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At least 865 records · Page 48Linked to original sources
PubMed2005

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny.

Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyze multigene data sets. Consensus methods provide an alternative, more inclusive, approach for analyzing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 21:1459-1461) to incorporate additional information. This additional information could come from bootstrap analysis, Bayesian analysis, or various methods to find confidence sets of trees. The new methods can be extended to include edge weights representing genetic distance. We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa.

Animals↗
PubMed1993

Detection of viremia by a one step polymerase chain reaction method in hepatitis C virus infection.

A simple, sensitive, and specific one step polymerase chain reaction (PCR) method for the detection of hepatitis C virus (HCV) RNA in infected patients' serum or plasma samples is described. We performed the one step PCR amplification in combination with the initial step of reverse transcription by using oligonucleotide primers derived from the conserved 5'-untranslated region (5'-UTR) of the HCV genome. By utilizing this strategy, there was no need for nested or second stage PCR amplification. The PCR products (cDNAs) were easily visualized by agarose gel electrophoresis and ethidium bromide staining. Furthermore, the PCR products were characterized by Southern blot hybridization and DNA sequencing. We then used the one step PCR amplification method to detect the presence of HCV RNA in several infected patients' samples with acute and chronic infections. There was a 100% concordance between the results of PCR and second generation recombinant immunoblot assay (RIBA II). In addition, this method was found to be useful in determining viremia in HCV infected patients with indeterminate RIBA II results. The 5'-UTR of the HCV genome, being the most conserved region among different viral isolates, could be amplified by PCR for the detection of HCV RNA, as shown here, as well as serving as a potential target for antiviral agents.

Base Sequence↗
PubMed2001

ViewFeature: integrated feature analysis and visualization.

Visualization interfaces for high performance computing systems pose special problems due to the complexity and volume of data these systems manipulate. In the post-genomic era, scientists must be able to quickly gain insight into structure-function problems, and require flexible computing environments to quickly create interfaces that link the relevant tools. Feature, a program for analyzing protein sites, takes a set of 3-dimensional structures and creates statistical models of sites of structural or functional significance. Until now, Feature has provided no support for visualization, which can make understanding its results difficult. We have developed an extension to the molecular visualization program Chimera that integrates Feature's statistical models and site predictions with 3-dimensional structures viewed in Chimera. We call this extension ViewFeature, and it is designed to help users understand the structural Features that define a site of interest. We applied ViewFeature in an analysis of the enolase superfamily; a functionally distinct class of proteins that share a common fold, the alpha/beta barrel, in order to gain a more complete understanding of the conserved physical properties of this superfamily. In particular, we wanted to define the structural determinants that distinguish the enolase superfamily active site scaffold from other alpha/beta barrel superfamilies and particularly from other metal-binding alpha/beta barrel proteins. Through the use of ViewFeature, we have found that the C-terminal domain of the enolase superfamily does not differ at the scaffold level from metal-binding alpha/beta barrels. We are, however, able to differentiate between the metal-binding sites of alpha/beta barrels and those of other metal-binding proteins. We describe the overall architectural Features of enolases in a radius of 10 Angstroms around the active site.

Algorithms↗
PubMed2025

Expanding kinetoplastid genome annotation through protein structure comparison.

Kinetoplastids belong to the Discoba supergroup, an early divergent eukaryotic clade. Although the amount of genomic information on these parasites has grown substantially, assigning gene functions through traditional sequence-based homology methods remains challenging. Recently, significant advancements have been made in in-silico protein structure prediction and algorithms for rapid and precise large-scale protein structure comparisons. In this work, we developed a protein structure-based homology search pipeline (ASC, Annotation by Structural Comparisons) and applied it to transfer biological information to all kinetoplastid proteins available in TriTrypDB, the reference database for this lineage. Our pipeline enabled the assignment of structural similarity to a substantial portion of kinetoplastid proteins, improving current knowledge through annotation transfer. Additionally, we identified structural homologs for representatives of 6,700 uncharacterized proteins across 33 kinetoplastid species, proteins that could not be annotated using existing sequence-based tools and databases. As a result, this approach allowed us to infer potential biological information for a considerable number of kinetoplastid proteins. Among these, we identified structural homologs to ubiquitous eukaryotic proteins that are challenging to detect in kinetoplastid genomes through standard genome annotation pipelines. The results (KASC, Kinetoplastid Annotation by Structural Comparison) are openly accessible to the community at kasc.fcien.edu.uy through a user-friendly, gene-by-gene interface that enables visual inspection of the data.

