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At least 613 records · Page 34Linked to original sources
PubMed1994

[Hepatitis C].

Hepatitis C virus (HCV) was recognized in 1989 as the main cause of transfusion-related hepatitis non-A, non-B (HNANB) as well as sporadically-acquired HNANB infections. The HCV genome has been sequenced but the virus has not yet been visualized. Anti-HCV antibody tests have been developed, namely enzyme-linked immunosorbent assays (ELISA) for screening and recombinant immunoblot assay (RIBA) for confirmative testing of ELISA positive results. Since May 1991 all Danish blood donations have been tested for anti-HCV antibodies. Approximately 0.04% of Danish blood donors are 4-RIBA positive and have signs of chronic HCV infection based on ALT, HCV-RNA or histological findings. High-risk groups are intravenous drug abusers, haemophiliacs, haemodialysis patients and recipients of multiple blood transfusions. Approximately one third of the cases are sporadic, i.e. without obvious risk factors. Sexual transmission of HCV may occur, but this route is uncommon. More than half of the patients with acute HCV infection progress to chronic hepatitis C. Of these a considerable proportion develops cirrhosis and some eventually hepatocellular carcinoma. At present interferon (IFN) is the only registered therapy against chronic hepatitis C. Approximately half of the patients respond to treatment. The majority, however, relapse after stopping IFN treatment and only 20% maintain their response.

Hepacivirus↗
PubMed2002

BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.

MOTIVATION: Understanding the biochemistry of a newly sequenced organism is an essential task for post-genomic analysis. Since, however, genome and array data grow much faster than biochemical information, it is necessary to infer reactions by comparative analysis. No integrated and easy to use software tool for this purpose exists as yet. RESULTS: We present a new software system--BioMiner--for analyzing and visualizing biochemical pathways and networks. BioMiner is based on a new comprehensive, extensible and reusable data model--BioCore--which can be used to model biochemical pathways and networks. As a first application we present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based on sequence similarity. We successfully tested PathFinder with a number of experiments, e.g. the well studied glycolysis in bacteria. Additionally, an application called PathViewer for the visualization of metabolic networks is presented. PathViewer is the first application we are aware of which supports the graphical comparison of metabolic networks of different organisms. AVAILABILITY: http://www.zbi.uni-saarland.de/chair/projects/BioMiner SUPPLEMENTARY INFORMATION: Additional information on experimental results can be found on our web site.

Biochemistry↗
PubMedDate not supplied

Altered drug resistance and recovery from paralysis in Drosophila melanogaster with a deficient histamine-gated chloride channel.

The recent identification and characterization of two genes, encoding histamine-gated chloride channel subunits from Drosophila melanogaster, has confirmed that histamine is a major neurotransmitter in the fruitfly. One of the cloned genes, hclA (synonyms: HisCl-alpha1; HisCl2), corresponds to ort (ora transientless), mutationsin which affect synaptic transmission in the Drosophila visual system. We identified a mutational change (a null mutation) in the genomic and RNA copies of hclA derived from mutants carrying the ort(1) allele. This correlates with new phenotypes observed in the mutant strain. We found hypersensitivity to the avermectin neurotoxins in both the ort(1) adult flies and third instar larvae compared to Oregon R wild-type animals. On the other hand, the mutation makes both male and female adult flies more resistant to treatment with diethyl ether, and the animals show substantially prolonged recovery from paralysis after diethylether anaesthesia, as well as from paralysis after mechanical shock, as revealed by the bang sensitivity test. Altogether, our data give direct evidence that in vivo a HCLA subunit-containing receptor has a distinct role in the neurotoxic action of the avermectins. They also provide new evidence for a function in the response to diethylether anaesthesia and, moreover, that HCLA function is not limited to the visual system.

Anesthetics, Inhalation↗
PubMed1992

Polymerase chain reaction-based DNA fingerprinting in the spontaneously hypertensive rat: potential source of cDNA library probes.

