MspI polymorphism at the human complement component C6 gene (C6).
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Chromosome Mapping↗
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Overrepresentation of elements recognized by TCP-domain transcription factors in the upstream regions of nuclear genes encoding components of the mitochondrial oxidative phosphorylation Machinery.
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Cell Nucleus↗
Arabidopsis genes encoding components of the chloroplastic protein import apparatus.
The process of protein import into plastids has been studied extensively using isolated pea (Pisum sativum) chloroplasts. As a consequence, virtually all of the known components of the proteinaceous apparatus that mediates import were originally cloned from pea. With the recent completion of the Arabidopsis genome sequencing project, it is now possible to identify putative homologs of the import components in this species. Our analysis has revealed that Arabidopsis homologs with high sequence similarity exist for all of the pea import complex subunits, making Arabidopsis a valid model for further study of this system. Multiple homologs can be identified for over one-half of the components. In all but one case it is known that more than one of the putative isoforms for a particular subunit are expressed. Thus, it is possible that multiple types of import complexes are present within the same cell, each having a unique affinity for different chloroplastic precursor proteins, depending upon the exact mix of isoforms it contains. Sequence analysis of the putative Arabidopsis homologs for the chloroplast protein import apparatus has revealed many questions concerning subunit function and evolution. It should now be possible to use the genetic tools available in Arabidopsis, including the generation of knockout mutants and antisense technology, to address these questions and learn more about the molecular functions of each of the components during the import process.
Amino Acid Sequence↗
Prevalence of human parvovirus B19 component NS1 gene in patients with Henoch-Schonlein purpura and hypersensitivity vasculitis.
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Adolescent↗
A novel mutation in the ARS (component B) gene encoding SLURP-1 in a Turkish family with mal de Meleda.
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Adolescent↗
Evolution of swine H3N2 influenza viruses in the United States.
During 1998, severe outbreaks of influenza were observed in four swine herds in the United States. This event was unique because the causative agents, H3N2 influenza viruses, are infrequently isolated from swine in North America. Two antigenically distinct reassortant viruses (H3N2) were isolated from infected animals: a double-reassortant virus containing genes similar to those of human and swine viruses, and a triple-reassortant virus containing genes similar to those of human, swine, and avian influenza viruses (N. N. Zhou, D. A. Senne, J. S. Landgraf, S. L. Swenson, G. Erickson, K. Rossow, L. Liu, K.-J. Yoon, S. Krauss, and R. G. Webster, J. Virol. 73:8851-8856, 1999). Because the U.S. pig population was essentially naive in regard to H3N2 viruses, it was important to determine the extent of viral spread. Hemagglutination inhibition (HI) assays of 4, 382 serum samples from swine in 23 states indicated that 28.3% of these animals had been exposed to classical swine-like H1N1 viruses and 20.5% had been exposed to the triple-reassortant-like H3N2 viruses. The HI data suggested that viruses antigenically related to the double-reassortant H3N2 virus have not become widespread in the U.S. swine population. The seroreactivity levels in swine serum samples and the nucleotide sequences of six additional 1999 isolates, all of which were of the triple-reassortant genotype, suggested that H3N2 viruses containing avian PA and PB2 genes had spread throughout much of the country. These avian-like genes cluster with genes from North American avian viruses. The worldwide predominance of swine viruses containing an avian-like internal gene component suggests that these genes may confer a selective advantage in pigs. Analysis of the 1999 swine H3N2 isolates showed that the internal gene complex of the triple-reassortant viruses was associated with three recent phylogenetically distinct human-like hemagglutinin (HA) molecules. Acquisition of HA genes from the human virus reservoir will significantly affect the efficacy of the current swine H3N2 vaccines. This finding supports continued surveillance of U.S. swine populations for influenza virus activity.
Animals↗
Characterization of protein kinase C beta isoform activation on the gene expression of transforming growth factor-beta, extracellular matrix components, and prostanoids in the glomeruli of diabetic rats.
