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PubMed2006

Quantitative genetics of cortical bone mass in healthy 10-year-old children from the Fels Longitudinal Study.

The genetic influences on bone mass likely change throughout the life span, but most genetic studies of bone mass regulation have focused on adults. There is, however, a growing awareness of the importance of genes influencing the acquisition of bone mass during childhood on lifelong bone health. The present investigation examines genetic influences on childhood bone mass by estimating the residual heritabilities of different measures of second metacarpal bone mass in a sample of 600 10-year-old participants from 144 families in the Fels Longitudinal Study. Bivariate quantitative genetic analyses were conducted to estimate genetic correlations between cortical bone mass measures, and measures of bone growth and development. Using a maximum likelihood-based variance components method for pedigree data, we found a residual heritability estimate of 0.71 for second metacarpal cortical index. Residual heritability estimates for individual measures of cortical bone (e.g., lateral cortical thickness, medial cortical thickness) ranged from 0.47 to 0.58, at this pre-pubertal childhood age. Low genetic correlations were found between cortical bone measures and both bone length and skeletal age. However, after Bonferonni adjustment for multiple testing, rho(G) was not significantly different from 0 for any of these pairs of traits. Results of this investigation provide evidence of significant genetic control over bone mass largely independent of maturation while bones are actively growing and before rapid accrual of bone that typically occurs during puberty.

Bone Density↗
PubMed2005

Testing the hypothesis of recent population expansions in nematode parasites of human-associated hosts.

It has been predicted that parasites of human-associated organisms (eg humans, domestic pets, farm animals, agricultural and silvicultural plants) are more likely to show rapid recent population expansions than are parasites of other hosts. Here, we directly test the generality of this demographic prediction for species of parasitic nematodes that currently have mitochondrial sequence data available in the literature or the public-access genetic databases. Of the 23 host/parasite combinations analysed, there are seven human-associated parasite species with expanding populations and three without, and there are three non-human-associated parasite species with expanding populations and 10 without. This statistically significant pattern confirms the prediction. However, it is likely that the situation is more complicated than the simple hypothesis test suggests, and those species that do not fit the predicted general pattern provide interesting insights into other evolutionary processes that influence the historical population genetics of host-parasite relationships. These processes include the effects of postglacial migrations, evolutionary relationships and possibly life-history characteristics. Furthermore, the analysis highlights the limitations of this form of bioinformatic data-mining, in comparison to controlled experimental hypothesis tests.

Animals↗
PubMed1992

Evaluation of a rapid peptide-based anti-human immunodeficiency virus-1 antibody immunoassay.

A qualitative, visually interpreted, rapid, and synthetic peptide-based anti-human immunodeficiency virus-1 (HIV) antibody immunoassay has been developed that may be of value in situations in which rapid determination of HIV-1 status is important. Because questions have been raised about the accuracy of rapid anti-HIV-1 assays, the sensitivity, specificity, interobserver and intraobserver variability of the Genie HIV-1 assay (Genetics Systems, Seattle, WA) were determined. Sera from 56 patients with HIV-1 infections documented by enzyme immunoassay and western blot tested positive by this assay. Enzyme immunoassay- and western blot-negative sera from 30 visceral organ transplant donors were negative using the Genie assay. Specificity was examined further by testing sera from 29 patients hospitalized with a variety of medical disorders, including acute bacterial pneumonia, acute myocardial infarction, monoclonal gammopathy, and high titer antinuclear or antimitochondrial antibodies. Two of these patients were reactive with the enzyme immunoassay, both of which tested negative by western blot. All 29 tested negative using the Genie assay. In addition, sera from five patients with repeatedly reactive enzyme immunoassays and negative western blots tested negative by the Genie system. There was 100% agreement in interobserver and intraobserver studies. With the western blot as the reference method, the Genie assay exhibited 100% sensitivity and specificity and there was no observer variability.

AIDS Serodiagnosis↗
PubMed2005

Aspirin and clopidogrel resistance: an emerging clinical entity.

