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PubMed2002

A compact view of isochores in the draft human genome sequence.

Prior to genome sequencing, information on base composition (GC level) and its variation in mammalian genomes could be obtained using density gradient ultracentrifugation. Analyses using this approach led to the conclusion that mammalian genomes are organized into mosaics of fairly homogeneous regions, called isochores. We present an initial compositional overview of the chromosomes of the recently available draft human genome sequence, in the form of color-coded moving window plots and corresponding GC level histograms. Results obtained from the draft human genome sequence agree well with those obtained or deduced earlier from CsCl experiments. The draft sequence now permits the visualization of the mosaic organization of the human genome at the DNA sequence level.

Base Composition↗
PubMed2006

BiologicalNetworks: visualization and analysis tool for systems biology.

Systems level investigation of genomic scale information requires the development of truly integrated databases dealing with heterogeneous data, which can be queried for simple properties of genes or other database objects as well as for complex network level properties, for the analysis and modelling of complex biological processes. Towards that goal, we recently constructed PathSys, a data integration platform for systems biology, which provides dynamic integration over a diverse set of databases [Baitaluk et al. (2006) BMC Bioinformatics 7, 55]. Here we describe a server, BiologicalNetworks, which provides visualization, analysis services and an information management framework over PathSys. The server allows easy retrieval, construction and visualization of complex biological networks, including genome-scale integrated networks of protein-protein, protein-DNA and genetic interactions. Most importantly, BiologicalNetworks addresses the need for systematic presentation and analysis of high-throughput expression data by mapping and analysis of expression profiles of genes or proteins simultaneously on to regulatory, metabolic and cellular networks. BiologicalNetworks Server is available at http://brak.sdsc.edu/pub/BiologicalNetworks.

Computer Graphics↗
PubMed1991

Organizational analysis of elav gene and functional analysis of ELAV protein of Drosophila melanogaster and Drosophila virilis.

Drosophila virilis genomic DNA corresponding to the D. melanogaster embryonic lethal abnormal visual system (elav) locus was cloned. DNA sequence analysis of a 3.8-kb genomic piece allowed identification of (i) an open reading frame (ORF) with striking homology to the previously identified D. melanogaster ORF and (ii) conserved sequence elements of possible regulatory relevance within and flanking the second intron. Conceptual translation of the D. virilis ORF predicts a 519-amino-acid-long ribonucleoprotein consensus sequence-type protein. Similar to D. melanogaster ELAV protein, it contains three tandem RNA-binding domains and an alanine/glutamine-rich amino-terminal region. The sequence throughout the RNA-binding domains, comprising the carboxy-terminal 346 amino acids, shows an extraordinary 100% identity at the amino acid level, indicating a strong structural constraint for this functional domain. The amino-terminal region is 36 amino acids longer in D. virilis, and the conservation is 66%. In in vivo functional tests, the D. virilis ORF was indistinguishable from the D. melanogaster ORF. Furthermore, a D. melanogaster ORF encoding an ELAV protein with a 40-amino-acid deletion within the alanine/glutamine-rich region was also able to supply elav function in vivo. Thus, the divergence of the amino-terminal region of the ELAV protein reflects lowered functional constraint rather than species-specific functional specification.

Amino Acid Sequence↗
PubMed2006

Visualization of the interaction between the precursors of VPg, the viral protein linked to the genome of turnip mosaic virus, and the translation eukaryotic initiation factor iso 4E in Planta.

The RNA genome of Turnip mosaic virus is covalently linked at its 5' end to a viral protein known as VPg. This protein binds to the translation eukaryotic initiation factor iso 4E [eIF(iso)4E]. This interaction has been shown to be important for virus infection, although its exact biological function(s) has not been elucidated. In this study, we investigated the subcellular site of the VPg-eIF(iso)4E interaction using bimolecular fluorescence complementation (BiFC). As a first step, eIF(iso)4E, 6K-VPg-Pro, and VPg-Pro were expressed as full-length green fluorescent protein (GFP) fusions in Nicotiana benthamiana, and their subcellular localizations were visualized by confocal microscopy. eIF(iso)4E was predominantly associated with the endoplasmic reticulum (ER), and VPg-Pro was observed in the nucleus and possibly the nucleolus, while 6K-VPg-Pro-GFP induced the formation of cytoplasmic vesicles budding from the ER. In BiFC experiments, reconstituted green fluorescence was observed throughout the nucleus, with a preferential accumulation in subnuclear structures when the GFP split fragments were fused to VPg-Pro and eIF(iso)4E. On the other hand, the interaction of 6K-VPg-Pro with eIF(iso)4E was observed in cytoplasmic vesicles embedded in the ER. These data suggest that the association of VPg with the translation factor might be needed for two different functions, depending of the VPg precursor involved in the interaction. VPg-Pro interaction with eIF(iso)4E may be involved in perturbing normal cellular functions, while 6K-VPg-Pro interaction with the translation factor may be needed for viral RNA translation and/or replication.

