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At least 847 records · Page 47Linked to original sources
PubMed2002

Genetic labelling of specific axonal pathways in the mouse central nervous system.

We report on transgenic mouse lines in which several sensory systems in the brain are specifically visualized genetically. We employed GAP-lacZ as an axon-targeted reporter protein that was constructed by fusing the membrane-anchoring domain of the GAP-43 protein to lacZ. The reporter gene was introduced into the genome under the control of a promoter element of Brn3b transcription factor to establish transgenic mouse lines. The individual lines thus generated afforded clear images of specific axonal pathways of the visual, vomeronasal, pontocerebellar, and auditory systems. The reporter protein labelled the entire axonal process as well as the cell body of developing and mature neurons on staining with X-gal. We show that these lines facilitate the developmental and anatomical study of these neural systems. This strategy should be applicable to a variety of neural systems by using various specific promoter elements.

Animals↗
PubMed2006

PATRIC: the VBI PathoSystems Resource Integration Center.

The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: 'breadth first' beginning with whole-genome and proteome curation using standardized protocols, a 'targeted' approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website (https://patric.vbi.vt.edu) will continually grow with the addition of data, analysis and functionality over the course of the project.

Bioterrorism↗
PubMed1986

Characterization of the DNA of the hamster papovavirus. III. Mapping of inverted repeated DNA sequences within the viral genome.

Sequences with 2-fold axis of symmetry (inverted repeated sequences) have been detected and mapped on the hamster papovavirus (HaPV) genome by their ability to form secondary structures like hairpins or stem-loops on single-stranded HaPV DNA. DNA regions with secondary structure were visualized by electron microscopy and mapped according to the physical map of HaPV. Eleven positions containing inverted repeats could be determined. The nucleotide sequence within all of these inverted repeats may be related since these regions can crosshybridize with each other. The possible functions of these sequences within the HaPV genome are discussed with respect to conditions found for genomes like those from SV40 and polyoma virus to get first indications for the localization of DNA regions representing the origin and termination of replication of HaPV DNA.

Animals↗
PubMed1998

Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome.

Diagnostic re-sequencing plays a central role in medical and evolutionary genetics. In this report we describe a process that applies fluorescence-based re-sequencing and an integrated set of analysis tools to automate and simplify the identification of DNA variations using the human mitochondrial genome as a model system. Two programs used in genome sequence analysis (Phred, a base-caller, and Phrap, a sequence assembler) are applied to assess the quality of each base call across the sequence. Potential DNA variants are automatically identified and 'tagged' by comparing the assembled sequence with a reference sequence. We also show that employing the Consed program to display a set of highly annotated reference sequences greatly simplifies data analysis by providing a visual database containing information on the location of the PCR primers, coding and regulatory sequences and previously known DNA variants. Among the 12 genomes sequenced 378 variants including 29 new variants were identified along with two heteroplasmic sites, automatically detected by the PolyPhred program. Overall we document the ease and speed of performing high quality and accurate fluorescence-based re-sequencing on long tracts of DNA as well as the application of new approaches to automatically find and view DNA variants among these sequences.

Base Sequence↗
PubMed2002

Molecular visualization of immunoglobulin switch region RNA/DNA complex by atomic force microscope.

Immunoglobulin heavy-chain (IgH) class switch recombination (CSR) is initiated by DNA breakage in the switch (S) region featuring tandem repetitive nucleotide sequences. Various studies have demonstrated that S-region transcription and splicing proceed to genomic recombination and are indispensable for CSR in vivo, although the precise molecular mechanism is largely unknown. Here, we show the novel physical property of the in vitro transcribed S-region RNA by direct visualization using an atomic force microscope (AFM). The S-region sense RNA, but not the antisense RNA, forms a persistent hybrid with the template plasmid DNA and changes the plasmid conformation from supercoil to open circle in the presence of spermidine. In addition, the S-region transcripts generate globular forms and are assembled on the template DNA into a large aggregate that may stall replication and increase the recombinogenicity of the S-region DNA.

