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Rapid DNA degradation in primary rat hepatocytes treated with diverse cytotoxic chemicals: analysis by pulsed field gel electrophoresis and implications for alkaline elution assays.

The use of genetic toxicology tests for hazard identification is complicated by the fact that some in vitro tests using cultured mammalian cells are subject to potential artifacts that can make it difficult to distinguish between direct, chemically-induced genotoxicity, and DNA damage that occurs secondary to chemically-induced cytotoxicity (e.g., mediated by endogenous nucleases). Recently, we demonstrated that cytotoxicity-induced DNA double strand breaks (dsb) can produce artifacts in the in vitro alkaline elution/rat hepatocyte assay [Elia et al., 1993]. To explore this further, we used pulsed field gel/DNA dsb assays to characterize the relationship between chemically-induced cytotoxicity and the degradation of genomic DNA to high molecular weight fragments. Two sets of compounds were tested: 17 cytotoxic agents judged to be neither genotoxic nor carcinogenic, and 10 known genotoxic carcinogens. We found a close correlation between chemically-induced cytotoxicity and the rapid degradation of DNA to high molecular weight, double-stranded fragments. In contrast, the classic genotoxic chemicals tested generally did not trigger DNA dsb fragmentation at doses that were genotoxic but not immediately cytotoxic. These data indicate that pulsed field gel/DNA dsb assays can be used with in vitro genetic toxicology assays to help distinguish between genotoxic and cytotoxic mechanisms of DNA damage.

Animals↗

Parasite-host specificity: experimental studies on the basis of parasite adaptation.

Specificity in parasitic interactions can be defined by host genotypes that are resistant to only a subset of parasite genotypes and parasite genotypes that are infective on a subset of host genotypes. It is not always clear if specificity is determined by the genotypes of the interactors, or if phenotypic plasticity (sometimes called acclimation) plays a larger role. Coevolutionary outcomes critically depend on the pervasiveness of genetic interactions. We studied specificity using the bacterial parasite Pasteuria ramosa and its crustacean host Daphnia magna. First, we tested for short-term adaptation of P. ramosa lines that had been rapidly shifted among different host genotypes. Adaptation at this time-scale would demonstrate the contribution of phenotypic plasticity to specificity. We found that infectivity was stable across lines irrespective of recent passage history, indicating that in the short term infection outcomes are fixed by genetic backgrounds. Second, we studied longer-term evolution with two host clones and two parasite lines. In this experiment, P. ramosa lines had the possibility to evolve adaptations to the host genotype (clone) in which they were serially passaged, which allowed us to test for a genetic component to specificity. Substantial differences arose in the two passaged lines: one parasite line gained infectivity on the host clone it was grown on, but it lost infectivity on the other host genotype (this line evolved specificity), while the other parasite line evolved higher infectivity on both host clones. We crossed the two host genotypes used in the serial passage experiment and found evidence that the number of host genes that underlies resistance variation is small. In sum, our results show that P. ramosa specificity is a stably inherited trait, it can evolve rapidly, and it is controlled by few genes in the host. These findings are consistent with the idea of a rapid, ongoing arms race between the bacterium and its host.

Adaptation, Physiological↗

Short-term testing--are we looking at wrong endpoints?

Short-term testing has been performed and interpreted on the basis of correlation between these tests and animal carcinogenicity. This empirical approach has been the only feasible one, due to a lack of knowledge of the actual genetic endpoints of relevance in carcinogenicity. However, the rapidly growing information on genetic alterations actually involved in carcinogenicity and in particular activation of oncogenes, provides facts of basic importance for the strategy of short-term testing. The presently used sets of short-term tests focus on standard genetic endpoints, mainly point mutations and chromosomal aberrations. Little attention has been paid in that connection to other endpoints, which have been shown or suspected to play an important role in carcinogenicity. These endpoints include gene amplification, transpositions, hypomethylation, polygene mutations and recombinogenic effects. Furthermore, indirect effects, for instance via radical generation and an imbalance of the nucleotide pool, may be of great significance for the carcinogenic and cocarcinogenic effects of many chemicals. Modern genetic and molecular technology has opened entirely new prospects for identifying genetic alterations in tumours and in its turn these prospects should be taken advantage of in order to build up more sophisticated batteries of assays, adapted to the genetic endpoints actually demonstrated to be involved in cancer induction. Development of new assay systems in accordance with the elucidation of genetic alterations in carcinogenicity will probably constitute one of the most important areas in genetic toxicology in the future. From a regulatory point of view the prerequisite for a development in this direction will be a flexibility of the handling of questions concerning short-term testing also at a bureaucratic level.

