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PubMed2002

Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and D.

Most HIV-1 infections in Uganda are caused by subtypes A and D. The prevalence of recombination and the sites of specific breakpoints between these subtypes have not been reported. HIV-1 pol sequences encoding protease (amino acids 1-99) and reverse transcriptase (amino acids 1-324) from 102 pregnant Ugandan women were analyzed by the Recombinant Identification Program, SimPlot, and examination of phylogenetically informative sites to identify sites of recombination between sequence segments belonging to different subtypes. Thirteen percent (13 of 102) of the pol sequences contained strong evidence of recombination between subtypes A and D. At least nine different patterns of recombination were observed. Five women infected with a recombinant virus transmitted the recombinant virus perinatally. In this population-based study, intersubtype recombinants were common. The large number of different types of pol recombinants identified suggests that recombination occurs readily in the pol region. Perinatal transmission of the recombinant viruses demonstrates their evolutionary stability.

Databases, Nucleic Acid↗
PubMed1978

Senescence: a stochastic molecular control theory.

A theoretical model of transcriptional control, in a preliminary form, is presented. The model has a critical boundary between a region of values in which the system is stable and essentially self-perpetuating and a region in which the essential macromolecules tend to disappear and not to be regenerated. The possibility of the transition results from cell division. Variation in the values of kinetic parameters or fluctuation in the partition of the macromolecules between the daughter cells of a division subject some cells in the population to the instability. Cells on the wrong side of the critical boundary may accumulate in G2, and will eventually die, at rates and frequencies depending on the specific peculiarities of various cell types (e.g., tissues). Such phenomena, in association with the characteristic division patterns predicted by the theory, have been observed in vitro and in vivo. "Programmed death" in morphogenesis may be an instance. Problems in the future development of the theory are outlined. The significance of clonal selection for atherogenesis and perhaps oncogenesis is noted. The theory is briefly contrasted with "damage" and "error" theories; and the eventual possibility of constructive intervention in ageing at the molecular level is suggested.

Aging↗
PubMed1996

Histone H1 overexpressed to high level in tobacco affects certain developmental programs but has limited effect on basal cellular functions.

Histone H1, a major structural component of chromatin fiber, is believed to act as a general repressor of transcription. To investigate in vivo the role of this protein in transcription regulation during development of a multicellular organism, we made transgenic tobacco plants that overexpress the gene for Arabidopsis histone H1. In all plants that overexpressed H1 the total H1-to-DNA ratio in chromatin increased 2.3-2.8 times compared with the physiological level. This was accompanied by 50-100% decrease of native tobacco H1. The phenotypic changes in H1-overexpressing plants ranged from mild to severe perturbations in morphological appearance and flowering. No correlation was observed between the extent of phenotypic change and the variation in the amount of overexpressed H1 or the presence or absence of the native tobacco H1. However, the severe phenotypic changes were correlated with early occurrence during plant growth of cells with abnormally heterochromatinized nuclei. Such cells occurred considerably later in plants with milder changes. Surprisingly, the ability of cells with highly heterochromatinized nuclei to fulfill basic physiological functions, including differentiation, was not markedly hampered. The results support the suggestion that chromatin structural changes dependent on H1 stoichiometry and on the profile of major H1 variants have limited regulatory effect on the activity of genes that control basal cellular functions. However, the H1-mediated chromatin changes can be of much greater importance for the regulation of genes involved in control of specific developmental programs.

Arabidopsis↗
PubMed2005

Use of autosomal loci for clustering individuals and populations of East Asian origin.

