efforts in genome mapping and sequencing is uncovering a number of novel genes whose functions cannot be predicted from their structures, thereby demonstrating the need for the systematic collection of biological information other than their sequences to exploit fully the genomic data. Since one of the most fundamental pieces of information is the expression profile of individual genes, various approaches to genome-wide gene-expression scanning are being explored, based on differential hybridization, comparative cDNA sequencing and message-display techniques. Although each approach has unique advantages and drawbacks, the accumulation of expression data on individual genes is expected to shed light on the functions of genes that are revealed by genome analysis but whose function is not known. At the same time, further improvements in these techniques, as well as the development of novel methodologies, are required to explore fully the genome expression status in various biological situations.

Chromosome Mapping↗

PubMed2001

Towards genetic genome projects: genomic library screening and gene-targeting vector construction in a single step.

We have developed technologies that simplify genomic library construction and screening, substantially reducing both the time and the cost associated with traditional library screening methods and facilitating the generation of gene-targeting constructs. By taking advantage of homologous recombination in Escherichia coli, we were able to use as little as 80 bp of total sequence homology to screen for a specific gene from a genomic library in plasmid or phage form. This method, called recombination cloning (REC), takes only a few days instead of the several weeks required for traditional plaque-lift methods. In addition, because every clone in the mouse genomic library we have constructed has a negative selection marker adjacent to the genomic insert, REC screening can generate gene-targeting vectors in one step, from library screening to finished construct. Conditional targeting constructs can be generated easily with minimal additional manipulation.

Animals↗

PubMed2026

Culture-free genomics: a shift toward genome-wide applications in Chagas disease and leishmaniasis.

INTRODUCTION: Chagas disease and leishmaniasis remain major neglected tropical diseases, with diagnosis and surveillance constrained by low parasite burden, multiclonal infections, and complex parasite biology. Traditional culture-dependent and targeted molecular approaches fail to capture the full genomic diversity of Trypanosoma cruzi and Leishmania spp. limiting clinical and epidemiological utility. AREAS COVERED: We review the evolution from early sequencing to second- and third-generation platforms, highlighting culture-free detection and genomic surveillance. We discuss enrichment strategies (selective whole-genome amplification (SWGA) and capture-enrichment sequencing (CES)) addressing low parasite DNA abundance in complex samples, alongside metagenomics and portable sequencing for field-based surveillance and diagnostics. We further explore how direct-from-host data can improve diagnostics, enhance transmission surveillance, support treatment monitoring, and guide control strategies. EXPERT OPINION: Culture-free genomic approaches represent a transformative advance in kinetoplastid research, providing resolution that culture-dependent methods cannot deliver. Their diagnostic contribution is at present largely indirect, operating through the identification of improved molecular and serological targets rather than through sequencing as the assay itself. Persistent barriers of cost, infrastructure, standardization, and bioinformatics capacity, together with the absence of formal clinical validation, currently confine these methods to research and surveillance settings.

Capture-enrichment sequencing↗

PubMed2025

Doubled Genomes, Divergent Fates: Genomic Insights Into Diversification in an Allotetraploid Cavefish.

Cave environments impose unique challenges that drive remarkable genetic and phenotypic changes in cave-dwelling organisms. In this study, we investigated the genomic basis of adaptation in the small eye golden-line fish (Sinocyclocheilus microphthalmus), an allotetraploid cavefish endemic to Guangxi, China. Using whole-genome resequencing data from 47 individuals across six cave locations, we examined how neutral and selective forces influence diversification. Our analyses uncovered significant population structure indicative of allopatric divergence, along with evidence of locus-specific selection contributing to genomic differentiation. We identified seven single outlier clusters (SOCs), each tied to the divergence of specific populations, underscoring the role of local processes in driving diversity. Genes associated with vision showed relaxed selection, likely reflecting adaptation to darkness, while positive selection on other loci revealed additional functional shifts. Notably, allopolyploidy was found to fuel divergence through subgenome-specific patterns and asymmetric evolution within SOCs and among homoeologs. Taken together, these findings provide valuable insights into mechanisms of cave evolution and illustrate how allotetraploid genomes can facilitate diversification, potentially contributing to speciation in extreme environments.

Animals↗

PubMed1984

Genomic structure of HTLV (human T-cell leukemia virus): detection of defective genome and its amplification in MT-2 cells.

We studied the genomic structure of human T-cell leukemia virus (HTLV) in the HTLV producer cell line MT-2. Southern blotting revealed that at least eight HTLV proviruses were integrated in the chromosomes of MT-2 cells. The genomic structure of these proviruses was analyzed using fragments of cloned HTLV that were specific to gag, pol, env, pXs and U3R genes as probes. We have identified a complete genome of HTLV in MT-2 (non-defective type). However, seven of the eight proviruses had defective genomes. Provirus T2-a contains only the U3R (LTR) of HTLV and T2-b corresponds to the non-defective genome. T2-c possesses only a portion of env, and pXs and U3R. T2-d consists of gag, pol, part of env and U3R. On the other hand, T2-e, f, g and h consist of gag, pXs and U3R. Northern blotting experiments with mRNA from MT-2 cells supported the evidence of amplification of the gag-pXs gene of HTLV. 26S mRNA is considered to be a subgenomic species of 35S RNA. 32S mRNA may represent the T2-d provirus which lacks a portion of env and pXs, while 20S mRNA was a subgenomic species. The gag-pXs gene may correspond to 24S mRNA, the amount which was amplified in MT-2 cells.

Base Sequence↗