1. Using the Polymerase Chain Reaction with a primer homologous to a repetitive unit found at irregular distances in the rat genome, we were able to synthesize DNA fragments spanning such units and visualize them as a ladder of discrete bands following electrophoresis. 2. Differences between fingerprint patterns generated using SHR, WKY and SD DNA, in the form of band deletions or duplications, were readily detected. 3. Unlike traditional fingerprinting, PCR fingerprints allow the ready extraction and characterization of polymorphic bands. Such bands could then be used as probes with which to screen a cDNA library that might, in turn, identify expressed genes involved in the development of hypertension.

Animals↗
PubMed2001

FhuA-mediated phage genome transfer into liposomes: a cryo-electron tomography study.

BACKGROUND: The transfer of phage genomes into host cells is a well established but only dimly understood process. Following the irreversible phage binding to a receptor in the bacterial outer membrane, the DNA is ejected from the viral capsid and transferred across the bacterial cell envelope. In Escherichia coli, the mere interaction of the phage T5 with its outer membrane receptor, the ferrichrome transporter FhuA, is sufficient to trigger the release of the DNA from the phage capsid. Although the structure of FhuA has been determined at atomic resolution, the understanding of the respective roles of phage and bacterial proteins in DNA channeling and the mechanisms by which the transfer of the DNA is mediated remains fragmentary. RESULTS: We report on the use of cryo-electron tomography to analyze, at a molecular level, the interactions of T5 phages bound to FhuA-containing proteoliposomes. The resolution of the three-dimensional reconstructions allowed us to visualize the phage-proteoliposome interaction before and after release of the genome into the vesicles. After binding to its receptor, the straight fiber of the phage T5 (the "tip" of the viral tail made of pb2 proteins) traverses the lipid bilayer, allowing the transfer of its double-stranded DNA (121,000 bp) into the proteoliposome. Concomitantly, the tip of the tail undergoes a major conformational change; it shrinks in length (from 50 to 23 nm), while its diameter increases (from 2 to 4 nm). CONCLUSIONS: Taking into account the crystal structure of FhuA, we conclude that FhuA is only used as a docking site for the phage. The tip of the phage tail acts like an "injection needle," creating a passageway at the periphery of FhuA, through which the DNA crosses the membrane. A possible mechanistic scenario for the transfer of the viral genome into bacteria is discussed.

Bacterial Outer Membrane Proteins↗
PubMed2003

Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans.

In this paper we present a new method for detecting block duplications in a genome. It is more stringent than previous ones in that it requires a more rigorous definition of paralogous genes and that it requires the paralogous proteins on the two blocks to be contiguous. In addition, it provides three criterion choices: (1) the same composition (i.e., having the same paralogues in the two windows), (2) the same composition and gene order, and (3) the same composition, gene order, and gene orientation. The method is completely automated, requiring no visual inspection as in previous methods. We applied it to analyze the complete genomes of S. cerevisiae and C. elegans. In yeast we detected fewer duplicated blocks than previously reported. In C. elegans, however, we detected more block duplications than previously reported, indicating that although our method has a more stringent definition of block duplication than previous ones, it may be more sensitive in detection because it considers every possible window rather than only fixed nonoverlapping windows. Our results show that block duplication is a common phenomenon in both organisms. The patterns of block duplication in the two species are, however, markedly different. The yeast shows much more extensive block duplication than the nematode, with some chromosomes having more than 40% of the duplications derived from block duplications. Moreover, in the yeast the majority of block duplications occurred between chromosomes, while in the nematode most block duplications occurred within chromosomes.

Animals↗
PubMed2003

GPCEG-A database for genomic polymorphism of Chinese ethnic groups.

This paper reports the construction of the database for Genomic Polymorphism of Chinese Ethnic Groups (GPCEG). GPCEG contains denomination and basic information of Chinese 56 ethnic groups, with introduction of their in geographic distribution, population quantity, spoken and written language, religious belief and physical characteristics. GPCEG collects the data of genomic polymorphism, cell lines, reference and links of other international related databases. The visualization, query and update system were also available. GPCEG laid the foundations of establishing a national database with Chinese characteristics.

Cell Line↗
PubMed2005

Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses.

MapMan is a user-driven tool that displays large genomics datasets onto diagrams of metabolic pathways or other processes. Here, we present new developments, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, the incorporation of statistics packages, and extensions of the software to incorporate more biological information including visualization of corresponding genes and horizontal searches for similar global responses across large numbers of arrays.

