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PubMed1992

An evaluation of the E. coli K-12 uvrB/recA DNA repair host-mediated assay. II. In vivo results for 36 compounds tested in the mouse.

The aim of this study was to further evaluate the E. coli K-12 DNA repair host-mediated assay, as a short-term in vivo genotoxicity test, to be used as a complement to the micronucleus test in the routine testing of chemicals and drugs. The assay involves the administration of the test substance to mice by the route of choice, followed by the intravenous administration of a mixture of DNA repair deficient and proficient derivatives of E. coli K-12. After an incubation period the relative survival of the two strains was determined in blood, liver, lungs, kidneys and testes of the host. A significant preferential reduction of the DNA repair deficient strain in any organ indicates that the test substance possesses genotoxic properties. A total of 36 substances, 26 carcinogens, 4 weak or non-carcinogens and 6 unclassified substances, were tested in this assay. Positive results were obtained for 23 compounds. Of the carcinogens 18 were positive and of the non-carcinogens 3 were negative. The overall concordance between the assay and carcinogenicity was 72%. In general, alkylating agents and direct-acting nitroso compounds showed genotoxic activity in all organs tested, while the other substances were positive in a limited number of organs. With oral administration, which was the most commonly used administration route in the study, the organ showing a positive response most often was the blood. The results from the present study were compared with results from the micronucleus test, which were available for 26 of the substances. Results were in agreement for 15 of the substances, while 8 substances were positive in the present assay and negative in the micronucleus test: 4-aminobiphenyl, 2-anisidine, epichlorohydrin, formaldehyde, 1- and 2-naphthylamine, 2-nitrophenylenediamine and 4-nitroquinoline-N-oxide. The substances negative in the E. coli DNA repair host-mediated assay, but positive in the micronucleus test were: benzene, catechol and cyclophosphamide. It is concluded from this evaluation that the E. coli K-12 DNA repair host-mediated assay detects a number of carcinogens that are negative in the micronucleus test, while detecting most of the compounds that are positive in the latter. The advantages of this test are that differential DNA repair measures a broad spectrum of genetic damage, an in vitro/in vivo comparison is possible with the same test organisms, results can be obtained from various organs and the test is rapid.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1992

Mapping human chromosomes by walking with sequence-tagged sites from end fragments of yeast artificial chromosome inserts.

Sequence-tagged sites (STSs) derived from end fragments of chromosome-specific yeast artificial chromosomes (YACs) can facilitate the assembly of an overlapping YAC/STS map. Contigs form rapidly by iteratively screening YAC collections with end-fragment STSs from YACs that have not yet been detected by any previous STS. The map is rendered rapidly useful during its assembly by incorporating supplementary STSs from genes and genetic linkage probes with known locations. Methods for the systematic development and testing of the end-fragments STSs are given here, and a group of 100 STSs is presented for the X chromosome. The mapping strategy is shown to be successful in simulations with portions of the X chromosome already largely mapped into overlapping YACs by other means.

Base Sequence↗
PubMed1997

Interspecific microsatellite markers for the study of pinniped populations.

Microsatellites have rapidly become the marker of choice for a wide variety of population genetic studies. Here we describe 20 pinniped microsatellite markers which have been tested across 18 pinniped species. The majority of these markers have broad utility in all pinnipeds and provide a strong base for detailed population genetic studies in the Pinnipedia.

Animals↗
PubMed1982

Histone H4 hyperacetylation and rapid turnover of its acetyl groups in transcriptionally inactive rooster testis spermatids.

In order to study the relationship between acetylation of histones, chromatin structure and gene activity, the distribution and turnover of acetyl groups among nucleosomal core histones and the extent of histone H4 acetylation were examined in rooster testis cell nuclei at different stages of spermatogenesis. Histone H4 was the predominant acetylated histone in mature testes. Hyperacetylation of H4 and rapid turnover of its acetyl groups are not univocally correlated with transcriptional activity since they were detected in both genetically active testicular cells and genetically inactive elongated spermatids. During the transition from nucleohistone to nucleoprotamine in elongated spermatids the chromatin undergoes dramatic structural changes with exposition of binding sites on DNA (1). Hyperacetylation of H4 and rapid turnover of its acetyl groups could be correlated with the particular conformation of chromatin in elongated spermatids and might represent a necessary condition for binding of chromosomal proteins to DNA.

Acetates↗
PubMed1996

Primed IN situ labelling (PRINS) as a rational procedure for identification of marker chromosomes using a panel of primers differentially tagging the human chromosomes.

PRimed IN Situ labelling (PRINS) is a highly specific and sensitive technique for detecting DNA sequences on human chromosomes in situ. PRINS is currently being introduced for research and routine analysis in clinical and cancer genetics. In this paper, we report a rational PRINS procedure for the rapid identification of marker chromosomes. Using this method it is possible to test a sample from a patient with up to eight different primers simultaneously on one slide. We have synthesized oligonucleotide primers that can differentially tag the human chromosomes, and with the protocol presented in this report we are able to identify the chromosomal origin of a marker chromosome within 2 hours.