Induction of protein kinase C (PKC) pathway in the vascular tissues by hyperglycemia has been associated with many of the cellular changes observed in the complications of diabetes. Recently, we have reported that the use of a novel, orally effective specific inhibitor of PKC beta isoform (LY333531) normalized many of the early retinal and renal hemodynamics in rat models of diabetes. In the present study, we have characterized a spectrum of biochemical and molecular abnormalities associated with chronic changes induced by glucose or diabetes in the cultured mesangial cells and renal glomeruli that can be prevented by LY333531. Hyperglycemia increased diacylglycerol (DAG) level in cultured mesangial cells exposed to high concentrations of glucose and activated PKC alpha and beta1 isoforms in the renal glomeruli of diabetic rats. The addition of PKC beta selective inhibitor (LY333531) to cultured mesangial cells inhibited activated PKC activities by high glucose without lowering DAG levels and LY333531 given orally in diabetic rats specifically inhibited the activation of PKC beta1 isoform without decreasing PKC alpha isoform activation. Glucose-induced increases in arachidonic acid release, prostaglandin E2 production, and inhibition of Na+-K+ ATPase activities in the cultured mesangial cells were completely prevented by the addition of LY333531. Oral feeding of LY333531 prevented the increased mRNA expression of TGF-beta1 and extracellular matrix components such as fibronectin and alpha1(IV) collagen in the glomeruli of diabetic rats in parallel with inhibition of glomerular PKC activity. These results suggest that the activation of PKC, predominately the beta isoform by hyperglycemia in the mesangial cells and glomeruli can partly contribute to early renal dysfunctions by alteration of prostaglandin production and Na+-K+ ATPase activity as well as the chronic pathological changes by the overexpression of TGF-beta1 and extracellular matrix components genes.
Administration, Oral↗
Preliminary evidence for genetic determination of intraerythrocytic sodium concentration in Utah pedigrees.
Intraerythrocytic sodium concentration has been reported to be increased in hypertensive individuals and some of their normotensive relatives. We investigated the "familiality" of this trait in 572 nonhypertensive subjects from 34 Utah kindreds. Most of these kindreds were selected because of a high incidence of hypertension, heart attack, or stroke. Intraerythrocytic sodium concentration was correlated with the sex of the subject and suprailiac skinfold thickness. Intraerythrocytic sodium concentration was adjusted by linear regression for these 2 factors. The residual values were positively correlated in parent-offspring pairs and among sibs, both those presumed to be living together and those presumed to be living apart. The spouse-spouse correlation was not significant. Pedigree analysis suggested a mixed major-gene/polygenic model of inheritance, but these data did not allow us to distinguish between dominant and recessive inheritance for the major gene component. Total heritability due to both major-gene and polygenic components was estimated to be 90-95%; the proportion of the total variance due to polygenes was estimated to be 60-75%. These results suggest that further study of the relationship between the inheritance of intraerythrocytic sodium and the pathophysiology of hypertension is warranted.
Epidemiologic Methods↗
Accessibility and the developmental regulation of V(D)J recombination.
Antigen receptor genes are assembled from their component gene segments by a highly regulated series of site-specific DNA recombination reactions known as V(D)J recombination. Proteins encoded by the RAG1 and RAG2 genes are responsible for the recognition and double-stranded cleavage of a highly conserved DNA sequence flanking all rearranging gene segments. It remains uncertain how this common lymphoid recombinase is targeted to distinct loci in developing B and T cells and to specific loci at successive stages of lymphocyte development. This review considers evidence that DNA sequences which regulate the transcription of antigen receptor genes also regulate the recombination reaction by determining the accessibility of individual loci to the V(D)J recombinase.
Animals↗
Sequence of the gene for murine complement component C4.
The gene for murine complement component C4 lies in the S region of the murine major histocompatibility (H-2) complex; in this paper, we report the nucleotide sequence of this gene. The present sequence extends from a SmaI restriction enzyme cleavage site near the 5' end of the gene to a KpnI restriction enzyme cleavage site 569 nucleotides 3' of the polyadenylation site. The sequence spans 15,956 base pairs and together with previously reported data provides a complete sequence extending from the site of transcriptional initiation to the polyadenylation site. The sequence reveals that the C4 gene has 40 introns which range from 75 to 1089 base pairs in length and which include three murine B1 middle repetitive elements, a MT repeat element, and an apparently novel repeat sequence that is also found in noncoding regions of the murine beta-glucuronidase, lymphotoxin (TNF-beta), and rat alpha-crystallin genes. An intron splits the protein coding sequence precisely at the site of proteolytic activation of C4 by complement protease C1s; however, except for this one case, the intron positions show no striking relationship to the structural features of the C4 protein. The length of the murine C4 gene relative to the isotypic C4A and C4B genes in man suggests the independent loss of a 6-kilobase intron from both murine and human C4 genes.
