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Results for “programmed genetic variation”

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PubMed1991

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↗
PubMed2001

Toward a new synthesis: population genetics and evolutionary developmental biology.

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.

Adaptation, Biological↗
PubMed1994

Random amplified polymorphic DNA polymerase chain reaction (RAPD PCR) fingerprints in forensic species identification.

The random amplified polymorphic DNA (RAPD) method was used to identify the species of forensic biological samples. Neither genomic DNA sequence nor two polymerase chain reaction (PCR) cycle programs is required. Only single 10-nt primer and one PCR program are used. We demonstrated that this method can be used to identify animals including bovine, goat, pig, dog, rat, rabbit, chicken, duck, and human by comparing their RAPD PCR fingerprints. This study provides a simple, fast and sensitive fingerprinting method in species identification for crime scene evidence or food products of endangered species.

Animals↗
PubMed2004

Identification and expression analysis of EST-based genes in the bud of Lycoris longituba.

To obtain a primary overview of gene diversity and expression pattern in Lycoris longituba, 4,992 ESTs (Expressed Sequence Tags) from L. longituba bud were sequenced and 4,687 cleaned ESTs were used for gene expression analysis. Clustered by the PHRAP program, 967 contigs and 1,343 singlets were obtained. Blast search showed that 179 contigs and 227 singlets (totally 1,066 ESTs) had homologues in GenBank and 3,621 ESTs were novel.

Base Composition↗
PubMedDate not supplied

Counting all possible ancestral configurations of sample sequences in population genetics.

Given a set D of input sequences, a genealogy for D can be constructed backward in time using such evolutionary events as mutation, coalescent, and recombination. An ancestral configuration (AC) can be regarded as the multiset of all sequences present at a particular point in time in a possible genealogy for D. The complexity of computing the likelihood of observing D depends heavily on the total number of distinct ACs of D and, therefore, it is of interest to estimate that number. For D consisting of binary sequences of finite length, we consider the problem of enumerating exactly all distinct ACs. We assume that the root sequence type is known and that the mutation process is governed by the infinite-sites model. When there is no recombination, we construct a general method of obtaining closed-form formulas for the total number of ACs. The enumeration problem becomes much more complicated when recombination is involved. In that case, we devise a method of enumeration based on counting contingency tables and construct a dynamic programming algorithm for the approach. Last, we describe a method of counting the number of ACs that can appear in genealogies with less than or equal to a given number R of recombinations. Of particular interest is the case in which R is close to the minimum number of recombinations for D.

Biological Evolution↗
PubMed1997

Reproduction of the owl monkey (Aotus spp.) in captivity.

The reproduction performance of captive owl monkeys, a breed used extensively in biomedical research, was observed at the Battelle Primate Facility (BPF). The colony grew through captive breeding, imports from the Peruvian Primatological Project, and others to a peak size of 730. It included seven karyotypes of Aotus sp. Results showed that owl monkeys can breed successfully in a laboratory in numbers sufficient to sustain modest research programs. Reproductive success increases when pairs are compatible, of the same karyotype, and stabilized; however, mated pairs of different karyotype are also productive. Under conditions of controlled lighting and heating, owl monkeys at BPF showed no birth peak nor birth season.

Animal Welfare↗
PubMed2002

NBLAST: a cluster variant of BLAST for NxN comparisons.

BACKGROUND: The BLAST algorithm compares biological sequences to one another in order to determine shared motifs and common ancestry. However, the comparison of all non-redundant (NR) sequences against all other NR sequences is a computationally intensive task. We developed NBLAST as a cluster computer implementation of the BLAST family of sequence comparison programs for the purpose of generating pre-computed BLAST alignments and neighbour lists of NR sequences. RESULTS: NBLAST performs the heuristic BLAST algorithm and generates an exhaustive database of alignments, but it only computes alignments (i.e. the upper triangle) of a possible N2 alignments, where N is the set of all sequences to be compared. A task-partitioning algorithm allows for cluster computing across all cluster nodes and the NBLAST master process produces a BLAST sequence alignment database and a list of sequence neighbours for each sequence record. The resulting sequence alignment and neighbour databases are used to serve the SeqHound query system through a C/C++ and PERL Application Programming Interface (API). CONCLUSIONS: NBLAST offers a local alternative to the NCBI's remote Entrez system for pre-computed BLAST alignments and neighbour queries. On our 216-processor 450 MHz PIII cluster, NBLAST requires ~24 hrs to compute neighbours for 850000 proteins currently in the non-redundant protein database.

