SEARCH · Search PubMed

Results for “programmed genetic variation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,243 records · Page 69Linked to original sources

PubMed2006

Low frequency of telomerase RNA mutations among children with aplastic anemia or myelodysplastic syndrome.

Mutations in TERC, the RNA component of telomerase, result in autosomal dominant dyskeratosis congenita (DC), a rare bone marrow failure syndrome. TERC mutations have been detected in a subset of patients previously diagnosed with aplastic anemia and myelodysplastic syndrome (MDS), and these TERC mutations are clinically relevant as patients with DC respond poorly to conventional therapies. We aimed to determine the frequency of TERC mutations in pediatric patients with aplastic anemia and MDS who required a hematopoietic stem cell transplant. We obtained 284 blood samples from the National Donor Marrow Program Research Sample Repository from children and adolescents with bone marrow failure who underwent an unrelated stem cell transplant. We screened these samples for mutations in the TERC gene using direct DNA sequencing. We found 2 patients with sequence alterations in TERC. We identified a 2 base pair deletion (-240delCT) in a 4-year-old child with MDS and a single nucleotide alteration (-99-->CG) in a 1-year-old child with juvenile myelomonocytic leukemia. Screening for TERC gene mutations is unlikely to diagnose occult DC in children with severe bone marrow failure who require a hematopoietic stem cell transplant.

Adolescent↗

PubMed2002

Breast cancer, consanguinity, and lethal tumor genes: simulation of BRCA1/2 prevalence over 40 generations.

Marriage between biological relatives is a social custom with a long history in many parts of the world. Today, hundreds of millions of individuals live in consanguineous families. The offspring of consanguineous parents are more likely to have the same two alleles (homozygosity) by descent. In consanguineous family with BRCA1/2 gene mutations, an offspring is more likely to be BRCA1/2 homozygous. The consequences of BRCA1/2 mutation homozygosity in humans are unknown. In knockout mice, BRCA1 or BRCA2 homozygotes die as embryos. Because tumor suppressor genes are conserved and less species-specific than other genes, human BRCA1/2 homozygotes are likely to be biologically non-viable and are unknown to exist. Among the conceptuses of consanguineous couples, there are excess deaths (abortions, stillbirths, perinatal and early-childhood deaths) as well as a decreased risk of breast cancer, especially in younger females. It has been suggested that, in part, the excess deaths are due to BRCA1/2 and other still undiscovered tumor gene homozygotes. To examine the consequences of the long-term practice of consanguineous marriage on the prevalence of lethal cancer genes, we simulated, by computer, the mating of non-consanguineous and consanguineous populations over 40 generations. The program was developed in Basic for a Macintosh computer. The input comprised the rates of consanguineous marriage types and the output parameter was the rate of heterozygotes (carriers) in each generation. The combined prevalence of BRCA1/2 mutation of 1% was used as a starting reference point. Absence of spontaneous mutations and gene flow were assumed. In a randomly mating population, the BRCA1/2 carrier rate decreases on average 0.0035% every 25 years. In a highly consanguineous population, the carrier rate decreases on average 0.022% every 25 years, or six times faster than in a non-consanguineous population. There is a worldwide trend of decreasing breast cancer incidence with an increasing consanguinity rate. In conclusion, the BRCA1/2 and possibly other undiscovered tumor gene carrier rates are significantly lower in consanguineous than in non-consanguineous populations. Gene frequency in a population depends on the rate of inbreeding and length of consanguineous practices. A drift phenomenon may exert a major effect on the carrier rate. Consanguinity may explain part of the worldwide variation of breast cancer incidence.

Breast Neoplasms↗

PubMed2006

Oncogenesis of RON receptor tyrosine kinase: a molecular target for malignant epithelial cancers.