We studied the genetic relationships among East Asian populations based on allele frequency differences to clarify the relative similarities of East Asian populations with a specific focus on the relationships among the Koreans, the Japanese, and the Chinese populations known to be genetically similar. The goal is to find markers appropriate for differentiating among the specific populations. In this study, no prior data existed for Koreans and the markers were selected to differentiate Chinese and Japanese. We typed, using AB TaqMan assays, single-nucleotide polymorphisms (SNPs) at 43 highly selected mostly independent diallelic sites, on 386 individuals from eight East Asian populations (Han Chinese from San Francisco, Han Chinese from Taiwan, Hakka, Koreans, Japanese, Ami, Atayal, and Cambodians) and one Siberian population (Yakut). We inferred group membership of individuals using a model-based clustering method implemented by the STRUCTURE program and population clustering by using computer programs DISTANCE, NEIGHBOR, LSSEARCH, and DRAWTREE, respectively, calculating genetic distances among populations, calculating neighbor-joining and least-squares trees, and drawing the calculated trees. On average 52% of individuals in the three Chinese groups were assigned into one cluster, and, respectively, 78 and 69% of Koreans and Japanese into a different cluster. Koreans differentiated from the Chinese groups and clustered with the Japanese in the principal component analysis (PCA) and in the best least-squares tree. The majority of Koreans were difficult to distinguish from the Japanese. This study shows that a relatively few highly selected markers can, within limits, differentiate between closely related populations.

Asian People↗
PubMed1990

Estimation of direct and maternal genetic variance for litter size in Canadian Yorkshire and Landrace swine using an animal model.

Estimates of additive direct heritability (h2a) for traits such as litter size may be biased by maternal effects. The size of these effects was estimated using a derivative-free restricted maximum likelihood procedure under an animal model. First-parity records from Yorkshire (Y) and Landrace (L) gilts were obtained from the Quebec Record of Performance sow productivity program for 21,127 litters born between 1977 and 1987. Direct (sigma 2a) and maternal (sigma 2m) additive genetic variances, their covariance (sigma am) and error variance (sigma 2e) were estimated for total numbers born (NOBN), born alive (NOBA) and weaned (NOWN). Analysis of purebred Y and crossbred litters indicated that estimates of sigma 2a were of similar magnitude for all traits, with h2a ranging from .06 to .13. Except for L litters, estimates of sigma 2m were relatively low for NOBN and NOBA, and increased in size for NOWN, with h2m ranging from 0 to .08. Also, estimates of sigma am were negative, except for NOBN and NOBA with crossbred litters, and became increasingly negative for NOWN. Results from purebred L litters indicated there was a stronger negative correlation between direct and maternal genetic effects for NOBN and NOBA than for NOWN.

Analysis of Variance↗
PubMed1986

Inheritance of human muscle enzyme adaptation to isokinetic strength training.

Five monozygotic twin pairs were submitted to a 10-week isokinetic strength training program and biochemical characteristics measured before and after training to determine the role of heredity in skeletal muscle adaptation, while 5 unrelated sedentary subjects served as control group. Experimental subjects performed twice 3 series of 5 bilateral reciprocal alternating knee flexions and extensions at a velocity of 90 degrees/s 5 times per week. Before and after the training period, for each subject, the peak muscular torque output was measured at the same velocity and the vastus lateralis muscle was biopsied for biochemical determinations. No significant change was observed in the control group. Training increased peak muscular torque output by 24%. The activities of hexokinase, malate dehydrogenase and 3-hydroxyacyl CoA dehydrogenase also increased significantly by 28, 26 and 38%, respectively. Interindividual variations in the response of these variables to training were noted but these were shown to be independent of the genotype. No overall effect of training was observed for oxoglutarate dehydrogenase activity (OGDH). However, changes were seen in individual pairs of twins and these were in opposite directions in some pairs compared to others, thus explaining the absence of a general training effect. Significant intrapair resemblance in the training response was present for OGDH (r = 0.76), indicating that the sensitivity to isokinetic strength training for OGDH was highly variable, not random and probably genetically determined.

3-Hydroxyacyl CoA Dehydrogenases↗
PubMed2002

NMR structures of two variants of bovine pancreatic trypsin inhibitor (BPTI) reveal unexpected influence of mutations on protein structure and stability.