Immunoglobulin Class Switching↗
PubMed2003

[Molecular epidemiology of Mycobacterium tuberculosis using by RFLP analysis between genomic DNA--its accomplishment and practice].

Recently, epidemiology of M. tuberculosis have been performed by molecular techniques as a probe with the insertion sequence (IS) 6110. In the traditional study of tuberculosis epidemiology, information about social contact of persons and patient's illness history used to be an only relevant basis for elucidating transmission of tuberculosis infection. Therefore, it was very difficult to give a clear conclusion of whether isolates from different patients derived from a common source of infection or not. The subspecies typing of M. tuberculosis strains by IS6110 has become possible, based on the visualization of multiple loci of an insertion sequence (IS6110) that is a relatively stable gene fragment existing in a specific region of the genome. The variability of the number of copies and locations of this IS6110 in a genome is the basis that enables this technique to be used for the above purpose, which is a unique tool applicable to the analysis of M. tuberculosis. Generally, this technique, i.e., restriction fragment length polymorphism (RFLP) analysis, depends on the diversity of pattern of any polymorphic marker found in a genome of a strain. Among various markers so far developed and examined, IS6110 has been proved most appropriate for the purpose of typing strains of M. tuberculosis complex, especially in such circumstances as in Japan where isolated strains' RFLP patterns are similar each with others so that finer subtyping is needed. In this time, I would like to review the following topics based on the world literature of molecular epidemiology and the findings of our own that we have achieved during 1992 through 2001 in our Institute; (1) typing for the tracking of source of infection, (2) diffuse infection, (3) the presence of region-specific influential strains, (4) cross-contamination of strains in the laboratory, (5) the stability of IS6110, (6) phylogeny of tuberculosis (genotypes in Okinawa prefecture), and (7) the distinction between M. tuberculosis and M. bovis BCG, (8) computer-assisted patients management system. We also investigated the mode of transmission and risk factors of tuberculosis, based on the tuberculosis epidemiological data obtained in many parts of the world as well as the findings we gathered in our country from 1992 to 2001.

DNA, Bacterial↗
PubMed2005

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.

BACKGROUND: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity. RESULTS: We describe the implementation of a search method for putative transcription factor binding sites (TFBSs) based on hidden Markov models built from alignments of known sites. We built 1,079 models of TFBSs using experimentally determined sequence alignments of sites provided by the TRANSFAC and JASPAR databases and used them to scan sequences of the human, mouse, fly, worm and yeast genomes. In several cases tested the method identified correctly experimentally characterized sites, with better specificity and sensitivity than other similar computational methods. Moreover, a large-scale comparison using synthetic data showed that in the majority of cases our method performed significantly better than a nucleotide weight matrix-based method. CONCLUSION: The search engine, available at http://mapper.chip.org, allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, fly, worm and yeast genomes. In addition it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Due to its extensive database of models, powerful search engine and flexible interface, MAPPER represents an effective resource for the large-scale computational analysis of transcriptional regulation.

Algorithms↗
PubMed2001

GABA and the ornithine delta-aminotransferase gene in vigabatrin-associated visual field defects.

Vigabatrin use in some epilepsy patients has been associated with persistent visual field constriction and retinal dysfunction. The mechanism is unknown, but could be related to vigabatrin, chronic epilepsy, GABA toxicity, or the effect of a metabolite in combination with a predisposing genotype. The aim of this study was to investigate the latter two hypotheses. Levels of brain gamma-aminobutyric acid (GABA) measured by nuclear magnetic resonance spectroscopy were similar in subjects taking vigabatrin who developed visual field constriction and those who did not. We tested whether allelic heterogeneity of the ornithine aminotransferase gene occurs in the affected patients. No clinically significant mutation was detected, although a common intronic polymorphism was identified.

Anticonvulsants↗
PubMed2002

TAIR: a resource for integrated Arabidopsis data.