Recepteur d'origine nantais (RON) belongs to a subfamily of receptor tyrosine kinases (RTK) with unique expression patterns and biological activities. RON is activated by a serum-derived growth factor macrophage stimulating protein (MSP). The RON gene transcription is essential for embryonic development and critical in regulating certain physiological processes. Recent studies have indicated that altered RON expression contributes significantly to cancer progression and malignancy. In primary tumors, such as colon and breast cancers, overexpression of RON exists in large numbers and is often accompanied by the generation of different splicing variants. These RON variants direct a unique program that controls cell transformation, growth, migration, and invasion, indicating that altered RON expression has the ability to regulate motile/invasive phenotypes. These activities were also seen in transgenic mice, in which targeted expression of RON in lung epithelial cells resulted in numerous tumors with pathological features of human bronchioloalveolar carcinoma. Thus, abnormal RON activation is a pathogenic factor that transduces oncogenic signals leading to uncontrolled cell growth and subsequent malignant transformation. Considering these facts, RON and its variants can be considered as potential targets for therapeutic intervention. Experiments using small interfering RNA and neutralizing monoclonal antibodies demonstrated that suppressing RON expression and activation decreases cancer cell proliferation, increases apoptotic death, prevents tumor formation in nude mice, and reduces malignant phenotypes. Thus, blocking RON expression and activation has clinical significance in reversing malignant phenotypes and controlling tumor growth.

Animals↗

PubMed2005

Phosphatases modulate the bistable sporulation gene expression pattern in Bacillus subtilis.

Summary Spore formation in the Gram-positive bacterium Bacillus subtilis is a last resort adaptive response to starvation. To initiate sporulation, the key regulator in this process, Spo0A, needs to be activated by the so-called phosphorelay. Within a sporulating culture of B. subtilis, some cells initiate this developmental program, while other cells do not. Therefore, initiation of sporulation appears to be a regulatory process with a bistable outcome. Using a single cell analytical approach, we show that the autostimulatory loop of spo0A is responsible for generating a bistable response resulting in phenotypic variation within the sporulating culture. It is demonstrated that the main function of RapA, a phosphorelay phosphatase, is to maintain the bistable sporulation gene expression. As rapA expression is quorum regulated, it follows that quorum sensing influences sporulation bistability. Deletion of spo0E, a phosphatase directly acting on Spo0A approximately P, resulted in abolishment of the bistable expression pattern. Artificial induction of a heterologous Rap phosphatase restored heterogeneity in a rapA or spo0E mutant. These results demonstrate that with external phosphatases, B. subtilis can use the phosphorelay as a tuner to modulate the bistable outcome of the sporulating culture. This shows that B. subtilis employs multiple pathways to maintain the bistable nature of a sporulating culture, stressing the physiological importance of this phenomenon.

Bacillus subtilis↗

PubMed2006

A gradient of epidermal growth factor receptor signaling determines the sensitivity of rbf1 mutant cells to E2F-dependent apoptosis.

The inactivation of retinoblastoma (Rb) family members sensitizes cells to apoptosis. This cell death affects the development of mutant animals and also provides a critical constraint to the malignant potential of Rb mutant tumor cells. The extent of apoptosis caused by the inactivation of Rb is highly cell type and tissue specific, but the underlying reasons for this variation are poorly understood. Here, we characterize a specific time and place during Drosophila melanogaster development where rbf1 mutant cells are exquisitely sensitive to apoptosis. During the third larval instar, many rbf1 mutant cells undergo E2F-dependent cell death in the morphogenetic furrow. Surprisingly, this pattern of apoptosis is not caused by inappropriate cell cycle progression but instead involves the action of Argos, a secreted protein that negatively regulates Drosophila epidermal growth factor receptor (EGFR [DER]) activity. Apoptosis of rbf1 mutant cells is suppressed by the activation of DER, ras, or raf or by the inactivation of argos, sprouty, or gap1, and inhibition of DER strongly enhances apoptosis in rbf1 mutant discs. We show that RBF1 and a DER/ras/raf signaling pathway cooperate in vivo to suppress E2F-dependent apoptosis and that the loss of RBF1 alters a normal program of cell death that is controlled by Argos and DER. These results demonstrate that a gradient of DER/ras/raf signaling that occurs naturally during development provides the contextual signals that determine when and where the inactivation of rbf1 results in dE2F1-dependent apoptosis.

Animals↗

PubMed2004

Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales.

