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Results for “programmed genetic variation”

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At least 991 records · Page 55Linked to original sources
PubMed1997

[Genetic diversity and phylogenetic relationships among Chinese Macacas based on protein electrophoresis].

In this paper, using protein electrophoresis method, we studied proteinpolymorphism and genetic divergence of 5 species in Genus Macaca: M. mulatta, M. arctoides, M. assamensis, M. thibetana, M. fascicularis. A total of 30 genetic loci were analyzed for 29 individuals, including 4 Nycticebus pygmaeus as outgroup. For the 19 M. mulatta, 9 loci were found to be polymorphic. Accordingly, the percentage of polymorphic loci, P = 0.3; the mean number of alleles, A = 1.4, and the mean heterozygosity, H = 0.1045, indicating a rather high level of genetic diversity in this species. Furthermore, 10 loci showed polymorphic among the 5 species, which can be used as information loci for phylogenetic reconstruction. Three programs (conml, neighbor, fitch) in PHYLIP 3.5 c were chosen to construct phylogenetic trees. All of the three trees show support a close relationship between M. mulatta and M. fascicularis. However, two trees have the same topology, suggesting that M. arctoides belongs to an independent species group, while M. assamensis and M. thibetana are closely related and belong to another species group, and the other tree gives a different topology which implies that M. arctoides, M. assamensis and M. thibetana belong to one species group.

Animals↗
PubMed1999

Treatment planning for brachytherapy: an integer programming model, two computational approaches and experiments with permanent prostate implant planning.

An integer linear programming model is proposed as a framework for optimizing seed placement and dose distribution in brachytherapy treatment planning. The basic model involves using 0/1 indicator variables to describe the placement or non-placement of seeds in a prespecified three-dimensional grid of potential locations. The dose delivered to each point in a discretized representation of the diseased organ and neighbouring healthy tissue can then be modelled as a linear combination of the indicator variables. A system of linear constraints is imposed to attempt to keep the dose level at each point to within specified target bounds. Since it is physically impossible to satisfy all constraints simultaneously, each constraint uses a variable to either record when the target dose level is achieved, or to record the deviation from the desired level. These additional variables are embedded into an objective function to be optimized. Variations on this model are discussed and two computational approaches--a branch-and-bound algorithm and a genetic algorithm--for finding 'optimal' seed placements are described. Results of computational experiments on a collection of prostate cancer cases are reported. The results indicate that both optimization algorithms are capable of producing good solutions within 5 to 15 min, and that small variations in model parameters can have a measurable effect on the dose distribution of the resulting plans.

Algorithms↗
PubMedDate not supplied

Hoxd13 expression in the developing limbs of the short-tailed fruit bat, Carollia perspicillata.

Bat forelimbs are highly specialized for sustained flight, providing a unique model to explore the genetic programs that regulate vertebrate limb diversity. Hoxd9-13 genes are important regulators of stylopodium, zeugopodium, and autopodium development and thus evolutionary changes in their expression profiles and biochemical activities may contribute to divergent limb morphologies in vertebrates. We have isolated the genomic region that includes Hoxd12 and Hoxd13 from Carollia perspicillata, the short-tailed fruit bat. The bat Hoxd13 gene encodes a protein that shares 95% identity with human and mouse HOXD13. The expression pattern of bat Hoxd13 mRNA during limb development was compared with that of mouse. In bat and mouse hindlimbs, the expression patterns of Hoxd13 are relatively similar. However, although the forelimb Hoxd13 expression patterns in both organisms during early limb bud stages are similar, at later stages they diverge; the anterior expression boundary of bat Hoxd13 is posterior-shifted relative to the mouse. These findings, compared with the Hoxd13 expression profiles of other vertebrates, suggest that divergent Hoxd13 expression patterns may contribute to limb morphological variation.

Animals↗
PubMedDate not supplied

[Mitochondrial DNA polymorphism reveals a genetic differentiation between ethnic groups in the population of Jerba].