Kinetoplastida↗
PubMed2006

Tandemly repeated DNA sequence instabilities induced by two promoters of morphological transformation in vitro: a short-term response to non-mutagenic agents in C3H/10T1/2 cells.

The ability of tumour promoters to alter DNA stability within regions that contain tandemly repeated sequences (TRSs), was studied in a cell culture model of multi-stage carcinogenesis. Non-cytotoxic concentrations of TPA (12-O-tetradecanoyl-phorbol-13-acetate) and xanthine oxidase with xanthine substrate, sufficient to promote morphological transformation in C3H/10T1/2 cultures, were tested for their effects on mutation frequencies in TRSs by a DNA fingerprinting approach. Specifically, restriction digests of genomic DNA samples from randomly selected, non-transformed clones, isolated from cultures after several days exposure to promoters, were visualized by Southern hybridizations with the multi-locus pentamer repeat sequence probe, Ms6-Hm (Pc-1). Basal and promoter-induced frequencies of sub-clone TRS fingerprint polymorphisms were estimated in five cell populations: an uncloned stock culture, three populations established from normal-appearing sub-clones, and one clonal population established from a 3-methylcholanthrene (MCA)-transformed focus. Basal variant fingerprint frequencies spanned a range from 0.0 to 0.43% mutants/band among cells from the four untransformed populations. Both TPA and xanthine oxidase treatments significantly increased recorded mutation frequencies, 2.3- and 2.7-fold, respectively, using combined data from the progenitor population and three untransformed clones. The untreated MCA-transformed clonal population appeared to contain a single, pre-existing mutant restriction fragment, but additional mutations were induced thereafter, in response to the promoting treatments. Taken together, the measured increases in mutations were highly significant and suggest that promoters of cell transformation in the C3H/10T1/2 cell line might induce a genome-wide instability targeted to regions containing Ms6-Hm sequence motifs.

Animals↗
PubMedDate not supplied

Development and validation of a CGH microarray for clinical cytogenetic diagnosis.

PURPOSE: We developed a microarray for clinical diagnosis of chromosomal disorders using large insert genomic DNA clones as targets for comparative genomic hybridization (CGH). METHODS: The array contains 362 FISH-verified clones that span genomic regions implicated in over 40 known human genomic disorders and representative subtelomeric clones for each of the 41 clinically relevant human chromosome telomeres. Three or four clones from almost all deletion or duplication genomic regions and three or more clones for each subtelomeric region were included. We tested chromosome microarray analysis (CMA) in a masked fashion by examining genomic DNA from 25 patients who were previously ascertained in a genetic clinic and studied by conventional cytogenetics. A novel software package implemented in the R statistical programming language was developed for normalization, visualization, and inference. RESULTS: The CMA results were entirely consistent with previous cytogenetic and FISH findings. For clone by clone analysis, the sensitivity was estimated to be 96.7% and the specificity was 99.1%. Major advantages of this selected human genome array include the following: interrogation of clinically relevant genomic regions, the ability to test for a wide range of duplication and deletion syndromes in a single analysis, the ability to detect duplications that would likely be undetected by metaphase FISH, and ease of confirmation of suspected genomic changes by conventional FISH testing currently available in the cytogenetics laboratory. CONCLUSION: The array is an attractive alternative to telomere FISH and locus-specific FISH, but it does not include uniform coverage across the arms of each chromosome and is not intended to substitute for a standard karyotype. Limitations of CMA include the inability to detect both balanced chromosome changes and low levels of mosaicism.

Chromosome Aberrations↗
PubMed1988

The genomic clone G-21 which resembles a beta-adrenergic receptor sequence encodes the 5-HT1A receptor.