The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) provides an integrated view of genomic data for Arabidopsis thaliana. The information is obtained from a battery of sources, including the Arabidopsis user community, the literature, and the major genome centers. Currently TAIR provides information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins. In addition, users can find Arabidopsis publications and information about Arabidopsis researchers. Our emphasis is now on incorporating functional annotations of genes and gene products, genome-wide expression, and biochemical pathway data. Among the tools developed at TAIR, the most notable is the Sequence Viewer, which displays gene annotation, clones, transcripts, markers and polymorphisms on the Arabidopsis genome, and allows zooming in to the nucleotide level. A tool recently released is AraCyc, which is designed for visualization of biochemical pathways. We are also developing tools to extract information from the literature in a systematic way, and building controlled vocabularies to describe biological concepts in collaboration with other database groups. A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site.

Arabidopsis↗
PubMed2024

Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation.

Flaviviruses replicate their genomes in replication organelles (ROs) formed as bud-like invaginations on the endoplasmic reticulum (ER) membrane, which also functions as the site for virion assembly. While this localization is well established, it is not known to what extent viral membrane remodeling, genome replication, virion assembly, and maturation are coordinated. Here, we imaged tick-borne flavivirus replication in human cells using cryo-electron tomography. We find that the RO membrane bud is shaped by a combination of a curvature-establishing coat and the pressure from intraluminal template RNA. A protein complex at the RO base extends to an adjacent membrane, where immature virions bud. Naturally occurring furin site variants determine whether virions mature in the immediate vicinity of ROs. We further visualize replication in mouse brain tissue by cryo-electron tomography. Taken together, these findings reveal a close spatial coupling of flavivirus genome replication, budding, and maturation.

Journal Article↗
PubMed2006

Accelerating the reconstruction of genome-scale metabolic networks.

BACKGROUND: The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method to accelerate the time-consuming process of network reconstruction for a query species. The method exploits the availability of well-curated metabolic networks and uses high-resolution predictions of gene equivalency between species, allowing the transfer of gene-reaction associations from curated networks. RESULTS: We have evaluated the method using Lactococcus lactis IL1403, for which a genome-scale metabolic network was published recently. We recovered most of the gene-reaction associations (i.e. 74 - 85%) which are incorporated in the published network. Moreover, we predicted over 200 additional genes to be associated to reactions, including genes with unknown function, genes for transporters and genes with specific metabolic reactions, which are good candidates for an extension to the previously published network. In a comparison of our developed method with the well-established approach Pathologic, we predicted 186 additional genes to be associated to reactions. We also predicted a relatively high number of complete conserved protein complexes, which are derived from curated metabolic networks, illustrating the potential predictive power of our method for protein complexes. CONCLUSION: We show that our methodology can be applied to accelerate the reconstruction of genome-scale metabolic networks by taking optimal advantage of existing, manually curated networks. As orthology detection is the first step in the method, only the translated open reading frames (ORFs) of a newly sequenced genome are necessary to reconstruct a metabolic network. When more manually curated metabolic networks will become available in the near future, the usefulness of our method in network prediction is likely to increase.

Bacillus subtilis↗
PubMed2003

New tools for quantifying and visualizing adoptively transferred cells in recipient mice.

Adoptive transfer of donor cells in mice is widely used in research on the function and metabolism of lymphocytes. We have evaluated new approaches for quantifying and visualizing adopted cells in recipient mouse tissue. We injected spleen cells from male beta-galactosidase (LacZ) transgenic mice into female wild type mice and assessed the robustness of real-time PCR for quantifying the accumulation of the donor cells in blood and tissues of the recipient mice. The clearance of donor cells from the blood and their recruitment in lung, spleen, liver, and kidney was almost identical when obtained with amplification of the donor cell-specific LacZ or sex-determining region on the Y-chromosome (SRY) gene. We found, however, a marked difference in the PCR amplification efficiency of genomic DNA of different tissues, which should be taken into account when comparing recruitment of donor cells in different tissues. To visualize adoptively transferred cells, we used either spleen cells from transgenic mice, which express a Green Fluorescent Protein (GFP) transgene or spleen cells that had been fluorescence labeled ex vivo with CellTracker Orange. Whereas ex vivo and in vivo labeled donor cells could easily be detected in recipient mouse tissue by laser scanning confocal microscopy, only CellTracker Orange-labeled cells could be detected by conventional fluorescence microscopy due to autofluorescence in the examined tissues. Importantly, CellTracker Orange labeling did not appear to affect the blood clearance or the tissue accumulation of the donor cells. Together, the results demonstrate the usefulness of new protocols for quantifying and visualizing adoptively transferred cells by genetic tracing or fluorescence labeling.