Amniocentesis↗
PubMed2000

Laboratory diagnosis of malaria.

Malaria particularly falciparum malaria is a major public health problem in India. Its correct and early diagnosis is very important for prompt treatment as a preventive and control measure. Microscopy is the traditional method for laboratory diagnosis of malaria, which is used widely. However, it is time consuming, needs expertism and the detection limit is 10-20 parasites/ml blood in thick film and 100 parasites/ml blood in thin film. Quantitative buffy coat technique (QBC) is highly sensitive method but expensive equipment is needed for this test. The serological methods involving antibody detection give information regarding exposure to malaria but do not differentiate between present and past infections. Genetic probes and PCR are highly sensitive methods but require expensive equipments. Parasite antigen detection tests are useful in field and PHC level for rapid diagnosis of P falciparum malaria.LDH based test for diagnosing malaria is sensitive but can not differentiate between species. For monitoring of drug resistance or follow-up of patients, methods which can quantify parasitaemia are needed. Simply microscopy is the best solution at present.

Clinical Laboratory Techniques↗
PubMed1992

Alternative models for early onset of childhood leukaemia.

This paper considers theoretical models for early-onset childhood leukaemia. The major focus of attention is the two-hit mutational model. A simple mathematical representation is used to explore mechanisms which might lead to onset of leukaemia at an unusually early age. Two such mechanisms are considered. The first of these, a germinal or very early embryonic first mutation is shown to imply that multiple independent leukaemic clones are likely to arise sequentially in very young patients. Clonal multiplicity could underlie the poor prognosis which has been associated with early onset childhood acute lymphoblastic leukaemia. It implies that curative therapy might require intensive treatment followed by bone marrow rescue to ensure eradication of all single-hit predisposed target cells. The prediction of multiple leukaemic clones might be tested in female patients by means of X-linked restriction fragment length polymorphisms and in patients with B-lineage neoplasms by determination of immunoglobin gene rearrangements. A second mechanism for early onset leukaemogenesis is the occurrence of a high cellular mutation rate in some patients. This is shown to result in leukaemia at significantly earlier age if the mutation rate is sufficiently high to influence target cell loss rate. This mechanism would enable more rapid clonal evolution of leukaemic cells and the early emergence of drug resistant variants. The prediction might be tested experimentally by sequential observation of genetic markers (e.g. Karyotypes, DNA fingerprint patterns) and the rate of emergence of drug resistant phenotypes. Other models, considered more briefly, include one-hit mutational 'dominants' in the developing embryo and faster growth kinetics in neoplasms of younger patients.(ABSTRACT TRUNCATED AT 250 WORDS)

Cell Division↗
PubMed2005

Molecular diagnosis in lymphoma.

The evolution of our ability to diagnose and classify lymphomas in an increasingly refined manner has paralleled the development of novel technologic approaches, with contemporary practice dependent upon the harnessing of a plethora of data that include microscopic, immunophenotypic, and genetic information. Although each of these components is currently indispensable, there is a purported progressive improvement in biologic objectivity as one maneuvers through these respective technologies. Accordingly, and in particular given the rapid pace at which key insights into lymphoma biology are emerging with microarray and other cutting-edge technologies, the role of molecular genetic testing is assuming even greater relevance. The ability to diagnose and classify lymphomas more accurately, precisely, and rationally by incorporating molecular data ought to lead to the development of more appropriate directed therapies.

Gene Rearrangement↗
PubMed2005

Detection of Salmonella enterica in naturally contaminated liquid eggs by loop-mediated isothermal amplification, and characterization of Salmonella isolates.

Loop-mediated isothermal amplification (LAMP) assay was effective in detecting Salmonella enterica in naturally contaminated liquid egg samples. Salmonella was detected in 110 samples taken from four egg-breaking plants. The egg samples were pre-enriched in buffered peptone water (BPW) at 37 degrees C for 20 h. The selective enrichment was done in Rappaport-Vassiliadis or tetrathionate broth and plated onto xylose lysine deoxycholate agar and brilliant green agar, modified. In addition, the PCR assay was used to detect Salmonella after pre-enrichment in BPW at 37 degrees C for 20 h. The culture method and PCR assay were compared to the LAMP assay, which was also performed after pre-enrichment in BPW. PCR failed to detect Salmonella in 10% of 110 samples, whereas the culture method and LAMP assay successfully identified Salmonella in all samples. However, the LAMP assay was found to be much more rapid than the culture method and as sensitive in detecting Salmonella from liquid eggs. In all of the egg-breaking plants studied, Salmonella was isolated on most tested days. The positive samples showed that more than 75% of the Salmonella strains had identical genetic patterns when analyzed by pulsed-field gel electrophoresis. This suggests that the same Salmonella strains having survived long periods of time in the plants were contaminating the production line. The LAMP assay is rapid, specific, and sensitive for Salmonella detection in liquid eggs and is able to monitor Salmonella contamination in egg-handling plants more reliably.

