Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “programmed genetic variation”

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

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

At least 1,117 records · Page 62Linked to original sources
PubMed2003

Use of SSRs for establishing heterotic groups in subtropical maize.

Heterotic groups and patterns are of fundamental importance in hybrid breeding. The objectives of our research were to: (1) investigate the relationship of simple sequence repeats (SSR) based genetic distances between populations and panmictic midparent heterosis (PMPH) in a broad range of CIMMYT maize germplasm, (2) evaluate the usefulness of SSR markers for defining heterotic groups and patterns in subtropical germplasm, and (3) examine applications of SSR markers for broadening heterotic groups by systematic introgression of other germplasm. Published data of two diallels and one factorial evaluated for grain yield were re-analyzed to calculate the PMPH in population hybrids. Additionally, 20 pools and populations widely used in CIMMYT's breeding program were assayed with 83 SSR markers covering the entire maize genome. Correlations of squared modified Roger's distance (MRD(2)) and PMPH were mostly positive and significant, but adaption problems caused deviations in some cases. For intermediate- and early-maturity subtropical germplasm, two heterotic groups could be suggested consisting of a flint and dent composite. We concluded that the relationships between the populations obtained by SSR analyses are in excellent agreement with pedigree information. SSR markers are a valuable complementation to field trials for identifying heterotic groups and can be used to introgress exotic germplasm systematically.

Alleles↗
PubMed2006

Gene-environment interactions differentially affect mouse strain behavioral parameters.

Systematic phenotyping of mouse strains and mutants generated through genome-wide mutagenesis programs promises to deliver a wealth of functional genetic information. To this end, the appropriation of a standard series of phenotyping protocols is desirable to produce data sets that are consistent within and across laboratories and across time. Standard phenotyping protocols such as EMPReSS (European Mouse Phenotyping Resource for Standardised Screens) provide a series of protocols aimed at phenotyping multiple body systems that could realistically be adopted and/or reproduced in any laboratory. This includes a series of neurologic and behavioral screens, bearing in mind that this class of phenotype is well represented in targeted mutants and mutagenesis screens. Having cross-validated screening batteries in a number of laboratories and in a number of commonly used inbred strains, our group was interested in establishing whether subtle changes in cage environment could affect behavioral test outcome. Aside from unavoidable quantitative differences in test outcome, we identified significant and distinct genotype-environment-test interactions. For example, specific strain order in open-field center entries and total distance traveled can be reversed depending on the form of enrichment used, while prepulse inhibition of the acoustic startle response is, even quantitatively, unaffected by the enrichment condition. Our findings argue that unless systematically recorded, behavioral studies conducted under subtle variations in cage environment may lead to data misinterpretation, although this could be limited to particular behaviors. Further investigations into the extent and limits of genetic and environmental variables are critical for the realization of both behavioral and functional genomics endpoints.

Animals↗
PubMed1998

DIAMOD: display and modeling of DNA bending.

MOTIVATION: DIAMOD (Displayandmodeling ofDNA) was created as a user-friendly software for exploring and better understanding DNA structural variations, particularly DNA bending. It was intended to be as open as possible so that any of the existing or future predictive models can be used with it. RESULTS: DIAMOD features graphic display and interactive manipulation of DNA molecules on the screen. Since it works with di-, tri- or tetranucleotide models supplied as external files of angular parameters, it was recently used to evaluate critically all available predictive models for DNA bending. The program has a unique option to insert bends at defined positions in DNA sequence independently of the currently used model, which enables the simulation of both intrinsic and protein-induced kinking. Finally, many output file formats facilitate the sharing of data with other programs and the creation of visually pleasing images. AVAILABILITY: The program is available on request to academic users free of charge. It will be distributed via the WWW (http://www-personal.umich.edu/ mensur/software.html). Users with no network access can get a copy directly from the author. CONTACT: mensur@umich.edu

Algorithms↗
PubMed1992

Linkage analysis of maturity-onset diabetes of the young (MODY): genetic heterogeneity and nonpenetrance.

