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PubMed1995

Impaired mitochondrial function in idiopathic dilated cardiomyopathy: biochemical and molecular analysis.

Mitochondrial defects at the biochemical and molecular levels are increasingly recognized in diseases involving the heart. The objective of this study was to assess the frequency and extent of mitochondrial defects in idiopathic dilated cardiomyopathy. Left ventricular tissues of 27 patients with idiopathic dilated cardiomyopathy undergoing orthotopic cardiac transplantation because of severe cardiac failure were examined to assess the specific activity levels of mitochondrial respiratory enzymes and changes in mtDNA structure and copy number. Abnormal specific activities of several mitochondrial enzymes were found in 55% of the cardiomyopathic tissues examined (15 patients), with six patients displaying single enzyme defects, including five in complex III and one in complex I. Multiple mitochondrial enzyme defects were found in nine patients, with the most frequent combination of defects seen in complex III and complex IV (5 cases). These enzymatic changes were shown not to be accompanied by changes in mtDNA copy number. In seven cases, however, including three young adults, there was a marked decrease in the levels of polymerase chain reaction products derived from specific mtDNA regions, which may be an indication of specific mtDNA damage. Specific mitochondrial abnormalities are frequently found in idiopathic dilated cardiomyopathy, with a variety of mitochondrial loci affected. These findings are not age dependent.

Adult↗

PubMed2005

Supercomplexes of IsiA and photosystem I in a mutant lacking subunit PsaL.

The cyanobacterium Synechocystis PCC 6803 grown under short-term iron-deficient conditions assembles a supercomplex consisting of a trimeric Photosystem I (PSI) complex encircled by a ring of 18 IsiA complexes. Furthermore, it has been shown that single or double rings of IsiA with up to 35 copies in total can surround monomeric PSI. Here we present an analysis by electron microscopy and image analysis of the various PSI-IsiA supercomplexes from a Synechocystis PCC 6803 mutant lacking the PsaL subunit after short- and long-term iron-deficient growth. In the absence of PsaL, the tendency to form complexes with IsiA is still strong, but the average number of complete rings is lower than in the wild type. The majority of IsiA copies binds into partial double rings at the side of PsaF/J subunits rather than in complete single or double rings, which also cover the PsaL side of the PSI monomer. This indicates that PsaL facilitates the formation of IsiA rings around PSI monomers but is not an obligatory structural component in the formation of PSI-IsiA complexes.

Bacterial Proteins↗

PubMed1999

Drunken-cell footprints: nuclease treatment of ethanol-permeabilized bacteria reveals an initiation-like nucleoprotein complex in stationary phase replication origins.

The nucleoprotein complex formed on oriC, the Escherichia coli replication origin, is dynamic. During the cell cycle, high levels of the initiator DnaA and a bending protein, IHF, bind to oriC at the time of initiation of DNA replication, while binding of Fis, another bending protein, is reduced. In order to probe the structure of nucleoprotein complexes at oriC in more detail, we have developed an in situ footprinting method, termed drunken-cell footprinting, that allows enzymatic DNA modifying reagents access to intracellular nucleoprotein complexes in E.coli, after a brief exposure to ethanol. With this method, we observed in situ binding of Fis to oriC in exponentially growing cells, and binding of IHF to oriC in stationary cells, using DNase I and Bst NI endonuclease, respectively. Increased binding of DnaA to oriC in stationary phase was also noted. Because binding of DnaA and IHF results in unwinding of oriC in vitro, P1 endonuclease was used to probe for intracellular unwinding of oriC. P1 cleavage sites, localized within the 13mer unwinding region of oriC ', were dramatically enhanced in stationary phase on wild-type origins, but not on mutant versions of oriC unable to unwind. These observations suggest that most oriC copies become unwound during stationary phase, forming an initiation-like nucleoprotein complex.

Bacterial Proteins↗

PubMed1982

Complexity of polysomal polyadenylated RNAs in Vicia faba meristematic root cells.

As a first step in quantifying gene expression during differentiation of the Vicia faba root cells we have analysed the mRNA population from meristematic cells. Using cDNA X mRNA hybridizations we have shown that this population can be divided into three abundance classes (abundant, intermediate and rate) representing 37%, 34% and 29% of the mRNAs and containing 26, 610 and 11700 sequences respectively. The total base-sequence complexity of the mRNA population, as determined by cDNA X mRNA hybridization, was found to be 1.6 x 10(7) nucleotides. This estimate was confirmed by the determination of the amount of single-copy genomic DNA hybridizing to the mRNA. Expressed as the number of structural gene transcripts, this complexity corresponds to about 13000 mRNA sequences.

