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Molecular epidemiology, pathogenesis and prevention of gastric cancer.

Cancer of the stomach is one of the most commonly diagnosed malignancies and remains an important cause of mortality world wide. This type of cancer is not uniformly distributed among populations but shows a marked variation in both incidence and mortality. Although gastric cancer is declining in many parts of the world, the reasons for this decline are not well understood and its etiology remains unclear. Several factors are suspected to play a role in gastric carcinogenesis, including the effects of diet, exogenous chemicals, intragastric synthesis of carcinogens, genetic factors, infectious agents and pathological conditions in the stomach (such as gastritis). A new look at the results of epidemiological and experimental studies is important for the establishment of strategies for control. Since cancer of the stomach has a very poor prognosis in its more advanced stages, such a control program must have its main focus on primary prevention. This review describes our knowledge about cancer of the stomach regarding epidemiology, pathogenesis and prevention.

Asia↗

The Second International Collaborative Study on Comparative Mutagenesis re-visited: analysis by multi-variate statistical methods.

Computerized data analysis methods were applied to a selected subset of the results generated by the International Program on Chemical Safety Collaborative Study on In Vitro Assays. The rationale of this study was the analysis of test performances and the comparison with the conclusions of a similar analysis previously performed on the results of the First International Study. The multi-variate data analysis techniques used in the present work proved to be particularly suitable for looking at the complex field of comparative mutagenesis in a logical and systematic fashion, and generated a clear classification of the assays on the basis of their experimental performances. This classification proved not to be consistent with the traditional categories that group tests according to genetic end-point and phylogenetic position, and afforded classes of assays distinct for their sensitivity and specificity in respect to carcinogens. In particular, two systems (Saccharomyces cerevisiae XV185-14C mutation and Syrian Hamster Embryo cells transformation assays) on the basis of the published results, seemed to show a considerable sensitivity in predicting carcinogenicity, although they do not show high specificity.

Animals↗

International training programs in reproductive sciences for conservation of Latin American felids.

Survival of the ten non-domestic felid species endemic to Latin America is imperiled by habitat loss, poaching and poor captive management. Over the past 10 years, conservation of these felids has been the primary focus of a reproductive research and training program conducted in Brazil, Mexico, and the USA. The objectives of this program were to: (1) provide intensive training in reproductive sciences to Latin American scientists, (2) conduct collaborative studies investigating basic and applied reproduction in endangered felids, and (3) establish a highly-trained scientific cohort to conduct independent conservation-based research. Four formal training courses, consisting of didactic lectures and hands-on instruction in research techniques, including semen collection, sperm cryopreservation and laparoscopic artificial insemination (AI), were taught in Brazil and Mexico between 1995 and 1998. Several of these scientists received further training in conducting fecal hormone analysis in the USA, and a number of research studies, many in collaboration with American scientists, were initiated in Latin American felids. Research findings have characterized basal reproductive traits in several felid species, including ocelots, margay, tigrinas and jaguars, and established that Latin American felids exhibit only minimal seasonal variation in most reproductive traits. Other studies have explored the impact of acute and chronic stressors on adrenocortical activity and demonstrated the importance of environmental enrichment in captivity, especially in small felids. Additional research has examined ovarian and immunological responsiveness of Latin American felids to exogenous gonadotropins and assessed the impact of nutrition on sperm production and oocyte quality. Applied reproductive studies have investigated sperm cryopreservation in both captive and wild felid populations and demonstrated the production of viable offspring in ocelots and tigrinas following laparoscopic AI. Ongoing studies are investigating the potential of in vitro fertilization (IVF), embryo cryopreservation and embryo transfer for genetic management of ocelots and tigrinas. To date, over 75 Brazilian ocelot and 50 tigrina IVF embryos have been cryopreserved and two pregnancies have been established in ocelots following transfer of frozen-thawed embryos. Findings from these studies are helping to improve husbandry, population management, and breeding of Latin American felids in captivity. Continued advances in assisted reproduction eventually may provide an alternative route for exchanging genetic material among Latin American felid populations. Most importantly, this collaborative program has been essential for building scientific capacity, within Brazil and Mexico, in establishing a core group of highly-trained reproductive biologists that will continue applying their new knowledge and skills to the conservation of Latin American felids.