The recent cloning of the complementary DNAs and/or genes for several receptors linked to guanine nucleotide regulatory proteins including the adrenergic receptors (alpha 1, alpha 2A, alpha 2B, beta 1, beta 2), several subtypes of the muscarinic cholinergic receptors, and the visual 'receptor' rhodopsin has revealed considerable similarity in the primary structure of these proteins. In addition, all of these proteins contain seven putative transmembrane alpha-helices. We have previously described a genomic clone, G-21, isolated by cross-hybridization at reduced stringency with a full length beta 2-adrenergic receptor probe. This clone contains an intronless gene which, because of its striking sequence resemblance to the adrenergic receptors, is presumed to encode a G-protein-coupled receptor. Previous attempts to identify this putative receptor by expression studies have failed. We now report that the protein product of the genomic clone, G21, transiently expressed in monkey kidney cells has all the typical ligand-binding characteristics of the 5-hydroxytryptamine (5-HT1A) receptor.

Animals↗
PubMed1994

Double-nested polymerase chain reaction for detection of caprine arthritis-encephalitis virus proviral DNA in blood, milk, and tissues of infected goats.

A nested polymerase chain reaction (PCR) for detecting proviral DNA of caprine arthritis-encephalitis virus (CAEV) in biological samples was developed. Primers for both gag and pol sequences of the CAEV genome were included in a single tube for simultaneous amplification ('double' PCR), and the resulting bands were resolved visually in ethidium bromide-stained agarose gels. Internal gag and pol probes were used to verify the identity of the amplified products by non-radioactive Southern hybridization. Final confirmation of the identity of representative PCR bands was provided by DNA sequence analysis. A comparison between the PCR and an antibody ELISA (with recombinant CAEV p28 as target) using 141 caprine blood samples indicated very strong agreement between the two assays (kappa = 0.912). Four of 7 goats with indeterminate ELISA results were PCR-positive as were 5 of 40 (12.5%) seronegative goats, most probably indicating delayed seroconversion. Eleven of 27 goats (41%) PCR-positive on blood had detectable CAEV proviral DNA in milk. Proviral DNA was also detected in lung, mesenteric lymph node, bone marrow, synovial membrane, and mammary gland of a seropositive, clinically affected goat, but not in equivalent tissues of a healthy seronegative goat.

Animals↗
PubMed2005

In vivo expression of GFP transgene delivered via a replicating feline leukemia virus.

We previously described replication-competent feline leukemia virus (FeLV) vectors with high-level and stable expression of a green fluorescent protein (GFP) or a suicide transgene in cell cultures in vitro. Considering that FeLV might potentially be used to deliver therapeutic genes in vivo, we first evaluated the expression of the GFP gene introduced in cats by the FeLV, Rickard subgroup A (FRA) construct. Eight newborn kittens were either inoculated with pFRA-GFP plasmid DNA intradermally, or challenged intraperitoneally with FRA-GFP-infected feline fibroblasts. During a 12-week observation period, five cats were shown to be progressively viremic. Quantitative PCR and RT-PCR analyses of plasma and tissue samples from these cats showed that GFP was retained in FeLV DNA or RNA to a variable degree, ranging from 0.002 to 27.890%. Tissue DNA samples were analyzed by PCR for the status of GFP and the env-transgene complex. While the proviruses carrying the GFP transgene were shown to be minor species, all tissues, however, retained the full-length GFP transgene. Despite the occurrence of predominant species with various deletions in the viral genome, approximately 1-3% of the total cell population was GFP-positive in the lymphoid tissues as visualized by laser confocal microscopy. Co-localization of immunofluorescent cells indicated that CD3-positive T cells, dendritic cells and macrophages were the major targets for GFP expression. These findings on the detectable in vivo expression of GFP for as long as a period of 3 months could be viewed positively for contemplating a therapeutic strategy for control of FeLV infection in the cats.

Animals↗
PubMed1998

The division apparatus of plastids and mitochondria.