DNA↗

PubMed1995

Cloning and sequencing a non-ATPase subunit of the regulatory complex of the Drosophila 26S protease.

We have cloned and sequenced a non-ATPase subunit of the regulatory complex of the Drosophila 26S protease. The gene is present in a single copy in the Drosophila genome. By comparing the nucleotide sequence of the genomic and cDNA clones three exons and two introns were localized. Two transcription start sites were identified 9 bp apart. The deduced protein sequence shows no significant similarity to any other protein in the database. In Drosophila embryos where the 26S protease is present in high concentration, the pool of free subunits of the regulatory complex is very low. Among the free subunits of the regulatory complex the cloned subunit is present in very large excess. This observation raises the possibility that this subunit is in a dynamic equilibrium, exchanging between a free and a particle-bound form, which may have important implications concerning its function.

Adenosine Triphosphatases↗

PubMed2003

Quantitation of antibody-bound and unbound Sin Nombre virus in the plasma of patient with hantavirus pulmonary syndrome.

Hantavirus pulmonary syndrome (HPS) is a rare but acute fulminant disease caused by Sin Nombre virus and other related hantaviruses. We reported earlier that HPS patients had high levels of viremia and the levels of viremia correlated with the severity of the disease. To determine whether the viruses are free in plasma or bound to antibodies to form immune complexes, we established a method to quantitate viral genomic RNA in antibody-bound viruses and in unbound viruses separately. To isolate immune complexes from plasma we used protein L, which binds to all classes of immunoglobulins and all subclasses of IgG, and we measured viral RNA copy number in antibody-bound viruses and unbound viruses by quantitative RT-PCR. We analyzed plasma samples collected on admission from 15 patients with HPS in the acute phase. The percentage of viral RNA in immune complexes versus total viral RNA varied from 9 to 91% among patients, and correlated with the total viral RNA copy numbers (P<0.05) and the neutralizing antibody titers of plasma (P<0.05). This quantitative method may be useful to examine diseases where immune complex formation or antibody-dependent enhancement may be involved in pathogenesis.

Antibodies, Viral↗

PubMed1993

Molecular cloning and characterization of contiguously located repetitive and single copy DNA sequences of Mycobacterium tuberculosis: development of PCR-based diagnostic assay.

Screening of a lambda gt11 genomic library has been used as an approach for molecular cloning of the Mycobacterium tuberculosis repetitive DNA shown to be present on a previously described 5.6-kb Alu I genomic fragment. The recombinant clone R18.8.2, which strongly hybridized with the radiolabeled 5.7-kb Alu fragment, carried two Eco RI inserts of 2 kb and 1.4 kb in size. Southern hybridization of each of these fragments to restriction endonuclease-cleaved M. tuberculosis DNA clearly demonstrated the 2 kb to contain the repetitive DNA sequence, while the 1.4 kb is represented in a single copy. When replica plaque lifts from the genomic library were probed, the 5.6-kb genomic fragment and the cloned 2-kb repetitive insert hybridized to an identical number of plaques, indicating the similarity and the high copy number of the repeating unit shared by the two fragments. Restriction mapping and Southern hybridization patterns indicated that the 2-kb repetitive and the 1.4-kb single-copy DNA sequences originated from a contiguous piece of genomic DNA. Both fragments were found to be unique to members of the M. tuberculosis complex, except that the 2-kb insert exhibited a weak hybridization with M. kansasii DNA. Finally, a 169-bp region from one end of the single-copy sequence has been amplified by polymerase chain reaction (PCR) in a manner specific to members of the M. tuberculosis complex. The sensitivity of the PCR was such that as few as 9-10 bacilli could be detected.

Base Sequence↗

PubMed1978

Measurement of the complexity and diversity of poly(adenylic acid) containing messenger RNA from rat liver.