Adoptive Transfer↗
PubMed2001

Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome.

With increases in the amounts of available DNA sequence data, it has become increasingly important to develop tools for comprehensive systematic analysis and comparison of species-specific characteristics of protein-coding sequences for a wide variety of genomes. In the present study, we used a novel neural-network algorithm, a self-organizing map (SOM), to efficiently and comprehensively analyze codon usage in approximately 60,000 genes from 29 bacterial species simultaneously. This SOM makes it possible to cluster and visualize genes of individual species separately at a much higher resolution than can be obtained with principal component analysis. The organization of the SOM can be explained by the genome G+C% and tRNA compositions of the individual species. We used SOM to examine codon usage heterogeneity in the E. coli O157 genome, which contains 'O157-unique segments' (O-islands), and showed that SOM is a powerful tool for characterization of horizontally transferred genes.

Algorithms↗
PubMed2006

A new measure for functional similarity of gene products based on Gene Ontology.

BACKGROUND: Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. RESULTS: We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; simRel and funSim. One measure (simRel) is applied in the comparison of the biological processes found in different groups of organisms. The other measure (funSim) is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. CONCLUSION: The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.

Algorithms↗
PubMed2005

Galaxy: a platform for interactive large-scale genome analysis.

Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.

Biological Evolution↗
PubMed1996

Fiber-FISH: experiences and a refined protocol.

One of the most time-consuming steps in positional cloning is the physical mapping of probes from the critical chromosomal region and the assembly of a genomic contig of large insert probes. New high-resolution Fiber-FISH techniques have significantly facilitated this tedious task by enabling rapid direct visualization of the order, degree of overlap and gap sizes of adjacent large insert clones. We have developed a method, where agarose-embedded DNA (PFGE block) is used as a source for preparing linearized DNA targets on microscope slides. This modification of the fiber-FISH technique has been successfully used in physical mapping in the 1-300 kb range as well as for detecting genomic rearrangements. Here, we present a refined protocol of our original technique. The application of this technique to agarose embedded yeast cells is also demonstrated. Finally, critical steps and trouble shooting of the method are addressed.

Chromosome Mapping↗
PubMed2004

Transgenerational genomic instability as revealed by a somatic mutation assay using the medaka fish.

We previously established a somatic mutation assay of the medaka wl (white leucophores) locus based on visual inspection, and showed that somatic mutations at paternally derived alleles frequently arise during the development of F1 embryos fertilized by sperm/late spermatids that had been exposed to gamma-rays. To further study such delayed mutations, we determined the frequency of mutant embryos obtained from three different crosses between irradiated males and non-irradiated females. When sperm and late spermatids were irradiated, the mutant frequency within non-irradiated maternally derived alleles was approximately 3 times higher than in the control group. In the F2 generation, however, no increase in mutant frequency was observed. Similarly, there was no significant increase in the F1 mutant frequency when stem spermatogonia were irradiated. These data suggest that irradiation of sperm and late spermatids can induce indirect mutations in F1 somatic cells, supporting the idea that genomic instability arises during F1 embryonic development. Moreover, such instability apparently arises most frequently when eggs are fertilized just after the sperm are irradiated.

Abnormalities, Radiation-Induced↗
PubMed2002

[Trends in the post-genomic pharmacological research].

With the advent of post-genome era, pharmacogenomics will be a new field in pharmacological sciences. In parallel, high-throughput screening, in silico research, as well as lots of visualization techniques are emerging as novel approaches in pharmacological researches. Some progress in the implementation of aforementioned new idea and methods in pharmacodynamics and pharmacokinetics research are also introduced in this review.

Genome, Human↗