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At least 109 records · Page 6Linked to original sources

Nested polymerase chain reaction on cellular DNA in plasma: a rapid method to investigate the collagen type I A2 MspI polymorphic restriction site in alcoholic patients.

We investigated the MspI restriction site of the human collagen type I A2 (COL1A2) gene in alcoholic subjects with and without liver disease, using the nested polymerase chain reaction to analyse trace cellular DNA in plasma samples. This procedure is rapid, it requires only 200 microliters plasma, and the results correlate perfectly with those of Southern blotting. Alcoholic subjects with acute alcoholic hepatitis had a significantly lower frequency of the minor allele than healthy controls or alcoholics with minimal liver abnormalities, i.e. steatosis. Our results reinforce the hypothesis of a genetic predisposition of certain alcoholics to liver damage.

Alcoholism↗

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

BACKGROUND: The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. RESULTS: By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. CONCLUSIONS: The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.

Animals↗

Population genetics of Y-chromosome STRs in a population of Podlasie, Northeastern Poland.

Haplotype and allele frequencies for the 12 Y-STRs were determined in a population sample of 186 Polish males. Five of the haplotypes were encountered in duplicate, while 176 haplotypes were unique. The overall gene diversity was 0.9973. This database study provides an essential precondition for applying Y-chromosomal STRs estimates in forensic identification of male DNA and tracing of paternal lineages.

Chromosomes, Human, Y↗

Identification and separation of DNA mixtures using peak area information.

We introduce a new methodology, based upon probabilistic expert systems, for analysing forensic identification problems involving DNA mixture traces using quantitative peak area information. Peak area is modelled with conditional Gaussian distributions. The expert system can be used for ascertaining whether individuals, whose profiles have been measured, have contributed to the mixture. It can also be used to predict DNA profiles of unknown contributors by separating the mixture into its individual components. The potential of our probabilistic methodology is illustrated on case data examples and compared with alternative approaches. The advantages are that identification and separation issues can be handled in a unified way within a single probabilistic model and the uncertainty associated with the analysis is quantified. Further work, required to bring the methodology to a point where it could be applied to the routine analysis of casework, is discussed.

DNA↗

Population genetics of Y-chromosome STRs in a population sample of the Lithuanian minority residing in the northeastern Poland.

Haplotype and allele frequencies for the 12 Y-STRs were determined in a population sample of 124 unrelated males--members of the Lithuanian minority residing in the northeastern Poland. Three of the haplotypes were encountered in duplicate, while 118 haplotypes were unique. The overall gene diversity was 0.9952. Analysis of molecular variance revealed that the Lithuanian minority can be distinguished from the autochthonous Poles, although these two populations are very close to each other. This database study provides an essential precondition for applying Y-chromosomal STRs estimates in forensic identification of male DNA and tracing of paternal lineages.

Chromosomes, Human, Y↗

Investigation of the link between visceral surface rib lesions and tuberculosis in a Medieval skeletal series from England using ancient DNA.

Seven human skeletons from a large assemblage from a rural English Medieval burial site show lesions, predominantly proliferative in nature, on the visceral surfaces of the ribs. In order to investigate whether these rib lesions were regularly associated with tuberculous infection, these individuals, together with a group of age- and sex-matched control skeletons without bony signs of infection, were subjected to polymerase chain reaction (PCR) assays aimed at detecting traces of DNA from infecting microorganisms of the Mycobacterium tuberculosis complex. The results provided no evidence for any regular association between visceral surface rib lesions and the presence of M. tuberculosis complex DNA in the study group. The significance of these findings for the paleopathological interpretation of visceral surface rib lesions is discussed.

Adolescent↗

Preliminary observations on interaction of 14C-metronidazole with macromolecules in vivo and in vitro.

Preliminary studies on the in vivo and in vitro interactions of 14C-metronidazole with macromolecules showed that the agent or its metabolite(s) can interact with nucleic acids and proteins in vivo. In vitro studies suggest that in absence of DNA synthesis trace amount of metronidazole does bind to DNA/protein and addition of metabolic activation system (from mouse liver) generates more reactive species from metronidazole.

Animals↗

VSQual: a visual system to assist DNA sequencing quality control.