Antiplatelet therapy is a cornerstone of cardiovascular medicine. Aspirin and clopidogrel have emerged as critical therapies in the treatment of cardiovascular disease. Despite their efficacy, patients on these medications continue to suffer complications. Millions of patients are currently on low-dose antiplatelet therapy but it is unknown how many of these patients are under-treated or on the wrong medication. Aspirin and clopidogrel resistance are emerging clinical entities with potentially severe consequences such as recurrent myocardial infarction, stroke, or death. The mechanism of resistance remains incompletely defined, but there are specific clinical, cellular, and genetic factors that influence therapeutic failure. These factors range from physicians who fail to prescribe these medications despite appropriate indications to polymorphisms of platelet membrane glycoproteins. Rapid and accurate diagnosis of antiplatelet resistance also remains an issue as new bedside tests are developed. By understanding the mechanism of therapeutic failure and by improving the diagnosis of this clinical entity, a new era of individualized antiplatelet therapy may arise with routine measurements of platelet activity in the same way that cholesterol, blood pressure, and blood sugar are followed, thus improving the care for millions of people.

Aged↗
PubMed2000

Mycobacterium kubicae sp. nov., a slowly growing, scotochromogenic Mycobacterium.

A previously uncharacterized, slowly growing, scotochromogenic Mycobacterium species was detected by HPLC analysis of the cell-wall-bound mycolic acids. The mycolic acid pattern standard was shown to be a late-eluting, contiguous peak cluster occurring at approximately 8-9 min. The mycolic acid pattern was noted to be most similar in number of peaks and range of elution to that reported previously for Mycobacterium asiaticum. However, the relative distribution of peaks within the elution range demonstrated a pattern with prominent peaks that started to emerge later than the characteristic M. asiaticum pattern. Standard biochemical identification test results were similar to those of the photochromogenic species M. asiaticum. Comparative 16S rRNA gene sequence analysis confirmed the genetic uniqueness of the strains and demonstrated the unclassified mycobacteria to be in a unique, intermediate position between slow and rapid growers in the phylogenetic tree of Mycobacterium. The name Mycobacterium kubicae sp. nov. is proposed for this taxon. The type strain is CDC 941078T (= ATCC 700732T = CIP 106428T).

Base Sequence↗
PubMed1994

Activation of the protein tyrosine kinase tyk2 by interferon alpha/beta.

We previously demonstrated that the gene tyk2 rescues the phenotype of a human mutant cell line unresponsive to alpha (IFN) and partially responsive to IFN-beta. Here, we describe functional complementation of the mutant cells with the corresponding cDNA. To characterize the putative non-receptor protein tyrosine kinase encoded by the gene tyk2 and begin to understand its functioning, we have raised polyclonal antibodies against a segment of the protein. Using these, we have identified tyk2 as a 134-kDa protein which is rapidly and transiently phosphorylated on tyrosine in response to IFN-alpha/beta and possesses an inducible kinase activity when tested in vitro. IFN-gamma has no effect on the phosphorylation state of the protein. In agreement with previous genetic evidence, these results assign a role to tyk2 in the IFN-alpha/beta signalling pathway and not in the IFN-gamma pathway. Fractionation of cell lysates have helped to localize the bulk of the protein in the cytoplasm, with a minor fraction associated with the cell membrane. Both protein pools undergo activation upon short-term IFN treatment of intact cells. Through the study of the effect of pervanadate on the phosphorylation level and the activity of tyk2, we conclude that activation of tyk2 by IFN-alpha does not require an intermediate regulatory tyrosine phosphatase.

Cell Membrane↗
PubMed2001

Acute liver graft failure due to emergence of lamivudine resistant hepatitis B virus: rapid resolution during treatment with adefovir.

BACKGROUND: Strategies for prevention of liver graft reinfection by hepatitis B virus (HBV) have been developed during recent years. Initially, passive immunoprophylaxis with high titre HBV immunoglobulin (HBIg), followed by lamivudine prophylaxis, and then the combination of lamivudine and HBIg have been employed. However, suboptimal use of the combination may be associated with failure of prophylaxis reflected by the emergence of HBV species with genetic changes that confer resistance to lamivudine and HBIg. Reinfection of the graft by HBV can be associated with rapid development of liver failure. CASE REPORT: A 43 year old HBV infected man received lamivudine before transplantation, and lamivudine and HBIg after transplantation. Despite prophylaxis, graft reinfection and severe hepatitis were observed. The observed serological evolution and genetic sequencing of the emergent HBV species suggested selection of lamivudine resistant and surface antigen escape mutants consecutively. Adefovir treatment began after the development of graft failure. OUTCOME: A rapid exponential decline in serum HBV titre was observed. Liver function tests normalised and signs of liver failure resolved. CONCLUSION: The use of HBIg and lamivudine permits prevention of graft reinfection by HBV for the majority of patients. Adefovir, a potent inhibitor of lamivudine resistant HBV, should be used when failure of prophylaxis is associated with graft hepatitis.