The complexity of rat liver poly (A)+ messenger RNA (mRNA) has been measured by analysis of the kinetics of hydridization with both complementary DNA (cDNA) and single copy DNA. The complementary DNA-poly(A)+ mRNA hybridization reaction demonstrates the existence of three abundance classes representing 18, 37, and 45% of the cDNA and 4, 290, and 24 000 different 1800-nucleotide sequences respectively. The poly(A)+ mRNA driven single copy DNA hybridization reaction reveals a single major transition accounting for 1.9% of the haploid rat genome. The kinetics of the poly(A)+ mRNA driven single copy DNA reaction suggest that approximately 45% of the mass of the mRNA population contains over 95% of the complexity. Although higher than previous estimates, the base sequence complexities of rat liver poly(A)+ mRNA measured in these two ways are in good agreement, suggesting that the technique of poly(A)+ mRNA-cDNA hybridization may be used in approximating the complexity as well as abundance of a messenger RNA population. DNA-driven cDNA reactions reveal that about 10% of rat liver poly(A)+ mRNA is transcribed from repetitive sequences in the rat genome.

Animals↗

PubMed2000

Locus-specific multifluor FISH analysis allows physical characterization of complex chromosome abnormalities in neoplasia.

Novel techniques in molecular cytogenetics have radically improved the ability to characterize genetic changes in neoplastic cells. In parallel, a rapid development in high-throughput genomics has resulted in detailed physical maps of the human genome. Combining these two fields, we have developed a method for the simultaneous visualization of several physically defined segments along a chromosome. Seven YAC clones and one subtelomeric cosmid clone from chromosome 12 were labeled with unique combinations of four fluors and hybridized to metaphase chromosomes from neoplastic cells. In a uterine leiomyoma and a myxoid liposarcoma with translocations 12;14 and 12;16, the breakpoints in chromosome 12 could be localized to the HMGIC and CHOP regions, respectively. In the other tumors, more complex aberrations were visualized, including two inversions in 12q with a common breakpoint between MDM2 and D12S332 in a pleomorphic adenoma, amplification of MDM2 and CDK4 in ring chromosomes from a malignant fibrous histiocytoma, and amplification of KRAS2 together with other unbalanced rearrangements in two pancreatic adenocarcinomas. Combinatorially labeled single-copy probes may thus simultaneously provide physical localization of breakpoints and an overview of complex structural rearrangements. Genes Chromosomes Cancer 28:347-352, 2000.

Chromosome Aberrations↗

PubMed1993

Schistosoma mansoni: comparison of cloned tropomyosin antigens shared between adult parasites and Biomphalaria glabrata.

Rabbit antisera, raised against whole, homogenized hepatopancreas from uninfected Biomphalaria glabrata, were used to screen a cDNA library prepared from adult Schistosoma mansoni. Of 1.8 x 10(5) recombinants screened, 34 clones were specifically immunoreactive with the antisera. Twenty of the clones were subcloned for further analysis, and 13 of the 20 were demonstrated to hybridize to a cDNA probe encoding schistosome tropomyosin I (pSMTM) at high stringency (Xu et al. Experimental Parasitology 69, 373-392, 1989). One partial cDNA clone (pSM4), which failed to hybridize to pSMTM, was used to rescreen the adult worm cDNA library and a 1381-bp cDNA clone, SmTMII, was identified and characterized. SmTMII contained a single 284-amino acid open reading frame and was shown to be 65.8% homologous to SMTM. Computer-assisted analysis of the predicted protein structure depicted a hydrophilic molecule with the extensive alpha helical secondary structure characteristic of tropomyosins. SmTMII was expressed in Escherichia coli and the resulting 45-kDa fusion protein was recognized by both a polyclonal antiserum specific for SMTM and the antiserum of mice chronically infected with S. mansoni. Northern analysis showed the SmTMII mRNA in the adult stage to be about 1.6 kb in size. Analysis of the SmTMII gene by Southern blot revealed a complex hybridization pattern suggesting the presence of introns or multiple gene copies. The 650-bp EcoRI fragment of SmTMII was used to screen a cDNA library prepared from uninfected Biomphalaria glabrata and two clones, each encoding a novel snail tropomyosin, BgTMII, were isolated and characterized. The two clones, consisting of 2816 and 2314 bp, respectively, differed from each other only in the polyadenylation signal used and each contained a single and identical 284-amino acid open reading frame having 94.7% homology with the previously reported snail tropomyosin, BG39 (Dissous et al. Molecular and Biochemical Parasitology 43, 245-256, 1990). BgTMII was shown to have a higher amino acid homology with SMTM (68.3%) than with BG39 (65.1%) and a higher amino acid homology with SMTM than the two schistosome tropomyosins (SMTM and SmTMII) have with each other (65.8%). Implications of these observations in relation to the concept of host-parasite antigen mimicry are discussed.