Animals↗

Perception and response in plant disease resistance.

Plants express sophisticated mechanisms for recognizing pathogens. The functionally defined repertoire of non-self perception is large; the number and nature of subsequent molecular events required for resistance is unknown. Recent cloning of disease resistance genes, and genetic identification of loci required for their function, allows dissection of the structure, evolution, and deployment within populations of pathogen-perception mechanisms. Roles for reactive oxygen species and programmed cell death in resistance have also been suggested recently. New results document a role for salicylic acid as a lynchpin in the establishment and maintenance of the 'effector functions' of disease resistance, and strategies for engineered plant protection are moving closer to reality.

Apoptosis↗

Two distinct events in lineage establishment of a biopotential hemopoietic cell line.

HL-60, a human myelomonocytic cell line can be induced to differentiate along either granulocyte or monocyte pathways and therefore is a good model to study lineage establishment. We have shown that there are two classes of reactions in the establishment of the granulocytic line distinguishable by their kinetics. The fast reaction occurs in hours and is induced by ouabain or A23187, agents which effect ions. The slow reactions occur at a constant rate over a period of 5 days and are induced by the surrogate inducers RA and D3 but also by the natural inducer GM-CSF. GM-CSF induces the enzyme markers which we use to characterize both granulocytes and monocytes in the same cell. If these markers are indeed unique to each of the lines this means that HL-60 has both gene programs initiated by GM-CSF and D3. Variant lines which do not respond to one or more of the inducers can be used to analyze this point since variants which are induced only to granulocytes or only to monocytes by GM-CSF have been isolated.

Calcimycin↗

Chromosomal aberrations and SCEs as biomarkers of cancer risk.

Previous studies have suggested that the frequency of chromosomal aberrations (CAs), but not of sister chromatid exchanges (SCEs), predicts cancer risk. We have further examined this relationship in European cohorts comprising altogether almost 22,000 subjects, in the framework of a European collaborative project (CancerRiskBiomarkers). The present paper gives an overview of some of the results of the project, especially as regards CAs and SCEs. The results confirm that a high level of CAs is associated with an increased risk of cancer and indicate that this association does not depend on the time between CA analysis and cancer detection, i.e., is obviously not explained by undetected cancer. The present evidence indicates that both chromatid-type and chromosome-type CAs predict cancer, even though some data suggest that chromosome-type CAs may have a more pronounced predictive value than chromatid-type CAs. CA frequency appears to predict cancers at various sites, although there seems to be a particular association with gastrointestinal cancers. SCE frequency does not appear to have cancer predictive value, at least partly due to uncontrollable technical variation. A number of genetic polymorphisms of xenobiotic metabolism, DNA repair, and folate metabolism affect the level of CAs and might collectively contribute to the cancer predictivity of CAs. Other factors that may influence the association between CAs and cancer include, e.g., exposure to genotoxic carcinogens and internal generation of genotoxic species. Although the association between CA level and cancer is seen at the group level, an association probably also exists for the individual, although it is not known if an individual approach could be feasible. However, group level evidence should be enough to support the use of CA analysis as a tool in screening programs and prevention policies in occupational and environmental health.

Chromosome Aberrations↗

Characterization of two new HLA-B alleles by sequence-based typing: HLA-B*0817 and HLA-B*1311.