A lack of pliant software tools that support small- to medium-scale DNA sequencing efforts is a major hindrance for recording and using laboratory workflow information to monitor the overall quality of data production. Here we describe VSQual, a set of Perl programs intended to provide simple and powerful tools to check several quality features of the sequencing data generated by automated DNA sequencing machines. The core program of VSQual is a flexible Perl-based pipeline, designed to be accessible and useful for both programmers and non-programmers. This pipeline directs the processing steps and can be easily customized for laboratory needs. Basically, the raw DNA sequencing trace files are processed by Phred and Cross_match, then the outputs are parsed, reformatted into Web-based graphical reports, and added to a Web site structure. The result is a set of real time sequencing reports easily accessible and understood by common laboratory people. These reports facilitate the monitoring of DNA sequencing as well as the management of laboratory workflow, significantly reducing operational costs and ensuring high quality and scientifically reliable results.

Database Management Systems↗

Herpes simplex virus type 1 (HSV-1) UL56 gene is involved in viral intraperitoneal pathogenicity to immunocompetent mice.

A comparison of the pathogenicity in mice of the recombinant herpes simplex virus type 1 (HSV-1) strain HSV-1-M-LacZ, in which the UL56 gene has been deleted, was made with its parental strain F, following infection in different mouse strains. The polymerase chain reaction (PCR) technique was used to study the migration of virus DNA in the mouse model. Tissues from adult mice infected intraperitoneally (IP) with one of three HSV-1 strains (F, HFEM or HSV-1-LacZ) were examined for the presence of viral DNA. DNA of the pathogenic strain F was detected in the adrenal glands, spinal cord, brain, liver and pancreas. DNA of HSV-1-M-LacZ was detected in the same tissues. However, DNA of the apathogenic strain HFEM was detected transiently (on days 2 and 3 p.i., but not days 1, 5 or 7), only in the adrenal glands and no viral DNA was detected in any of the other tissues. HSV-1 pathogenic strains injected intraperitoneally into newborn mice (7 days old) killed most of the mice. In the surviving mice viral DNA of the three virus strains was found in peritoneal exudate cells (PEC), adrenal glands, spinal cord, liver and spleen. It was found that HSV-1-M-LacZ, which lacks the UL56 gene, resembled in pathogenicity to the newborn mice the pathogenic HSV-1 strains F and KOS. The PCR technique was used to trace viral DNA in tissues of the mice which survived HSV-1 infection at 7 weeks of age. Only HSV-1 (KOS) DNA was detected in the pancreas. The brains of these mice did not contain viral DNA. It is suggested that HSV-1 DNA may reside in surviving HSV-1- infected newborn mice in a "latent" state in nonneural tissues.

Adrenal Glands↗

Mycobacterium tuberculosis transmission between cluster members with similar fingerprint patterns.

Molecular epidemiologic studies provide evidence of transmission of Mycobacterium tuberculosis within clusters of patients whose isolates share identical IS6110-DNA fingerprint patterns. However, M. tuberculosis transmission among patients whose isolates have similar but not identical DNA fingerprint patterns (i.e., differing by a single band) has not been well documented. We used DNA fingerprinting, combined with conventional epidemiology, to show unsuspected patterns of tuberculosis transmission associated with three public bars in the same city. Among clustered TB cases, DNA fingerprinting analysis of isolates with similar and identical fingerprints helped us discover epidemiologic links missed during routine tuberculosis contact investigations.

Adult↗

[Connection between 2 tuberculosis outbreaks demonstrated after 8 years by DNA-fingerprinting of the causative mycobacteria].

OBJECTIVE: To determine the possible connection between two outbreaks of tuberculosis at an 8-year interval by DNA fingerprinting of the causative mycobacteria. DESIGN: Descriptive. SETTING: Regional Public Health Services Zeeland and Noord-Holland, the Netherlands. METHOD: The source patients of the tuberculosis explosions in an island in the province of Zeeland (28 persons infected) and an island of the Noord-Holland area (36 persons infected) were identified in 1986 and 1994 respectively. In 1994. spoligotyping was performed on dead bacteria from the suspected source from 1986. to analyse the chain of transmission. RESULTS: Identical spoligotyping patterns of the source patients proved the transmission of a Mycobacterium tuberculosis strain from a father to his son around 1986. Lack of a positive Mantoux test in the son prohibited prevention of the 1994 explosion. CONCLUSION: Thanks to the applicability of spoligotyping on non-vital mycobacteria this DNA method contributed retrospectively to demonstration of a connection between two out-breaks of tuberculosis at an 8-year interval.