Acute Disease↗
PubMed2000

Evaluation of the oestrogen-receptor activating potency of environmental samples by means of yeast oestrogen assays.

A bioassay based on genetically modified yeast strains was applied to screen environmental samples for their oestrogen-like activity. The yeast system was selected from the vast number of "oestrogen bioassays" available because it permits rapid and easy handling at low costs. The test protocol developed allowed the examination of dimethyl sulfoxide-dissolved samples within one day, with an EC50 between 1.5 nM and 3.5 nM 17 beta-oestradiol and a detection limit between 0.3 nM and 0.5 nM 17 beta-oestradiol for yeast strain I. Advantages and disadvantages as well as future prospects of this kind of oestrogen bioassay will be considered by discussing selected results.

Biological Assay↗
PubMed1998

Polymorphisms of twelve short tandem repeat loci in a Taiwanese population and their application in parentage testing.

With the advancement of techniques in molecular biology, rapid, sensitive, and reliable methods of DNA typing for parentage testing have become available. In this study, we evaluated the usefulness of multiplex polymerase chain reaction (PCR) with 12 unlinked short tandem repeat (STR) loci for paternity testing in Taiwan. The genetic informativeness of this test was then compared with that of conventional human leukocyte antigen (HLA) analysis in 167 parentage studies. The 12 STR loci alone provided a cumulative power of exclusion of up to 0.9998. Paternity was excluded in 59 (35.3%) cases, including 40 of 112 paternity trios and 19 of 55 paternity duos. In the 40 trios in which paternity was excluded, a mean of 6 (range, 3-9) incompatible STR markers were in the 19 duos in which paternity was excluded, a mean of 4 (range, 1-8) incompatible STR markers were noted. In the 72 trios in which the alleged paternity could not be excluded, the mean probabilities of paternity (PP) were 90.6863% with HLA testing alone, 99.9847% with STR analysis alone, and 99.9972% with combined HLA and STR analysis. In the 36 duos in which the alleged paternity could not be excluded, the mean PPs were 81.4768% with HLA testing alone, 99.6124% with STR analysis alone, and 99.9145% with combined HLA and STR analysis. These results suggest that STR analysis is very powerful when used alone for paternity trio testing and when combined with conventional serologic HLA typing for duo parentage testing in the Taiwan population.

Chromosome Mapping↗
PubMed2002

Rapid genetic analysis of Helicobacter pylori gastric mucosal colonization in suckling mice.

Previously described animal models for Helicobacter pylori infection have been limited by cumbersome host requirements (e.g., germ-free conditions or unusual species) or are applicable to only special subsets of H. pylori strains (e.g., fresh clinical isolates or animal-adapted derivatives). Here, we report that 5- to 6-day-old outbred CD-1 (ICR) suckling mice support 24-h colonization of all H. pylori strains tested (SS1, 26695 SmR-1, 43504 SmR-1, and G27 SmR-1), including lab-passaged strains that cannot be adapted for colonization of adult animals. Total colony-forming units (cfu) recovered from infection with lab-passaged strains did not differ from those with mouse-adapted SS1. We also tested this model's ability to detect colonization defects in strains carrying mutations in known virulence genes by coinfecting with wild-type H. pylori and measuring differential recovery. This competition assay identified colonization defects in several classes of known attenuated mutants, including those defective in acid resistance (ureA), metabolism (frdA), motility (motB), and chemotaxis (cheY). A mutant defective in copA (copper transporting P-type ATPase) is nonattenuated in adult and infant mice. Possibly because of the limited duration of infection, our model did not identify defects in vacuolating cytotoxin (vacA) or gamma-glutamyltranspeptidase (ggt) as attenuating, in contrast to results from other animal models. We also identified a new virulence gene (HP0507) encoding a conserved hypothetical protein, which is important for colonization in our model. The suckling mouse model offers a rapid method to identify colonization defects in any H. pylori strain and may have utility as a new tool for studying immunity to primary infection.

