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At least 991 records · Page 55Linked to original sources
PubMed2000

Some aspects of plant karyology and karyosystematics.

The significance of the 4C value (where C is the amount of DNA in the unreplicated haploid genome) in angiosperm plants is discussed. The DNA amount is a stable feature used in biosystematics. Although this parameter varies even in closely related taxa, there is no correlation between the DNA amount and the structural and functional organization of plants. The role of DNA amount, including "excess" DNA, in plant evolution is considered. Some rules governing the distribution of DNA amount among different plant taxa are postulated, together with the possibility of using the data in systematics, phylogeny, and solutions of problems of genetic apparatus organization and evolution. The decrease in DNA value per genome during plant evolution and the high level of species formation in taxa with large DNA values have been shown. Plant taxa with a small DNA value per genome have a high percentage and higher degree of polyploidy. The nature of the differential staining of euchromatin and heterochromatin bands of prophase and metaphase chromosomes is also discussed. Data that could explain the mechanism of heterochromatin visualization under cold pretreatment of cells are reviewed. Phenomena involved in the arrangement of chromocenters in interphase nuclei and chromosomes in metaphase during consecutive cell generations are discussed.

Gene Expression Regulation, Plant↗
PubMed2003

Plant metabolomics: large-scale phytochemistry in the functional genomics era.

Metabolomics or the large-scale phytochemical analysis of plants is reviewed in relation to functional genomics and systems biology. A historical account of the introduction and evolution of metabolite profiling into today's modern comprehensive metabolomics approach is provided. Many of the technologies used in metabolomics, including optical spectroscopy, nuclear magnetic resonance, and mass spectrometry are surveyed. The critical role of bioinformatics and various methods of data visualization are summarized and the future role of metabolomics in plant science assessed.

Computational Biology↗
PubMed2000

Genomic control for association studies: a semiparametric test to detect excess-haplotype sharing.

Individuals who share a disease mutation from a common ancestor often share alleles at genetic markers adjacent to the mutation, even if the common ancestor is remote. The alleles at these adjacent markers, called the haplotype, can be visualized as a string of realizations of random variables, which may be dependent when individuals are related in some fashion. Ideally, for a sample of individuals all having the same (genetic) disease, this dependence-measured as haplotype-sharing-will be greater in the vicinity of disease genes than in other regions of the genome. In this paper we present a semiparametric test for haplotype-sharing. We begin by developing a model assuming that the ancestral haplotype is known and thus the extent of haplotype-sharing from a common ancestor can be determined unambiguously. The amount of overlap at markers far from the disease is treated as a random variable with an unknown distribution F, which we estimate non-parametrically. Overlap of markers surrounding disease genes are modeled as a mixture pF(x - theta) + (1 - p)F(x), in which p is the fraction of subjects with the disease mutation. Testing for a disease gene then amounts to testing whether p = 0. Next we drop the assumption that the ancestral haplotype is known. To detect excess clustering of haplotypes, we measure the pairwise overlap of a set of haplotypes. As in the simpler scenario, this distribution is modeled as a location-shift mixture. To test the hypothesis we construct a score test with a simple limiting distribution.

Journal Article↗
PubMed1998

Integration of human herpesvirus 6 in a Burkitt's lymphoma cell line.

Human herpesvirus 6 (HHV-6) genome has been found in several human lymphoid malignancies, but configuration of the HHV-6 genome has not been well delineated. We established the HHV-6-positive, Epstein-Barr virus-negative Burkitt's lymphoma cell line Katata. In this study we investigated the status of the HHV-6 genome in Katata cells. Neither linear nor circular HHV-6 DNA was detected by Gardella gel analysis. The fluorescence in situ hybridization technique enabled us to directly visualize the integrated HHV-6 DNA at the single-cell level. Only one integrated site of viral DNA was detected in metaphase chromosomes and it was preferentially located at the long arm of chromosome 22 (22q13). Treatment of the cells with 12-O-tetradecanoyl-phorbol-13-acetate (TPA) or with calcium ionophore A23187 led to induction of the HHV-6 immediate-early gene as well as the late gene. Sodium n-butyrate also gave rise to expression of the HHV-6 genes. The TPA inducibility was synergistically enhanced when combined with A23187 or n-butyrate. Our study provides, for the first time, an in vitro model system of latent HHV-6 infection whose genome is integrated into host DNA of lymphoma cells.

Blotting, Southern↗
PubMed1995

Molecular cytogenetic quantitation of gains and losses of genetic material from human gliomas.