Animals↗

Frequency of mutations in rpoB and codons 315 and 463 of katG in rifampin- and/or isoniazid-resistant Mycobacterium tuberculosis isolates from northeast Mexico.

A total of 48 isoniazid (INH)- and rifampin (RIF)-resistant Mycobacterium tuberculosis isolates, 19 INH-resistant isolates, and 9 RIF-resistant isolates were randomly selected and tested for detecting mutations at codons 315 and 463 of katG by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and/or for detecting mutations at a 69-bp region of the rpoB gene by the INNO-LiPA Rif TB assay. Of the 67 INH-resistant isolates tested, 36 (53.7%) showed the mutation at codon 315 of katG; however, none of them showed the mutation at codon 463. The majority of the RIF-resistant samples analyzed (49 of 57, 86.0%) reacted positive with one of the four R-type probes. The R5-pattern (S531L mutation) was the most frequently observed (31 of 57, 54.4%), followed by R4a-pattern (H526Y mutation) 13 isolates (22.8%), R4b-pattern (H526D mutation) 4 isolates (7.0%), and R2-pattern (D516V mutation) 1 isolate (1.8%). Overall, there was agreement between the line probe kit and phenotypic RIF-susceptibility test for 56 (98.2%) of 57 RIF-resistant isolates tested. These results show that the mutation analysis at codon 315 of katG could be used as a screening assay prior to standard susceptibility testing, whereas mutations in the rpoB gene could be used successfully as genetic markers to rapidly detect RIF-resistant M. tuberculosis clinical isolates from northeast Mexico.

Antitubercular Agents↗

A simple VNTR-PCR method for detecting maternal cell contamination in prenatal diagnosis.

The effectiveness of variable number tandem repeats (VNTRs) was evaluated in the detection of maternal cell contamination. Nonradioactive PCRs were performed on 30 sets of prenatal tissue using VNTRs as primers. The combination of two VNTRs (YNZ22 and APOB) provided information on all 30 cases, distinguishing maternal-fetal genotype patterns and detecting maternal cell contamination in 5 of 30 prenatal cases. The amplification of these two VNTRs does not require radioactive or fluorescence labeling, and a small gel electrophoresis is sufficient to see the maternal-fetal genotype pattern. By this method, detection of maternal cell contamination in prenatal tissues can be obtained in 1 day, without the use of expensive instruments, thus providing DNA laboratories a very sensitive, rapid, and simple proof pretest on all prenatal tissues before performing the final genetic diagnostic testing.

Amniocentesis↗

The limb-girdle muscular dystrophies-multiple genes, multiple mechanisms.

In the field of muscular dystrophy, advances in understanding the molecular basis of the various disorders in this group have been rapidly translated into readily applicable diagnostic tests, allowing the provision of more accurate prognostic and genetic counselling. The limb-girdle muscular dystrophies (LGMD) have recently undergone a major reclassification according to their genetic basis. Currently 13 different types can be recognized. Amongst this group, increasing diversity of the mechanisms involved in producing a muscular dystrophy phenotype is emerging. Recent insights into the involvement of the dystrophin glycoprotein complex in muscular dystrophy suggests that its members may play distinct or even multiple roles in the maintenance of muscle fibre integrity. In other forms of LGMD, proteins have been implicated which may be important in intracellular signalling, vesicle trafficking or the control of transcription. As these various mechanisms are more fully elucidated, further insights will be gained into the pathophysiology of muscular dystrophy. At a practical level, despite the marked heterogeneity of this group real progress can at last be made in determining a precise diagnosis.

Calpain↗

Canine inherited retinal degenerations: update on molecular genetic research and its clinical application.

Inherited retinal degenerations in the dog include generalised progressive retinal atrophy, retinal pigment epithelial dystrophy, congenital stationary night blindness and day blindness (hemeralopia). The clinical phenotype and pathology of these diseases closely resemble some types of human inherited retinal degeneration, in particular retinitis pigmentosa, one of the most common inherited causes of blindness in man. Molecular genetic investigations aim to identify the genetic mutations underlying the canine inherited retinal degenerations. Two major research strategies, candidate gene analysis and linkage analysis, have been used. To date, candidate gene analysis has definitively identified the genetic mutations underlying nine inherited retinal degenerations, each in a different breed of dog, and linkage studies have identified genetic markers for a further retinal degeneration which is found in at least six different breeds. This review outlines the research strategy behind candidate gene and linkage studies and summarises recent results in the search for genetic causes of canine inherited retinal degenerations. The aim is to increase awareness of this rapidly changing field and to show how the research can be used to develop genetic tests for these diseases and thereby reduce the incidence of inherited eye disease in dogs.