Here we determined NMR solution structures of two mutants of bovine pancreatic trypsin inhibitor (BPTI) to reveal structural reasons of their decreased thermodynamic stability. A point mutation, A16V, in the solvent-exposed loop destabilizes the protein by 20 degrees C, in contrast to marginal destabilization observed for G, S, R, L or W mutants. In the second mutant introduction of eight alanine residues at proteinase-contacting sites (residues 11, 13, 17, 18, 19, 34, 37 and 39) provides a protein that denatures at a temperature about 30 degrees C higher than expected from additive behavior of individual mutations. In order to efficiently determine structures of these variants, we applied a procedure that allows us to share data between regions unaffected by mutation(s). NOAH/DYANA and CNS programs were used for a rapid assignment of NOESY cross-peaks, structure calculations and refinement. The solution structure of the A16V mutant reveals no conformational change within the molecule, but shows close contacts between V16, I18 and G36/G37. Thus, the observed 4.3kcal/mol decrease of stability results from a strained local conformation of these residues caused by introduction of a beta-branched Val side-chain. Contrary to the A16V mutation, introduction of eight alanine residues produces significant conformational changes, manifested in over a 9A shift of the Y35 side-chain. This structural rearrangement provides about 6kcal/mol non-additive stabilization energy, compared to the mutant in which G37 and R39 are not mutated to alanine residues.

Amides↗
PubMed2001

[Preliminary study on cytochrome C oxidase 1 gene of Oncomelania hupensis from Miao River area in Hubei province].

OBJECTIVE: To study the mitochondrial cytochrome C oxidase 1(CO1) gene of Oncomelania snails from Miao River area in Hubei Province. METHODS: Oncomelania snails were collected from Miao River area, including upstream and downstream. Genomic DNA was extracted from the tissue of the snail. PCR was used to amplify a fragment of the CO1 gene. Sequences of the CO1 fragment were determined directly from the purified PCR products by an automated sequencer. Sequences for each individual were assembled and edited using ESEE 3.0 s. A distance matrix was computed using program DNADISt of PHYLIP(3.57). Unrooted maximum likelihood trees were calculated from program FITCH. RESULTS: The amplified CO1 gene of the snail was a fragment of 638 bp in length. Sequence analysis showed that the accumulated variable sites were significant different between upstream and downstream populations, being 29 and 46, respectively. From the number of variable sites in the gene, snails in this area were roughly separated into two groups. Each of them was a mixture of both upstream and downstream snails. Same haplotypes were confirmed to be present among the collected sites along the river. From the distance matrix of sequence divergence, the population upstream vs downstream differed by 0.0221 +/- 0.0105. CONCLUSION: There were more variation in downstream population than that in upstream. Gene flow was identified in these populations. The phylogenetic trees suggest the existence of two groups, but all of them belong to 0. h. hupensis.

Animals↗
PubMed1994

A theoretical study of the socioecology of ungulates. II. A dynamic programming study of the stochastic formulation.

We develop a stochastic version of a previously discussed model of optimal herd size selection in ungulates. We assume that a large herd size confers to the animals a high level of protection against predators, but reduces the amount of food which can be eaten by each individual; on the contrary animals belonging to small herds would have access to large amounts of food but would bear a high risk of being killed by predators. Employing a dynamic programming approach we analyze the optimal trade-off between starvation and predation risks under the hypothesis that the animals would try to maximize their expected reproductive fitness during the incoming breeding period. We compare the optimal strategy in environments described by different kinds of stochastic food distributions (including the deterministic limit) for different values of predation pressure and of overall food availability. We obtain general information about the effect of the level of randomness of food distribution on the mean individual fitness and on the number of reproducers (the animals which survive to the beginning of the reproductive season). Moreover we discuss how a certain number of behavioral and ecological processes--which have been often described in natural populations of ungulates and which are usually explained in terms of phenological variations of the ecological landscape--may be interpreted as caused by intrinsic variations of the animals' strategy.

Animal Nutritional Physiological Phenomena↗
PubMed2006

Heart rate recovery after maximal exercise is associated with acetylcholine receptor M2 (CHRM2) gene polymorphism.