Jerba is an island situated in the South-East of Tunisia were some ethnic groups (Arabs, Berbers, Blacks, Jewishs and others) cohabit for centuries. The religion and cultural differences have represented an obstacle to a mixture between these groups. In order to evaluate the genetic differentiation between the muslim groups (Arabs, Berbers and Blacks), we have analysed the polymorphism of a mitochondrial DNA coding region. The cytochrome oxydase coding region (COII) was amplified by PCR in 57 Arabs, 42 Berbers and 16 Blacks. The amplified products were analysed by Restriction Fragment Length Polymorphism (RFLP). Genetic distances were calculated by using the AMOVA program. The values of these distances were significantly different between Arabs and Blacks, and between Berbers and Blacks but not between Arabs and Berbers. So That, to refine the evaluation of genetic diversity between Arabs and Berbers, we have analysed the polymorphism of a second mitochondrial coding region which encodes for the fifth unit of NADH deshydrogenase (ND5). Eleven haplotypes were defined from the resulting data of mitochondrial COII and ND5 polymorphism and a significant genetic distance between Arabs and Berbers was computed.

Analysis of Variance↗
PubMed2004

A probabilistic model of 3' end formation in Caenorhabditis elegans.

The 3' ends of mRNAs terminate with a poly(A) tail. This post-transcriptional modification is directed by sequence features present in the 3'-untranslated region (3'-UTR). We have undertaken a computational analysis of 3' end formation in Caenorhabditis elegans. By aligning cDNAs that diverge from genomic sequence at the poly(A) tract, we accurately identified a large set of true cleavage sites. When there are many transcripts aligned to a particular locus, local variation of the cleavage site over a span of a few bases is frequently observed. We find that in addition to the well-known AAUAAA motif there are several regions with distinct nucleotide compositional biases. We propose a generalized hidden Markov model that describes sequence features in C.elegans 3'-UTRs. We find that a computer program employing this model accurately predicts experimentally observed 3' ends even when there are multiple AAUAAA motifs and multiple cleavage sites. We have made available a complete set of polyadenylation site predictions for the C.elegans genome, including a subset of 6570 supported by aligned transcripts.

3' Untranslated Regions↗
PubMed2004

A versatile statistical analysis algorithm to detect genome copy number variation.

We have developed a versatile statistical analysis algorithm for the detection of genomic aberrations in human cancer cell lines. The algorithm analyzes genomic data obtained from a variety of array technologies, such as oligonucleotide array, bacterial artificial chromosome array, or array-based comparative genomic hybridization, that operate by hybridizing with genomic material obtained from cancer and normal cells and allow detection of regions of the genome with altered copy number. The number of probes (i.e., resolution), the amount of uncharacterized noise per probe, and the severity of chromosomal aberrations per chromosomal region may vary with the underlying technology, biological sample, and sample preparation. Constrained by these uncertainties, our algorithm aims at robustness by using a priorless maximum a posteriori estimator and at efficiency by a dynamic programming implementation. We illustrate these characteristics of our algorithm by applying it to data obtained from representational oligonucleotide microarray analysis and array-based comparative genomic hybridization technology as well as to synthetic data obtained from an artificial model whose properties can be varied computationally. The algorithm can combine data from multiple sources and thus facilitate the discovery of genes and markers important in cancer, as well as the discovery of loci important in inherited genetic disease.

Algorithms↗
PubMed1988

[The role of hereditary and environmental factors in the variability of the components comprising the mass of the human upper extremity at various stages of postnatal ontogeny].

The investigation has been performed in mono- and dizygotic twins of the Ukrainian ethnic and territorial groups. As a whole 196 pairs of twins, among them 80 pairs of mono- and 116 pairs of dizygotes of both sex at the age of 12-60 years have been undergone the examination. The twins selected are divided into two age groups--period of sex maturation (12-17 years of age) and that of maturity (30-60 years of age). Quantitative parameters on composition of the components of the upper extremity mass (fatty, muscular and osseous) are studied in all the twins. Coefficients of intrapaired correlation and indices of Holzinger's heritability are calculated according to an original program, using the microcomputer "Electronika B3-34". The degree of hereditary and environmental influences for development and formation of the main components of the upper extremity mass at certain stages of individual development are characterized with ontogenic changeability. With age the degree of hereditary dependence of the development and formation of the upper extremity mass components decreases, and sex dimorphism according to the degree of the hereditary dependence of the components studied is displayed as a greater hereditary determination in male persons.

