Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis

X inactivation is a chromosome-specific form of genetic regulation in which thousands of genes on one homologue become silenced early in female embryogenesis. Although many aspects of X inactivation are now understood, the spread of the X inactivation signal along the entire length of the chromosome remains enigmatic. Extending the Gartler-Riggs model [Gartler, S. M. & Riggs, A. D. (1983) Annu. Rev. Genet. 17, 155-190], Lyon recently proposed [Lyon, M. F. (1998) Cytogenet. Cell Genet. 80, 133-137] that a nonrandom organization of long interspersed element (LINE) repetitive sequences on the X chromosome might be responsible for its facultative heterochromatization. In this paper, we present data indicating that the LINE-1 (L1) composition of the human X chromosome is fundamentally distinct from that of human autosomes. The X chromosome is enriched 2-fold for L1 repetitive elements, with the greatest enrichment observed for a restricted subset of LINE-1 elements that were active <100 million years ago. Regional analysis of the X chromosome reveals that the most significant clustering of these elements is in Xq13-Xq21 (the center of X inactivation). Genomic segments harboring genes that escape inactivation are significantly reduced in L1 content compared with X chromosome segments containing genes subject to X inactivation, providing further support for the association between X inactivation and L1 content. These nonrandom properties of L1 distribution on the X chromosome provide strong evidence that L1 elements may serve as DNA signals to propagate X inactivation along the chromosome.

Precise quantitative determination of phytosterols, stanols, and cholesterol metabolites in human serum by capillary gas-liquid chromatography

Total lipid extraction, solid-phase extraction, saponification, derivatization to trimethylsilyl ether derivatives, then capillary gas-liquid chromatography were used for quantitative analysis of sitosterol, campesterol, stigmasterol, sitostanol, campestanol, lathosterol, desmosterol, and lanosterol in human serum. Details of quality control integral to the accuracy and precision of analyses are included. The method limits of detection and quantitation, respectively, ranged from 0.05 microg/ml and 0.2 microg/ml for sitostanol to 0.4 microg/ml and 1.2 microg/ml for campesterol and campestanol. Analytes were measured at concentrations of 120 ng/ml to 6 microg/ml with standard deviations of 0.02 to 0.12 microg/ml for 55 analyses of a control serum sample conducted over a 2-month period.

GIST: A web tool for collecting gene information

As the human genome is sequenced and annotated, an important step in future genetic studies of complex traits and diseases will be the identification of relevant candidate genes. To enable such compilations, it would be useful to collate all necessary and available genetic information for each candidate gene. To this end, we have created a web tool (http://genome.cwru.edu/gist/gist.html+ ++) to allow the rapid cataloging of currently available genetic data. This tool, called GIST (or "Gene Information Search Tool"), allows an investigator to search the major genomic databases containing gene and marker information from a single query point. To prove the utility of GIST, a catalog of 150 hypertension candidate genes was created. This resource collates all available nucleotide and amino acid sequence data, expression data, chromosomal map location, and genetic marker interval for each gene, collected from on-line databases. These data can be used to guide genetic studies of hypertension.

Alkylpurine-DNA-N-glycosylase knockout mice show increased susceptibility to induction of mutations by methyl methanesulfonate

Alkylpurine-DNA-N-glycosylase (APNG) null mice have been generated by homologous recombination in embryonic stem cells. The null status of the animals was confirmed at the mRNA level by reverse transcription-PCR and by the inability of cell extracts of tissues from the knockout (ko) animals to release 3-methyladenine (3-meA) or 7-methylguanine (7-meG) from 3H-methylated calf thymus DNA in vitro. Following treatment with DNA-methylating agents, increased persistence of 7-meG was found in liver sections of APNG ko mice in comparison with wild-type (wt) mice, demonstrating an in vivo phenotype for the APNG null animals. Unlike other null mutants of the base excision repair pathway, the APNG ko mice exhibit a very mild phenotype, show no outward abnormalities, are fertile, and have an apparently normal life span. Neither a difference in the number of leukocytes in peripheral blood nor a difference in the number of bone marrow polychromatic erythrocytes was found when ko and wt mice were exposed to methylating or chloroethylating agents. These agents also showed similar growth-inhibitory effects in primary embryonic fibroblasts isolated from ko and wt mice. However, treatment with methyl methanesulfonate resulted in three- to fourfold more hprt mutations in splenic T lymphocytes from APNG ko mice than in those from wt mice. These mutations were predominantly single-base-pair changes; in the ko mice, they consisted primarily of AT-->TA and GC-->TA transversions, which most likely are caused by 3-meA and 3- or 7-meG, respectively. These results clearly show an important role for APNG in attenuating the mutagenic effects of N-alkylpurines in vivo.