We have analyzed the inheritance of maturity-onset diabetes of the young (MODY) on chromosome 20 in a large multigeneration family, the R.-W. family, and in two other MODY families. Of the four branches of the R.-W. pedigree which have been studied, two have documented early onset of non-insulin-dependent diabetes mellitus (NIDDM), while there is no evidence of early onset in the other two branches. The early-onset branches have apparently inherited the same D20S16 allele from the affected parent, while another D20S16 allele was inherited in the two branches without evidence of early onset. A test for homogeneity, the M-test, using the results of two-point linkage analysis with D20S16 indicates heterogeneity between early- and late-onset branches of the R.-W. family (P less than or equal to .014). In addition, analysis strongly suggests that MODY as expressed in the EDI and WIS families is unlinked to loci on chromosome 20 (P less than or equal to .018-.004). Comparable results are seen when the data are analyzed by the HOMOG program. Three polymorphic loci-D20S16, D20S17, and ADA--show no recombination with the MODY locus when two-point linkage analysis is used in the early-onset branches of the family. The multipoint lod score in the early-onset branches of the R.-W. family is 10.16, with the most likely location being between D20S4 and D20S17. Multipoint linkage analysis using the CHROMPICS option of the program CRI-MAP has been used to follow inheritance of the MODY disease locus. This analysis has identified two cases of possible nonpenetrance in the early-onset branches of the family (odds of at least 156:1), as determined by the appearance of apparent isolated double crossovers at the MODY locus in these unaffected individuals.

Adolescent↗
PubMed2003

The cryopreservation of ovarian tissue: uses and indications in veterinary medicine.

Animal experiments have shown that cryopreservation of the ovarian cortex, containing primordial follicles, could be used to preserve gametes thereby restoring fertility in humans and animals. During the last 100 years, many hundreds of species have been lost, and a third of the breeding animals are threatened with extinction. To preserve genetic diversity, notably for the conservation of endangered species, it is essential to conserve female and male gametes. Today, biotechnologies such as artificial insemination and embryo transfer are used in breeding programs and are well developed. However, even using these advanced techniques, there are problems due to the limited number of individuals used as the source of gametes, so that the risk of inbreeding is high, even in large populations. To preserve genetic diversity, it is necessary to create gene banks of male and female gametes and embryos, using a very large number of individual donors. Cryopreservation of ovarian tissue could present a means for enlarging the gene pool. Cryopreserved ovarian tissue could be used in auto- or xenografts, or for in vitro maturation (IVM) of primordial follicles. In this review, we describe the processes for cryopreservation of ovarian tissue and the various possibilities for using it.

Animals↗
PubMed2004

Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases.

A unified, bioinformatics-driven, single nucleotide polymorphism (SNP)-based approach to microbial genotyping has been developed. Multilocus sequence typing (MLST) databases consist of known variants of standardized housekeeping genes. Normally, seven fragments are defined; a sequence type (ST) consists of the variants of these fragments that are found in a particular isolate. A computer program that can identify highly informative sets of SNPs in entire MLST databases has been constructed. The SNPs either define a particular user-specified ST or provide a high value for Simpson's index of diversity (D), and may thus be generally applicable to that species. SNP sets that are diagnostic for Neisseria meningitidis ST-11 and ST-42, and high-D SNP sets for N. meningitidis and Staphylococcus aureus, were identified and real-time PCR methods to interrogate these SNPs were demonstrated. High-D SNP sets were also identified in other MLST databases. This widely applicable approach allows rapid genetic fingerprinting of infectious agents.

Algorithms↗
PubMed2006

Brain derived neurotrophic factor (BDNF) gene variants and Alzheimer's disease, affective disorders, posttraumatic stress disorder, schizophrenia, and substance dependence.

Genetic variation at the locus encoding the brain derived neurotrophic factor (BDNF) has been implicated in some neuropsychiatric disorders such as Alzheimer's disease (AD), affective disorders (AFDs), schizophrenia, and substance dependence. We therefore performed a mutation scan of the BDNF gene to identify novel gene variants and examined the association between BDNF variants and several neuropsychiatric phenotypes in European American (EA) subjects and controls. Using denaturing high performance liquid chromatography (dHPLC), we identified a novel variant (G-712A) in the putative promoter region. This variant and two previously reported BDNF SNPs (C270T and Val66Met) were genotyped in 295 patients with AD, 108 with AFDs, 96 with posttraumatic stress disorder (PTSD), 84 with schizophrenia, 327 with alcohol and/or drug dependence, and 250 normal control subjects. No association was found between these three BDNF gene variants and AD, AFDs, PTSD, or schizophrenia. However, there was a nominally higher frequency of the G-712A G-allele and the G/G genotype in subjects with substance dependence than in controls (Allele: chi(2) = 4.080, df = 1, P = 0.043; Genotype: chi(2) = 7.225, df = 2, P = 0.027). Although after correction for multiple testing, the findings are not considered significant (threshold P-value was set at 0.020 by the program SNPSpD), logistic regression analyses confirmed the modest association between SNP G-712A and substance dependence, when the sex and age of subjects were taken into consideration. The negative results for AFDs, PTSD, and schizophrenia could be due to the low statistical power. Further study with larger samples is warranted.