The determinants of heart rate (HR) recovery after exercise are not well known, although attenuated HR recovery is associated with an increased risk of cardiovascular mortality. Because acetylcholine receptor subtype M2 (CHRM2) plays a key role in the cardiac chronotropic response, we tested the hypothesis that, in healthy individuals, the CHRM2 gene polymorphisms might be associated with HR recovery 1 min after the termination of a maximal exercise test, both before and after endurance training. The study population consisted of sedentary men and women (n = 95, 42 +/- 5 yr) assigned to a training (n = 80) or control group (n = 15). The study subjects underwent a 2-wk laboratory-controlled endurance training program, which included five 40-min sessions/wk at 70-80% of maximal HR. HR recovery differed between the intron 5 rs324640 genotypes at baseline (C/C, -33 +/- 10; C/T, -33 +/- 7; and T/T, -40 +/- 11 beats/min, P = 0.008). Endurance training further strengthened the association: the less common C/C homozygotes showed 6 and 12 beats/min lower HR recovery than the C/T heterozygotes or the T/T homozygotes (P = 0.001), respectively. A similar association was found between A/T transversion at the 3'-untranslated region of the CHRM2 gene and HR recovery at baseline (P = 0.025) and after endurance training (P = 0.005). These data suggest that DNA sequence variation at the CHRM2 locus is a potential modifier of HR recovery in the sedentary state and after short-term endurance training in healthy individuals.

Adaptation, Physiological↗
PubMed1995

Exploratory analysis of population genetic assessment as a water quality indicator. I. Pimephales notatus.

Biological sampling has been implemented to assess water quality in many states. The purpose of this study was to examine whether genetic diversity and structure of Pimephales notatus could serve as effective biomarkers of exposure to anthropogenic stressors by comparing genetic measures with other biological indicators of water quality. Fish were collected from 15 sites on eight streams by the Ohio Environmental Protection Agency as part of their stream water quality evaluation program. Values for the Index of Biotic Integrity (IBI) and the Invertebrate Community Index (ICI) were determined for these 15 sites. Starch gel electrophoresis was used to collect genetic data for seven variable enzyme loci. Genetic diversity measures were not associated with site IBI or ICI values. However, the range of site IBI and ICI values was limited. The proportion of individuals not expressing esterase locus 3 could be used to predict IBI; IBI decreased as the proportion of nonexpression increased. Allele and genotype frequency differences were observed between sites on the Little Scioto River, the one stream with a large difference in IBI and ICI values between sites. This study suggested that allele and genotype frequencies may have been impacted without affecting overall species diversity.

Alleles↗
PubMedDate not supplied

[Concept of the effect of low doses of ionizing radiation on cells and its possible use in the interpretation of medical-biological consequences].

A concept is proposed where the events induced by low doses of ionizing radiation with low linear energy transfer have different script than those induced by high doses. Its essence consist in the existence of a small fraction (subpopulation) in clonal heterogeneous population whose cells are determined for a specific programmed response induced by a number of action that are potentially able (at high doses) to decrease the survival of the given population. The function of the postulated cell is a deliberate sacrifice necessary for formation of evolutionary reserve. A mechanism of this response is based on an autogeneration of wide-scale genome rearrangements in cells and is not connected with direct influence of genetically hazardous agents on DNA. This leads to arising of a number of genetic variants (evolutionary reserve cells). Selection among them enhancing survival of the population may in the same time lead to harmful consequences for the organism (if there are malfunctions of the immune system). Medical-biological consequences of the effect of low doses are associated with the appearance of such clones and biologically active products secreted from the exposed cells. Mechanisms responsible for the above phenomena are discussed.

Cell Nucleus↗
PubMed2000

Body weight and tail length divergence in mice selected for rate of development.