clk1, a serine/threonine protein kinase-encoding gene, is involved in pathogenicity of Colletotrichum lindemuthianum on common bean

A random insertional mutagenesis in Colletotrichum lindemuthianum, the causal agent of common bean anthracnose, generated four mutants that showed altered pathogenicity when tested on intact seedlings, excised leaves, and/or excised hypocotyls. One of these mutants, H290, produced very few lesions on bean leaves and appeared affected in its ability to penetrate the leaf cuticle. Molecular analyses showed that the border sequences of the unique integration site of the disrupting pAN7-1 plasmid in the mutant exhibited homology with conserved domains of serine/threonine protein kinases. The corresponding wild-type sequences were cloned and a gene replacement vector with a mutated copy harboring a selection marker constructed. Transformation of the wild-type pathogen produced a strain with a phenotype identical to the original mutant. Genomic and cDNA sequences indicated that the disrupted gene is a member of the serine/threonine protein kinase family. The gene, called clk1 (Colletotrichum lindemuthianum kinase 1), was weakly expressed in the mycelium of the wild-type strain grown on rich and minimal synthetic media but was undetectable during the infection even when a sensitive reverse transcriptase-polymerase chain reaction methodology was used. This study represents the first characterization of altered pathogenicity mutants in C. lindemuthianum produced by random mutagenesis and demonstrates the involvement of a member of the serine/threonine kinase gene family in the early steps of the infection process.

Fourier transform infrared evidence for connectivity between CuB and glutamic acid 286 in cytochrome bo3 from Escherichia coli

Photodissociation of fully reduced, carbonmonoxy cytochrome bo3 causes ultrafast transfer of carbon monoxide (C triple bond O) from heme iron to CuB in the binuclear site. At low temperatures, the C triple bond O remains bound to CuB for extended times. Here, we show that the binding of C triple bond O to CuB perturbs the IR stretch of an un-ionized carboxylic acid residue, which is identified as Glu286 by mutation to Asp or to Cys. Before photodissociation, the carbonyl (C=O)-stretching frequency of this carboxylic acid residue is 1726 cm-1 for Glu286 and 1759 cm-1 for Glu286Asp. These frequencies are definitive evidence for un-ionized R-COOH and suggest that the carboxylic acids are hydrogen-bonded, though more extensively in Glu286. In Glu286Cys, this IR feature is lost altogether. We ascribe the frequency shifts in the C=O IR absorptions to the effects of binding photodissociated C triple bond O to CuB, which are relay ed to the 286 locus. Conversely, the 2065 cm-1 C triple bond O stretch of CuB-CO is markedly affected by both mutations. These effects are ascribed to changes in the Lewis acidity of CuB, or to displacement of a CuB histidine ligand by C triple bond O. C triple bond O binding to CuB also induces a downshift of an IR band which can be attributed to an aromatic C-H stretch, possibly of histidine imidazole, at about 3140 cm-1. The results suggest an easily polarizable, through-bond connectivity between one of the histidine CuB ligands and the carboxylic group of Glu286. A chain of bound water molecules may provide such a connection, which is of interest in the context of the proton pump mechanism of the heme-copper oxidases.

Flow-flash kinetics of O2 binding to cytochrome c oxidase at elevated [O2]: observations using high pressure stopped flow for gaseous reactants

A high-pressure stopped-flow apparatus developed in our laboratories provides the capability to use dissolved gaseous reactants at elevated concentrations in solution (in equilibrium with gas pressures up to ca. 30 atm) for measurement of reaction kinetics. We have used this apparatus to follow the reaction of dioxygen with bovine cytochrome c oxidase following photolysis of the fully reduced CO ligated enzyme up to a dioxygen concentration of 16 mM. The observed rate dependence on [02] follows saturation kinetics and was fit to a limiting rate of 1.0 X 10(6) s(-1). This value is approximately the same as that for the thermal loss of CO to solution from the transient CuB bound state formed upon photolysis of the heme-CO complex. Implications for the mechanism of O2 binding and reduction by the heme-copper oxidases are discussed.