Aging↗
PubMed2003

Adenovirus vector library: an approach to the discovery of gene and protein function.

A method was developed to generate a complex cDNA expression library within an adenovirus type 5 (Ad5)-based vector backbone, termed AdLibrary. Construction of the AdLibrary entailed the conversion of an Ad5 genome-containing cosmid to infectious virus particles. The Ad5 genome was modified by replacing the E1A and E1B genes with a Rous sarcoma virus-driven expression cassette. Conversion was accomplished by liberating the viral genome by restriction enzyme digestion and transfection in HEK 293 cells, which support the growth of E1A/E1B-deficient virus. A test AdLibrary demonstrated the possibility of converting and identifying a marker gene present at a frequency of 1/10(5) in the cosmid library. To demonstrate the utility of this technology, an AdLibrary was used to isolate a viral gene by its biological function. Virus growth was selected for with an AdLibrary on A549 cells, which do not complement for E1A/E1B function. The AdLibrary was generated with cDNAs derived from HeLa cells productively infected with Ad5. A cDNA corresponding to Ad5 E1A 13S was selected and isolated from the AdLibrary using this strategy. Since multiple genes are assayed simultaneously, this technology should expedite the discovery of genes affecting defined biological activities. This AdLibrary approach provides an opportunity to exploit the efficient gene delivery capabilities of adenovirus vectors for the rapid discovery of gene and protein function.

Adenoviridae↗
PubMed2001

Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes.

Organisms producing resting stages provide unique opportunities for reconstructing the genetic history of natural populations. Diapausing seeds and eggs often are preserved in large numbers, representing entire populations captured in an evolutionary inert state for decades and even centuries. Starting from a natural resting egg bank of the waterflea Daphnia, we compare the evolutionary rates of change in an adaptive quantitative trait with those in selectively neutral DNA markers, thus effectively testing whether the observed genetic changes in the quantitative trait are driven by natural selection. The population studied experienced variable and well documented levels of fish predation over the past 30 years and shows correlated genetic changes in phototactic behavior, a predator-avoidance trait that is related to diel vertical migration. The changes mainly involve an increased plasticity response upon exposure to predator kairomone, the direction of the changes being in agreement with the hypothesis of adaptive evolution. Genetic differentiation through time was an order of magnitude higher for the studied behavioral trait than for neutral markers (DNA microsatellites), providing strong evidence that natural selection was the driving force behind the observed, rapid, evolutionary changes.

Adaptation, Physiological↗
PubMed2005

A short-term test adapted to detect the genotoxic effects of environmental volatile pollutants (benzene fumes) using the filamentous fungus Aspergillus nidulans.

With the recent focus on environmental problems, increasing awareness of the harmful effects of industrial and agricultural pollution has created a demand for progressively more sophisticated pollutant and toxicity detection methods. Using Aspergillus nidulans strains this work presents a new short term-test that, most importantly, enables the rapid and inexpensive detection of volatile pollutants that induce genotoxic/carcinogenic effects in animals. The main aim is to contribute to environmental health protection, and special attention is directed to monitoring the hazard posed by benzene (as a carcinogenic agent model) mainly because its ubiquitous presence often leads to severe noxious effects in humans among whom increased rates of human leukemia have been reported. To evaluate even the submutagenic effects of benzene fumes, two Aspergillus nidulans diploid strains, heterozygous for several auxotrophic mutations, were used. The DNA lesions produced stimulate mitotic recombination and homozygotization of auxotrophic recessive mutations. Conidial exposure to a saturated atmosphere of benzene fumes for 20 s was enough to increase the mitotic recombination frequencies significantly. Genetic analyses of treated diploids evidenced alterations related to mitotic recombination frequencies, gene expression, and allelic segregation rates. Altogether they reflect the potential of benzene to induce alterations in the fungal DNA, and albeit indirectly, they also respond for the genotoxic/carcinogenic harmful side effects widely connected to benzene. This is the first description of a sensitive, rapid and inexpensive test able to detect the submutagenic dose effects of volatile environmental compounds. In addition, despite concentrating on benzene the same test can be applied to many other pollutants, volatile or not. Additionally, the test can also be used to detect the antigenotoxic properties of foods and drugs.