Mitochondria and plastids in eukaryotic cells contain distinct genomes and multiply in the cytoplasm by binary division of preexisting organelles. Mitochondrial and plastid nuclei are easily visualized as compartments in the matrix of organelles by high-resolution fluorescence microscopy and by immunoelectron microscopy using anti-DNA antibodies. Plastid and mitochondrial division can be clearly separated into two main events: division of the organelle nuclei, and then division of the rest of the organelles, the process of organellokinesis (mitochondriokinesis and plastidokinesis). The mechanical apparatus that regulates organellokinesis has remained undetermined. In 1986, the plastid-dividing apparatus (PD ring) for plastidokinesis was first identified by us in the primitive red alga Cyanidium caldarium RK-1. The PD ring is located in the cytoplasm outside the organelle envelope at the constricted isthmus of dividing organelles and has subsequently been found in all eukaryotic plants examined. We were also the first to identify the mitochondrion-dividing apparatus (MD ring) for mitochondriokinesis in the unicellular red alga Cyanidioschyzon merolae in 1993. Eukaryotic cell division is therefore controlled by at least three dividing apparata (rings), a contractile ring, an MD ring, and a PD ring, while bacterial division is controlled by a single bacterial contractile FtsZ ring. The aims of this review are to present the fine structure, process of formation, and contraction of the organelle-dividing apparatus, focusing on evolutionary conservation and diversion from the bacterial contractile ring.

Cell Division↗
PubMed2004

Network structures and algorithms in Bioconductor.

UNLABELLED: In this paper, we review the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T Graphviz) and network algorithms (Boost) have been developed to support analysis of graphical structures in genomics and computational biology. AVAILABILITY: Packages graph, Rgraphviz, RBGL of Bioconductor (www.bioconductor.org).

Algorithms↗
PubMed1997

A locus for autosomal recessive pseudoxanthoma elasticum, with penetrance of vascular symptoms in carriers, maps to chromosome 16p13.1.

Pseudoxanthoma elasticum (PXE) is a heritable systemic disorder characterized by calcification of the elastic fibers of the connective tissue. Symptoms are predominantly noted in the eye, the skin, and the cardiovascular system, resulting in visual loss, skin lesions, and life-threatening vascular disease. In the study we combined homozygosity mapping and genome scanning with 374 markers in affected individuals from a PXE family from a genetically isolated population in The Netherlands. Initial homozygosity in two or three patients was found with up to 20 markers, among which D16S292 located in 16p13.1. Upon refined and more extensive family screening of the latter region, close linkage without recombination was found with the marker D16S764 (Zmax = 6.27). Despite clear autosomal recessive inheritance of the ocular symptoms in PXE, vascular symptoms appear in 40%-50% of the heterozygotes.

Chromosome Mapping↗
PubMed2005

Subspace-based prototyping and classification of chromosome images.

Chromosomes are essential genomic information carriers. Chromosome classification constitutes an important part of routine clinical and cancer cytogenetics analysis. Cytogeneticists perform visual interpretation of banded chromosome images according to the diagrammatic models of various chromosome types known as the ideograms, which mimic artists' depiction of the chromosomes. In this paper, we present a subspace-based approach for automated prototyping and classification of chromosome images. We show that 1) prototype chromosome images can be quantitatively synthesized from a subspace to objectively represent the chromosome images of a given type or population, and 2) the transformation coefficients (or projected coordinate values of sample chromosomes) in the subspace can be utilized as the extracted feature measurements for classification purposes. We examine in particular the formation of three well-known subspaces, namely the ones derived from principal component analysis (PCA), Fisher's linear discriminant analysis, and the discrete cosine transform (DCT). These subspaces are implemented and evaluated for prototyping two-dimensional (2-D) images and for classification of both 2-D images and one-dimensional profiles of chromosomes. Experimental results show that previously unseen prototype chromosome images of high visual quality can be synthesized using the proposed subspace-based method, and that PCA and the DCT significantly outperform the well-known benchmark technique of weighted density distribution functions in classifying 2-D chromosome images.

Algorithms↗
PubMed1997

[Nucleotide sequence of cDNA and organization of the gene for alpha-subunit of photoreceptor phosphodiesterase of cyclic GMP in human retinal cones].

Five clones were isolated from a human retina cDNA library whose cDNA inserts allowed reconstruction of the total sequence of the human clone cGMP phosphodiesterase alpha'-subunit cDNA comprising 3455 bp. The protein's deduced sequence contains 858 amino acids residues with molecular mass 99,169 Da. A substantial homology was revealed between the amino acid sequence of the human cones cGMP-phosphodiesterase alpha'-subunit and the corresponding sequences of alpha, beta, and alpha' subunits of visual cGMP-phosphodiesterase of bovine, murine, chicken and human retinas. Four recombinant bacteriophages were isolated from a genomic library whose inserts made it possible to reconstruct a 32-kb fragment of the human cones cGMP-phosphodiesterase alpha'-subunit gene. 5'-Flanking region of the gene and first 14 exons, encoding an N-terminal segment of the protein, along with the adjacent intron segments were sequenced.