Precise identification of Bacillus anthracis isolates has aided forensic and epidemiological analyses of natural anthrax cases, bioterrorism acts and industrial scale accidents by state-sponsored bioweapons programs. Because there is little molecular variation among B. anthracis isolates, identifying and using rare variation is crucial for precise strain identification. We think that mutation is the primary diversifying force in a clonal, recently emerged pathogen, such as B. anthracis, since mutation rate is correlated with diversity on a per locus basis. While single nucleotide polymorphisms (SNPs) are rare, their detection is facilitated by whole genome discovery approaches. As highly stable phylogenetic markers, SNPs are useful for identifying long branches or key phylogenetic positions. Selection of single, diagnostic "Canonical SNPs" (canSNPs) for these phylogenetic positions allows for efficient and defining assays. We have taken a nested hierarchal strategy for subtyping B. anthracis, which is consistent with traditional diagnostics and applicable to a wide range of pathogens. Progressive hierarchical resolving assays using nucleic acids (PHRANA) uses a progression of diagnostic genomic loci that are initially highly stable but with low resolution and, ultimately, very unstable but with high resolution. This approach mitigates the need for data weighting and provides both a deeply rooted phylogenetic hypothesis and high resolution discrimination among closely related isolates.

Animals↗

PubMed2000

Use of three different marker systems to estimate genetic diversity of Indian elite rice varieties.

Genetic diversity among 42 Indian elite rice varieties, which is important for selection of parents for conventional breeding and hybrid program, was evaluated using three different types of DNA markers and parentage analysis. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers resulted in mean heterozygosity values of 0.429, 0.675 and 0.882 over all loci, respectively, and marker index values of 2.21, 4.05 and 5.49, respectively. The three molecular marker systems together provide wider genome coverage and, therefore, would be a better indicator of the genetic relationships among the 42 elite rice cultivars than those revealed using individual molecular markers. A total of 153 bands (91%) were polymorphic out of 168 bands amplified, considering all the markers together. The average genetic similarity coefficient across all the 861 cultivar pairs was 0.70 while the average coefficient of parentage was 0.10. Cluster analysis revealed that there was a very poor correlation (correlation coefficient <0.1) between dendrograms generated using coefficients of parentage and molecular marker generated genetic similarities, which can be attributed to selection pressure, genetic drift, sampling of loci and unknown relationships among supposedly unrelated ancestors.

DNA, Plant↗

PubMed1999

Protein folds and families: sequence and structure alignments.

Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from http://www.embl-ebi.ac.uk/dali/

Databases, Factual↗

PubMed2001

Macro-evolution of the hairy enhancer in Drosophila species.

It has been suggested that many of the changes in the developmental program might be in the cis-acting promoters and enhancer regions. Here I study the macro-evolutionary changes of an enhancer region for the early developmental gene hairy in Drosophila melanogaster, D. simulans, D. pseudoobscura, D. willistoni, D. nebulosa, D. hydei, and D. virilis. The enhancer region is characterized by small, highly conserved blocks interspersed among highly variable regions. Nevertheless, species phylogenies constructed by the enhancer sequences agree with the widely accepted phylogeny of these species. The evolution of the variable regions is consistent with a molecular clock, while the evolution of the conserved blocks is significantly different from a clock. In particular, the D. pseudoobscura lineage shows the highest degree of species-specific change consistent with changes in expression timing reported in an earlier study. It has been suggested that the variation in sequence length between highly conserved blocks may play a role in the coordination of regulatory processes, such as protein-protein interactions; thus, stabilizing selection has been suggested to act on the length variations. Here I develop a test for stabilizing selection on length variation and show that the hairy enhancer does not show statistically significant evidence for stabilizing selection. J. Exp. Zool. (Mol. Dev. Evol.) 291:175-185, 2001.

Amino Acid Sequence↗

PubMed2004

The National Pork Producers Council Maternal Line National Genetic Evaluation Program: a comparison of six maternal genetic lines for female productivity measures over four parities.