The unregulated growth that is characteristic of human malignant gliomas is accompanied by, and may result from, losses and/or gains of genetic material. Understanding the mechanisms that underlie how particular genetic aberrations cause dysfunctional growth will help elucidate the pathogenesis of this disease. Two techniques are proving useful in evaluating the clinical relevance of specific genetic aberrations in malignant gliomas. Fluorescence in situ hybridization (FISH) permits direct visualization of gains and losses of genetic material in single cells and quantitation of cellular subpopulations that have particular genetic aberrations. Comparative genomic hybridization can identify regions of genetic gain and loss in tumor DNA.

Brain Neoplasms↗
PubMed1997

Polymorphism of the LMP2 gene and disease phenotype in ankylosing spondylitis: no association with disease severity.

Although a number of reports have now described an association between polymorphism of the LMP2 gene and disease phenotype in HLA-B27 positive individuals with ankylosing spondylitis (AS), some describe associations with acute anterior uveitis, others with juvenile onset disease, and one report provides no association. A recent study describes yet a further association with disease severity in patients with juvenile rheumatoid arthritis. We therefore hypothesized that the discrepant findings in adult disease may be a reflection of an underlying association with disease severity. Our study population consisted of 100 HLA-B27 positive Caucasians with AS of ten or more years duration. Clinical assessment of disease severity was based on a metrology index scoring five measurements, the modified health assessment questionnaire for the spondyloarthropathies, and a disease activity index consisting of a visual analog scale to score the amount of pain, stiffness and fatigue. LMP2 genotypes were assigned following polymerase chain reaction amplification from genomic DNA and restriction enzyme digestion with CfoI. Despite confirmation of a significantly higher prevalence of the LMP2 BB genotype in AAU positive (66.0%) versus AAU negative (45.2%) patients (P < 0.05), we observed no association between LMP2 genotypes and any of the indices of disease severity. Furthermore, although a significant association was noted between the presence of peripheral synovitis and the functional index score (P < 0.05), a history of AAU was not associated with more severe disease. Our data is thus internally consistent in demonstrating no association between LMP2 genotypes and either disease severity or peripheral arthritis, and supports the notion that polymorphism of LMP2 primarily influences the development of AAU and not some other phenotype of AS.

Adult↗
PubMed2001

Differential gene expression profile of glucocorticoids, testosterone, and dehydroepiandrosterone in human cells.

Glucocorticoids are the major immunomodulating hormones in the human body. Recently, increasing interest in androgens as immunomodulators has emerged. In particular, Dehydroepiandrosterone (DHEA) has been suggested as beneficial in the treatment of some autoimmune disorders. However, the action and role of testicular and adrenal androgens on human immune cells remains unclear. This is the first study to provide large-scale gene expression data on the action of different steroids (DHEA, glucocorticoids, and testosterone) on human peripheral blood mononuclear cells using the recently developed genomic-scale technology of microarrays. Novel computational tools and techniques such as Principal Component Analysis (PCA) were used for analysis, clustering and visualization. We have demonstrated that each steroid has its distinct gene expression profile, although DHEA and testosterone co-regulated most genes in a similar direction while glucocorticoids frequently regulated the same genes in an opposite direction. Our data suggest an important and a complex regulatory role for androgens on human immune cells that should be considered in androgen replacement or treatment strategies.

Dehydroepiandrosterone↗
PubMed1992

Effects of different DNA polymerases in ligation-mediated PCR: enhanced genomic sequencing and in vivo footprinting.

We have developed a simplified procedure for the ligation-mediated polymerase chain reaction (LMPCR) using Thermococcus litoralis DNA polymerase (Vent DNA polymerase). We show that Vent DNA polymerase produces correct, blunt-ended primer extension products with substantially higher efficiency than Thermus aquaticus (Taq) DNA polymerase or modified T7 DNA polymerase (Sequenase). This difference leads to significantly improved genomic sequencing, methylation analysis, and in vivo footprinting with LMPCR. These improvements include representation of all bands with more uniform intensity, clear visualization of previously difficult regions of sequence, and reduction in the occurrence of spurious bands. It also simplifies the use of DNase I cut DNA for LMPCR footprinting.

Animals↗
PubMed1989

Rapid detection and sequencing of alleles in the 3' flanking region of the interleukin-6 gene.