Animals↗
Optimization of a stochastically simulated gene network model via simulated annealing.
By rearranging naturally occurring genetic components, gene networks can be created that display novel functions. When designing these networks, the kinetic parameters describing DNA/protein binding are of great importance, as these parameters strongly influence the behavior of the resulting gene network. This article presents an optimization method based on simulated annealing to locate combinations of kinetic parameters that produce a desired behavior in a genetic network. Since gene expression is an inherently stochastic process, the simulation component of simulated annealing optimization is conducted using an accurate multiscale simulation algorithm to calculate an ensemble of network trajectories at each iteration of the simulated annealing algorithm. Using the three-gene repressilator of Elowitz and Leibler as an example, we show that gene network optimizations can be conducted using a mechanistically realistic model integrated stochastically. The repressilator is optimized to give oscillations of an arbitrary specified period. These optimized designs may then provide a starting-point for the selection of genetic components needed to realize an in vivo system.
Algorithms↗
Proteoglycan-19, laminin and collagen type IV production is correlated with the levels of mRNA in F9 cell aggregates differentiating in the presence or absence of cyclic AMP.
F9 embryonal carcinoma cells differentiate to embryoid bodies containing an outer epithelial layer of visceral endoderm cells when cultured as aggregates in medium containing retinoic acid (RA). Another pathway of differentiation to parietal endoderm is followed when dibutyryl cyclic AMP (cAMP) is added to the medium. We have measured the accumulated levels of RNA transcripts from a chondroitin sulfate proteoglycan gene (PG-19), the type IV collagen alpha 1, alpha 2 subunit genes, and laminin B1, B2 subunit genes during these differentiation processes. Laminin B2 gene is uniquely regulated among the extracellular matrix component genes studied. The level of laminin B2 RNA remains almost invariant during RA induction of differentiation but is induced 11-fold by cAMP with RA. In contrast, laminin B1, collagen IV alpha 1, and alpha 2 genes are induced in two stages with six- to sevenfold accumulation of RNA induced by RA and fourfold greater levels by cAMP (19- to 28-fold overall). All of these matrix-encoding genes except proteoglycan are expressed at low levels in unstimulated F9 cells, whereas PG-19 is completely undetectable and is observed only after 2 days of stimulation with RA. Its increased expression with RA and cAMP induction is at least 100-fold during F9 differentiation. Extracellular matrix transcripts are relatively stable and this accounts in part for high accumulated levels during differentiation. We conclude that several kinds of gene regulation occur among the matrix components and other differentiation markers, and this makes the F9 model system useful to study the differential effects of hormone treatments on cellular events leading to differentiation and loss of tumorigenicity.
Bucladesine↗
The gene for component-II of botulinum C2 toxin.
The gene encoding component-II of the Clostridium botulinum C2 toxin was cloned from the chromosomal DNA of C. botulinum type C strain (C)-203U28, and the nucleotide sequence was determined. The gene (bc2h) encodes a protein with 721 amino acid residues and is located at 247 bp downstream of the gene for component-I. The N-terminal 16 amino acids were identical to those obtained by analysis of the purified component-II toxin. The ORF for bc2h had only 39% homology at the amino acid level with the C.perfringens iota-Ib protein and an ATP/GTP binding site which is present in the iota-Ib protein is missing from the protein encoded by bc2h. Both genes had a homologous region that predicts a transmembrane segment.
Amino Acid Sequence↗
Monolignol radical-radical coupling networks in western red cedar and Arabidopsis and their evolutionary implications.
The discovery of a nine-member multigene dirigent family involved in control of monolignol radical-radical coupling in the ancient gymnosperm, western red cedar, suggested that a complex multidimensional network had evolved to regulate such processes in vascular plants. Accordingly, in this study, the corresponding promoter regions for each dirigent multigene member were obtained by genome-walking, with Arabidopsis being subsequently transformed to express each promoter fused to the beta-glucuronidase (GUS) reporter gene. It was found that each component gene of the proposed network is apparently differentially expressed in individual tissues, organs and cells at all stages of plant growth and development. The data so obtained thus further support the hypothesis that a sophisticated monolignol radical-radical coupling network exists in plants which has been highly conserved throughout vascular plant evolution.
Arabidopsis↗
GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.