Adolescent↗
PubMed1995

High diversity of alpha-globin haplotypes in a Senegalese population, including many previously unreported variants.

RFLP haplotypes at the alpha-globin gene complex have been examined in 190 individuals from the Niokolo Mandenka population of Senegal: haplotypes were assigned unambiguously for 210 chromosomes. The Mandenka share with other African populations a sample size-independent haplotype diversity that is much greater than that in any non-African population: the number of haplotypes observed in the Mandenka is typically twice that seen in the non-African populations sampled to date. Of these haplotypes, 17.3% had not been observed in any previous surveys, and a further 19.1% have previously been reported only in African populations. The haplotype distribution shows clear differences between African and non-African peoples, but this is on the basis of population-specific haplotypes combined with haplotypes common to all. The relationship of the newly reported haplotypes to those previously recorded suggests that several mutation processes, particularly recombination as homologous exchange or gene conversion, have been involved in their production. A computer program based on the expectation-maximization (EM) algorithm was used to obtain maximum-likelihood estimates of haplotype frequencies for the entire data set: good concordance between the unambiguous and EM-derived sets was seen for the overall haplotype frequencies. Some of the low-frequency haplotypes reported by the estimation algorithm differ greatly, in structure, from those haplotypes known to be present in human populations, and they may not represent haplotypes actually present in the sample.

Genetic Variation↗
PubMed2003

Tests of linkage and association of the COL1A2 gene with bone phenotypes' variation in Chinese nuclear families.

In the present study, we simultaneously test linkage and/or association of the collagen type I alpha 2 (COL1A2) gene with bone mineral density (BMD) and bone area. A total of 1280 subjects from 407 Chinese nuclear families (including both parents and their daughters) were genotyped for an intragenic marker MspI in the COL1A2 gene. BMD and bone area at the lumbar spine and hip were measured by dual-energy X-ray absorptiometry. Applying the QTDT (quantitative transmission disequilibrium test) program, we performed tests for population stratification, within-family association (via transmission disequilibrium test), total association, linkage, and linkage while modeling association. Significant or marginal within-family associations were found with BMD at the lumbar spine (P = 0.013), trochanter (P = 0.004), and total hip (P = 0.053) and with bone area at the intertrochanteric region (P = 0.024) and total hip (P = 0.048). The positive associations were confirmed in permutations except for bone area at total hip (P > 0.10). A small proportion (<1%) of the population variance of bone phenotypes can be explained by the MspI polymorphism; however, it may be underestimated given the significant population stratification detected in our sample. Due to the limited number of sib pairs in this sample, we did not find evidence of linkage. In summary, the MspI polymorphism is likely to be in linkage disequilibrium with a nearby functional mutation affecting BMD and bone area.

Adult↗
PubMedDate not supplied

Repeated sequences in bacterial chromosomes and plasmids: a glimpse from sequenced genomes.

To gain insight into the extent of exact DNA repeats in sequenced bacterial genomes and their plasmids, we analyzed the collection of completely sequenced bacterial genomes available at GenBank using the program Miropeats. This program draws graphical representations of exact DNA repeats in whole genomes. In this work, we present maps showing the extent and type (inverted or direct) of exact DNA repeats longer than 300 bp for the whole collection. These repeats may participate in a variety of events relevant for bacterial genome plasticity, such as amplifications, deletions, inversions, and translocations (via homologous recombination), as well as transposition. Additionally, we review recent data showing that high-frequency architectural variations in genomic structure occur at both the interspecies and interstrain levels.

Bacteria↗
PubMed2004

Sequence variability in the fibroin-H intron of domesticated and wild silk moths.