Animals↗

Modification in penicillin-binding proteins during in vivo development of genetic competence of Haemophilus influenzae is associated with a rapid change in the physiological state of cells.

By using whole-cell labeling assay with 125I-penicillin V, we observed a reduction in the binding of the radiolabeled beta-lactam to four or five penicillin-binding proteins (PBPs) in Haemophilus influenzae cells cultivated under specific conditions. PBPs 3A, 3B, 4, and 6 were altered after the growth of bacteria in diffusion chambers implanted in the peritoneal cavity of rats. PBP 2 was also modified when cells were cultivated in human cerebrospinal fluids. Because this observation may have important consequences on the efficacy of beta-lactams during antibiotic therapy, we characterized the physiological state of bacteria cultivated in animals in the hope of explaining how such important changes in cell properties develop in vivo. Since the development of natural genetic competence occurs at the stationary phase of growth in H. influenzae, we used a DNA transformation assay to evaluate the physiological state of bacteria grown in diffusion chambers implanted in rats. Chromosomal DNA isolated from an antibiotic-resistant donor strain was mixed with bacteria in diffusion chambers. At different times during a 5-h incubation period, recipient bacteria were collected from the chambers, CFU were determined by plate counting, and antibiotic-resistant transformants were isolated on selective plates. Genetic competence rapidly developed in cells grown in rats, and the frequency of transformation by test DNA was elevated. Electron microscopy revealed an irregular cell shape and blebs at the surface of bacteria cultivated in animals and in cerebrospinal fluids. In an attempt to induce a similar physiological state in vitro, we supplemented broth cultures with cyclic AMP or synchronized cultures by a nutritional upshift. No changes in PBPs were observed with supplemental cyclic AMP or during a single cell cycle. Finally, a reduction in the affinity of PBPs for 125I-penicillin V identical to that observed in bacteria grown in rats was observed in cells isolated from the stationary phase of growth in vitro. These results clearly indicate that H. influenzae cells grown in animals undergo a rapid change to a physiological state similar to that found in late-stationary-phase cultures in vitro. This observation indicates that the rational design of future and improved antibiotic therapy of H. influenzae infections should consider cell properties of slow-growing or latent bacteria.

Animals↗

Temperature-sensitive mutants of yeast exhibiting a rapid inhibition of protein synthesis.

Certain temperature-sensitive (ts(-)) mutants of yeast which cannot be corrected by nutritional supplementation exhibited a rapid cessation of protein synthesis after a shift to the restrictive temperature. Genetic and biochemical tests permitted a division of these mutants into four classes. This division was based upon genetic complementation patterns among the mutants and an investigation of glucose incorporation into macromolecules and polyribosome content in the mutants after a shift to the restrictive temperature. A study of these parameters in the parent strain (ts(+)) in the presence of certain well-characterized inhibitors allowed a tentative identification of the biochemical defects in each of the four classes. The properties of the mutants in class IA were consistent with the hypothesis that they result from a defect in the initiation of polypeptide chains or in ribonucleic acid synthesis; mutants in class IB from a defect in the elongation of polypeptide chains; mutants in class IIA from a defect in energy metabolism; and mutants in class IIB from a lesion affecting membrane function.

Arsenic↗

Genotype at the -174G/C polymorphism of the interleukin-6 gene is associated with common carotid artery intimal-medial thickness: family study and meta-analysis.

BACKGROUND AND PURPOSE: Studies in unrelated individuals have produced conflicting findings concerning the putative association between the interleukin-6 (IL-6) -174G/C polymorphism and carotid intimal-medial thickness (IMT). We have used a family-based genetic association design to assess the heritability of carotid IMT and to investigate the hypothesized association of carotid IMT with the IL-6 to -174G/C polymorphism. METHODS: We studied 854 members of 224 white British families. The heritability of carotid IMT was determined using Multipoint Engine for Rapid Likelihood Inference. Genetic association analyses were carried out using ANOVA and family-based tests of association implemented in Quantitative Transmission Disequilibrium Test. A meta-analysis of previous studies of the association was conducted to place our result in context. RESULTS: The heritability of carotid IMT was 24%. Under a recessive model (GG+GC versus CC), there was significant evidence of association between IL-6 to the -174G/C genotype and adjusted log(e) maximal carotid IMT (F=5.469; P=0.02). Family-based analyses using Quantitative Transmission Disequilibrium Test showed no evidence of population stratification as a cause of the observed association (chi2(1)=0.469; P=0.4934). The CC genotype was associated with a 4.8% increase in maximal carotid IMT and accounted for 0.6% of the observed variation in the trait, which is equivalent to 2.5% of the heritable component. A meta-analysis of the present and 2 previous large studies, which enrolled a total of 2930 subjects, confirmed the recessive effect of the C allele on carotid IMT (P=0.0014). CONCLUSIONS: The genotype at the IL-6 to -174G/C polymorphism is associated with common carotid artery IMT, although the size of the genetic effect is small.