A series of mouse lines has been produced by 19 generations of restricted index selection for rate of development during early and late ontogeny. The selection program was based on an index with the following four replicated selection treatments: E(+) and E(-) were selected to alter birth to 10-day body weight gain while holding late gain for both selection lines constant; correspondingly, L(+) and L(-) were selected to alter 28- to 56-day body weight gain holding early gain for both lines constant. Herein, we characterize response to selection for growth rate by analyzing age-specific mouse body weight and tail lengths and for growth curves using a logistics model. Selection on developmental rate has resulted in divergence in both age-specific and growth curve traits. E(+) and L(+) lines reached identical weights during the late selection interval, then diverged to unique mature weights. E(-) and L(-) lines similarly achieved identical weights during late selection and diverged to unique mature weights. However, the shapes of early and late growth curves were significantly divergent, and at least two distinct growth patterns are shown to result from selection. Response in body weight gain was accompanied by similar, though less pronounced, change in tail length traits. Significant response during intervals of restricted growth was also found, especially in lines selected for late gain. The evolution of the growth trajectory under restricted index selection is discussed in terms of drift and available additive genetic variation and covariation.

Aging↗
PubMed2006

Novel DNA variations to characterize low molecular weight glutenin Glu-D3 genes and develop STS markers in common wheat.

Low-molecular-weight glutenin subunits (LMW-GS) play an important role in bread and noodle processing quality by influencing the viscoelasticity and extensibility of dough. The objectives of this study were to characterize Glu-D3 subunit coding genes and to develop molecular markers for identifying Glu-D3 gene haplotypes. Gene specific primer sets were designed to amplify eight wheat cultivars containing Glu-D3a, b, c, d and e alleles, defined traditionally by protein electrophoretic mobility. Three novel Glu-D3 DNA sequences, designated as GluD3-4, GluD3-5 and GluD3-6, were amplified from the eight wheat cultivars. GluD3-4 showed three allelic variants or haplotypes at the DNA level in the eight cultivars, which were designated as GluD3-41, GluD3-42 and GluD3-43. Compared with GluD3-42, a single nucleotide polymorphism (SNP) was detected for GluD3-43 in the coding region, resulting in a pseudo-gene with a nonsense mutation at the 119th position of deduced peptide, and a 3-bp insertion was found in the coding region of GluD3-41, leading to a glutamine insertion at the 249th position of its deduced protein. The coding regions for GluD3-5 and GluD3-6 showed no allelic variation in the eight cultivars tested, indicating that they were relatively conservative in common wheat. Based on the 12 allelic variants of three Glu-D3 genes identified in this study and three detected previously, seven STS markers were established to amplify the corresponding gene sequences in wheat cultivars containing five Glu-D3 alleles (a, b, c, d and e). The seven primer sets M2F12/M2R12, M2F2/M2R2, M2F3/M2R3, M3F1/M3R1, M3F2/M3R2, M4F1/M4R1 and M4F3/M4R3 were specific to the allelic variants GluD3-21/22, GluD3-22, GluD3-23, GluD3-31, GluD3-32, GluD3-41 and GluD3-43, respectively, which were validated by amplifying 20 Chinese wheat cultivars containing alleles a, b, c and f based on protein electrophoretic mobility. These markers will be useful to identify the Glu-D3 gene haplotypes in wheat breeding programs.

Alleles↗
PubMed1993

Development of an animal model for across-herd genetic evaluation of number born alive in swine.

An animal model and computer software were developed to conduct across-herd genetic evaluations using data from producers participating in the Sow Productivity Index program of the American Yorkshire Club. The final data set consisted of 61,596 litter records from 1986 to early 1990. The animal model included fixed contemporary group effects and random additive direct, service sire, permanent environmental, and residual effects. Additive genetic relationships among animals were included. A separate relationship matrix for service sires and their sires was also included. A data set similar to the Yorkshire field data was simulated to use in testing the animal model. The simulated data set consisted of 40 herds, each with 120 reproducing dams and either four or five sires. Six generations of simulated data were produced, resulting in 20,605 litter records. These records were then evaluated using the animal model for number of pigs born alive. Finally, correlations between the true breeding values from the simulation and the predicted breeding values were computed. The correlation between the 918 true and predicted sire breeding values was considerably lower for the animal model without a service sire effect than when it was included (.53 vs .74, respectively). However, the difference was cut in half (.66 vs .77) when only sires with greater than five daughter records were included. The high accuracy of the animal model with a random service sire effect indicates that the proposed model adequately accounts for the variation found in records for number of pigs born alive.