Arabidopsis Proteins↗
PubMed2026

Malaria-GENOMAP: a web-based tool for exploring genomic variation of malaria parasites.

MOTIVATION: Malaria, caused by Plasmodium parasites, imposes a significant public health burden. While Plasmodium falciparum remains the primary target of elimination strategies due to its high mortality rate, lesser-known species such as P. malariae, P. vivax, and P. knowlesi continue to contribute to substantial human morbidity. Genomic approaches, including whole-genome sequencing, offer powerful tools for understanding the biology, transmission, and emerging drug resistance of these neglected Plasmodium species. However, there is an urgent need for informatic tools to summarize and visualize the high-dimensional and complex genomic data generated. RESULTS: We developed Malaria-GENOMAP, a user-friendly web-based tool, which integrates genomic variant data, such as allele frequencies, with geographical maps and chromosome-wide to gene views for in-depth exploration. The tool includes variation from P. knowlesi (n = 139), P. malariae (n = 158), P. ovale curtisi (n = 36), P. ovale wallikeri (n = 47), P. simium (n = 38), and P. vivax (n = 1359). It enables the investigation of population structure, geographic associations of mutations, and putative drug resistance markers, offering valuable insights for malaria control efforts. AVAILABILITY AND IMPLEMENTATION: Malaria-GENOMAP is available online at https://genomics.lshtm.ac.uk/malaria-genomaps.

Internet↗
PubMed2006

Combo: a whole genome comparative browser.

SUMMARY: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats. AVAILABILITY: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms and is freely available for download at http://www.broad.mit.edu/annotation/argo/.

Algorithms↗
PubMed1997

Genetic variations in human benign prostatic hyperplasia detected by restriction landmark genomic scanning.

Alterations in the genomic DNAs of benign prostatic hyperplasias were examined using restriction landmark genomic scanning. This methodology allows the visual comparison of a large number of loci as spots within a gel that has been electrophoresed in 2 dimensions. Within each of the 16 hyperplasias examined, we found 2 to 10 spots with altered intensities, as compared to equivalent spots from normal prostate, but could detect few common spot profiles for any hyperplasia samples. These data conflict with data from previous studies and suggest that there may be no consistent genetic changes in the pathogenesis of some forms of human benign prostatic hyperplasia.

Aged↗
PubMed2005

Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics.

Bacterial comparative genomics has been revolutionized by microarrays, but the power of any microarray is dependent on the number and diversity of gene reporters it contains. Staphylococcus aureus is an important human pathogen causing a wide range of invasive and toxin-mediated diseases, and more than 20% of the genome of any isolate consists of variable genes. Seven whole-genome sequences of S. aureus are available, and we exploited this rare opportunity to design, build, and validate a comprehensive, nonredundant PCR product microarray carrying reporters that represent every predicted open reading frame (3,623 probes). Such a comprehensive microarray necessitated a novel design strategy. Validation with the seven sequenced strains showed correct identification of 93.9% of genes present or absent/divergent but was dependent on the method of analysis chosen. Microarray data were highly reproducible, reducing the need for many replicate slides. Interpretation of microarray data was enhanced by focusing on the major areas of variation--the presence or absence of mobile genetic elements (MGEs). We compiled "composite genomes" of every individual MGE and visualized their distribution. This allowed the sensitive discrimination of related isolates, including the first clear description of how isolates of the same clone of epidemic methicillin-resistant S. aureus differ substantially in their carriage of MGEs. These MGEs carry virulence and resistance genes, suggesting differences in pathogenic potential. The novel methods of design and interpretation of data generated from this microarray will enable further studies of S. aureus evolution, epidemiology, and pathogenesis.

Bacterial Proteins↗
PubMed1995

Multiparameter in situ analysis of trophoblast cells in mixed cell populations by combined DNA and RNA in situ hybridization.

We developed a non-radioactive assay for simultaneous detection of cytoplasmic mRNA and nuclear genomic DNA in fetal trophoblast cells by sequential in situ hybridization. Trophoblast-specific mRNA is detected with a digoxigenin-labeled RNA probe complementary to HLA-G, followed by visualization through the generation of stable contrast-rich DAB/Ni complexes. Genomic target DNA is subsequently visualized in labeled cells by fluorescent in situ hybridization using biotin-labeled chromosome-specific DNA probes. Simultaneous visualization of both targets is made possible using a fluorescence microscope with FITC filter and conventional brightfield light. This method allows detection of trophoblast cells within a mixed cell population and, at the same time, analysis of chromosome anomalies in the trophoblast cells identified. For prenatal diagnosis of fetal cells enriched from maternal peripheral blood during pregnancy, this multiparameter in situ analysis of immobilized fetal trophoblast cells will be very useful.