The 3' flanking region of the interleukin 6 gene is polymorphic due to insertions of different size. Within this region lies a sequence of approximately 500 base pairs that is AT rich. Based on flanking sequence information we have constructed oligonucleotides which prime the polymerase chain reaction (PCR) and amplify this AT rich region. The amplification products visualized by agarose gel electrophoresis gave fragment sizes for both homozygous and heterozygous individuals that were concordant with those observed by conventional genomic blotting techniques. Alleles that could not be typed by Southern analysis were resolved with this approach. These results illustrate the value of PCR for the rapid detection of length polymorphisms such as those due to variable numbers of tandem repeats. In contrast to RFLP analysis this procedure takes less than a day to perform, is cheaper, avoids the use of radioactivity and requires far less substrate DNA. Three different human alleles were sequenced, and differences were detected that were due to both large duplications and loss of one or two bases, suggesting that AT rich regions identify highly polymorphic loci. The same primers also amplified non-human primate DNA, allowing a comparison of the human sequence with that of the common chimpanzee and baboon.

Alleles↗
PubMed2001

The small world inside large metabolic networks.

The metabolic network of the catabolic, energy and biosynthetic metabolism of Escherichia coli is a paradigmatic case for the large genetic and metabolic networks that functional genomics efforts are beginning to elucidate. To analyse the structure of previously unknown networks involving hundreds or thousands of components by simple visual inspection is impossible, and quantitative approaches are needed to analyse them. We have undertaken a graph theoretical analysis of the E. coli metabolic network and find that this network is a small-world graph, a type of graph distinct from both regular and random networks and observed in a variety of seemingly unrelated areas, such as friendship networks in sociology, the structure of electrical power grids, and the nervous system of Caenorhabditis elegans. Moreover, the connectivity of the metabolites follows a power law, another unusual but by no means rare statistical distribution. This provides an objective criterion for the centrality of the tricarboxylic acid cycle to metabolism. The small-world architecture may serve to minimize transition times between metabolic states, and contains evidence about the evolutionary history of metabolism.

Escherichia coli↗
PubMed1979

Electron microscopic mapping of RNA transcribed from the late region of polyoma virus DNA.

The polyoma virus (Py) RNA species transcribed from the L DNA strand of the "late" region of the Py genome in Py-infected mouse cells have been mapped by hybridization with specific fragments of Py DNA followed by electron microscopic visualization of the hybrids. Total cellular polyadenylated Py-specific RNA molecules having an S value in the range of 16S to 20S were purified by oligodeoxythymidylic acidcellulose column chromatography, preparative hybridization with Py DNA, and sucrose gradient centrifugation. Cytoplasmic Py-specific RNA was similarily purified, except that it was not fractionated by sucrose gradient centrifugation. Hybrids of these RNA molecules and Py DNA fragments were spread for electron microscopy by either the cytochrome c technique or the bacteriophage T4 gene 32 protein method. The polyadenylic acid at the 3'-end of the RNA in the hybrids was identified by labeling with simian virus 40 DNA circles to which polybromodeoxyuridylic acid tails had been covalently attached. These experiments revealed the presence of three L DNA strand transcripts in both RNA preparations. Two of these RNA molecules were found to be spliced from chains transcribed from two noncontiguous parts of the late region. The third molecule either is a continuous transcript of the entire late region or contains a splicing feature which is too small to be reliably observed by the electron microscope methods used. The 5'-ends of the three RNA species map within a region extending from 68 to 70 map units on the Py restriction endonuclease map. Each of the two spliced molecules contains a 5'-terminal leader sequence transcribed from a DNA segment with an estimated length of 60 to 110 nuvleotides. The 3'-ends of the leaders map at 66.7 +/- 1.0 and 66.4 +/- 0.50 map units. In these molecules the 5'-ends of the other part (the main body) map at 59.4 +/- 0.90 and 49.4 +/- 2.0 map units, respectively. The 3'-termini of all three RNA species map at 24 to 25 map units.

DNA, Viral↗
PubMed1993

Application of the random amplified polymorphic DNA technique for the detection of polymorphism among wild and cultivated tetraploid wheats.

