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PubMed2005

Study on genetic diversity of Magnaporthe grisea using PCR and determination of the mating type alleles distribution in Mazandaran province, Iran.

The population structure of Magnaporthe grisea, the causal agent of the rice blast, was analyzed in Mazandaran province, using DNA fingerprinting based on RAPD-PCR by means of three primers including "I", "D" and "H". Total DNA of 47 isolates was extracted and amplified according to a specific PCR program. As a result, variable length fragments were generated. Each isolate was subjected to DNA fingerprinting and clonal lineages were determined. Phenetic analysis differentiated three distinct fingerprint lineages. In order to study on fertility status and distribution of the mating type idiomorphs (alleles), 72 monoconidial isolates from Mazandaran province were paired with four standard fertile hermaphrodite isolates. The mating type of 36 isolates was determined as Mat 1-1. The others (36 isolates) did not form any perithecia in pairing with standard isolates

DNA Fingerprinting↗
PubMed2004

Catalase deficiency drastically affects gene expression induced by high light in Arabidopsis thaliana.

In plants, hydrogen peroxide (H(2)O(2)) plays a major signaling role in triggering both a defense response and cell death. Increased cellular H(2)O(2) levels and subsequent redox imbalances are managed at the production and scavenging levels. Because catalases are the major H(2)O(2) scavengers that remove the bulk of cellular H(2)O(2), altering their levels allows in planta modulation of H(2)O(2) concentrations. Reduced peroxisomal catalase activity increased sensitivity toward both ozone and photorespiratory H(2)O(2)-induced cell death in transgenic catalase-deficient Arabidopsis thaliana. These plants were used as a model system to build a comprehensive inventory of transcriptomic variations, which were triggered by photorespiratory H(2)O(2) induced by high-light (HL) irradiance. In addition to an H(2)O(2)-dependent and -independent type of transcriptional response during light stress, microarray analysis on both control and transgenic catalase-deficient plants, exposed to 0, 3, 8, and 23 h of HL, revealed several specific regulatory patterns of gene expression. Thus, photorespiratory H(2)O(2) has a direct impact on transcriptional programs in plants.

Arabidopsis↗
PubMed2002

Control of developmental timing by micrornas and their targets.

In Caenorhabditis elegans the timing of many developmental events is regulated by heterochronic genes. Such genes orchestrate the timing of cell divisions and fates appropriate for the developmental stage of an organism. Analyses of heterochronic mutations in the nematode C. elegans have revealed a genetic pathway that controls the timing of post-embryonic cell divisions and fates. Two of the genes in this pathway encode small regulatory RNAs. The 22 nucleotide (nt) RNAs downregulate the expression of protein-coding mRNAs of target heterochronic genes. Analogous variations in the timing of appearance of particular features have been noted among closely related species, suggesting that such explicit control of developmental timing may not be exclusive to C. elegans. In fact, some of the genes that globally pattern the temporal progression of C. elegans development, including one of the tiny RNA genes, are conserved and temporally regulated across much of animal phylogeny, suggesting that the molecular mechanisms of temporal control are ancient and universal. A very large family of tiny RNA genes called microRNAs, which are similar in structure to the heterochronic regulatory RNAs, have been detected in diverse animal species and are likely to be present in most metazoans. Functions of the newly discovered microRNAs are not yet known. Other examples of temporal programs during growth include the exquisitely choreographed temporal sequences of developmental fates in neurogenesis in Drosophila and the sequential programs of epidermal coloration in insect wing patterning. An interesting possibility is that microRNAs mediate transitions on a variety of time scales to pattern the activities of particular target protein-coding genes and in turn generate sets of cells over a period of time. Plasticity in these microRNA genes or their targets may lead to changes in relative developmental timing between related species, or heterochronic change. Instead of inventing new gene functions, even subtle changes in temporal expression of pre-existing control genes can result in speciation by altering the time at which they function.

Animals↗
PubMed1976

Response to selection for hatchability in turkeys at three altitudes.