Litter (n = 8,424) and female performance records were collected in two breed-to-wean production units in order to evaluate genetic line differences for sow longevity and maternal performance over four parities. Lines evaluated were American Diamond Genetics, Danbred North America, Dekalb-Monsanto DK44, Dekalb-Monsanto GPK347, Newsham Hybrids, and National Swine Registry. Females within a line were derived from a minimum of 65 sires, 197 dams (three dams per sire), and a maximum of three daughters per dam, except in the GPK347, which were produced using semen from 12 Nebraska Index boars mated with Dekalb-Monsanto Line 34 females. All lines expressed 100% maternal heterosis. Mixed model statistical procedures were used with fixed effects including genetic line, parity, production unit, and two-way interactions. Random effects included a contemporary week of production and female for repeated records. Lactation length (average 15 d) was included as a linear covariate where appropriate. In total, 3,599 females entered as early-weaned pigs, 3,283 entered the breeding herd, 2,592 farrowed at least a single litter, and 1,656 and completed four parities. Line (P < 0.001) and parity (P < 0.001) effects were observed for virtually all traits measured. Ranges of genetic line differences averaged across parities were 1.76 pigs for total born, 1.45 pigs born alive, and 0.31 stillborn pigs per litter. Ranges of line differences in total and live litter weight were 1.4 and 1.3 kg, respectively. Ranges among lines, within Parities 1 through 4, for litter size at weaning were 0.56, 1.08, 0.91, and 0.64 pigs per litter, respectively. Line differences for weight (33.8 kg) and backfat depth (6.4 mm) at farrowing, lactation feed intake (8.7 kg), weight loss (5.0 kg), and backfat loss (0.87 mm) were observed. Extended wean-to-estrus interval was related to variation in weight, feed intake, and backfat loss in all lines except the GPK347. The GPK347 females farrowed and weaned the largest number of pigs, ate less feed in lactation, and lost more backfat and weight during lactation, yet they had the largest litters and the shortest wean-to-estrus intervals. Line x parity interactions existed for many traits due to small rank changes, but in general, the high- and low-ranked lines did not change. Genetic line differences in reproductive efficiency through four parities exist and must be recognized when choosing a female line.

Adipose Tissue↗

PubMed2006

Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis.

Understanding the ecology of drug-resistant pathogens is essential for devising rational programs to preserve the effective lifespan of antimicrobial agents and to abrogate epidemics of drug-resistant organisms. Mathematical models predict that strain fitness is an important determinant of multidrug-resistant Mycobacterium tuberculosis transmission, but the effects of strain diversity have been largely overlooked. Here we compared the impact of resistance mutations on the transmission of isoniazid-resistant M. tuberculosis in San Francisco during a 9-y period. Strains with a KatG S315T or inhA promoter mutation were more likely to spread than strains with other mutations. The impact of these mutations on the transmission of isoniazid-resistant strains was comparable to the effect of other clinical determinants of transmission. Associations were apparent between specific drug resistance mutations and the main M. tuberculosis lineages. Our results show that in addition to host and environmental factors, strain genetic diversity can influence the transmission dynamics of drug-resistant bacteria.

Alleles↗

PubMed2004

IL10 gene polymorphisms are associated with asthma phenotypes in children.

IL10 is an anti-inflammatory cytokine that has been found to have lower production in macrophages and mononuclear cells from asthmatics. Since reduced IL10 levels may influence the severity of asthma phenotypes, we examined IL10 single-nucleotide polymorphisms (SNPs) for association with asthma severity and allergy phenotypes as quantitative traits. Utilizing DNA samples from 518 Caucasian asthmatic children from the Childhood Asthma Management Program (CAMP) and their parents, we genotyped six IL10 SNPs: 3 in the promoter, 2 in introns, and one in the 3' UTR. Using family-based association tests, each SNP was tested for association with asthma and allergy phenotypes individually. Population-based association analysis was performed with each SNP locus, the promoter haplotypes and the 6-loci haplotypes. The 3' UTR SNP was significantly associated with FEV(1) as a percent of predicted (FEV(1)PP) (P=0.0002) in both the family and population analyses. The promoter haplotype GCC was positively associated with IgE levels and FEV(1)PP (P=0.007 and 0.012, respectively). The promoter haplotype ATA was negatively associated with lnPC(20) and FEV(1)PP (P=0.008 and 0.043, respectively). Polymorphisms in IL10 are associated with asthma phenotypes in this cohort. Further studies of variation in the IL10 gene may help elucidate the mechanism of asthma development in children.