Adult↗

Thin film biosensor for rapid visual detection of nucleic acid targets.

BACKGROUND: We have developed a silicon-based biosensor that generates a visual signal in response to nucleic acid targets. METHODS: In this system, capture oligonucleotide probes are immobilized on the surface of the biosensor. Interaction of the capture probes with a complementary target and a biotinylated detector oligonucleotide allows initiation of formation of an organic thin film on the biosensor. Thin film formation is completed by enzymatic activity of peroxidase conjugated to an anti-biotin antibody. Peroxidase catalyzes deposition of an insoluble product onto the silicon surface, generating a uniform thin film. The increased thickness on the surface alters the perceived color of the biosensor through changes in the interference patterns of reflected light from the surface, causing a color change from gold to purple. RESULTS: The biosensor results may be evaluated by direct visual inspection or quantified by ellipsometry. Results are obtained in 25 min with a detection limit of 5 pmol/L (150 amol/sample). Selectivity of the biosensor is demonstrated by discrimination of single nucleotide mismatches. Multitarget arrays are also analyzed with the thin film biosensor, and the system is capable of detecting targets from human serum and urine. CONCLUSIONS: The biosensor surface is inexpensive to produce, and the assay format is simple and rapid. The thin film biosensor is adaptable to a wide variety of nucleic acid detection applications, including rapid diagnostic testing for infectious disease panels, antibiotic resistance panels, or allelic discrimination of specific genetic markers.

Base Sequence↗

[New evidence for detecting Helicobacter pylori in clinics].

A part of diagnostic tests for Helicobacter pylori was approved as National Health Insurance system in Ministry of Health and Welfare Japan on last November 2000. The gold standard for the presence of most infectious diseases is successful culture of the organism. H. pylori is fastidious and time consuming for growth in media. Instead of bacterial culture of H. pylori from biopsy sample, we need to effort to develop rapid methods to identify gene segment of H. pylori and its antibiotic resistance. Even the genetic methods would be developed, circular antigen product of H. pylori must be important for diagnosis of its clinical pathology. Here we listed the available diagnostic tests for histology, bacterial culture, rapid urease test, urea breath testing, and serological testing for H. pylori in Japan.

Bacteriological Techniques↗

A rational use of laboratory tests in the diagnosis and management of hepatitis C virus infection.

The prevalence of HCV infection is very diversified according to geographical areas and ranges from 1% in the Northern regions of the world to more than 20% as we move South. Due to the presence of HCV-associated liver diseases and the development of effective treatments, the diagnosis of HCV infection is a growing medical need. Several tests are available, from simple screening to identify the presence of anti-HCV antibodies to the more sophisticated quantification of viral load and genotyping. However, these tests are to be used in a logical, consequential and cost-effective manner. This review article will report on the protocol in use in the North-Eastern part of Italy for the screening and diagnosis of HCV infection. The protocol is based on a consensus among several experts and may be the basis for a more rational approach in this rapidly growing field.

Genetic Testing↗

Selection line x diet interactions for two lines of pigs fed 12 or 24% protein diets.

An experiment with crossbred swine was conducted over six generations of selection based on an index (Index) of average daily gain in weight (ADG) in a test period from 56 d of age to 91 kg gross weight and average backfat thickness (ABF) measured from ultrasonic scans at 91 kg. Test pigs of the high protein select (HS) and control (HC) lines were fed a 24% crude protein (CP) diet and pigs of the low protein select (LS) and control (LC) lines were fed a 12% CP diet during the test period. The extent of genetic (selection line) x environmental (dietary) interaction effects was determined based on feeding closely related boars and gilts from both the HS and LS lines on both diets. Tests were conducted in 1986 and 1987 with progeny of the fifth and sixth generations of selection. Records for 472 pigs sired by 37 boars and out of 101 dams were analyzed for effects of selection and diets on AGE of pig at 91 kg, ADG, ABF, LMA (longissimus muscle area at the last rib) and Index. Statistically significant interactions effects of line x diet were noted (P less than .01) for AGE, ADG and Index, traits with low to moderate heritabilities (h2). For ABF and LMA, body composition traits with moderate or higher h2, interaction effects of line x diet were near zero. These results suggest that for best all-around future performance, traits such as AGE and ADG, selection probably should be practiced under dietary conditions under which future populations will be produced. For body composition traits such as ABF and LMA, selection probably would be more effective if pigs were fed a more enriched protein diet. However, as a practical matter, to more rapidly improve the genetic merit of the swine population, both the central station and on-the-farm testing programs should be conducted under standard commercial production systems.