Adolescent↗

Molecular characterization of a voltage-gated potassium channel expressed in rat testis.

Potassium (K(+)) channels are present in both mammalian testis and spermatozoa. Immunofluorescent detection of sperm-bound biotinylated charybdotoxin, an inhibitor of Ca(2+)-activated and of delayed rectifier K(+) channels, indicated that these ion channels are uniformly distributed over the surface of both heads and tails of unfixed rat epididymal spermatozoa. Reverse transcription-polymerase chain reaction (RT-PCR) analysis on rat testis RNA with PCR primers, based on known nucleotide sequences of different classes of K(+) channels, amplified sequences homologous to delayed rectifier K(+) channels. In-situ RT-PCR on rat testis sections showed that these K(+) channel transcripts are present in the cytoplasm of primary spermatocytes and post-meiotic elongating spermatids. Northern blot analysis of various rat tissues identified multiple K(+) channel transcripts, some of which were observed only in testis. An attempt to obtain a full length rat testis K(+) channel cDNA sequence gave an assembled sequence of 2693 base pairs with >90% homology to a delayed rectifier K(+) channel, Kv1.3. A method for rapid amplification of cDNA ends was employed to amplify the 5' sequences of the rat testis cDNA but a unique sequence could not be obtained. DNA sequencer traces suggest that multiple related K(+) channels which differed at their 5' ends were amplified in rat testis.

5' Untranslated Regions↗

On the in vitro cytotoxicity of 1-chloroethyl-2-chloromethyl-2-imidazoline hydrochloride.

The cytotoxic activity of the monofunctional alkylating agent 1-chloroethyl-2-chloromethyl-2-imidazoline hydrochloride (chlorimidazine), synthesized according to predetermined properties, is characterized. The data obtained show that the substance has a cell-cycle state nonspecific cytotoxic effect. The interaction of chlorimidazine with cellular DNA is traced. It is found that the substance does not induce a break in the macromolecule, apurine sites or intercalation. Ensuing from the chemical structure of the compound, the probable mechanism of its cytotoxic action is discussed.

Animals↗

Transmission of Mycobacterium tuberculosis through casual contact with an infectious case.

BACKGROUND: An ongoing restriction fragment length polymorphism study of Mycobacterium tuberculosis isolates from tuberculosis cases showed an identical 12-band IS6110 pattern unique to 3 unrelated patients (Patients A-C) diagnosed as having tuberculosis within a 9-month period. METHODS: In an attempt to identify epidemiologic links between the 3 patients, we performed site visits to the retail business work site of patient A and conducted detailed interviews with all 3 patients and their contacts. RESULTS: Patient B had visited patient A's work site 3 times during patient A's infectious period, spending no more than 15 minutes each time. Patient C visited patient A's work site on 6 to 10 occasions during this period for no more than 45 minutes at any one time. There were no other epidemiologic links between these 3 cases other than the contact at the store. Contact investigation identified 4 tuberculin skin test conversions among 8 (50%) of patient A's coworkers, 6 positive tests among 15 household contacts (40%), and 8 positive tests among 16 identified customers who were casual contacts (50%). Patient B and patient C were most likely infected by patient A during one of their brief visits to patient A's work site. CONCLUSIONS: These data demonstrate that some tuberculosis is spread through casual contact not normally pursued in traditional contact investigations and that, in certain situations, M tuberculosis can be transmitted despite minimal duration of exposure. In addition, this outbreak emphasizes the importance of DNA fingerprinting data for identifying unusual transmission in unexpected settings.

Adult↗

DNA knotting abolishes in vitro chromatin assembly.