In this brief communication we report the characterization of two new HLA-B variants officially named HLA-B*0817 and HLA-B*1311. The HLA-B*0817 allele was identified in a Caucasoid male candidate for renal transplantation in the North Italy Transplant program. The nucleotidic sequence of exons 2, 3 and 4 of this novel allele is identical to that of HLA-B*0804 except for three point mutations in exon 2: from A to G at position 259, from C to G at position 261 and from G to A at position 302. These mutations are responsible for two aminoacidic substitutions [Asn (r) Glu, codon 63, and Ser (r) Asn, codon 77]. HLA-B*1311 was found in a volunteer donor belonging to National Marrow Donor Program(R). This new variant is identical to that of HLA-B*1301 except for three nucleotide substitutions at positions 353, 355 and 369 leading to two aminoacidic variations from Ile to Thr at codon 94 and from Ile to Leu at codon 95 and a silent mutation at codon 99.

Alleles↗

Modeling interindividual variation in physiological factors used in PBPK models of humans.

Modeling interindividual variation in internal doses in humans using PBPK models requires data on the variation in physiological parameters across the population of interest. These data should also reflect the correlations between the values of the various parameters in a person. In this project, we develop a source of data for human physiological parameters where (1) the parameter values for an individual are correlated with one another, and (2) values of parameters capture interindividual variation in populations of a specific gender, race, and age range. The parameters investigated in this project include: (1) volumes of selected organs and tissues; (2) blood flows for the organs and tissues; and (3) the total cardiac output under resting conditions and average daily inhalation rate. These parameters are expressed as records of correlated values for the approximately 30,000 individuals evaluated in the NHANES III survey. A computer program, Physiological Parameters for PBPK Modeling (P3M), is developed that allows records to be retrieved randomly from the database with specification of constraints on age, sex, and ethnicity. P3M is publicly available. The database and accompanying software provide a convenient tool for parameterizating models of interindividual variation in human pharmacokinetics.

Computer Simulation↗

Genetic basis for innovations in floral organ identity.

Of the many innovations associated with the radiation of the angiosperms, the evolution of a petal identity program is among the best understood from a genetic standpoint. Although the existing data do indicate that similar genetic mechanisms control petal development across diverse taxa, there is also considerable evidence for variability in petal identity programs, likely due to a number of factors. These points are illustrated through a review of our current knowledge on the subject, integrating phylogenetic, morphological, and genetic studies. Comparative studies of petal identity highlight the complex nature of homology in plants and stand as a cautionary tale for the interpretation of gene expression data.

Biological Evolution↗

Recovering haplotype structure through recombination and gene conversion.

MOTIVATION: Understanding haplotype evolution subject to mutation, recombination and gene conversion is fundamental to understand genetic specificities of human populations and hereditary bases of complex disorders. The goal of this project is to develop new algorithmic tools assisting the reconstruction of historical relationships between haplotypes and the inference of haplotypes from genotypes. RESULTS: We present two new algorithms. The first one finds an optimal pathway of mutations, recombinations and gene conversions leading to a given haplotype of size m from a population of h haplotypes. It runs in time O(mhs(2)), where s is the maximum number of contiguous sites that can be exchanged in a single gene conversion. The second one finds an optimal pathway of mutations and recombinations leading to a given genotype, and runs in time O(mh(2)). Both algorithms are based on a penalty score model and use a dynamic programming approach. We apply the second one to the problem of inferring haplotypes from genotypes, and show how it can be used as an independent tool, or to improve the performance of existing methods. AVAILABILITY: The algorithms have been implemented in JAVA and are available on request.

Algorithms↗

Segregation and linkage analysis.

Computer programs are available in the software package SAGE to perform a variety of segregation and linkage analyses used by human geneticists. These methods are designed specifically to uncover major gene segregation in pedigree data coming from non-inbred populations. With the aid of a closely linked polymorphic marker, they can detect a locus that contributes as little as 10% to the variation of a quantitative trait in a pedigree sample of several hundred individuals.

Animals↗

Absence of geographic chromosomal variation in the roan and sable antelope and the cytogenetics of a naturally occurring hybrid.