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed2002

A novel method for the construction of genome wide transcriptome maps.

Expression profiling by cDNA-AFLP is commonly used to display the transcriptome of a specific tissue, treatment or developmental stage. In this paper, cDNA-AFLP has been used to study transcripts expressed in segregating populations from Arabidopsis thaliana and potato (Solanum tuberosum). The genetic differences between the offspring genotypes are thus visualized as polymorphisms in the transcriptome. We show that polymorphic transcripts can be used as genetic markers and allow the construction of a linkage map. The resulting map shows that, in contrast to genomic markers, the transcriptome-derived markers did not cluster in particular areas of the chromosome, and that cDNA-AFLP markers are targeted specifically to transcriptionally active regions. The cDNA-AFLP markers used in mapping are derived from DNA polymorphisms in transcripts, rather than differences in expression regulation. The high potential of transcriptome markers as opposed to (anonymous) genomic markers for applications in genetic analyses, marker-assisted breeding and map-based cloning is discussed.

Arabidopsis↗
PubMed2006

Go with the glow: fluorescent proteins to light transgenic organisms.

Once a biological novelty known for their role in bioluminescence, fluorescent proteins (FPs) from marine invertebrates have revolutionized the life sciences. Organisms from all kingdoms have been transformed with the Aequorea victoria green fluorescent protein (GFP), and biotechnology has been advanced by the use of FPs. This article reviews the current uses of FPs in whole transgenic organisms and genomics and looks beyond GFP to the complete color palette and spectral properties afforded by FPs from other marine organisms. Coupled with electronic devices for visualizing and quantifying FPs, recently cloned FP genes might be useful for the ecological monitoring of transgenic organisms in the environment. Therefore, this review also addresses the in vivo labeling of organisms with an emphasis on plants.

Animals↗
PubMed2002

HapScope: a software system for automated and visual analysis of functionally annotated haplotypes.

We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The HapScope analysis pipeline supports: (i) computational haplotype construction with an expectation-maximization or Bayesian statistical algorithm; (ii) SNP classification by protein coding change, homology to model organisms or putative regulatory regions; and (iii) minimum SNP subset selection by either a Brute Force Algorithm or a Greedy Partition Algorithm. The HapScope viewer displays genomic structure with haplotype information in an integrated environment, providing eight alternative views for assessing genetic and functional correlation. It has a user-friendly interface for: (i) haplotype block visualization; (ii) SNP subset selection; (iii) haplotype consolidation with subset SNP markers; (iv) incorporation of both experimentally determined haplotypes and computational results; and (v) data export for additional analysis. Comparison of haplotypes constructed by the statistical algorithms with those determined experimentally shows variation in haplotype prediction accuracies in genomic regions with different levels of nucleotide diversity. We have applied HapScope in analyzing haplotypes for candidate genes and genomic regions with extensive SNP and genotype data. We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research.

Algorithms↗
PubMed2002

Predictome: a database of putative functional links between proteins.

The current deluge of genomic sequences has spawned the creation of tools capable of making sense of the data. Computational and high-throughput experimental methods for generating links between proteins have recently been emerging. These methods effectively act as hypothesis machines, allowing researchers to screen large sets of data to detect interesting patterns that can then be studied in greater detail. Although the potential use of these putative links in predicting gene function has been demonstrated, a central repository for all such links for many genomes would maximize their usefulness. Here we present Predictome, a database of predicted links between the proteins of 44 genomes based on the implementation of three computational methods--chromosomal proximity, phylogenetic profiling and domain fusion--and large-scale experimental screenings of protein-protein interaction data. The combination of data from various predictive methods in one database allows for their comparison with each other, as well as visualization of their correlation with known pathway information. As a repository for such data, Predictome is an ongoing resource for the community, providing functional relationships among proteins as new genomic data emerges. Predictome is available at http://predictome.bu.edu.

Animals↗