Genes, Plant↗
PubMed1992

Intron requirement for expression of the human purine nucleoside phosphorylase gene.

Abbreviated purine nucleoside phosphorylase (PNP) genes were engineered to determine the effect of introns on human PNP gene expression. PNP minigenes containing the first intron (complete or shortened from 2.9 kb down to 855 bp), the first two introns or all five PNP introns resulted in substantial human PNP isozyme expression after transient transfection of murine NIH 3T3 cells. Low level human PNP activity was observed after transfection with a PNP minigene containing the last three introns. An intronless PNP minigene construct containing the PNP cDNA fused to genomic flanking sequences resulted in undetectable human PNP activity. Heterogeneous, stable NIH 3T3 transfectants of intron-containing PNP minigenes (verified by Southern analysis), expressed high levels of PNP activity and contained appropriately processed 1.7 kb message visualized by northern analysis. Stable transfectants of the intronless PNP minigene (40-45 copies per haploid genome) contained no detectable human PNP isozyme or mRNA. Insertion of the 855 bp shortened intron 1 sequence in either orientation upstream or downstream of a chimeric PNP promoter-bacterial chloramphenicol acetyltransferase (CAT) gene resulted in a several-fold increase in CAT expression in comparison with the parental PNP-CAT construct. We conclude that human PNP gene expression at the mRNA and protein level is dependent on the presence of intronic sequences and that the level of PNP expression varies directly with the number of introns included. The disproportionately greatest effect of intron 1 can be explained by the presence of an enhancer-like element retained in the shortened 855 bp intron 1 sequence.

3T3 Cells↗
PubMed2004

Visualizing chromosome structure/organization.

With the rapid development of sequencing technologies in the past decade, many eukaryotic genomes have been resolved at the primary sequence level. However, organization of the genome within nuclei and the principles that govern such properties remain largely unclear. Optimization of fluorescence probe-based hybridization technologies combined with new advances in the instrumentation for microscopy has steadily yielded more structural information on chromosome organization in eukaryote model systems. These studies provide static snapshots of the detailed organization of chromatin. More recently, the successful application of a chromatin tagging strategy utilizing auto fluorescent fusion proteins opened a new era of chromatin studies in which the dynamic organization of the genome can be tracked in near real time. This review focuses on these new approaches to studying chromatin organization and dynamics in plants, and on future prospects in unraveling the basic principle of chromosome organization.

Chromatin↗
PubMed2003

Layout search of a gene regulatory network for 3-D visualization.

In recent years, base sequences have been increasingly unscrambled through attempts represented by the human genome project. Accordingly, the estimation of the genetic network has been accelerated. However, no definitive method has become available for drawing a large effective graph. This paper proposes a method which allows for coping with an increase in the number of nodes by laying out genes on planes of several layers and then overlapping these planes. This layout involves an optimization problem which requires maximizing the fitness function. To demonstrate the effectiveness of our approach, we show some graphs using actual data on 82 genes and 552 genes. We also describe how to lay out nodes by means of stochastic searches, e.g., stochastic hill-climbing and incremental methods. The experimental results show the superiority and usefulness of two search methods in comparison with the simple random search.

Gene Expression Regulation↗
PubMed2005

Computational cluster validation in post-genomic data analysis.

MOTIVATION: The discovery of novel biological knowledge from the ab initio analysis of post-genomic data relies upon the use of unsupervised processing methods, in particular clustering techniques. Much recent research in bioinformatics has therefore been focused on the transfer of clustering methods introduced in other scientific fields and on the development of novel algorithms specifically designed to tackle the challenges posed by post-genomic data. The partitions returned by a clustering algorithm are commonly validated using visual inspection and concordance with prior biological knowledge--whether the clusters actually correspond to the real structure in the data is somewhat less frequently considered. Suitable computational cluster validation techniques are available in the general data-mining literature, but have been given only a fraction of the same attention in bioinformatics. RESULTS: This review paper aims to familiarize the reader with the battery of techniques available for the validation of clustering results, with a particular focus on their application to post-genomic data analysis. Synthetic and real biological datasets are used to demonstrate the benefits, and also some of the perils, of analytical clustervalidation. AVAILABILITY: The software used in the experiments is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/. SUPPLEMENTARY INFORMATION: Enlarged colour plots are provided in the Supplementary Material, which is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/.