3' Untranslated Regions↗

PubMed1996

NTP technical report on the toxicity studies of 1-Nitropyrene (CAS No. 5522-43-0) Administered by Inhalation to F344/N Rats.

1-Nitropyrene is a by-product of combustion. It is the predominant nitrated polycyclic aromatic hydrocarbon emitted in diesel engine exhaust and has been found at concentrations of up to 57 pg/m(3) in the air over urban and suburban areas. 1-Nitropyrene is detoxified mainly to 1-aminopyrene by nitro reduction. 1-Nitropyrene can also undergo ring oxidation, depending on the concentration of oxygen. Aryl nitrenium ions generated by nitro reduction or K-region nitropyrene epoxides generated by ring oxidation can react with DNA, forming adducts. 1-Nitropyrene was nominated for toxicity study because it is mutagenic, it is found in the environment, and it has potential for human exposure. Administration by inhalation was chosen because humans are exposed to 1-nitropyrene mainly by inhalation. Nose-only inhalation was chosen because whole-body inhalation exposure would require a large quantity of purified 1-nitropyrene that is expensive and difficult to procure. The study was performed in rats because of technical problems with conducting nose-only inhalation studies in mice and because mice are known to be more resistant to 1-nitropyrene toxicity. In the base study, groups of 10 male and 10 female 7-week-old F344/N rats were exposed to 0, 0.5, 2, 8, 20, or 50 mg/m(3) 1-nitropyrene aerosol, 6 hours per day, 5 days per week, for 13 weeks. At 13 weeks, rats were evaluated for histopathology, clinical pathology, and reproductive system effects. In a supplemental evaluation, toxicokinetic effects were assessed in male F344/N rats exposed to 1-nitropyrene for 13 weeks. All rats survived to the end of the 13-week exposure. For all groups, body weight gains of exposed rats were similar to those of concurrent controls (but lower than those of historical whole body inhalation study control rats); however, liver weights of exposed male rats were higher than those of the controls. There were slight variations in certain hematology and clinical chemistry parameters for some groups, but these were not considered related to 1-nitropyrene exposure. Squamous metaplasia of the respiratory mucosa was observed in the larynx of male rats exposed to 1-nitropyrene at a concentration of 2 mg/m(3) or greater and of female rats at all exposure concentrations. Squamous metaplasia of the bronchial epithelium also occurred in male and female rats in the higher exposure groups. Cytoplasmic alteration of the nasal respiratory epithelium was observed in both sexes exposed to 1-nitropyrene at a concentration of 8 mg/m(3)or greater. No treatment-related effects on sperm motility or vaginal cytology were noted. However, testicular atrophy was observed in all male rats and was considered a secondary effect resulting from the daily confinement within the exposure tubes. The elimination half-life of 1-nitropyrene in the lungs was about 1 hour for rats exposed to 8 mg/m(3)and 6 hours for rats exposed to 50 mg/m(3). Lung burdens of 1-nitropyrene in rats exposed to 8 mg/m(3) remained the same for the 13-week duration; however, lung burdens in rats exposed to 50 mg/m(3) increased with time indicating that the rats were unable to clear the 1-nitropyrene between exposures. The half-life of 1-nitropyrene in the plasma of rats exposed to 50 mg/m(3) was about 1 hour. Based on data contained in this report and previously published reports on the genetic toxicity, carcinogenicity, and toxicokinetics of 1-nitropyrene, it is the opinion of the National Toxicology Program (NTP) that 1-nitropyrene has a high likelihood of being carcinogenic to the respiratory tract, particularly under exposure conditions that lead to significant accumulations of 1-nitropyrene in the lungs, and perhaps other organs of F344/N rats. In summary, nose-only inhalation exposure to 1-nitropyrene for 13 weeks induced squamous metaplasia of the laryngeal and bronchial respiratory epithelium in male and female rats. Cytoplasmic alteration in the nasal respiratory epithelium were also induced in male and female rats. The no-observed-adverse-effect level (NOAEL) for male rats was 0.5 mg/m(3). A NOAEL for female rats could not be determined from these studies. Synonyms: 3-Nitropyrene; Pyrene, 1-nitro.