Animals↗
PubMed2006

Rapid ethanol tolerance mediated by adaptations in acute tolerance in inbred mouse strains.

It has been postulated that decreased acute sensitivity to ethanol is an important genetically-mediated risk factor for the development of alcoholism. Previous work in mice and rats has indicated that ethanol sensitivity can be reduced in a genotype-dependent manner by a single dose of ethanol 24 h prior to testing, so-called 'rapid' tolerance. The current studies were undertaken to determine if the observed rapid tolerance was mediated by alterations in initial sensitivity or acute functional tolerance (AFT), the two primary components of acute sensitivity. Separate groups of C57BL/6, DBA/2, ILS, and ISS inbred mouse strains were administered a single pretreatment dose of saline or ethanol (5 g/kg). The original and modified versions of the loss of righting reflex test, ethanol-induced hypothermia, and ataxia on a stationary dowel rod were tested 24 h later. Dependent on the test and strain, varying degrees of rapid tolerance were observed; a pronounced sensitization was detected in one case. There was a concomitant increase in the rate and/or magnitude of AFT with little change in initial sensitivity suggesting that rapid tolerance was mediated primarily by alterations in AFT. This conclusion may have implications for the contribution of acute sensitivity to human alcoholism.

Alcohol Drinking↗
PubMed1997

Variation within Mycobacterium scrofulaceum.

The purpose of this study was to identify Mycobacterium scrofulaceum reliably and rapidly and investigate diversity within the species. Fifty-four cultures were identified as Myco. scrofulaceum by preliminary cultural and biochemical tests, thin-layer chromatography and double diffusion. These strains were examined by PCR based on the 65 kDa heat stress protein gene, followed by restriction enzyme analysis of the product with BstEII and HaeIII. This produced seven groups, most with fewer fragments than had been reported previously. The technique was a rapid and reliable method for studying variation within Myco. scrofulaceum but alone, was unable to discriminate between some of these variants and other genetically similar species. When PCR-RFLP results were combined with biochemical tests, the major groups appeared to relate to different disease situations and thus, may have some epidemiological value.

DNA, Bacterial↗
PubMedDate not supplied

An indexed genomic library for Paramecium complementation cloning.

Recent pioneering work opened the way for cloning genes in Paramecium by functional complementation of mutants. We present here the construction and pilot utilization of a new indexed library of Paramecium macronuclear DNA. The library is made of 61,440 clones containing inserts mostly between 6 and 12 kilobases. It has already allowed the complementation cloning of four new genes, and this library has proven to be very useful for rapid hybridization cloning.

Animals↗
PubMed2000

High throughput genetic screening for the detection of hereditary non-polyposis colon cancer (HNPCC) using capillary electrophoresis.

Approximately 5-10% of all colorectal carcinomas arise from cancer predisposition syndromes caused by heterozygote germline mutations in post-replicative DNA mismatch repair (MMR) genes. In contrast to gastrointestinal polyposis syndromes, carcinomas in these patients do not occur on the background of increased numbers of polyps and hence are refered to as hereditary non-polyposis colorectal cancers (HNPCC). Six different MMR genes, MSH2, MSH3, MSH6, MLH1, MLH3 and PMS2, have been identified in the human genome. In the majority of HNPCC patients, heterozygote germline mutations are present in the MSH2 or MLH1 gene. Detection of mutations by conventional sequencing technology is expensive and labor intensive due to the complex intron and/or exon structures. In this study, we therefore have explored whether capillary electrophoresis-based single strand conformation polymorphism (SSCP-CE) provides a reliable means for mutation screening. We have tested different MLH1 mutations in exons 9 and 16 and find that SSCP-CE produces reliable electrophoretic patterns that allow recognition of wild-type alleles, microdeletions and point mutations. In summary, SSCP-CE provides a rapid, automated, and cost-effective technology for MSH2 and MLH1 mutation screening and will facilitate genetic diagnostics for HNPCC patients.

Colonic Neoplasms↗
PubMedDate not supplied

Genetic heterogeneity among nutritionally deficient streptococci.