The determination of geographic chromosomal variation in rare or endangered species, or those of special management concern, is important, since geographically defined cytotypes can negatively influence breeding programs involving founders drawn from widely divergent localities. We cytogenetically analyzed specimens of the roan (Hippotragus equinus) and sable antelope (H. niger) collected from widely divergent localities throughout their respective ranges. Each species was characterized by a diploid number of 60 and an invariant karyotype. In contrast to the absence of intraspecific variation, however, the two species differ with respect to centromeric constitutive heterochromatin and numbers of nucleolar organizer regions. These cytogenetic landmarks were subsequently used to verify an anecdotal account of a naturally occurring roan x sable hybrid. The data show that, despite their markedly distinct phenotypes, the roan and sable antelope are nonetheless sufficiently similar genetically to produce viable offspring. Hybridization, although a rare event between these species, is probably partly promoted by behavioral differences which are not always sufficient to prevent mating between them.

Africa↗

Progeny testing and selection intensity for Holstein bulls in different countries.

International Bull Evaluation Service (Interbull) Holstein evaluations from February 1995 through February 2003 were used to determine characteristics of progeny testing for Holstein bulls in Australia, Canada, Denmark, France, Germany, Italy, New Zealand, Sweden, The Netherlands, and the United States. The decision to graduate a bull from progeny test (PT) was assumed to have been made based on the second Interbull evaluation, and graduation was defined as the addition of 200 daughters in the period 2.5 to 4.5 yr later. Mean bull age at PT decision varied across countries by 12 mo. Mean numbers of herds and daughters ranged from 39 to 111 and 54 to 144, respectively. Countries with higher requirements for official evaluations generally had more herds and daughters but older bulls at PT decision. Mean estimated breeding values for yield traits of sires of tested bulls were most similar across countries for fat, differing by only 6.4 kg. The four countries highest for sire protein differed only by 1 kg; however, the range was 12 kg. Percentages of bulls graduated ranged from 4.4 to 14.7 across countries. Selection intensities (standardized selection differentials) tended to be about 1.0 for yield traits. Selection intensities for somatic cell score were generally unfavorable, reflecting selection for negatively correlated yield traits. Reflecting variation in national breeding goals, selection intensities for stature were positive for most countries and highly negative for New Zealand. Selection intensity for fore udder was generally the lowest among the traits examined. All but one country showed positive selection for udder support. These statistics permit comparison of the components of PT programs across country, illustrating possible opportunities for improvement.

Animals↗

Catechol O-methyltransferase val158met genotype and neural mechanisms related to affective arousal and regulation.

CONTEXT: Catechol O-methyltransferase (COMT), the major enzyme determining cortical dopamine flux, has a common functional polymorphism (val(158)met) that affects prefrontal function and working memory capacity and has also been associated with anxiety and emotional dysregulation. OBJECTIVES: To examine COMT val(158)met effects on corticolimbic circuitry reactivity and functional connectivity during processing of biologically salient stimuli, as well as the relationship to the temperamental trait of novelty seeking. DESIGN: Within-subject functional magnetic resonance imaging study. SETTING: National Institute of Mental Health, Genes, Cognition, and Psychosis Program, Bethesda, Md. Patients One hundred one healthy subjects of both sexes. RESULTS: We found that the met allele was associated with a dose-dependent increase in hippocampal formation and ventrolateral prefrontal cortex activation during viewing of faces displaying negative emotion. In met/met homozygotes, limbic and prefrontal regions showed increased functional coupling. Moreover, in these same subjects, the magnitude of amygdala-orbitofrontal coupling was inversely correlated with novelty seeking, an index of temperamental inflexibility. CONCLUSIONS: Our results indicate that heritable variation in dopamine neurotransmission associated with the met allele of the COMT polymorphism results in heightened reactivity and connectivity in corticolimbic circuits. This may reflect a genetic predisposition for inflexible processing of affective stimuli, a mechanism possibly accounting for aspects of arousal and behavioral control that contribute to emotional dysregulation previously reported in met/met individuals.