Development of a high-density genetic linkage map of cultivated wheats using conventional molecular markers has lagged behind the other major food crops such as rice and tomato because of the large genome size and limited levels of genetic polymorphisms. Recently, random amplified polymorphic DNAs (RAPDs) have been suggested to provide an alternative to visualize more polymorphism. For the construction of a genetic linkage map in tetraploid wheats, one can use a strategy of intersubspecific crosses between the most dissimilar wild and cultivated tetraploid wheats that are easy to hybridize and result in fertile progeny. An assessment of the level of RAPDs among different accessions and varieties of wild and cultivated tetraploid wheats is required to fulfill this objective. We present here the data obtained using RAPD analysis of 40 primers in 20 accessions of wild tetraploid emmer wheats (Triticum turgidum L. ssp. dicoccoides) and 10 genotypes of cultivated tetraploid durum wheats (Triticum turgidum L. ssp. durum) selected from geographically diverse locations. We have observed a higher level of polymorphism among different accessions of wild emmer wheat from Israel. Turkey, and Jordan than the group of cultivated American, Turkish, and Syrian durum wheats. These data have been used to generate a dendrogram suggesting the genetic relationships among these genotypes, and the most dissimilar genotypes are identified for future mapping and gene tagging work.

Base Sequence↗
PubMed2005

Characterization of Bietti crystalline dystrophy patients with CYP4V2 mutations.

PURPOSE: Mutations of the CYP4V2 gene, a novel family member of the cytochrome P450 genes on chromosome 4q35, have recently been identified in patients with Bietti crystalline dystrophy (BCD). The aim of this study was to investigate the spectrum of mutations in this gene in BCD patients from Singapore, and to characterize their phenotype. METHODS: Nine patients with BCD from six families were recruited into the study. The 11 exons of the CYP4V2 gene were amplified from genomic DNA of patients by polymerase chain reaction and then sequenced. Detailed characterization of the patients' phenotype was performed with fundal photography, visual field testing, fundal fluorescein angiography, and electroretinography (ERG). RESULTS: Three pathogenic mutations were identified; two mutations, S482X and K386T, were novel and found in three patients. The third mutation, a previously identified 15-bp deletion that included the 3' splice site for exon 7, was found in all nine patients, with six patients carrying the deletion in the homozygous state. Haplotype analysis in patients and controls indicated a founder effect for this deletion mutation in exon 7. Clinical heterogeneity was present in the patients. Compound heterozygotes for the deletion in exon 7 seemed to have more severe disease compared to patients homozygous for the deletion. There was good correlation between clinical stage of disease and ERG changes, but age did not correlate with disease severity. CONCLUSIONS: This study identified novel mutations in the CYP4V2 gene as a cause of BCD. A high carrier frequency for the 15-bp deletion in exon 7 may exist in the Singapore population. Phenotype characterization showed clinical heterogeneity, and age did not correlate with disease severity.

Adult↗
PubMed1992

[Epstein-Barr virus associated lymphocyte proliferation].

In recent years, techniques, probes, and reagents became available to reliably visualize individual Epstein-Barr virus (EBV)-infected cells, to assess EBV gene expression, and to analyze the clonal composition of EBV genomes in human tissues. Application of these techniques to more than 1000 lymphoid tissue specimens revealed (1) characteristic cellular and compartmental distribution patterns of EBV-infected cells in normal lymph nodes, reflecting the interference of EBV with physiologic B cell differentiation pathways, (2) an association of EBV with various mono- and oligoclonal lymphoproliferations ranging from benign conditions to overtly malignant lymphomas, and (3) characteristic patterns of EBV gene expression among EBV-associated lymphoproliferations. In the context of the established immortalizing and transforming properties of EBV, the findings support the concept of an etiologic role of EBV for cases of certain lymphomas such as Burkitt's lymphoma, anaplastic large cell lymphoma, Hodgkin's disease, and lymphomas arising in immunocompromised individuals. In contrast, lymphomas harboring EBV in only proportions of the tumor cells (such as cases of peripheral T cell lymphoma and some B cell lymphoma types) argue against an etiologic role in the primary process of malignant transformation for the virus in these instances. Since in many of these cases a proportion of the EBV infected tumor cells express the EBV oncoprotein LMP (latent membrane protein) the virus may influence, however, the proliferative properties as well as the morphological and molecular phenotype of the neoplastic cells.

B-Lymphocytes↗
PubMed1992

VNTR polymorphism of the collagen type II, alpha 1 (COL2A1) gene detected by PCR.

The 3' side of the human type II collagen alpha 1 (COL2A1) gene contains a region consisting of a variable number of tandemly repeated short A + T-rich DNA sequences (VNTR). We amplified this region accurately by the polymerase chain reaction (PCR). Genomic DNA was purified from isolated buffy-coat cells, and thermostable Taq polymerase was used to amplify the target region. The amplification products were directly visualized after polyacrylamide gel electrophoresis. In this way, five alleles were distinguished in chromosomes from 33 unrelated Japanese, and named A, B, C, D, and E in decreasing order of length. The relative frequencies of the COL2A1 3' VNTR alleles A through E were 0.045, 0.075, 0.469, 0.015, and 0.393, respectively. Co-dominant segregation was observed in two informative families. The COLA2A1 3' VNTR locus was estimated to have a heterozygosity index of 62% and a polymorphic information content of 0.55.