Algorithms↗
PubMed2001

Comparative evaluation of three commercial software packages for analysis of DNA polymorphism patterns.

OBJECTIVE: In the present study we have compared three commercial software packages, GelCompar, Molecular Analyst Fingerprinting, and BioImage, to determine if the results generated by the programs were comparable and correlated adequately with visual interpretation of electrophoretic gels, in the analysis of several well characterized incidents of infections. METHODS: Infections caused by Pseudomonas aeruginosa, Candida dubliniensis, C. albicans, and serotypes of Salmonella were characterized by restriction endonuclease analysis, macrorestriction analysis of genomic DNA with pulsed-field gel electrophoresis, and random amplified polymorphic DNA. The genotypes were visually detected based on band presence or absence in the different gels. The similarity values of DNA profiles were computed using Dice coefficient and were presented in dendrograms by UPGMA. The concordance or agreement between the number of genotypes obtained and their clustering, using the computerized programs, was determined. RESULTS: In general, agreement in number of genotypes obtained visually and by using the commercial DNA analysis software was achieved, but discrepancies were also denoted between the systems. The concordance between the visual and the computerized analysis ranged from 72% to 100%. CONCLUSION: In our experience, although the programs evaluated in the present study performed acceptably well, such programs may be used as an aid in the analysis of complex banding patterns, and they do not provide an indisputably correct analysis in genotype definition.

Animals↗
PubMed2025

Visualizing the conformational landscape of CRISPR-Cas9 through kinetics-informed structural studies.

CRISPR-Cas9 has transformed genome editing through its programmability and versatility. Its DNA cleavage activity involves dynamic conformational changes during gRNA binding, DNA recognition, R-loop formation, and endonuclease activation. Understanding these molecular transitions is critical for improving the specificity and efficiency of Cas9, but this remains challenging precisely due to these rapid structural rearrangements. Early structural studies provided foundational insights but were limited to static states under catalytically inactive conditions. Cryo-EM has since enabled visualization of the dynamic nature of active Cas9, by enriching for specific conformations. This chapter introduces a kinetics-informed cryo-EM approach to capture the stepwise activation of Cas9 in real time. With thorough kinetic analyses, such as stopped-flow measurements of R-loop formation, we describe how to identify optimal timepoints to visualize key conformational states with cryo-EM. Integration of kinetic and structural data enables precise mapping of the conformational landscape of Cas9 and other dynamic enzymes, advancing our understanding of their molecular mechanisms and providing a framework for engineering enhanced variants.

Cryoelectron Microscopy↗
PubMed2004

Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data.

Integration of the large variety of genome maps from several organisms provides the mechanism by which physiological knowledge obtained in model systems such as the rat can be projected onto the human genome to further the research on human disease. The release of the rat genome sequence provides new information for studies using the rat model and is a key reference against which existing and new rat physiological results can be aligned. Previously, we described comparative maps of the rat, mouse, and human based on EST sequence comparisons combined with radiation hybrid maps. Here, we use new data and introduce the Integrated Genomics Environment, an extensive database of curated and integrated maps, markers, and physiological results. These results are integrated by using VCMapview, a java-based map integration and visualization tool. This unique environment allows researchers to relate results from cytogenetic, genetic, and radiation hybrid studies to the genome sequence and compare regions of interest between human, mouse, and rat. Integrating rat physiology with mouse genetics and clinical results from human by using the respective genomes provides a novel route to capitalize on comparative genomics and the strengths of model organism biology.

Animals↗
PubMed2002

Triplex-forming DNAs in the human interphase nucleus visualized in situ by polypurine/polypyrimidine DNA probes and antitriplex antibodies.