Eggs from a commerical flock of Small White turkeys established at 76 meters above sea level were used to develop five lines of turkeys. Hatchability of fertile eggs was the only criterion used to establish selected lines at 76, 1524, and 2182 meters. Control lines were maintained at the 76 and 1524-meter locations. The objective of this study was to evaluate effects of the selection program on organ weights, body weight, and packed cell volumes (PCV). For two generations, eggs from one hatch at each of the three elevations were divided into three groups, two of which were exchanged for hatching and rearing. Twenty poults from the five lines at all three locations were sacrificed at 1-day, 2-weeks, and 4-weeks of age. Heart. liver spleen, adrenals, pancreas, lungs, kidneys, and gonads were removed, weighed, and the weight expressed as a percent of body weight. Blood samples were collected and PCV values determined at ages 1-day, 2-weeks, and 4-weeks at the 1524-meter elevation. Selection for hatchability had no adverse effect upon 1-day, 2, and 4-week body weights. Variations in body weight between locations were not due to natural environmental conditions, but rather to variations in management. Selection for hatchability coupled with natural selection resulted in the development of lines of turkeys with higher PCV values than the original control population. Exposure of turkey poults from the five genetic lines developed at an altitude of 2182 meters lead to an increase in relative weights of the heart and adrenal glands compared to birds at the 76 and 1524-meter locations. Exposure at the 2182-meter location also resulted in lighter spleens, pancreata, kidneys, and ovaries compared to birds at the 76 and 1524-meter locations. Selection for hatchability favors larger adrenals, livers, pancreata, kidneys, and lungs, but smaller hearts. Natural selection at higher elevations compounds the situation by favoring smaller adrenals and livers, but larger spleens, pancreata, and kidneys.

Altitude↗
PubMed1997

The epidemiology of soft tissue sarcoma.

Soft tissue sarcoma (STS) accounts for approximately 1% of all cancers diagnosed annually in the United States. Population-based data from Connecticut covering the years 1935-1989 have shown an increasing incidence of STS in both genders, with a greater increase among men than women. The recent increase in acquired immune deficiency syndrome-related Kaposi's sarcoma does not explain the upward trend in STS, dating back decades. Etiologic heterogeneity is suggested by epidemiologic variations that have been observed by subsite and cell type. Among the environmental factors associated with STS are external radiation therapy, Thorotrast, arsenical pesticides and medications, phenoxyherbicides, dioxin, vinyl chloride, immunosuppressive drugs, alkylating agents, androgen-anabolic steroids, human immunodeficiency virus, and human herpes virus type 8. In addition, STS occurs excessively among persons with certain heritable states including retinoblastoma, Li-Fraumeni syndrome, Gardner's syndrome, Werner's syndrome, nevoid basal cell carcinoma syndrome, neurofibromatosis type 1, and some immunodeficiency syndromes. These risk factors account for a minority of STS cases but provide leads for further epidemiologic and interdisciplinary studies into the genetic and environmental determinants of various forms of STS.

Environmental Exposure↗
PubMed2004

A bioeconomic approach to derive economic values for pasture-based sheep genetic improvement programs.

Economic values for a range of different maternal and carcass sheep performance traits were derived for hill sheep in the United Kingdom. A bioeconomic model that includes estimates of available energy supply and herbage intake for sheep from hill and mountain pastures, together with that from improved grassland, has provided a base from which to define the economic limitations to genetic improvement in harsh environments. The degree to which different farm systems can accommodate changes in animal performance as a result of genetic improvement was explored. Results showed that genetic improvement in harsh environments is likely to be of greater benefit to farms with fewer constraints to improvements in production, such as better quality pasture or a higher ratio of improved grassland to hill pasture. For farm types in the harshest locations, the economic value of improving litter size was only positive within defined production limits. Increasing litter size beyond these limits resulted in diminishing marginal returns because the costs of additional inputs outweighed the benefits of extra returns. Results also showed that relative improvements in maternal characteristics are at least as economically important as improvements in lamb carcass quality. The effects of variation in market prices on economic values for the major costs and returns of the sheep enterprises showed that, in general, economic values are robust. The methodology described could be adapted and applied to other extensive sheep systems worldwide.

Animal Feed↗
PubMed1984

A non-motile Salmonella mutant (6, 7:-:-) and two serological variants encountered in Saudi Arabia.

A non-motile mutant of Salmonella group C1 and two serological variants were isolated during the performance of a national Salmonella surveillance program in Saudi Arabia. Most of the biochemical reactions of the strains conformed to those of the genus Salmonella except for some atypical reactions. The three strains exhibited different susceptibility patterns to 21 antimicrobial agents. The serological analysis revealed the following antigenic structures: 1, 4, 12, 27:b: - Salmonella sofia var. monophasic; 1, 42:z4, z23: - Salmonella gera var. monophasic and a Salmonella strain reported as a non-motile strain of group C1 by the World Health Organization International Collaborating Center for Reference and Research on Salmonella.