The single intron of the heavy-chain fibroin gene in domesticated (Bombyx mori) and wild (B. mandarina) silk moths has a length of approximately 1000 nucleotides. It is located only 57 bp from the gene's core promoter and harbors multiple AT-rich regulatory elements that have been found to enhance the basal level of transcription in vitro. In this work, the intronic nucleotide variability among members of both Bombyx species is analyzed. The intron sequences of B. mori strains k120 and Nistari, as well as B. mandarina specimens from Japan and Korea, were obtained. This information was compared with the previously reported sequences of B. mori strains p50 and C-108, as well as an additional B. mandarina specimen collected in Japan. We found a total of 26 variant positions, including variants shared by members of both species and species-specific changes. The potential functional role of these variants was investigated by using the program MatInspector to search for putative binding sites of transcription factors within the intron. We detected a multitude of putative binding elements distributed along the entire intronic sequence. Among them, 22 correspond to protein binding domains that are known to regulate fibroin transcription. The mapping of multiple variant positions within these putative binding sequences as well as in known regulatory elements of the intron argue for functional significance on the regulation of transcription.

Animals↗
PubMed2005

Cost comparison of natural service sires and artificial insemination for dairy cattle reproductive management.

Despite the widespread popularity of artificial insemination, many dairymen still prefer the use of natural service sires due to a variety of reasons, including a common perception that it is easier to manage and less expensive than AI. Little has been done to estimate the explicit and implicit costs, including the probable loss of genetic progress associated with the use of natural service sires in dairy herds. A partial budget approach was used to stochastically model the expected costs and returns of reproductive management options in large, western, Holstein dairies. Option one was natural service sires managed using currently recommended approaches including breeding soundness evaluations, bull vaccination, and a rotational breeding system. Option two was an AI system using a modified Presync-Ovsynch timed AI program in conjunction with estrus detection and inseminations performed by a commercial route breeder. Stochastic variables in the model included the cost of the lactating ration and purchased bulls, as well as the value received for milk, market bulls, and net merit gains. All other variables were treated deterministically. Under the model's assumptions, the use of natural service sires averaged approximately US dollar 10 more in cost per cow per year as compared to an AI program. Sixty percent of the time, AI was less expensive than using bulls. However, there was wide variation in expected differences in cost between the two systems with net merit estimates having the largest impact, followed by prices received for milk sold and market bulls.

Animals↗
PubMed1994

On the molecular nature of the Duarte variant of galactose-1-phosphate uridyl transferase (GALT).

Galactosemia is an inborn error of galactose metabolism secondary to deficiency of galactose-1-phosphate uridyl transferase (GALT). GALT is a polymorphic enzyme and Duarte (D) is the most common enzyme variant. This variant is characterized by faster electrophoretic mobility and reduced activity. Duarte/galactosemia compound heterozygotes (D/G) are commonly identified in galactosemia newborn screening programs. However, these patients do not generally require treatment. By using a "candidate mutation" approach to define the molecular basis of the Duarte variant of GALT, a close association between the previously reported N314D polymorphism and the Duarte variant of GALT was found. We suggest that N314D encodes the D variant of GALT and that molecular testing for N314D might be useful to confirm a biochemical diagnosis of Duarte variant of GALT.

Alleles↗
PubMed1995

Phylogenetic relationships of the Prodontria (Coleoptera; Scarabaeidae; subfamily Melolonthinae), derived from sequence variation in the mitochondrial cytochrome oxidase II gene.

The beetle genus Prodontria is of importance to New Zealand conservation programs. All Prodontria species are brachypterous (having reduced wings), and the genus presents some interesting evolutionary and biogeographic questions that are testable using phylogenetic reconstruction. A phylogeny was produced for 14 flightless Prodontria species, 2 macropterous (fully winged) Odontria species, and single representatives of 2 outgroup genera using sequence data from the mitochondrial COII gene. The data support probable conspecificity of the morphologically similar P. modesta and P. bicolorata but do not support their hypothesized sister-species relationship with the geographically proximate P. lewisi. The alpine P. capito is found to be a paraphyletic group, with the most eastern population diverging after the western populations made their appearance. Many interesting biogeographic disjunctions are here proposed to be anomalous and the result of morphological convergence. The data do not support the idea of a common flightless ancester for Prodontria, but suggest that brachyptery has evolved numerous times. In some instances, this appears to have led to contemporaneous speciation resulting in little resolution of phylogenetic relationships in some parts of the tree. These data allow for a new interpretation of the origin and diversification of the southern New Zealand flightless melolonthine fauna. Multiple speciation events involving wing reduction are suggested to involve at least one widespread flighted ancestor that has given rise to brachypterous forms.