Vasoactive intestinal peptide stimulates neuropeptide Y gene expression and causes neurite extension in PC12 cells through independent mechanisms

Vasoactive intestinal peptide (VIP) is widely recognized as a regulator of tyrosine hydroxylase via a mechanism of trans-synaptic activation. Subsets of adrenal medullary cells and postganglionic sympathetic nerves coexpress the peptide neurotransmitter neuropeptide Y (NPY) with catecholamines. Using PC12 cells transiently expressing a fusion gene in which the bacterial enzyme chloramphenicol acetyltransferase (CAT) is under the control of 700 base pairs of the 5' flanking region of the NPY gene, we have studied the role of VIP and the related peptide pituitary adenylate cyclase activating peptide (PACAP) in regulating NPY gene transcription. Both VIP and PACAP stimulated expression of the NPY gene through activation of cAMP-dependent protein kinase. PACAP was 1000-fold more potent in eliciting this response compared to VIP and activity resided in its N-terminal 27 amino acids. Both VIP and PACAP caused a subpopulation (approximately 50%) of PC12 cells to undergo profound morphological changes in that the cells extended long, slender neurites with prominent growth cones. This change in morphology was unaffected by preincubating cells with inhibitors of either cAMP-dependent protein kinase or calcium/phospholipid-dependent protein kinase. A trophic role for either VIP or PACAP in regulating sympathetic nerve function is proposed.

Resistance of cowpea [Vigna unguiculata (L.) Walp.] to Striga gesnerioides (Willd.) Vatke, a parasitic angiosperm

An in vitro growth system was used to investigate the expression of resistance of cowpea [Vigna unguiculata (L.) Walp.] varieties B301 and 58-57 to the angiosperm parasite Striga gesnerioides (Willd.) Vatke. Variety Blackeye was included in experiments as a susceptible control. Seeds of S. gesnerioides germinated on the roots of all varieties. Two different mechanisms of resistance were expressed in B301 and 58-57 after penetration of host roots by parasite radicles. The first mechanism was expressed in both varieties; host tissue around invading Striga radicles became necrotic in association with the early death of the parasite and lack of tubercle formation. On variety 58-57, the necrosis response was expressed only when the roots were inoculated with Striga from Burkina Faso but Striga from Mali successfully parasitized the roots of variety 58-57. The second mechanism was observed only on variety B301. Striga radicles infected cowpea roots, tubercles were formed but remained at 1-2 mm in diameter with very limited stem growth. No further development of the parasite occurred in vitro or when infected cowpeas were grown in soil or vermiculite. Similarities between the expression of resistance of cowpea to Striga and ot plants to plant pathogenic fungi are discussed.

Serologic investigations in a New York City cohort of parenteral drug users

Human immunodeficiency virus (HIV) infection continues to be a major health problem for society. Intravenous drug users are the second largest risk group for HIV infection. The disease primarily affects immunologic functioning. This study examined the inherent immunologic dysfunction by measuring the seroprevalence of infection against pathogens often associated with HIV infection. Additionally, chi square analysis was used to compare intravenous drug users with a non-drug-using control group to see if any difference existed in the prevalence of antinuclear antibody, rheumatoid factor, abnormal titer of antibody to Toxoplasma gondii, cytomegalovirus, and herpes simplex virus (types 1 and 2). The intravenous drug users had a significantly greater level of antibody titers for antinuclear antibody and Toxoplasma gondii than did controls. Abnormal serologic results were not significantly associated with HIV seropositivity. The findings of this study suggest that intravenous drug users experience a greater prevalence of alteration in serologic markers unrelated to HIV exposure.