DNA↗
PubMed2005

eQTL Explorer: integrated mining of combined genetic linkage and expression experiments.

The development of computational resources to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. eQTL Explorer stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer provides a new and powerful tool to interrogate these very large and complex datasets.

Algorithms↗
PubMed2004

MolliGen, a database dedicated to the comparative genomics of Mollicutes.

Bacteria belonging to the class Mollicutes were among the first ones to be selected for complete genome sequencing because of the minimal size of their genomes and their pathogenicity for humans and a broad range of animals and plants. At this time six genome sequences have been publicly released (Mycoplasma genitalium, Mycoplasma pneumoniae, Ureaplasma urealyticum-parvum, Mycoplasma pulmonis, Mycoplasma penetrans and Mycoplasma gallisepticum) and as the number of available mollicute genomes increases, comparative genomics analysis within this model group of organisms becomes more and more instructive. However, such an analysis is difficult to carry out without a suitable platform gathering not only the original annotations but also relevant information available in public databases or obtained by applying common bioinformatics methods. With the aim of solving these difficulties, we have developed a web-accessible database named MolliGen (http://cbi.labri.fr/outils/molligen/). After selecting a set of genomes the user can launch various types of search based on annotation, position on the chromosomes or sequence similarity. In addition, relationships of putative orthology have been precomputed to allow differential genome queries. The results are presented in table format with multiple links to public databases and to bioinformatic analyses such as multiple alignments or BLAST search. Specific tools were also developed for the graphical visualization of the results, including a multi- genome browser for displaying dynamic pictures with clickable objects and for viewing relationships of precomputed similarity. MolliGen is designed to integrate all the complete genomes of mollicutes as they become available.

Computational Biology↗
PubMed1994

A flexible approach to genome map assembly.

A major goal of the Human Genome Project is to construct detailed physical maps of the human genome. A physical map is an assignment of DNA fragments to their locations on the genome. Complete maps of large genomes require the integration of many kinds of experimental data, each with its own forms of noise and experimental error. To facilitate this integration, we are developing a flexible approach to map assembly based on logic programming and data visualization. Logic programming provides a convenient and mathematically rigorous way of reasoning about data, while data visualization provides layout algorithms for assembling and displaying genome maps. To demonstrate the approach, this paper describes numerous rules for map assembly implemented in a data-visualization system called Hy+. Using these rules, we have successfully assembled contigs (partial maps) from real and simulated mapping data-data that is noisy, imprecise and contradictory. The main advantage of the approach is that it allows a user to rapidly develop, implement and test new rules for genome map assembly, with a minimum of programming effort.

Chromosome Mapping↗
PubMed2002

Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks.

We have developed a new tool to visualize expression data on metabolic pathways and to evaluate which metabolic pathways are most affected by transcriptional changes in whole-genome expression experiments. Using the Fisher Exact Test, the method scores biochemical pathways according to the probability that as many or more genes in a pathway would be significantly altered in a given experiment by chance alone. This method has been validated on diauxic shift experiments and reproduces well known effects of carbon source on yeast metabolism. The analysis is implemented with Pathway Analyzer, one of the tools of Pathway Processor, a new statistical package for the analysis of whole-genome expression data. Results from multiple experiments can be compared, reducing the analysis from the full set of individual genes to a limited number of pathways of interest. The pathways are visualized with OpenDX, an open-source visualization software package, and the relationship between genes in the pathways can be examined in detail using Expression Mapper, the second program of the package. This program features a graphical output displaying differences in expression on metabolic charts of the biochemical pathways to which the open reading frames are assigned.

Energy Metabolism↗
PubMed1981

Immunochemical visualization of binding of the chemical carcinogen benzo(a)pyrene diol-epoxide 1 to the genome.

antisera against DNA modified with r-7,t-8-dihydroxy-9,10-oxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE-1) was elicited in rabbits. Such sera reached with either single- or double-stranded modified DNA but not with unmodified DNA, free benzo(a)pyrene, or proteins modified by BPDE-1. Indirect immunofluorescence studies indicated that the immunoglobulin G in the sera bound specifically to the nuclei of KD cells which were treated with BPDE-1. The intensity of fluorescence was proportional to the dose of BPDE-1 used to treat the cells. About 50% of the BPDE-1-DNA adducts remained bound to DNA 24 hr after the removal of the carcinogen. The location of BPDE-1-modified bases in Col E1 DNA was visualized by immunoelectron microscopy.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1999

Focal sites of DNA repair synthesis in human chromosomes.