Air Pollutants↗
PubMed2005

The use of behavioral test batteries, II: effect of test interval.

Test batteries are commonly used to assess the behavioral phenotype of genetically modified and inbred strains of mice. However, few systematic studies have been employed to address several key issues concerning the use of a test battery. The current study was designed to address whether inter-test interval affects behavioral performance. Male mice of 3 different inbred strains and one F1 hybrid strain were randomly assigned to either a test battery with 1 week inter-test intervals, or a rapid test battery with 1-2 day inter-test intervals. The test battery included a neurological exam, open-field activity, light-dark exploration, rotarod test, prepulse inhibition, and startle habituation. The experiment was repeated with female animals of 2 different strains. As expected, there were strain differences on each of the behavioral assays; however, there was no major difference in performance between mice of the standard test battery and the rapid test battery. Similar results were found with females. These results indicate that the interval between most tests could be as little as 1-2 days, with little significant effect on overall performance. Thus, it is possible with the current test battery to reduce the inter-test interval to facilitate the rate of studying and identifying behavioral phenotypes in mice.

Analysis of Variance↗
PubMed1998

Rapid genotyping of mice with hemoglobinopathies and globin transgenes.

The hematology of the laboratory mouse has been well characterized. Normal genetic differences at the alpha- and beta-globin gene loci serve as useful markers for a wide variety of types of experimental studies. There are a number of naturally occurring or induced mutations that disrupt globin expression and produce thalassemic phenotypes. In addition, much has been learned of the workings of the globin locus control region from studies of transgenic mice, including those with mutations induced by targeted site-specific modifications. After a new mutation or transgene has been created, it must be maintained in living mice, and the genotypes of the offspring must be ascertained. While it is possible to determine genotypes by DNA analyses, such assays are time consuming and relatively expensive. An osmotic challenge test--originally developed for the genotyping of large-deletion alpha-thalassemia mutations in mice--has proven useful in detecting both severe and milder alpha- and beta-thalassemias, as well as some transgenic genotypes in mice carrying human globin genes. Reliable genotyping can, in some cases, be completed within a few minutes with minimal expense. Quantification of red cell fragility for a variety of thalassemic and transgenic mice is described here, along with a simplified test suitable for rapid, routine genotyping. The osmotic challenge test is perfectly reliable for distinguishing genotypes that cause significantly decreased release of hemoglobin from the red cells, but it is also useful for some of the conditions in which overall erythrocyte osmotic fragility is essentially normal.

Animals↗
PubMedDate not supplied

Alterations of BAT-26 identify a subset of gastric cancer with distinct clinicopathologic features and better postoperative prognosis.

BACKGROUND/AIMS: Gastrointestinal tumors with microsatellite instability represent a replication error-positive phenotype. BAT-26, a repeat of 26 deoxyadenosine localized in intron 5 of hMSH2 gene, has been reported as a reliable indicator of replication error phenotype in colorectal cancers. This study investigated whether BAT-26 is a useful marker for a mutator phenotype with distinct clinicopathologic features in gastric cancer. METHODOLOGY: One hundred and nineteen gastric cancer tissues and matched non-tumor tissue were examined by polymerase chain reactions with electrophoresis for 9 dinucleotide microsatellites and BAT-26, and frameshift mutations of transforming growth factor-beta type II receptor. The relation between BAT-26 alterations and relevant clinicopathological or genetic parameters were analyzed. RESULTS: Gastric cancer with BAT-26 alterations was highly correlated with multiple microsatellite alterations (> or = 3 loci) and frameshift mutations of transforming growth factor-beta type II receptor, and predominantly showed antral location, intestinal histologic subtype, advanced stage, a higher rate of Helicobacter pylori infection, a better postoperative survival and less lymph node metastasis. CONCLUSIONS: These results show testing of BAT-26 alterations is a convenient and rapid screening method for identifying a subset of gastric cancer with a mutator phenotype and better prognosis.

Adenocarcinoma↗