Algorithms↗
PubMed2003

Hetero: a program to simulate the evolution of DNA on a four-taxon tree.

We present a computer program to simulate the evolution of a nucleotide sequence on a phylogenetic tree with four tips. The program, Hetero, allows users to assign lineage-specific differences in the rate matrices used to describe the evolutionary process. It has a simple user interface and output, making it equally useful in the teaching and research of phylogenetics.

Algorithms↗
PubMed1992

A pharmacodynamic model of erythropoietin therapy for uremic anemia.

Fifty-seven patients receiving chronic high-flux hemodialysis began receiving recombinant alpha-human erythropoietin (rHuEPO). The mean initial rHuEPO dose used in 54 evaluable patients was 9963 +/- 4364 U/week; the final dose was 8972 +/- 4058 U/week. Treatment over a mean period of 154 +/- 40 days (84 to 224 days) resulted in an average increase in hematocrit from 24.7% +/- 3.7% to 32.5% +/- 4.4%. We present a model for these data that describes changes in hematocrit during rHuEPO therapy and that allows simultaneous estimation of red blood cell lifespan and rHuEPO-induced increases in red blood cell production rate. Analysis of the hematocrit values of the patients with the model, by use of NONMEM, a computer program for analysis of population data, reveals a nonlinear dose-response relationship with large interindividual variability (coefficient of variation) of about 50%. The estimated mean red blood cell lifespan is 64 days, with interindividual variability of about 30% (coefficient of variation). The intraindividual random variability in hematocrit about its prediction is +/- 5% of the prediction. For clinical dose adjustment, we present a method that uses only simple calculations.

Anemia↗
PubMed2002

QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice ( Oryza sativa) using microsatellite markers.

Rice ( Oryza sativa) cultivar development currently faces the task of overcoming yield plateaus, which is difficult due to the narrow genetic base of breeding programs. Oryza glumaepatula is a diploid wild relative of cultivated rice, native to Central and South America, and is therefore a potential source of alleles of agronomic importance to rice breeding programs. We studied 11 agronomic traits in BC(2)F(2) families of the interspecific cross Oryza sativa x O. glumaepatula. Transgressive lines which are almost isogenic to the elite recurrent O. sativa parent were identified for most of these traits. Quantitative trait locus (QTL) analysis was performed by single-point and interval mapping using a molecular map based on 157 microsatellite and STS markers. Marker regions accounting for 14.5 to 72.9% of a phenotypic variation trait were identified in 9 of the 12 rice chromosomes. Positive QTL effects from O. glumaepatula were observed in chromosomal regions associated with tillering and panicle-number traits.

Journal Article↗
PubMed2000

Novel HLA-B*15 alleles identified in potential marrow donors.

Several methods for low-resolution class I typing of potential bone marrow donors are available. The National Marrow Donor Program (NMDP) has initiated pilot projects for large-scale DNA-based class I typing to initially characterize donors. Sequence-specific oligonucleotide probe hybridization and sequence-specific primer polymerase chain reaction (PCR) screening of 3,500 NMDP potential donors suggested the presence of variants of known HLA-B*15 variants in 3 donors. PCR products encompassing HLA-B locus exons 1 through 3 were prepared and subcloned. Sequencing revealed 3 alleles differing from known HLA-B*15 alleles by nucleotide substitutions resulting in predicted novel HLA-B antigens. The new alleles occur in distinct ethnic groups. These findings further illustrate the substantial genetic variation present at the HLA-B locus within human populations.

Alleles↗
PubMed1980

Effect of alcohol on genetically determined variants of the normal electroencephalogram.

The effect of a single dose of alcohol on the electroencephalograms (EEGs) of healthy male carriers of extreme variants of the EEG was examined. The EEG variants included: low voltage, borderline alpha, diffuse beta, and monotonous alpha EEG. The EEGs were analyzed on a small processor by means of a program for interval-amplitude analysis. The synchronizing effect of alcohol (increase of alpha activity and decrease of variance of frequency) was most pronounced in the borderline alpha EEG. As the interindividual variability of the resting EEG is known to be genetically determined, it can be concluded that the differential effects of ethanol on the EEG have a genetic basis.