Animals↗
PubMed1995

Analysis of annual Medicago species using RAPD markers.

Annual species of the genus Medicago have attracted interest as green manure and temporary forage crops. This study was conducted to determine if randomly amplified polymorphic DNA (RAPD) markers could be used to assess the variability within and among species. Several accessions of each six species (M. scutellata Mill., M. disciformis DC., M. murex Willd., M. truncatula Gaertn., M. polymorpha L., and M. rugosa Desr.) were studied. A phylogeny reconstructed with the computer program Phylogenetic Analysis Using Parsimony (PAUP) showed the same relationships as traditional taxonomy. Variation was present among accessions of all species. Several accessions were considerably different from others within the species (one of each M. scutellata and M. polymorpha) and four accessions of M. murex were differentiated by both morphology and RAPD banding patterns from the other accessions. These accessions may be useful to include in a core collection. Variation within accessions was present. Although the species are autogamous, the original seed collections may have been made from a number of plants in the same area. Also, some outcrossing or seed mixing may have occurred. Finally, at least 10 RAPD primers appear to be necessary in order to develop reliable estimates of relatedness among annual Medicago accessions.

Base Sequence↗
PubMed1988

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids.

An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment. Central to this approach is the definition of a function describing simultaneously the curvature of the nucleic acid segment in question and the corresponding stepwise variation of helicoidal parameters along the segment. Minimisation of this function leads to an optimal distribution of the conformational irregularity of the segment between these two components. Further, it is shown that this approach can be applied equally easily to single or double stranded nucleic acids. The results of this analysis yield both the absolute helicoidal parameters of individual bases/base pairs and the relative helicoidal parameters between successive bases/base pairs as well as the overall locus of the helical axis. The possibilities of this mathematical approach are demonstrated with the help of a computer program termed "Curves" which is applied to the study of a number of different nucleic acid structures.

Algorithms↗
PubMed2006

Allele frequency misspecification: effect on power and Type I error of model-dependent linkage analysis of quantitative traits under random ascertainment.

BACKGROUND: Studies of model-based linkage analysis show that trait or marker model misspecification leads to decreasing power or increasing Type I error rate. An increase in Type I error rate is seen when marker related parameters (e.g., allele frequencies) are misspecified and ascertainment is through the trait, but lod-score methods are expected to be robust when ascertainment is random (as is often the case in linkage studies of quantitative traits). In previous studies, the power of lod-score linkage analysis using the "correct" generating model for the trait was found to increase when the marker allele frequencies were misspecified and parental data were missing. An investigation of Type I error rates, conducted in the absence of parental genotype data and with misspecification of marker allele frequencies, showed that an inflation in Type I error rate was the cause of at least part of this apparent increased power. To investigate whether the observed inflation in Type I error rate in model-based LOD score linkage was due to sampling variation, the trait model was estimated from each sample using REGCHUNT, an automated segregation analysis program used to fit models by maximum likelihood using many different sets of initial parameter estimates. RESULTS: The Type I error rates observed using the trait models generated by REGCHUNT were usually closer to the nominal levels than those obtained when assuming the generating trait model. CONCLUSION: This suggests that the observed inflation of Type I error upon misspecification of marker allele frequencies is at least partially due to sampling variation. Thus, with missing parental genotype data, lod-score linkage is not as robust to misspecification of marker allele frequencies as has been commonly thought.

Alleles↗
PubMed2006

Evidence of structural genomic region recombination in Hepatitis C virus.

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. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there have been few studies reporting recombination on natural populations of HCV. Recombination break-points have been identified in non structural proteins of the HCV genome. Given the implications that recombination has for RNA virus evolution, it is clearly important to determine the extent to which recombination plays a role in HCV evolution. In order to gain insight into these matters, we have performed a phylogenetic analysis of 89 full-length HCV strains from all types and sub-types, isolated all over the world, in order to detect possible recombination events. METHOD: Putative recombinant sequences were identified with the use of SimPlot program. Recombination events were confirmed by bootscaning, using putative recombinant sequence as a query. RESULTS: Two crossing over events were identified in the E1/E2 structural region of an intra-typic (1a/1c) recombinant strain. CONCLUSION: Only one of 89 full-length strains studied resulted to be a recombinant HCV strain, revealing that homologous recombination does not play an extensive roll in HCV evolution. Nevertheless, this mechanism can not be denied as a source for generating genetic diversity in natural populations of HCV, since a new intra-typic recombinant strain was found. Moreover, the recombination break-points were found in the structural region of the HCV genome.