Adult↗

Evidence of recombination in quasispecies populations of a Hepatitis C Virus patient undergoing anti-viral therapy.

BACKGROUND/AIM: Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. HCV circulates in vivo as a complex population of different but closely related viral variants, commonly referred to as a quasispecies. The extent to which recombination plays a role in the evolution of HCV quasispecies when patients are undergoing anti-viral therapy is currently unknown. In order to gain insight into these matters, we have performed a phylogenetic analysis of HCV quasispecies populations from six patients undergoing anti-viral therapy. METHODS: Putative recombinant sequences were identified with the use of SimPlot program. Recombination events were confirmed by bootscaning, using putative recombinant sequence as a query. Statistical support for the presence of a recombination event was done by the use of LARD program. RESULTS: A crossing-over event in the NS5A gene in a HCV strain recovered after four weeks of treatment was identified in quasispecies from a patient with sustained response. Putative parental-like strains were identified as strains circulating in previous weeks on the same patient. CONCLUSION: Only one recombinant strain was detected in all patient quasispecies populations studied. The recombination break-point is situated on the PKR-binding region of NS5A. Although recombination may not appeared to be extensive in NS5A genes of HCV quasispecies populations of patients undergoing antiviral therapy, this possibility should be taken into account as a mechanism of genetic variation for HCV.

Amino Acid Sequence↗

[RbcL sequence analysis of Belamcanda chinensis and related medicinal plants of Iris].

AIM: To identify "Shegan" [Belamcanda chinensis (L.) DC.] and relative medicinal plants of Iris including Iris tectorum Maxim., I. dichotoma Pall., I. germanica L. and I. japonica Thunb. by ribulose 1,5-bisphosphate carboxylase Large Gene (rbcL) sequence analysis. METHODS: General DNA was isolated from the fresh leaves of Belamcanda chinensis and 4 Iris spp. by CTAB. A pair of primers was designed to amplify the rbcL gene and PCR Preps DNA kit was used to purify the PCR products. The rbcL sequences were determined by ABI (Applied Biosystems Inco.) Prism 310 Genetic Analyzer. RESULTS: A fragment of about 750 bp of rbcL gene from Belamcanda chinensis and 4 Iris spp. were amplified and sequenced. The rbcL sequences of Iris tectorum, I. dichotoma Pall. and I. japonica were reported for the first time. The rbcL sequences of 5 species of Iridaceae were aligned and analyzed using Clustal (Version 8.0) and MEGA (Version 2.0.) programs. The nucleotide number of difference is from 1.000 to 20.000. The tranversions is from 0.000 to 9.000 and the transitions is from 0.000 to 14.000. Phylogenetic tree based on rbcL partial sequence data indicated that the eleven samples of 5 species clustered separately. CONCLUSION: The sequence variation of rbcL can be used to identify Belamcanda chinensis and 4 species of relative medicinal plants of Iris. The molecular phylogenetic tree accords with the classical taxonomy.

Base Sequence↗

Nutrient composition and anti-nutritional factors in selected vegetable soybean (Glycine max [L.] Merr.).

The genetic variation in the nutrient composition and anti-nutritional factors of 17 vegetable soybean genotypes were determined and a wide variation in protein %, total phosphorus (TPi) and available phosphorus (AP) was found among these genotypes. Variations in Ca, K, Fe, Mn, and Cu were also documented. Variation was also found for trypsin inhibitor (TI) activity and Phytate (PA) content. A highly significant and negative correlation (r = -0.533, P less than 0.01) was observed between TI and total protein. Strong positive correlation (r = 0.90) was also found between TPi and AP. Several genotypes (Sooty, Emperor, Wilson-5, PI 416771, PI 417322) showed good nutritional potential and can be used in the breeding program. High protein %, TPi, and minerals are desirable qualities for vegetable-type soybeans that make it as food with high nutrient density. Studies on the nutritional evaluation of immature vegetable type soybean seeds at different reproductive stages are also underway.

Analysis of Variance↗