Topological knots can be formed in vitro by incubating covalently closed double stranded DNA and purified topoisomerase II from the yeast Saccharomyces cerevisiae in an ATP-dependent reaction. Knotting production requires a starting enzyme/DNA mass ratio of 1. Analysis of knotted DNA was carried out by using both one- and two-dimensional agarose gel electrophoresis. The knots generated are efficiently untied, and give relaxed DNA rings, by catalytic amounts of topoisomerase II, but not by topoisomerase I. Time course analysis shows the knotting formation over relaxed and supercoiled DNA. When supercoiled DNA was used as a susbtrate, knots appear immediately whereas no transient relaxed rings were observed. The cell-free extract from Xenopus oocytes S-150 cannot assemble nucleosomes on knotted DNA templates as revealed by topological and micrococcal nuclease analysis. Nevertheless, the presence of knotted DNA templates does not inhibit the assembly over the relaxed plasmid. Finally, a pretreatment of knotted DNA with trace amounts of topoisomerase II before the addition of the S-150 yields a canonical minichromosome assembled in vitro. Taking into account these results, I suggest a mechanism of chromatin assembly regulation directed by topoisomerase II.

Adenosine Triphosphate↗

Reversibly contractile nuclear matrix. Its isolation, structure, and composition.

From Tetrahymena macronuclei we have isolated a reversibly contractile nucleo-skeleton, i.e., an "expanded" nuclear matrix which reversibly contracts when the total concentration of the bivalent cations, Ca and Mg (3:2), is decreased to 5 mM or increased to 125 mM. During contraction the average diameter of the expanded matrix becomes reduced by about 24%; this corresponds to a volume contraction of about 55%. The reversible contraction of the nuclear matrix does not depend on ATP and cannot be inhibited by salygran. The expanded matrix is obtained by removing carefully from the macronuclei 89.7% of the phospholipid, 99.6% of the DNA, 98.5% of the RNA, and 74.8% of the protein by treatment with Triton X-100 and digestion with DNase and RNase followed by an extraction with 2 M NaCl. Electron microscopy reveals, within the expanded matrix, residual equivalents to the structures characteristic for macronuclei: (a) a residual nuclear envelope with nuclear pore complexes; (b) residual nucleoli at the periphery; (c) a fibrillar internal network. The expanded matrix is essentially composed of proteins (96.2%) and traces of DNA (0.8%), RNA (0.5%), phospholipid (1.6%), and carbohydrates (0.9%). The last, which have been determined by gas chromatography, contain glucose, mannose, and an unidentified sugar in the ratio 1:5.4:5.7. The ratio of acidic to basic amino acids of the expanded matrix is 1.55. Sodium dodecyl sulfate (SDS) gel electrophoresis reveals a predominant protein with a mol wt of 18,000 which is apparently involved in the reversible contractile process. The mechanism of this reversible contraction of the expanded matrix remains to be elucidated, but it differs both from actin-myosin contraction systems and from the contractile spasmoneme system in vorticellids.

Calcium↗

Tuberculosis outbreaks in prison housing units for HIV-infected inmates--California, 1995-1996.

During 1995-1996, staff from the California departments of corrections and health services and local health departments investigated two outbreaks of drug-susceptible tuberculosis (TB). The outbreaks occurred in two state correctional institutions with dedicated HIV housing units. In each outbreak, all cases were linked by IS6110-based DNA fingerprinting of Mycobacterium tuberculosis isolates. This report describes the investigations of both outbreaks; the findings indicated that M. tuberculosis can spread rapidly among HIV-infected inmates and be transmitted to their visitors and prison employees, with secondary spread to the community.

California↗

Sequence variation in the noncoding region of human papillomavirus type 16 detected by single-strand conformation polymorphism analysis.

Human papillomavirus (HPV) type 16 variants were found by single-strand conformation polymorphism (SSCP) analysis of the noncoding region of the viral genome. Two sets of primers were used to analyze a 1018 bp region spanning nucleotides 7109-222. Twelve SSCP patterns were demonstrated among HPV 16 DNAs purified from 48 anal specimens from 24 homosexual men. Seven patterns were detected among 10 HPV 16 isolates from cervical carcinomas. In two pairs of sex partners, identical variants were recognized in each partner of the pair. Infection with two variants of HPV 16 from 2 specimens was observed in 1 of 21 subjects for whom there were multiple samples over time. DNA sequence analysis of 7 isolates confirmed that the SSCP technique showed polymorphisms only in fragments that had base substitutions and that all of these base substitutions resulted in detectable shifts in fragment mobility.

Anal Canal↗