Adult↗
PubMed1995

Quantification of apoptosis (programmed cell death) in mammalian testis by DNA-fragmentation ELISA.

Apoptosis (programmed cell death) could contribute to fluctuations in sperm production and involution of testis in dependence on seasonal, genetic, environmental or individual factors. Investigations of such factors require a reliable quantitative examination of apoptotic processes. Therefore, a standardized procedure was developed for quantification of apoptosis in samples of testicular parenchyma in bull. This test is based on a highly sensitive DNA-fragmentation ELISA which was used originally for somatic cells in culture. Aliquots of testicular parenchyma were minced and homogenized by freezing/thawing and subsequent sonification at 4 degrees C. In comparison, aliquots were lysed in original buffer from the cell death detection ELISA-kit. Nucleosomes from the cell cytoplasm were obtained in supernatant of homogenate or lysate after centrifugation. The absorbance was linear over the range of sample concentrations from 5 to 20 microg testis equivalent/100 microl solution. Therefore, samples were standardized to a final concentration of 10 microg testis equivalent/100 microl. The recorded values were expressed in units per mg tissue (U/mg). The method was used to study testicular apoptotic processes in the guinea pig and roe deer. The results showed that apoptosis can be detected in testicular homogenate prepared from 0.01 mg testis parenchyma within 24 h after recovery of testes without significant variations. Detectable apoptosis levels showed differences among sexually active guinea pig (7.08 +/- 1.95 U/mg), roe deer (16.32 +/- 3.45 U/mg), and cattle (29.0 +/- 7.1 U/mg). This species-specificity suggests different cross reactivity of the monoclonal antibody used in the ELISA. A significantly higher amount of testicular apoptosis was detected in a population of guinea pigs with increased inbreeding coefficients (f = 0.785 - 0.998) than in outbred animals (11.41 +/- 3.50 U/mg and 7.08 +/- 1.95 U/mg, respectively). The inverse relationship of testicular apoptosis and proliferation in these two populations was significant (r = -0.531; P < 0.05). In conclusion, the relative simplicity and high sensitivity of this nonradioactive method provides a useful approach to investigate spermatogenesis under different conditions. Results in the guinea pig showed that apoptosis plays an important role in the regulation of gonadal efficiency.

Journal Article↗
PubMed1996

Increased urinary testosterone/epitestosterone ratios found in Swedish athletes in connection with a national control program. Evaluation of 28 cases.

In connection with a national anti-doping control program, including analysis of 8946 urine samples, 28 athletes were found to have delivered samples free from xenobiotic anabolic steroids but with an increased testosterone/epitestosterone (T/E) ratio (> 6). Unannounced testing of the above athletes produced 2-4 additional urine samples during the next 2-3 months. A low degree of variation of the T/E ratio, with a C.V. below 30% was found in 17 of the subjects whereas 10 had a C.V. varying from 31% to 43%. One subject with a high urinary T/E ratio (10.5) had a C.V. of this ratio of 126% and also an extremely high ratio between testosterone and LH in urine. It has been reported that non-users of testosterone have T/E ratios fluctuating around a mean with a C.V. that will not exceed 30%. We found that administration of testosterone to seven healthy volunteers resulted in urinary T/E ratios that varied with a C.V. ranging from 67% to 130% during the following 4 weeks. It is concluded that among the above 28 cases, only one can be regarded as a clear case of testosterone doping. Although the vast majority of Swedish athletes have urinary T/E ratios below six, there is a subfraction with a constant higher ratio, possibly due to genetic factors.

Doping in Sports↗
PubMed1995

The interrelationship between ethnicity and gestational diabetes in fetal macrosomia.

OBJECTIVE: To determine the possibility of an ethnic influence on the development of macrosomia (birth weight > 90th percentile for gestational age) in gestational diabetes mellitus (GDM). RESEARCH DESIGN AND METHODS: We prospectively followed all African-American and Latino women enrolled in the Temple diabetes-in-pregnancy program. GDM was diagnosed in 103 African-American and 36 Latino women during the study period (1991-1994) according to the criteria of Carpenter and Coustan. All women were treated according to our previously published protocols. Data were collected on gestational weight gain, previous history of macrosomia, body mass index (BMI), and level of maternal glycemic control. RESULTS: Insulin therapy was required in 53 women (37.5%) to maintain fasting blood glucose levels at < 95 mg/dl and 2-h postprandial levels at < 120 mg/dl. Macrosomia developed in 50% of the neonates of Latino women versus 19% of neonates of African-American women (relative risk 2.68; 95% confidence interval 1.57-4.59). Potential confounding factors were not significantly different between the Latino and African-American women: mean blood glucose 96.6 +/- 15.7 vs. 96.5 +/- 22.4 mg/dl; BMI 29.0 +/- 5.5 vs. 31.5 +/- 8.2 kg/m2; pregnancy weight gain 29.2 +/- 12.7 vs. 30.9 +/- 20.5 lb; and parity 1.8 +/- 1.5 vs. 1.6 +/- 1.4, respectively. CONCLUSIONS: We have demonstrated that Latino women with GDM are at higher risk for having macrosomic infants in comparison with African-American women. This ethnic variation in fetal growth may be due to varying influences of in utero growth promoters among these populations as well as underlying genetic factors.