Differential accumulation of plant defense gene transcripts in a compatible and an incompatible plant-pathogen interaction

Phenylalanine ammonia-lyase and chalcone synthase catalyze the first reaction of phenylpropanoid biosynthesis and the first reaction of a branch pathway specific for flavonoid-isoflavonoid biosynthesis, respectively. These enzymes are key control elements in the synthesis of kievitone, phaseollin, and related isoflavonoid-derived phytoalexins. RNA blot hybridization with 32P-labeled cDNA sequences was used to demonstrate marked accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs in excision-wounded hypocotyls of Phaseolus vulgaris L. (dwarf French bean) and during race-cultivar-specific interactions between hypocotyls of P. vulgaris and the partially biotrophic fungus Colletotrichum lindemuthianum, the causal agent of anthracnose. In an incompatible interaction (host resistant), early concomitant accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs, localized mainly but not entirely in tissue adjacent to the site of infection, was observed prior to the onset of phytoalexin accumulation and expression of localized, hypersensitive resistance. In contrast, in a compatible interaction (host susceptible) there was no early accumulation of these transcripts; instead, there was a delayed widespread response associated with phytoalexin accumulation during attempted lesion limitation. Two-dimensional gel electrophoresis of [35S]methionine-labeled polypeptides synthesized in vitro by translation of isolated polysomal RNA demonstrated stimulation of the synthesis of characteristic sets of phenylalanine ammonia-lyase and chalcone synthase isopolypeptides in directly infected tissue and distant, hitherto uninfected tissue in both compatible and incompatible interactions. Our data show that specific accumulation of plant defense gene transcripts is a key early component in the sequence of events leading to expression of defense responses in wounded tissue and in infected tissue during race-cultivar-specific interactions and that an elicitation signal is transmitted intercellularly in response to infection.

Co-ordinated synthesis of phytoalexin biosynthetic enzymes in biologically-stressed cells of bean (Phaseolus vulgaris L.)

Changes in the rates of synthesis of three enzymes of phenyl-propanoid biosynthesis in Phaseolus vulgaris L. (dwarf French bean) have been investigated by immunoprecipitation of [S]methionine-labeled enzyme subunits with mono-specific antisera. Elicitor causes marked, rapid but transient co-ordinated increases in the rate of synthesis of phenyl-alanine ammonia-lyase, chalcone synthase and chalcone isomerase concomitant with the phase of rapid increase in enzyme activity at the onset of accumulation of phenyl-propanoid-derived phytoalexin antibiotics in suspension cultures of P. vulgaris. Co-ordinate induction of enzyme synthesis is also observed in hypocotyl tissue during race:cultivar-specific interactions with Colletotrichum lindemuthianum, causal agent of anthracnose. In an incompatible interaction (host resistant) there are early increases apparently localized to the initial site of infection prior to the onset of phytoalexin accumulation and expression of hypersensitive resistance. In contrast, in a compatible interaction (host susceptible) there is no induction of synthesis in the early stages of infection, but a delayed widespread response at the onset of lesion formation associated with attempted lesion limitation. It is concluded that expression of the phytoalexin defense response in biologically stressed cells of P. vulgaris characteristically involves co-ordinate induction of synthesis of phytoalexin biosynthetic enzymes.

Experience with a simplified trauma registry: profile of trauma at a university hospital

A simplified computer-based trauma registry system with well-defined limits of data capture is presented. This registry was utilized to describe the profile of trauma at a university hospital. In 1 year there were 882 trauma victims hospitalized, with an overall mortality of 3.3%. The majority of the patients had relatively minor injuries, primarily involving soft tissue and bone. Severe multiple trauma was associated with a significant mortality. Intracranial or intra-abdominal injuries occurred in less than 10% of the patients. Transport accidents, falls, and assaults were the cause of injury in 70%. Key access to specific information about the trauma patient population demonstrated the potential of the registry system. The advantages and limitations of the registry are discussed.

Column chromatographic separation of deoxynucleotide monomethyl esters and related products of the reaction of n-methyl-n-nitrosourea with deoxynucleoside monophosphates

Dowex 1 (HCOO-) column chromatographic procedures are described for the resolution of deoxynucleoside monophosphate monomethyl esters and other related products of the reaction of the carcinogen N-methyl-N-nitrosourea with deoxynucleoside monophosphates. These procedures provide convenient methods for the isolation and estimation of the products of these reactions.

Some lethal and semilethal forms of disproportionate short stature

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Bilateral femoral dysgenesis

Three patients with bilateral femoral dysgenesis are described, and the pathogenesis and clinical significance discussed. Af fected patients are often surprisingly agile, but surgery may be required for painful hips or to remove portions of poste riorly projecting femurs if these cause discomfort on sitting.

Elevation of the upper extremity by use of a simple "towel sling"

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