Nucleotide excision repair (NER) is the principle pathway by which the human cells eliminate UV-induced lesions from their genomic DNA. The process can be visualized through the labelling of the nucleotides that are incoporated into repair patches, following the excision of the damaged stretch of DNA. In this study we have visualized sites of DNA repair synthesis (DRS) in human interphase and metaphase chromosomes after very short times (2.5-30 min) of postirradiation labelling in vivo with 5-iododeoxyuridine. A limited number (<50 per nucleus) of discrete nuclear DRS sites were seen in cells fixed immediately after labelling and the sites are also detectable in interphase and metaphase chromosomes visualized 48h after irradiation (3 J/m2). These observations strongly support the view that within a given short time window distinct chromosome domains are under extensive repair while in many other domains NER is slow. They argue against the general distributative NER process but are consistent with a processive scanning of damaged domains.

Biotin↗
PubMed2000

Spatial distribution of GC- and AT-rich DNA sequences within human chromosome territories.

Previous topological analyses of DNA sequence organization in the interphase chromosome mainly focused on the spatial distribution of individual gene copies within chromosome territories. In order to achieve a more comprehensive view into the subchromosomal arrangement of DNA, we isolated the GC-richest/gene-richest fraction (H3 isochores) as well as AT-richest/gene-poorest fraction of human genomic DNA (L1+L2 isochores) and visualized the respective DNA within individual chromosome territories by means of dual-color FISH. Application of confocal laser scanning microscopy and dedicated 3D image analysis software, which differentiated territory subvolumes by peeling shells one voxel in width, revealed a significant difference in the intraterritorial distribution of these two DNA sequence classes. While the H3 isochores were found localized in all subvolumes of the territories at similar frequency, simultaneously detected L1+L2 isochores were observed more to the interior of the same chromosome territories. Thus the GC-rich sequences display a much higher variability in their intraterritorial localization than AT-rich DNA fragments.

Chromosomes, Human↗
PubMed1993

Baculovirus expression of the ADRV gene 5 encoded protein produces an oligomerized, antigenic, and immunogenic VP6 protein.

Adult diarrheal rotavirus (ADRV) is a currently noncultivatable group B human rotavirus responsible for epidemic outbreaks of gastroenteritis in China. Gene segment 5 of ADRV encodes the major inner capsid protein, VP6. ADRV gene 5 was inserted into a recombinant baculovirus by homologous recombination between baculovirus shuttle plasmid pACYM1-AD5 and AcNPV genomic DNA. Baculovirus recombinants were selected visually and plaque purified and VP6 expression was detected by Coomassie staining of PAGE-separated proteins. The baculovirus-expressed gene 5 polypeptide is 44 kDa, the same as for the major inner capsid protein present on EDTA-treated ADRV virions and in vitro-expressed VP6 protein. The expressed protein is oligomeric and in the absence of reducing agents multimerizes to apparent trimer, hexamer, and greater molecular mass as assayed by SDS-PAGE. The VP6 protein is immunoprecipitable by hyperimmune serum to ADRV, human ADRV convalescent serum, by a group B-specific monoclonal antibody and by porcine group B rotavirus infection serum. The baculovirus-expressed protein is immunogenic and antibodies to the expressed protein recognize ADRV virions. The ADRV VP6 protein should be useful for developing diagnostic assays for serum antibodies to group B rotavirus as well as for generating hyperimmune serum and monoclonal antibodies for detecting viral antigen from ADRV and other group B rotaviruses.

Antibodies, Monoclonal↗
PubMed1987

A method for nucleic acid hybridization to isolated chromosomes in suspension.

A procedure was developed to provide differential fluorescent staining of metaphase chromosomes in suspension following nucleic acid hybridization. For this purpose metaphase chromosomes were isolated from a Chinese hamster X human hybrid cell line. After hybridization with biotinylated human genomic DNA, the human chromosomes were visualized by indirect immunofluorescence using antibodies against biotin and fluoresceine-isothiocyanate-(FITC)-labeled second antibodies. This resulted in green fluorescent human chromosomes. In contrast, Chinese hamster chromosomes revealed red fluorescent staining only when counterstained with propidium iodide. Notably, interspecies chromosomal rearrangements could be easily detected. After hybridization and fluorescent staining, chromosomes still showed a well-preserved morphology under the light microscope. We suggest that this procedure may have a useful application in flow cytometry and sorting.

Animals↗