Adult↗
PubMed1994

Regulation of gene expression programs during Arabidopsis seed development: roles of the ABI3 locus and of endogenous abscisic acid.

The accumulation kinetics of 18 mRNAs were characterized during Arabidopsis silique development. These marker mRNAs could be grouped in distinct classes according to their coordinate temporal expression in the wild type and provided a basis for further characterization of the corresponding regulatory pathways. The abscisic acid (ABA)-insensitive abi3-4 mutation modified the expression pattern of several but not all members of each of these wild-type temporal mRNA classes. This indicates that the ABI3 protein directly participates in the regulation of several developmental programs and that multiple regulatory pathways can lead to the simultaneous expression of distinct mRNA markers. The ABI3 gene is specifically expressed in seed, but ectopic expression of ABI3 conferred the ability to accumulate several seed-specific mRNA markers in response to ABA in transgenic plantlets. This suggested that expression of these marker mRNAs might be controlled by an ABI3-dependent and ABA-dependent pathway(s) in seed. However, characterization of the ABA-biosynthetic aba mutant revealed that the accumulation of these mRNAs is not correlated to the ABA content of seed. A possible means of regulating gene expression by developmental variations in ABA sensitivity is apparently not attributable to variations in ABI3 cellular abundance. The total content of ABI3 protein per seed markedly increased at certain developmental stages, but this augmentation appears to result primarily from the simultaneous multiplication of embryonic cells. Our current findings are discussed in relation to their general implications for the mechanisms controlling gene expression programs in seed.

Abscisic Acid↗
PubMed2005

Influenza vaccines: recent advances in production technologies.

In spite of ongoing annual vaccination programs, the seasonal influenza epidemics remain a major cause of high morbidity and mortality. The currently used "inactivated" vaccines provide very short-term and highly specific humoral immunity due to the frequent antigenic variations in the influenza virion. These intra-muscularly administered vaccines also fail to induce protective mucosal immunity at the portal of viral entry and destruction of the virally infected cells by induction of cytotoxic T lymphocytes. Therefore, it is necessary to develop immunologically superior vaccines. This article highlights some of the recent developments in investigational influenza vaccines. The most notable recent developments of interest include the use of immunopotentiators, development of DNA vaccines, use of reverse genetics, and the feasibility of mammalian cell-based production processes. Presently, due to their safety and efficacy, the cold-adapted "live attenuated" vaccines are seen as viable alternatives to the "inactivated vaccines". The DNA vaccines are gaining importance due to the induction of broad-spectrum immunity. In addition, recent advances in recombinant technologies have shown the possibility of constructing pre-made libraries of vaccine strains, so that adequately preparations can be made for epidemics and pandemics.

Adjuvants, Immunologic↗
PubMed1996

Unraveling the chronic toxicity of lead: an essential priority for environmental health.

Although population exposure to lead has declined, chronic lead toxicity remains a major public health problem in the United States affecting millions of children and adults. Important gaps exist in knowledge of the pathophysiology of chronic lead intoxication. These gaps have impeded development of control strategies. To close current gaps in knowledge of chronic lead toxicity, we propose an integrated, multidisciplinary, marker-based research program. This program combines a) direct measurement of individual lead burden by 109Cd X-ray fluorescence analysis of lead in bone, b) determination of ALA-D phenotype, an index of individual susceptibility to lead, and c) assessments of subclinical injury produced by lead in the kidneys, nervous system and, reproductive organs. Data from this research will provide answers to questions of great public health importance: a) Are current environmental and occupational standards adequate to prevent chronic lead intoxication? b) is lead mobilized from the skeleton during pregnancy or lactation to cause fetal toxicity? c) Is lead mobilized from bone during menopause to cause neurotoxicity? d) What is the significance of genetic variation in determining susceptibility to lead? e) What is the contribution of lead to hypertension, renal disease, chronic neurodegenerative disease or declining sperm counts? f) Is chelation therapy effective in reducing body lead burden in persons with chronic overexposure to lead?

Acetylglucosaminidase↗
PubMed2005

Hepatic lipase gene variant -514C>T is associated with lipoprotein and insulin sensitivity response to regular exercise: the HERITAGE Family Study.