Journal Article↗

PubMed1997

Nested DNA inversion of Campylobacter fetus S-layer genes is recA dependent.

Wild-type strains of Campylobacter fetus are covered by a monomolecular array of surface layer proteins (SLPs) critical for virulence. Each cell possesses eight SLP gene cassettes, tightly clustered in the genome, that encode SLPs of 97 to 149 kDa. Variation of SLP expression occurs by a mechanism of nested DNA rearrangement that involves the inversion of a 6.2-kb sapA promoter-containing element alone or together with one or more flanking SLP gene cassettes. The presence of extensive regions of identity flanking the 5' and 3' ends of each SLP gene cassette and of a Chi-like recognition sequence within the 5' region of identity suggests that rearrangement of SLP gene cassettes may occur by a generalized (RecA-dependent) homologous recombination pathway. To explore this possibility, we cloned C. fetus recA and created mutant strains by marker rescue, in which recA is disrupted in either S+ or S- strains. These mutants then were assessed for their abilities to alter SLP expression either in the presence or absence of a complementary shuttle plasmid harboring native recA. In contrast to all previously reported programmed DNA inversion systems, inversion in C. fetus is recA dependent.

Bacterial Outer Membrane Proteins↗

PubMed2005

Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program.

Differences in gene expression underlie many of the phenotypic variations between related organisms, yet approaches to characterize such differences on a genome-wide scale are not well developed. Here, we introduce the "differential clustering algorithm" for revealing conserved and diverged co-expression patterns. Our approach is applied at different levels of organization, ranging from pair-wise correlations within specific groups of functionally linked genes, to higher-order correlations between such groups. Using the differential clustering algorithm, we systematically compared the transcription program of the fungal pathogen Candida albicans with that of the model organism Saccharomyces cerevisiae. Many of the identified differences are related to the differential requirement for mitochondrial function in the two yeasts. Distinct regulation patterns of cell cycle genes and of amino acid metabolic genes were also revealed and, in some cases, could be linked to the differential appearance of cis-regulatory elements in the gene promoter regions. Our study provides a comprehensive framework for comparative gene expression analysis and a rich source of hypotheses for uncharacterized open reading frames and putative cis-regulatory elements in C. albicans.

Candida albicans↗

PubMed1999

Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences.

A total of 1000 expressed sequence tags (ESTs) corresponding to 760 unique sequence sets were identified using random sequencing of clones from a cDNA library constructed from mycelial RNA of Phytophthora infestans. A number of software programs, represented by a relational database and an analysis pipeline, were developed for the automated analysis and storage of the EST sequence data. A set of 419 nonredundant sequences, which correspond to a total of 632 ESTs (63.2%), were identified as showing significant matches to sequences deposited in public databases. A putative cellular identity and role was assigned to all 419 sequences. All major functional categories were represented by at least several ESTs. Four novel cDNAs containing sequences related to elicitins, a family of structurally related proteins that induce the hypersensitive response and condition avirulence of P. infestans on Nicotiana plants, were among the most notable genes identified. Two of these elicitin-like cDNAs were among the most abundant cDNAs examined. The set also contained several ESTs with high sequence similarity to unique plant genes.

Actins↗

PubMed2006

Polymorphisms in TGF-beta1 gene and the risk of lung cancer.