Adipose Tissue↗

Rapid evolution through gene duplication and subfunctionalization of the testes-specific alpha4 proteasome subunits in Drosophila.

Gene duplication is an important mechanism for acquiring new genes and creating genetic novelty in organisms. Evidence suggests that duplicated genes are retained at a much higher rate than originally thought and that functional divergence of gene copies is a major factor promoting their retention in the genome. We find that two Drosophila testes-specific alpha4 proteasome subunit genes (alpha4-t1 and alpha4-t2) have a higher polymorphism within species and are significantly more diverged between species than the somatic alpha4 gene. Our data suggest that following gene duplication, the alpha4-t1 gene experienced relaxed selective constraints, whereas the alpha4-t2 gene experienced positive selection acting on several codons. We report significant heterogeneity in evolutionary rates among all three paralogs at homologous codons, indicating that functional divergence has coincided with genic divergence. Reproductive subfunctionalization may allow for a more rapid evolution of reproductive traits and a greater specialization of testes function. Our data add to the increasing evidence that duplicated genes experience lower selective constraints and in some cases positive selection following duplication. Newly duplicated genes that are freer from selective constraints may provide a mechanism for developing new interactions and a pathway for the evolution of new genes.

Animals↗

Comparative microsatellite analysis in discerning origin of disseminated tumor: the case of a patient with malignant ascites and a history of multiple tumors.

The origin of metastatic carcinoma is now always easily resolved on the basis of conventional dinical and pathological parameters, particularly in patients with more than 1 primary tumor. When 1 of the tumors is a renal cell carcinoma, the clinical picture is further confounded by the tendency of these tumors to be locally silent, to metastasize to unusual sites, and to disseminate long after removal of the primary tumor. We compared tumors for loss (ie, deletion) of loci on chromosomal arms 3p, 5q, 11q, and 18q in a patient with a malignant ascites fluid, a remote history of renal and colonic neoplasms, and a strong clinical suspicion of disseminated gastrointestinal adenocarcinoma. DNA from microdissected tumors and normal tissues was subjected to polymerase chain reaction-based microsatellite analysis. Even though the clinical picture suggested a gastrointestinal origin, comparison of genetic alterations clearly showed that the malignant ascites represented recurrence of the renal cell carcinoma. The malignant ascites and the primary renal cell carcinoma showed identical patterns of allelic loss at all loci tested. In contrast, the malignant ascites and colonic adenoma showed discordant patterns of allelic loss. Comparative microsatellite analysis provides a rapid genetic approach for discerning the origin of metastatic tumor spread. This may be a useful diagnostic adjunct when tumor origin is not clear on clinical or morphological grounds. In some instances, it may even provide a reasonable alternative to an extensive and costly conventional work-up.

Adenoma↗

Rapid genetic diagnosis at 7-9 weeks gestation: diagnosis of sex, single gene defects and DNA fingerprint from coelomic samples.

Prenatal diagnosis (chorionic villus sampling (CVS) or amniocentesis) is performed at a relatively late stage of pregnancy (11-18 weeks). Such tests have significant disadvantages including increased risk of miscarriage and delay before results are known. Earlier prenatal diagnosis (< 11 weeks) has been discontinued because of the risk of fetal abnormalities. Recently fetal cells have been recovered from the coelomic cavity at 7-12 weeks gestation (coelocentesis). This study has established that highly sensitive fluorescent polymerase chain reaction (PCR) can provide rapid (4-5 h), reliable and accurate multiple genetic diagnoses (sexing and single-gene diagnosis) from coelomic cells. As prenatal diagnosis has a significant risk of contamination, we have also shown that coelomic cells can be simultaneously DNA fingerprinted to determine that contamination has not occurred. This earlier method of prenatal diagnosis would be very valuable, as it may overcome some problems of later conventional prenatal diagnosis and allow reassurance/treatment to be undertaken at a much earlier stage. Successful application of these techniques may supersede alternative methods of prenatal diagnosis. Although these techniques appear very promising, extensive clinical trials must be undertaken to determine safety of coelocentesis, diagnostic reliability and accuracy in a clinical setting.

Adult↗