The nutritionally deficient (variant) streptococci (NDS) share the auxotrophic characteristic of requiring pyridoxal or thiol group supplementation for growth. The deoxyribonucleic acid relatedness of these organisms among themselves is unknown. Improved speciation of NDS would lead to a better knowledge of their pathogenesis and possible insight into improved clinical management. Therefore, DNA-DNA hybridization and biotyping of 23 nutritionally deficient streptococci were performed. Biochemical testing using the API Rapid Strept Identification method revealed that the organisms in this study were characterized among three broad biotype groups. Only one strain was nontypeable. DNA-DNA hybridization among the nutritionally deficient streptococci that we compared revealed genetic heterogeneity. Only four (17%) of 23 isolates were highly homologous; all were of biotypes 2 and 3. Reference viridans streptococcal strains had minimal homology to the NDS strains. The data indicate that the NDS are genetically heterogeneous.

Bacterial Typing Techniques↗
PubMed1994

Rapid and simple method for preparation of genomic DNA from easily obtainable clotted blood.

A method was developed for the preparation of genomic DNA from clotted blood that is usually discarded after extraction, for other laboratory tests. The method, which involves proteinase K digestion, salt/chloroform extraction and 90% ethanol precipitation of DNA from clotted blood, is rapid, simple, and easy because it does not impose an extra burden on the patient.

DNA↗
PubMed2006

DNA analysis: what and when to request?

Over the last 15 years genetic testing by DNA analysis has expanded enormously both in volume and range due to advances in scientific knowledge and analytical technology. This type of analysis has the potential to provide rapid, cost effective, and accurate diagnostic information but also has its limitations. Some of the changes detected may be of ambiguous consequence and as the knowledge base expands so too does the recognition that other factors can influence the clinical picture. In many cases outcomes may be predicted only on a statistical basis rather than individually. Careful attention should therefore be given to the clinical question that is being addressed before such testing is requested.

DNA↗
PubMed1996

Identification of genetic markers for initial sensitivity and rapid tolerance to ethanol-induced ataxia using quantitative trait locus analysis in BXD recombinant inbred mice.

Rapid tolerance to rotarod ataxia has previously been demonstrated in mice after sequential ethanol injections. Here we tested DBA/2J and C57BL/6J mice for initial ethanol sensitivity; DBA/2J mice were more sensitive (0.40 +/- 0.17 mg/g brain) than C57BL/6J mice (1.44 +/- 0.12 mg/g). We then monitored the development of tolerance by quantifying blood ethanol concentrations at the recovery from ataxia over five sequential injections; tolerance reached a plateau in about 5 hr. DBA/2J mice became very tolerant (final ethanol threshold 3.47 +/- 0.16 mg/ml, an increase of 3.07 mg/ml, or 8.7-fold above base line); B6 became slightly tolerant (final ethanol threshold 2.62 +/- 12 mg/ml, and increase of 1.18, or 1.8-fold above base line). Therefore, by the end of the treatment regimen, the rank order of sensitivity of the two strains had reversed. We then tested 25 recombinant inbred strains from among strains representing a cross between C57BL/6J and DBA/2J inbred strains, followed by a quantitative trait locus analysis with a database of 1522 markers to identify provisional loci. This procedure identified 19 markers on 11 chromosomes for initial sensitivity, 18 markers on 9 chromosomes for tolerance (delta) and 21 markers on 11 chromosomes for tolerance (fold-increase). Of these, 17 markers were in common, which suggests that initial sensitivity and tolerance share substantial genetic codetermination. Major candidate loci will be confirmed by genotyping B6D2F2 offspring that have been tested for initial sensitivity and tolerance.

Animals↗
PubMed1987

Induction of prophage lambda by chlorinated pesticides.

Chlorinated organics represent an important class of environmental carcinogens. However, only a small percentage of the carcinogens of this chemical class are genotoxic in prokaryotic bioassays such as the Salmonella assay. In an effort to identify a short-term assay sensitive to chlorinated carcinogens, we have tested a group of chlorinated pesticides, most of which are carcinogenic in rodents, in a prophage-induction assay developed by Rossman et al. (1984). The Microscreen phage-induction assay is a rapid, inexpensive, miniaturized system that uses the induction of prophage lambda in Escherichia coli as an indicator of genetic damage. It has been used successfully to screen complex environmental samples for genotoxicants and has detected carcinogenic metals that are refractory in the Salmonella assay. The pesticides tested were malathion, monuron, p,p'-DDT, mirex, lindane, nitrofen, chlordane, toxaphene, captan, and dichlorvos. All but the first 4 induced prophage. The remaining pesticides were ranked as follows according to induction potency in the presence of S9: captan greater than dichlorvos greater than toxaphene greater than lindane greater than nitrofen greater than chlordane. Rankings were similar in the absence of S9. Of these 6 pesticides, only nitrofen required S9 to induce prophage. Comparisons with mutagenesis data in Salmonella indicated that the Microscreen assay detected as genotoxic each of the pesticides that were mutagenic in Salmonella; moreover, it detected 2 additional carcinogens (chlordane and lindane) that were not mutagenic in the Salmonella assay. The possible use of the Microscreen phage-induction assay to detect chlorinated organics is discussed.

Animals↗