Adult↗
PubMed2003

Ancient Wings: animating the evolution of butterfly wing patterns.

Character optimization methods can be used to reconstruct ancestral states at the internal nodes of phylogenetic trees. However, seldom are these ancestral states visualized collectively. Ancient Wings is a computer program that provides a novel method of visualizing the evolution of several morphological traits simultaneously. It allows users to visualize how the ventral hindwing pattern of 54 butterflies in the genus Bicyclus may have changed over time. By clicking on each of the nodes within the evolutionary tree, the user can see an animation of how wing size, eyespot size, and eyespot position relative the wing margin, have putatively evolved as a collective whole. Ancient Wings may be used as a pedagogical device as well as a research tool for hypothesis-generation in the fields of evolutionary, ecological, and developmental biology.

Animals↗
PubMed2004

VizStruct: exploratory visualization for gene expression profiling.

MOTIVATION: DNA arrays provide a broad snapshot of the state of the cell by measuring the expression levels of thousands of genes simultaneously. Visualization techniques can enable the exploration and detection of patterns and relationships in a complex data set by presenting the data in a graphical format in which the key characteristics become more apparent. The dimensionality and size of array data sets however present significant challenges to visualization. The purpose of this study is to present an interactive approach for visualizing variations in gene expression profiles and to assess its usefulness for classifying samples. RESULTS: The first Fourier harmonic projection was used to map multi-dimensional gene expression data to two dimensions in an implementation called VizStruct. The visualization method was tested using the differentially expressed genes identified in eight separate gene expression data sets. The samples were classified using the oblique decision tree (OC1) algorithm to provide a procedure for visualization-driven classification. The classifiers were evaluated by the holdout and the cross-validation techniques. The proposed method was found to achieve high accuracy. AVAILABILITY: Detailed mathematical derivation of all mapping properties as well as figures in color can be found as supplementary on the web page http://www.cse.buffalo.edu/DBGROUP/bioinformatics/supplementary/vizstruct. All programs were written in Java and Matlab and software code is available by request from the first author.

Algorithms↗
PubMed2003

Molecular analysis of gene expression in tumor pathology.

Human cancers are diverse in their pathology and responsiveness to clinical treatment. This diversity is at least in part due to variations in cellular gene expression programs. Although the analyis of proteins--the key players in cells and potential drug targets--is advancing rapidly, there are situations in which the analysis of RNA rather than proteins can provide valuable information for the diagnosis of cancer. These situations include absense of an antibody for the protein of interest, expression of functionally defective proteins, expressed small nucleotide polymorphisms (SNPs), analysis of alternatively or abnormally spliced molecules, and functional analysis of splice site mutations. In this chapter we will focus on the analysis of RNA from clinical samples and will summarize how gene expression studies on the RNA level using a variety of new tools can be useful for discovering new classes of tumors, for predicting clinical outcome or therapy response, and for designing novel personalized clinical interventions that can not be achieved with histology alone.

Cadherins↗
PubMed1996

Cryopreservation of stallion spermatozoa.

The main advantage to using frozen semen in any breeding program is faster genetic gain for the inherited trait desired. Milk production of dairy cows doubled (from 26,000 to 52,000 kg of milk/cow per year) between 1950 and 1980, because the dairy industry was using semen only from bulls with the greatest genetic potential for milk production. This genetic gain could have been achieved without the use of frozen semen; however, the time required to achieve that same genetic progress would have been lengthened exceedingly. Fertility rates using frozen stallion spermatozoa are not equal to that of fresh semen, but with careful management of both the stallion and the mare fertility rates of 40% to 60% can be achieved for a single mare reproductive cycle and fertility rates of 60% to 75% during the course of a breeding season can be expected for a number of stallions. Because pregnancy rates have increased and because many breed registries now condone the use of frozen stallion semen, more people in the equine industry are using frozen semen. It has been the attempt of this article to make the practitioner aware of some of the problems that can occur when processing, freezing, storing, and using frozen semen, and how to control those problems. The practitioner also should be aware that there is large variation in semen quality from stallions, and that spermatozoa from some of the problem stallions can be improved by altering a "standard protocol," but that semen from some stallions will not cryopreserve effectively, regardless of the efforts put forth.