The polypurine/polypyrimidine (PuPy) tracts present in the human genome are known to be scattered among and within chromosomes. In PuPy tract sequences, triplex formation occurs readily under physiological conditions, leaving single-stranded DNAs capable of hybridization with complementary single-stranded DNAs and RNAs. The formation of single-strands and transmolecular triplexes is thought to enable sequences spaced distantly along the genome to associate with each other and organize nuclear DNA into ordered configurations. Triplex-forming DNAs in the human interphase nucleus were analyzed by combining fluorescence in situ "nondenaturing" hybridization employing PuPy tract probes and immunodetection by antitriplex antibodies. The nondenaturing hybridization technique, which has been used to detect RNA, may detect single-stranded DNAs in nondenatured nuclei, if present. Probes such as (GA/TC)(n) and (GAA/TTC)(n) sequences gave sequence-specific signals that overlapped with or were closely associated with triplexes immunolocalized by using known antitriplex antibodies. Pretreatment of nuclei with antitriplex antibodies blocked probe signal formation. Signal formation was resistant to pretreatment of nuclei with RNases but sensitive to single strand-specific nucleases. Triplexes visualized differentially with distinct PuPy tract probes were associated spatially with centromeric sequences in the interphase nucleus in a sequence-specific manner.

Cell Line↗
PubMed2005

Identification and visualization of the dimerization initiation site of the prototype lentivirus, maedi visna virus: a potential GACG tetraloop displays structural homology with the alpha- and gamma-retroviruses.

Dimerization of retroviral genomic RNA is essential for efficient viral replication and is mediated by structural interactions between identical RNA motifs in the viral leader region. We have visualized, by electron microscopy, RNA dimers formed from the leader region of the prototype lentivirus, maedi visna virus. Characterization by in vitro assays of the domains responsible for this interaction has identified a 20 nucleotide sequence that functions as the core dimerization initiation site. This region is predicted to form a GACG tetraloop and therefore differs significantly from the kissing loop palindromes utilized to initiate dimerization in primate lentiviruses. The motif is strongly conserved across the ovine and caprine lentiviruses, implying a critical functional role. Furthermore, the proposed GACG tetraloop exhibits marked structural homology with similar structural motifs present in the leader regions of the alpha- and gamma-retroviruses, and the maedi visna virus dimer linkage region is capable of forming heterodimeric species with the Moloney murine leukemia virus Psi domain. This may be indicative of commonality of origin of the two viruses or convergent evolution.

Animals↗
PubMed1996

Structural analysis of mitochondrial DNA molecules from fungi and plants using moving pictures and pulsed-field gel electrophoresis.

The size and structure of mitochondrial DNA (mtDNA) molecules was investigated by conventional and pulsed-field gel electrophoresis (PFGE) and by analyzing moving pictures during electrophoresis of individual fluorescently labelled mtDNA molecules. Little or no mtDNA that migrated into the gel was found in circular form for fungi (Schizosaccharomyces pombe, Saccharomyces cerevisiae and Neurospora crassa) or plants (Brassica hirta, tobacco, voodoo lily and maize). Most mtDNA migrated as a smear of linear DNA sizes from about 50 to 100 or 250 kilobases (kb), depending on the species, irrespective of the size of the mitochondrial genome over a range of 0.06 to 570 kb. S. cerevisiae, B. hirta and tobacco also yielded a linear mtDNA fraction containing molecules > 1000 kb in size. About half the mtDNA remained in the well of the gel after PFGE. Moving pictures revealed that this well-bound (wb) mtDNA contained molecules larger than the genome size in linear form for all species (except N. crassa) and in multi-fibered, comet-like forms for most of the wb mtDNA of N. crassa and Sc. pombe. A minor amount of the wb mtDNA with visually interpretable structure was circular: circle sizes were both larger and smaller than the 80-kb genome of S. cerevisiae, larger than the 19-kb genome of Sc. pombe and smaller than the 208-kb and 570-kb genomes of B. hirta and maize, respectively. About 25 to 75% of the wb mtDNA from cultured tobacco cells was found in circles smaller than its genome size. Partial digestion of Sc. pombe mtDNA with restriction endonucleases that cleave once per genome revealed gel bands at about 38 kb and 19 kb with a smear of sizes between the bands and below the 19-kb band, suggesting a head-to-tail genomic concatemer as the most prominent form in extracted mtDNA. A pattern of bands with smears was also found for complete digests (with multiply cleaving enzymes) of mtDNA from Sc. pombe, S. cerevisiae and N. crassa, but bands without smears were found for digests of DNA from phage lambda and several plasmids.

DNA, Fungal↗