Amino Acid Sequence↗
PubMed2006

How valid is single nucleotide polymorphism (SNP) diagnosis for the individual risk assessment of breast cancer?

The number of reports investigating disease susceptibility based on the carriage of low-penetrance, high-frequency single nucleotide polymorphisms (SNPs) has increased in recent years. Evidence is accumulating defining specific individual variations in breast cancer susceptibility. Genetic variations of estradiol and xenobiotics metabolisms as well as genes involved in cell-cycle control have been described as significant contributors to breast cancer susceptibility, with variations depending on ethnic background and co-factors such as smoking and family history of breast cancer. In sum, the highest level of evidence to date linking SNPs and breast cancer comes from nested case-control studies within the prospective Nurses' Health Study. These data establish seven SNPs - hPRB +331G/A, AR CAG repeat, CYP19 (TTTA)10, CYP1A1 MspI, VDR FOK1, XRCC1 Arg194Trp and XRCC2 Arg188His - as small but significant risk factors for spontaneous, non-hereditary breast cancer. In addition, meta-analysis of data in the literature establishes the TGFBR1*6A, HRAS1, GSTP Ile105Val and GSTM1 SNPs as low-penetrance genetic risk factors of sporadic breast cancer. The clinical consequences of such a risk elevation may be detailed instruction of the patient as to general measures of breast cancer prevention such as a low-fat diet, optimization of body mass index, physical exercise, avoidance of alcohol and long-term hormone replacement therapy, and participation in a breast cancer screening program between the ages of 50 and 70 years. Specific surgical or drug interventions such as prophylactic mastectomy and oophorectomy or prophylactic intake of tamoxifen are not indicated based on SNP analysis at this time.

Breast Neoplasms↗
PubMed2004

Accuracy improvement for identifying translation initiation sites in microbial genomes.

MOTIVATION: At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3' end), but a much lower accuracy of the translation initiation site (TIS, 5' end). The latter is important to the analysis and the understanding of the putative protein of a gene and the regulatory machinery of the translation. Improving the accuracy of prediction of TIS is one of the remaining open problems. RESULTS: In this paper, we develop a four-component statistical model to describe the TIS of prokaryotic genes. The model incorporates several features with biological meanings, including the correlation between translation termination site and TIS of genes, the sequence content around the start codon; the sequence content of the consensus signal related to ribosomal binding sites (RBSs), and the correlation between TIS and the upstream consensus signal. An entirely non-supervised training system is constructed, which takes as input a set of annotated coding open reading frames (ORFs) by any gene finder, and gives as output a set of organism-specific parameters (without any prior knowledge or empirical constants and formulas). The novel algorithm is tested on a set of reliable datasets of genes from Escherichia coli and Bacillus subtillis. MED-Start may correctly predict 95.4% of the start sites of 195 experimentally confirmed E.coli genes, 96.6% of 58 reliable B.subtillis genes. Moreover, the test results indicate that the algorithm gives higher accuracy for more reliable datasets, and is robust to the variation of gene length. MED-Start may be used as a postprocessor for a gene finder. After processing by our program, the improvement of gene start prediction of gene finder system is remarkable, e.g. the accuracy of TIS predicted by MED 1.0 increases from 61.7 to 91.5% for 854 E.coli verified genes, while that by GLIMMER 2.02 increases from 63.2 to 92.0% for the same dataset. These results show that our algorithm is one of the most accurate methods to identify TIS of prokaryotic genomes. AVAILABILITY: The program MED-Start can be accessed through the website of CTB at Peking University: http://ctb.pku.edu.cn/main/SheGroup/MED_Start.htm.

Algorithms↗
PubMed2004

SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history.

UNLABELLED: We present an extension of the program SIMCOAL, which allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias. AVAILABILITY: http://cmpg.unibe.ch/software/simcoal2/.

Algorithms↗
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↗