We investigated the associations between the hepatic lipase gene (LIPC) -514C>T polymorphism and lipases, lipoproteins, and insulin sensitivity (Si) responses to exercise training. Hepatic lipase and lipoprotein lipase activities, plasma lipoprotein levels, and Si were measured in the sedentary state and post-exercise training in the Health, Risk Factors, Exercise Training, and Genetics (HERITAGE) Family Study (n=662). The LIPC -514C allele frequency was 0.516 (blacks) and 0.796 (whites). Baseline and post-exercise training hepatic lipase activities were 40% higher in CC homozygotes (P < 0.0001) in both races. Black CC homozygotes had lower baseline lipoprotein lipase activity, HDL cholesterol, HDL3, and apolipoprotein (apo)A-1 concentrations. White CC homozygotes had lower baseline HDL cholesterol, apoA-1, LDL cholesterol, and apoB levels that remained low post-exercise training. Baseline Si was not associated with the LIPC genotypes. However, training-induced improvements in Si both in blacks and whites were greater in CC homozygotes (+1.25 +/- 0.2 and +0.22 +/- 0.2 microU.min(-1).ml(-1)) than in the TT genotype (+0.27 +/- 0.3 and -0.97 +/- 0.3 microU.min(-1).ml(-1)) (P = 0.008 and P = 0.002, respectively). The LIPC -514C allele was associated with higher hepatic lipase activity in sedentary and physically active states and better Si responses to regular exercise both in black and white individuals. The benefits from an exercise program on Si are likely to be substantial in the general population given the high frequency of the LIPC -514C allele, particularly in whites.

Adult↗
PubMed1996

[Hereditary biochemical diversity in the processes of evolution and individual development].

Results of long-term studies of Russian authors on regularities of expression of hereditary biochemical diversity in evolution and development are reviewed. Primary attention is given to the concepts of genetic monomorphism and genetic stability of population systems, principles of adaptive gene pool structure and optimum genetic diversity, historical and conservation genetics, the concept of the multilevel gene expression, and temporal regulation of ontogenetic functioning of gene clusters coding for enzymes. A universal genetic approach to the problems of evolution and ontogeny is proposed. A population is regarded as a superorganism whose key property is the hierarchic structure of its genetic stability from the stability of monomorphic genes via stability of polymorphic gene frequencies in a multilevel population system to the stability of the total amount of gene diversity in this system. A multicellular organism is also regarded as a developing hierarchical system of populations of cells and genes interacting in a nonrandom fashion. This maintains stability of metabolic processes and is expressed in consistent correlations between monogenic and polygenic morphophysiological characters. Properties of both organisms are determined by the adaptive heterozygosity optimum, the disturbance of which has negative consequences for both individuals and populations. On the basis of these results and the concept on the common nature of evolutionary and ontogenetic processes, the following conclusions are drawn: genetic processes can be either favorable or adverse for developing organisms and populations; the state of genetic processes can be determined by analysis of gene diversity and their deviations from the optimum, taking into account the adaptive gene pool structure; and negative hazardous consequences of extreme external effects at both the individual and population levels can be detected by methods of biochemical genetics in specially planned monitoring programs. Knowledge of normal processes of realization of hereditary information in evolution of populations and in ontogeny opens up new perspectives in detection of unfavorable processes and their correction. This approach proved promising both for preventive and clinical medicine and for exploitation and artificial reproduction of biological resources.

Adaptation, Physiological↗
PubMed1997

Protein nutrition of gestating sows.

Dietary amino acid requirements of gestating sows vary depending on genetic strain, energy intake, body weight, and other factors. Estimation of amino acid requirements for gestating sows in a defined situation should be directed toward achieving a high rate of protein accretion and a modest rate of fat accretion. More information is needed to set target accretion rates precisely. A simple mathematical model was developed with the limited objectives of 1) aiding in understanding the interactions among energy intake, amino acid intake, protein accretion potential, and body weight in affecting the amount of body protein and fat accreted by pregnant sows and 2) providing general guidelines for feeding programs. Predictions from the model suggest that the daily lysine requirement varies markedly with variation in ME intake but that the requirement as a percentage of the diet is more stable as ME intake varies. At moderate ME intake, the lysine requirement seems greater during late gestation than earlier. The lysine requirement of heavy sows is less than that of light gilts at a similar ME intake, and this offers opportunity for modest cost savings in pork production. A compromise is necessary between the goals of a high rate of protein accretion and a modest rate of fat accretion. It seems that a sow's potential protein accretion rate is rarely limiting.

Animal Nutritional Physiological Phenomena↗