Amino Acid Sequence↗

PubMed2000

An expressed sequence tag database of T-cell-enriched activated chicken splenocytes: sequence analysis of 5251 clones.

The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. A chicken EST Web site (http://udgenome. ags.udel. edu/chickest/chick.htm) has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank (Accession Nos. AI979741-AI982511). Our new Web site (http://www. chickest.udel.edu) will be active as of March 3, 2000, and will also provide keyword-searching capabilities for BLASTX and BLASTN hits of all our clones.

Animals↗

PubMed1989

Electron microscopical analysis of Drosophila polytene chromosomes. V. Characteristics of structures formed by transposed DNA segments of mobile elements.

An electron microscopical (EM) analysis was performed on regions of polytene chromosomes which contained DNA segments of different genetic composition, inserted by P element-mediated transformation into the Drosophila melanogaster genome. In seven of ten regions examined, containing insertions of the hsp28-ry, hsp70-Adh, ryhsp 70-beta-gal genes and of the ry gene tetramer, new bands appeared. Lack of new bands in three other strains is apparently connected with the fusion of the inserted material to preexisting bands. The new bands do not differ morphologically from the usual bands of polytene chromosomes, and their formation is likely due to predominant insertion of DNA segments into interbands. Among the constructs examined, the minimal length of a DNA segment which appears as a new band is about 5 kb; the DNA packing ratio in the new bands varies from 30 to 50. Activation of the inserted genes by heat shock has enabled us to observe the puffing characteristics of new bands. A sequence of some one kb forms a large interband, or micropuff; the puff size is correlated with the length of the genes being activated. If a DNA segment contains a single gene, then its activation causes the decompaction of the whole band; however, when a DNA segment consists of two genes and the promoter element of the activated gene is positioned in the middle of the sequence, the band splits and only part is decompacted and puffed. The DNA packing ratio in the puffs is 1.4-3.5. The subsequent deletion of the hsp70 promoter but retention of 23, 59, and 73 by from the transcription start points leads to failure of puff formation. In all the transformed sites an increase in the total length of the interbands adjacent to the insert as compared with the initial interband was observed. This increase appears to be due to decompaction of the P element DAN flanking the inserted segments. It is shown that a DNA segment, consisting of four tandemly repeated ry gene copies and interspersed by material which includes P DNA, forms a complex of loose chromatin in which, however, four bands can be resolved. We also observed a lengthening of interband regions containing only the P element sequence itself. Insertion of the complete 2.9 kb P element into the large single 10A1-2 bound of the X chromosome (an insertion in the region approximately 10 kb to the right of the v gene) causes splitting of the band into two parts and formation of a new interband.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1992

Fine-structure mapping of the complex locus Odc-rs5 relative to Igk and distal loci.

Odc-rs5 was previously identified as a complex locus closely linked to the Igk complex on mouse Chromosome (Chr) 6 and comprising at least five copies of a sequence related to the mRNA encoding ornithine decarboxylase (ODC) in the genomes of mice of some inbred strains and at least seven copies in others (Richards-Smith and Elliott, Mammalian Genome 2: 215, 1992). In the present study, Odc-rs5 was shown to be composed of at least seven copies of the ODC sequence in both the Odc-rs5a and Odc-rs5b haplotypes. Based upon the distribution of DNA restriction fragments (RFs) that had previously been associated with Odc-rs5a or Odc-rs5b among 42 mice of inbred laboratory strains having various haplotypes at Igk and in mice of two congenic strains [B6.PL-Ly-2a, Ly-3a(75NS)/Cy and B6.PL-Ly-2a,Ly-3a(85NS)/Cy] and a backcross-derived stock (NAK) known to be recombinant within Igk, a fine structure map of Odc-rs5 was deduced relative to Igk and more distal loci. Odc-rs5-derived RFs were located to three distinct regions within and/or distal to Igk and to a fourth site between (Ly-3, Ly-2) and Raf-1. Additionally, DNAs from 19 mice of inbred strains and random-bred stocks derived from wild progenitors trapped at various locations were analyzed and found to exhibit an unexpected variety of combinations of RFs associated with the two Odc-rs5 haplotypes most frequently observed among inbred laboratory strains of mice.

Animals↗

PubMed2005

An FB-NOF mediated duplication of the white gene is responsible for the zeste1 phenotype in some Drosophila melanogaster unstable strains.