We describe a method (implemented in a program, GAZE) for assembling arbitrary evidence for individual gene components (features) into predictions of complete gene structures. Our system is generic in that both the features themselves, and the model of gene structure against which potential assemblies are validated and scored, are external to the system and supplied by the user. GAZE uses a dynamic programming algorithm to obtain the highest scoring gene structure according to the model and posterior probabilities that each input feature is part of a gene. A novel pruning strategy ensures that the algorithm has a run-time effectively linear in sequence length. To demonstrate the flexibility of our system in the incorporation of additional evidence into the gene prediction process, we show how it can be used to both represent nonstandard gene structures (in the form of trans-spliced genes in Caenorhabditis elegans), and make use of similarity information (in the form of Expressed Sequence Tag alignments), while requiring no change to the underlying software. GAZE is available at http://www.sanger.ac.uk/Software/analysis/GAZE.
Algorithms↗
Expression and localization of the renin-angiotensin system in the rat pancreas.
The possibility of an intrinsic renin-angiotensin system (RAS) in the pancreas has been raised by previous studies in which immunohistochemical examination showed the presence of angiotensin II and its receptor subtypes, type 1 (AT1) and type 2 (AT2). In the present study, gene expression of several key RAS components was investigated by reverse-transcription PCR. mRNA expression for angiotensinogen, renin and angiotensin II receptor subtypes, AT1a, AT1b and AT2 was shown. The presence of angiotensinogen protein, the mandatory component for an intrinsic RAS, was demonstrated by Western blotting and localized by immunohistochemistry to the epithelia and endothelia of pancreatic ducts and blood vessels respectively. Immunoblot analysis detected a predominant protein band of about 60 kDa in the pancreas. This was consistent with the predicted value for angiotensinogen as reported in other tissues. Together with previous findings, the present study shows that the rat pancreas expresses the major RAS component genes, notably angiotensinogen and renin, required for intracellular formation of angiotensin II. The data support the notion of an intrinsic RAS in the rat pancreas which may play a role in the regulation of pancreatic functions.
Angiotensin II↗
Characterization of recombinant thioesterase and acyl carrier protein domains of chicken fatty acid synthase expressed in Escherichia coli.
Fatty acid synthase of animal tissue is a multifunctional enzyme comprised of two identical subunits, each containing seven partial activities and a site for the prosthetic group, 4'-phosphopantetheine (acyl carrier protein). We have recently isolated cDNA clones of chicken fatty acid synthase coding for the dehydratase, enoyl reductase, beta-ketoacyl reductase, acyl carrier protein, and thioesterase domains (Chirala, S.S., Kasturi, R., Pazirandeh, M., Stolow, D.T., Huang, W.Y., and Wakil, S.J. (1989) J. Biol. Chem. 264, 3750-3757). To gain insight into the structure and function of the various domains, the portion of the cDNA coding for the acyl carrier protein and thioesterase domains was expressed in Escherichia coli by using an expression vector that utilizes the phage lambda PL promoter. The recombinant protein was efficiently expressed and purified to near homogeneity using anion-exchange and hydroxyapatite chromatography. As expected from the coding capacity of the cDNA expressed, the protein has a molecular weight of 43,000 and reacts with antithioesterase antibodies. The recombinant thioesterase was found to be enzymatically active and has the same substrate specificity and kinetic properties as the native enzyme of the multifunctional synthase. Treatment of the recombinant protein with alpha-chymotrypsin results in the cleavage of the acyl carrier protein and thioesterase domain junction sequence at exactly the same site as with native fatty acid synthase. The amino acid composition of the purified recombinant protein revealed the presence of 0.6 mol of beta-alanine/mol of protein, indicating partial pantothenylation of the recombinant acyl carrier protein domain. These results indicate that the expressed protein has a conformation similar to the native enzyme and that its folding into functionally active domains is independent of the remaining domains of the multifunctional synthase subunit. These conclusions are consistent with the proposal that the multifunctional synthase gene has evolved from fusion of component genes.
Acyl Carrier Protein↗
Structure of the mouse C-reactive protein gene.
A genomic DNA clone corresponding to the mouse C-reactive protein (CRP) has been isolated and characterized. The mouse CRP gene is 1.9-kilobase pairs in length and contains a single intron of 213-base pairs which interrupts the codon for the 2nd amino acid residue of the mature CRP protein. We compared nucleotide sequences of the mouse and human CRP genes and discussed structures of possible regulatory sequences. With this characterization, the isolation and sequence analyses of a set of mouse and human pentraxin genes, i.e. CRP and serum amyloid P component genes is not complete.
Amino Acid Sequence↗