Animals↗
PubMed2006

[Comparison of nucleotide and deduced amino acid sequences of E gene of the newly isolated Japanese encephalitis virus strains and inactivated vaccine strain P3].

BACKGROUND: To analyze the difference of nucleotides and deduced amino acids sequences E gene between the newly isolated Japanese encephalitis (JE) virus strains from mosquitoes or patients and P3 strain. METHODS: The E gene sequences of corresponding strains of JE virus were obtained from GenBank. Computer analyze of nucleic acid data and deduced amino acid sequence were accomplished using the Clustal X (1.8), DNASTAR, GENEDOC (3.2) programs. RESULTS: The result showed that compared with the Fujian strains and P3 strain the nucleotide sequence homology was up to 98.3%, and the amino acid sequence homology was up to 98.2%, respectively. Compared with the Shanghai strains and P3 strain, the nucleotide sequence differences were 12%, and the amino acid sequence homology was up to 98.2%, respectively. Compared with P3 strain, there were nineteen amino acid variations in E gene of all the newly isolated strains. Between P3 and all the newly isolated JE virus strains, there are three common variations at E-129, E-222, E-366. And two common variations E-160 and E-487 were found only in Fujian strains, common variations at E-129, E-222, E-227, E-366 in Shanghai strains. CONCLUSION: There are some differences between P3 strain and JE viruses which were isolated from mosquitoes belonging to genotype I in Shanghai and from patients belonging to genotype III from Fujian province. But these variations are not in the important locations affecting the biological characteristic of the viruses.

Amino Acid Sequence↗
PubMed1992

Evidence for orthologous seed weight genes in cowpea and mung bean based on RFLP mapping.

A well saturated genomic map is a necessity for a breeding program based on marker assisted selection. To this end, we are developing genomic maps for cowpea (Vigna unguiculata 2N = 22) and mung bean (Vigna radiata 2N = 22) based on restriction fragment length polymorphism (RFLP) markers. Using these maps, we have located major quantitative trait loci (QTLs) for seed weight in both species. Two unlinked genomic regions in cowpea contained QTLs accounting for 52.7% of the variation for seed weight. In mung bean there were four unlinked genomic regions accounting for 49.7% of the variation for seed weight. In both cowpea and mung bean the genomic region with the greatest effect on seed weight spanned the same RFLP markers in the same linkage order. This suggests that the QTLs in this genomic region have remained conserved through evolution. This inference is supported by the observation that a significant interaction (i.e., epistasis) was detected between the QTL(s) in the conserved region and an unlinked RFLP marker locus in both species.

Fabaceae↗
PubMed1995

Glial transplants: an in vivo analysis of extrinsic and intrinsic determinants of dysmyelination in genetic variants.

Myelination in the CNS depends on the ability of oligodendrocytes (Ols) to efficiently colonize the brain, differentiate, and express a precise balance of specific genes necessary for myelin synthesis. Mutations in these genes produce different types of dysmyelination in animal as in human. Defects in the synthesis of myelin constituents usually lead to mild dysmyelinations. IN contrast, mutations affecting the gene encoding the proteolipid, another major protein of myelin, produce various perturbations of Ols biology suggesting a pleiotropic effect of the gene in the development of the CNS. Studies on expansion of cell population and survival have provided contradictory information on the extrinsic and intrinsic action of the gene on Ols biology. On one hand, in vitro studies using conditioned media as in vivo studies on heterozygotes, and transplantations experiments suggest that excess of programmed cell death in these mutants is ruled out by intrinsic factors which could act during embryonic life. On the other hand, attempts to compensate the gene defect by transgenic correction demonstrate a dominant negative effect of the jp mutation on both survival and functional potential of Ols. Finally, total suppression of PLP gene expression has a restricted effect on myelin structure without excess of cell death. These contradictory results are discussed in the perspective of regulation of cell death by competition for growth factors in limiting amount. The proposed model suggests that this contradiction is only apparent, and that excess of cell death in PLP/DM20 mutant is intrinsically determined by diminished competitivity of the mutant Ols for limited amounts of environmental factors.

Animals↗