The males of the Drosophila melanogaster M115 mutant strain and of its spontaneous revertant strain RM115 are phenotypically similar to those carrying the w(+UZ) and w(+UR) alleles. The molecular description of these mutant strains could be extended to the unstable-zeste system, which has been used as a genotoxicity test, and could be of use for a better understanding of the assay. An FB element in the 3' vicinity of the white gene, actually into the second intron of the newly predicted CG32795 gene, was found and precisely located in our M115 and RM115 strains, and also in w(+UZ) as expected. We demonstrate the presence of NOF sequences in the M115 and w(+UZ) insertions. However, we found that the z1 phenotype in these males might not be due to the FB-NOF interference on the zeste-white interaction but to a duplication of the white gene unnoticed in previous studies. The reversion of RM115 correlates with the loss of the duplication, probably by a complex recombination event. Furthermore, a FISH experiment suggests that the two copies of white are nearby or tandemly duplicated.

ATP-Binding Cassette Transporters↗

PubMed2006

Genome-wide investigation on the genetic variations of rice disease resistance genes.

Exploitation of plant disease resistance (R) gene in breeding programs has been proven to be the most efficient strategy for coping with the threat of pathogens. An understanding of R-gene variation is the basis for this strategy. Here we report a genome-wide investigation on the variation of NBS-LRR-encoding genes, the common type of R genes, between two sequenced rice genomes, Oryza sativa L. var. Nipponbare and 93-11. We show that the allelic nucleotide diversity in 65.0% of 397 least-divergent pairs is not high (0.344% on average), while the remaining 35% display a greater diversity (5.4% on average). The majority of conserved R genes is single-copy and/or located as a singleton. The clustered, particularly the complex-clustered, R-genes contribute greatly to the rich genetic variation. Surprisingly only 11.2% of R-genes have remarkably high ratios of non-synonymous to synonymous rates, which is much less than the 17.4% observed between Arabidopsis genomes. Noticeable "artificially selective sweeping" could be detected in a large proportion of the conserved R-genes, a scenario described in the "arms race" co-evolutionary model. Based on our study, a variation pattern of R-genes is proposed and confirmed by the analysis of R-genes from other rice lines, indicating that the observed variation pattern may be common in all rice lines.

Genes, Plant↗

PubMed1976

Informational complexity of the nuclear and chloroplast genomes of Chlamydomonas reinhardi.

DNA - DNA reassociation kinetics analyzed by hydroxylapatite chromatography have been used to determine the informational content of the Chlamydomonas reinhardi nuclear and chloroplast genomes. The kinetics indicate that nuclear DNA, with the exception of ribosomal cistrons, renatures as a single component with an informational complexity 25 times that of the Escherichia coli genome. The chloroplast genome has less than 0.3% of the informational complexity of the nuclear genome, but is present in about 50 copies in the vegetative cell. Chloroplast DNA shows about a 10-12% zero-time binding component.

Cell Nucleus↗

PubMed1994

Maltose transport system of Escherichia coli: an ABC-type transporter.

The maltose transport system of E. coli is composed of a periplasmic maltose-binding protein (MBP), the presumed transmembrane channel made up of MalF and MalG proteins, and two copies of the ATPase subunit, MalK. The membrane-associated transporter complex was purified in a functional form both from the wild-type strain and from mutants that do not require MBP for transport, and was reconstituted into proteoliposomes. A major function of MBP is to send a transmembrane signal, in the presence of ligands, to the ATPase subunits on the inner side of the membrane. In addition, MBP performs a special function in the translocation of the larger ligands, maltodextrins, perhaps by aligning them for entry into the channel.

ATP-Binding Cassette Transporters↗

PubMed1991

Gene expression of nonsegmented negative strand RNA viruses.

Nonsegmented negative strand RNA viruses comprise major human and animal pathogens in nature. This class of viruses is ubiquitous and infects vertebrates, invertebrates, and plants. Our laboratory has been working on the gene expression of two prototype nonsegmented negative strand RNA viruses, vesicular stomatitis virus (a rhabdovirus) and human parainfluenza virus 3 (a paramyxovirus). An RNA-dependent RNA polymerase (L and P protein) is packaged within the virion which faithfully copies the genome RNA in vitro and in vivo; this enzyme complex, in association with the nucleocapsid protein (N), is also involved in the replication process. In this review, we have presented up-to-date information of the structure and function of the RNA polymerases of these two viruses, the mechanisms of transcription and replication, and the role of host proteins in the life-cycle of the viruses. These detailed studies have led us to a better understanding of the roles of viral and cellular proteins in the viral gene expression.

Animals↗