BACKGROUND: Transforming growth factor-beta1 (TGF-beta1) functions as a suppressor of tumor initiation by inhibiting cellular proliferation or by promoting cellular differentiation or apoptosis in the early phase of cancer development. Variations in the DNA sequence in the TGF-beta1 gene may lead to altered TGF-beta1 production and/or activity, and so this can modulate an individual's susceptibility to lung cancer. To test this hypothesis, we investigated the association of the TGF-beta1 -509C > T and 869T > C (L10P) polymorphisms and their haplotypes with the risk of lung cancer in a Korean population. METHODS: The TGF-beta1 genotypes were determined in 432 lung cancer patients and in 432 healthy control subjects who were frequency-matched for age and gender. The TGF-beta1 haplotypes were predicted using a Bayesian algorithm in the Phase program. RESULTS: Individuals with at least one -509T allele were at a significantly decreased risk of adenocarcinoma (AC) and small cell carcinoma (SM), as compared with carriers with the -509CC genotype [adjusted odds ratio (OR), 0.63; 95% confidence interval (CI), 0.42-0.96; P = 0.04; and adjusted OR, 0.45; 95% CI, 0.27-0.76; P = 0.002; respectively]. For the 869T > C polymorphism, the combined TC + CC genotype was associated with a significantly decreased risk of SM compared with the TT genotype (adjusted OR, 0.52; 95% CI, 0.31-0.88; P = 0.01). Consistent with the results of the genotyping analyses, the -509T/869C haplotype was associated with a significantly decreased risk of AC and SM as compared with the -509C/869T haplotype (adjusted OR, 0.75; 95% CI, 0.57-0.98; P = 0.04; and adjusted OR, 0.67; 95% CI, 0.47-0.96; P = 0.02; respectively). CONCLUSION: The TGF-beta1 -509C > T and 869T > C polymorphisms and their haplotypes may contribute to genetic susceptibility to AC and SM of the lung.

Adenocarcinoma↗

PubMed2003

Molecular epidemiology of porcine reproductive and respiratory syndrome virus (PRRSV) in Québec.

Porcine reproductive and respiratory syndrome virus (PRRSV) strains identified in samples from 226 field cases originating from Québec herds and submitted over a 4-year period (March 1998-July 2002) were studied. Sequencing of PRRSV strains was performed on the ORF5 gene amplified product and restriction fragment length polymorphism (RFLP) patterns for enzymes MluI, HincII and SacII were determined on these sequences. Twenty-four other PRRSV isolates including three vaccine strains were also included for comparison purposes and the total of 250 PRRSV strains were used in a phylogenetic analysis. Clinical and epidemiological data were collected through a questionnaire for each of the submitted field cases. About 75% of the cases were submitted during autumn and winter. Over 60% of the cases were submitted for reproductive problems, 33% for respiratory problems and 6% for increased PRRSV serological titers in the herd in absence of clinical signs. In 69% of the cases there was a PRRS vaccination program for the herd. However, only 26% of the animals from which samples were obtained had been vaccinated themselves. The genomic analysis of this large number of strains revealed a great variability of PRRSV ORF5 with 59% of amino acid positions being polymorphic. A total of 29 RFLP patterns were obtained. The main RFLP patterns obtained were 1-8-4 (28%), 1-4-4 (16%), 1-2-4 (9%) and 1-11-4 (9%). The global findings derived from the molecular analysis of 226 PRRSV strains suggest that PRRSV circulating in Québec represent a different sub-population of strains. Vaccine-like strains were identified in 10% of the cases. A phylogenetic tree enabled the identification of 44 groupings comprising two to 23 strains each. Of the 250 sequences analyzed, 183 (73%) could be included in one of these groupings. The data collected from the questionnaires were used to establish epidemiological links between strains within groupings. The main relationships between strains within a grouping were the introduction of infected animals (19%) and area spread (33%). In 40% of the cases from which an area spread was suspected, herds were located within 3 km from another. Aerosol transmission was suspected in several cases, more than half of which belonged to different owners. In 41 herds, more than one strain (2-8) were identified over a period varying from 3 months to 4 years. Data indicated that a PRRSV strain can persist in a herd up to 3.5 years displaying as little as 2% variation in ORF5 during this time. In 78% of the herds with multiple submissions genetically different strains were identified; often within 1 year of the original identification. These genetically distinct strains were often associated with a recrudescence of moderate to severe clinical signs. Coexistence on the same farm of different PRRSV strains was also observed.

Animals↗