Evolution, Molecular↗
PubMed1977

Congenital malformations in pigs in a post mortem material.

Pigs which died during the preweaning period in 17 herds were examined post mortem over a 2-year period. In total 6,669 pigs, including 1,884 stillborn, from 2,936 litters died. The total number of pigs born constituted 29,886. Congenital malformations were registered in 410 pigs equalizing 1.4 per cent of the pigs born (Table I). The various malformations were analysed and related to a number of herd parameters. The herd to herd variation was 0.6--2.4 per cent, with a mean of 1.4 per cent. The incidence of affected litters was 11.8 per cent, showing a variation between the herds of 6.4 to 17.6 per cent. The frequency of malformed pigs was found to be higher in closed herds as compared to herds in which breeding stock was purchased (1.6 per cent versus 1.2 per cent). The relative importance of the various malformations is presented in Table II. The individual malformations are discussed, and it is concluded that the present investigation cannot contribute to a further genetical elucidation. Test matings with closely related animals, which is unrealizable in commercially run herds, are needed for that purpose. About 70 per cent of the recorded malformations appeared as phenotypic and could easily be recognized by a laid person. Malformations may therefore persist on a fairly low level as long as natural insemination is used. The present level of hereditary malformations may easily change with an increasing use of artificial insemination, and systematic monitoring of malformations becomes imperative in avoiding an unacceptable increase in the frequency of malformations. In processing collected data from sow/litter records and boar records, the data processing program applied in this study is supposed to be suitable.

Anal Canal↗
PubMed2005

Evaluation of the Bio-Rad VARIANT II HbA2/HbA1C Dual Program for measurement of hemoglobin concentrations and detection of variants.

In this work data obtained on the VARIANT II hemoglobin analyzer using the Dual Kit elution system were compared to those obtained with the beta-Thalassemia Short Program. Since many laboratories still use an earlier model of the hemoglobin analyzer, the Variant 1, these data were also compared to those obtained with the latter instrument. Our study is divided into two parts. The first is an evaluation of the precision of the VARIANT II for determining the levels of hemoglobin (Hb)A2 and Hb F. This was carried out for normal subjects, thalassemic patients and patients with HbS. The second part concerns the potential of this instrument in the presumptive identification of Hb variants.

Fetal Hemoglobin↗
PubMed2002

Molecular typing of Mycobacterium tuberculosis strains with a common two-band IS6110 pattern.

We conducted a program of population-based molecular typing of all Mycobacterium tuberculosis isolates obtained in Alabama since 1994. Of 2452 isolates, 1013 (41%) had fewer than 6 bands of IS6110; 348 (14%) had a single two-band pattern (JH2). With conventional epidemiologic methods, we identified three groups of related patients with JH2 isolates. Spoligotyping and pattern of variable number of tandem repeats identified 10 molecular groups; two found by conventional methods were subdivided.

Alabama↗
PubMed2004

Maternal constraint of fetal growth and its consequences.

The major non-genetic factor determining the size of the fetus at term is maternal constraint. This term refers to a set of poorly defined processes by which maternal and uteroplacental factors act to limit the growth of the fetus, presumably by limiting nutrient availability and/or the metabolic-hormonal drive to grow. Maternal constraint can be divided into supply-limited constraint (e.g. maternal size) and demand-driven constraint (e.g. twinning). Maternal constraint acts in all pregnancies, but is greater in some situations, particularly those involving young maternal age, small maternal size, nulliparous and multiple pregnancies. Maternal constraint is an important physiological cause of the variation in birth size, but is not without longer-term consequences. There is increasing evidence that maternal constraint is an important factor in determining the increased risk of adult diseases in those who have poor fetal growth due to pathophysiological factors. The evidence is reviewed and placed in the context of discussing the evolutionary significance of maternal constraint. The role of predictive adaptive responses as the basis of programming, and the effects of maternal constraint on these responses are discussed. Changing demography means that maternal constraint must increasingly be considered as a significant factor in determining the pattern of disease.