Alleles↗
PubMed2005

Isolation and characterization of visual pigment kinase-related genes in carp retina: polyphyly in GRK1 subtypes, GRK1A and 1B.

PURPOSE: Visual pigment is phosphorylated and inactivated after light stimulus. The responsible enzyme is known as rhodopsin kinase or G-protein-coupled receptor kinase 1 (GRK1) in rods. We recently showed that the kinase in cones (GRK7) has much higher activity than GRK1 in rods in carp retina. During the course of these studies, we realized that there are several subtypes of GRK1 and GRK7. In the present study, therefore, to identify the GRK1 and GRK7 subtypes expressed in carp photoreceptors, we determined their nucleotide sequences together with their expression patterns in carp retina. We also analyzed their relationships to other GRK1s and GRK7s phylogenetically. METHODS: Oligonucleotides corresponding to the amino acid sequences conserved in GRK1 or GRK7 were synthesized to screen the GRK subtypes in a carp retinal cDNA library. The isolated partial cDNAs were used to determine the full length of GRK subtypes. Genomic Southern hybridization was performed to learn whether each of the isolated GRKs is encoded by a single gene or it is an allelic variation. Tissue localization of the isolated GRKs was examined with in situ hybridization. RESULTS: A novel subtype of GRK1, GRK1B, was found in addition to the conventional GRK1 (called GRK1A subtype in this study) in carp retina. The GRK1A subtype, more specifically the GRK1A-1 subtype, which is related to the mammalian-type GRK1, was expressed in rods, while the GRK1B subtype, related to chicken GRK1, was expressed in cones. Since GRK7-1 was also expressed in cones, carp cones express both GRK7-1 and GRK1B. There were two paralogous genes in all of the GRK1 and GRK7 subtypes in carp retina: GRK1A-1a and 1A-1b, GRK1Ba and 1Bb, and GRK7-1a and 7-1b. Each of these genes was suggested to be encoded by a single gene in the carp genome, and each pair was found to be expressed in the same type of photoreceptors. CONCLUSIONS: Carp rods and cones express at least two kinds of visual pigment kinases. Phylogenetic analysis suggested that GRK7-1 together with GRK1A-1 and GRK1B appeared before divergence of vertebrates and that some of these genes were lost during evolution in a species-dependent manner. This evolutional process probably explains why the expression pattern of GRK1 and GRK7 is complex among vertebrate species.

Amino Acid Sequence↗
PubMed2005

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/.

Chromosomes, Plant↗
PubMed1984

Structure of poliovirus replicative intermediate RNA. Electron microscope analysis of RNA cross-linked in vivo with psoralen derivative.

The structure of the poliovirus replicative intermediate RNA was examined by electron microscopy after cross-linking in vivo with 4'-aminomethyl-4,5',8-trimethylpsoralen. After purification from infected cells, undenatured RI appeared as a double-stranded backbone of genome length, with an average of three (and occasionally up to eight) nascent, single-stranded tails. After denaturation, however, only single strands of heterogeneous length were visualized, indicating that the RI in the cell contains little or no duplex structure, and thus nascent chains are only transiently hydrogen-bonded to their template over short regions. The double-stranded backbone of undenatured RI, observed previously by others and in these experiments, is due to collapse of complementary chains during the deproteinization and purification procedures. The effectiveness of the in vivo cross-linking procedure was demonstrated by the complete inhibition of viral RNA synthesis in treated cells and by direct binding of [3H]AMT to RI molecules in vivo. Mature polio virions are impermeable to AMT; however, growth of virus in cells incubated with AMT in the dark resulted in normal yields of virus particles containing RNA genomes, whose infectivity could be subsequently photo-inactivated. The frequency of AMT-induced cross-linking was determined by analyses of double-stranded poliovirus RNA (RF). Cross-linking in vitro followed by spreading for electron microscopy under denaturing conditions yielded bubbled duplex structures with a minimum of one interstrand cross-link per 80 base-pairs. RF cross-linked in vivo also showed extensive cross-linking, decreased about fivefold from the in vitro cross-linked value. Thus, the failure to detect cross-linked RI under these conditions indicates that extensive base-pairing does not exist in vivo.

Base Composition↗