Adolescent↗
PubMed2004

[Trends in genetic diversity change of spring bread wheat cultivars released in Russia in 1929-2003].

Using genealogy analysis, we studied genetic diversity of 340 cultivars of spring bread wheat that were released on the territory of Russia in 1929-2003. Trends in the temporal change of genetic diversity were inferred from analysis of a set of n x m matrices, where n is the number of the released cultivars and m is the number of original ancestors. The pool of original ancestors of the spring bread wheat cultivars for the total period of study included 255 landraces, of which 88 were from the former USSR and modern Russia. The original ancestors showed great differences in their presence in the cultivar sets examined and, consequently, in their importance for the gene pool of Russian spring wheats. The distributions of contributions of dominant original ancestors to cultivar diversity were significantly different in different regions, indicating that the ancestors were specific for the cultivation conditions. During the last 75 years, the genetic diversity of the spring bread wheat cultivars has been increasing owing to the wide use of foreign material in Russian breeding programs. However, our analysis showed that about 60 landraces, including the Russian ones, were lost during the studied time period. The lost part makes up 35% of the gene pool of the Russian original ancestors. It is reasonable to assume that the lost landraces carried a gene complex f or adaptation to specific Russian environments. Specificity of the contributions of the original ancestors in the sets of cultivars produced in different breeding centers was established. A comparative analysis of genetic similarity of cultivars was carried out using coefficients of parentage. Significant differences in this parameter between breeding institutes and regions of cultivation were revealed.

Cluster Analysis↗
PubMed2005

Ivermectin imposes selection pressure on P-glycoprotein from Onchocerca volvulus: linkage disequilibrium and genotype diversity.

Widespread use of ivermectin (IVM) as part of the Onchocerciasis Control Program (OCP) in West Africa could influence the evolution of the human filarial parasite Onchocerca volvulus. Use of IVM, in some areas for 15 years, may have restricted genetic diversity of O. volvulus, resembling effects attributed to a population bottleneck. Large population-based chemotherapy programmes, such as the OCP, may impose strong selection pressure on parasites and an examination of possible genetic selection by IVM in O. volvulus is warranted. IVM is a substrate for P-glycoprotein; a homologue from O. volvulus (OvPGP) has been linked with IVM sensitivity. Linkage disequilibrium (LD) patterns of 28 genetic markers spanning the OvPGP locus were examined in 4 O. volvulus populations from the Volta Region of Ghana, West Africa. Reduced gene diversity, increased heterozygosity and an increase in the number of markers not in Hardy-Weinberg equilibrium were associated with increasing IVM treatment. The number of regions in LD decreased with treatment and with time. However, between 1999 and 2002, seven regions of OvPGP were always in complete LD, while surrounding areas showed a reduction in genetic variation. The use of IVM for onchocerciasis control has imposed strong selection on O. volvulus populations, reducing genetic variation and disrupting LD.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2006

Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: alternative structures, developmental expression, and biophysical variations.

We describe the regulated transcriptome of CACNA1G, a human gene for T-type Ca(v)3.1 calcium channels that is subject to extensive alternative RNA splicing. Fifteen sites of transcript variation include 2 alternative 5'-UTR promoter sites, 2 alternative 3'-UTR polyadenylation sites, and 11 sites of alternative splicing within the open reading frame. A survey of 1580 fetal and adult human brain full-length complementary DNAs reveals a family of 30 distinct transcripts, including multiple functional forms that vary in expression with development. Statistical analyses of fetal and adult transcript populations reveal patterns of linkages among intramolecular splice site configurations that change dramatically with development. A shift from nearly independent, biased splicing in fetal transcripts to strongly concerted splicing in adult transcripts suggests progressive activation of multiple "programs" of splicing regulation that reorganize molecular structures in differentiating cells. Patch-clamp studies of nine selected variants help relate splicing regulation to permutations of the gating parameters most likely to modify T-channel physiology in expressing neurons. Gating behavior reflects combinatorial interactions between variable domains so that molecular phenotype depends on ensembles of coselected domains, consistent with the observed emergence of concerted splicing during development. We conclude that the structural gene and networks of splicing regulatory factors define an integrated system for the phenotypic variation of Ca(v)3.1 biophysics during nervous system development.

Alternative Splicing↗