Animals↗
PubMed1987

Growth-associated traits in parental and F1 populations of chickens under different feeding programs. 1. Ad libitum feeding.

Two experiments were conducted to compare body composition, plasma concentrations of glucose, lipid and protein, gastrointestinal tract (GIT) morphology, and digestive enzyme activities among populations of chickens exhibiting wide differences in growth. In the first experiment, males from a high weight (HW) line, a low weight (LW) line, and crosses between the lines (HL) were examined. In the second experiment, the same high weight (HW') line, a White Leghorn (LEG) line and their crosses (HLEG) were compared. In both experiments, comparisons were made at both 25 and 61 days of age. The HW chicks were heavier and had larger breasts and longer shanks than the LW or LEG chicks. Although the crosses (HL, HLEG) exhibited values for these traits intermediate to those of the parental lines, HLEG chicks tended to resemble one of the parental lines more closely than did the HL chicks. Differences among all mating combinations were significant for body fat, but the crosses (HLEG, HL) tended to more closely resemble their HW parental line. The HW chicks had significantly higher concentrations of glucose, lipid, and protein in plasma at 25 but not 61 days of age. No differences in glucose, lipid, or protein concentrations in plasma were observed in the second experiment. When expressed as a percentage of body weight, LW and LEG chicks tended to have larger GIT than HW chicks, whereas crosses more closely resembled the HW line. Although significant differences in digestive enzyme activities were obtained, these differences were generally associated with differences in body weight. It was concluded that genetic variation in the traits examined was dependent on both population and age.

Animals↗
PubMed2003

Gene expression profiling in porcine fetal thymus.

To obtain an initial overview of gene diversity and expression pattern in porcine thymus, 11,712 ESTs (Expressed Sequence Tags) from 100-day-old porcine thymus (FTY) were sequenced and 7,071 cleaned ESTs were used for gene expression analysis. Clustered by the PHRAP program, 959 contigs and 3,074 singlets were obtained. Blast search showed that 806 contigs and 1,669 singlets (totally 5,442 ESTs) had homologues in GenBank and 1,629 ESTs were novel. According to the Gene Ontology classification, 36.99% ESTs were cataloged into the gene expression group, indicating that although the functional gene (18.78% in defense group) of thymus is expressed in a certain degree, the 100-day-old porcine thymus still exists in a developmental stage. Comparative analysis showed that the gene expression pattern of the 100-day-old porcine thymus is similar to that of the human infant thymus.

Animals↗
PubMed2004

Variability of the Chlamydia trachomatis omp1 gene detected in samples from men tested in male-only saunas in Melbourne, Australia.

A recent screening program in Melbourne, Victoria, Australia, has shown that Chlamydia trachomatis is an important infection among men who frequent male-only saunas. To evaluate the C. trachomatis isolates circulating in local saunas, the C. trachomatis-positive samples collected during the program underwent amplification and sequencing of the omp1 gene, and the corresponding serovars were deduced. Forty-seven C. trachomatis-positive samples collected (from October 2001 to September 2002) from 39 men were evaluated. The deduced serovars found, in descending order of prevalence, were D, G, and J; and serovars B, E, F, and H were each found in single samples. The seven different serovars identified in the study sample indicate that local saunas are a reservoir of multiple C. trachomatis strains, possibly maintained by the introduction of new patrons or regular patrons who have been exposed to C. trachomatis elsewhere. No significant genetic variants were found, as most variable positions were silent and were detected only in single samples.

Anal Canal↗
PubMed2026

Impact of genomic selection for disease resistance on the spread of infection in a simulated aquaculture population.

BACKGROUND: In aquaculture, selection for disease resistance is typically based on mortality records from challenge tests performed on relatives of selection candidates. However, commercial success depends on limiting disease transmission, particularly the incidence and severity of outbreaks. It remains unclear whether selecting for lower mortality also reduces disease transmission. Both these outcomes are influenced by three underlying epidemiological host traits: susceptibility, infectivity, and infection-induced mortality. This simulation study evaluated the impact of genomic selection against mortality on disease transmission in a salmon population exposed to a pathogen with a fast transmission rate. METHODS: Mortality was assumed to be recorded on sibs of selection candidate, either as binary dead/alive status or as time to death during cohabitation/bath challenge tests. Phenotypes were simulated using a stochastic compartmental Susceptible-Infected-Removed epidemiological model, with genetic variation for the three underlying traits. Scenarios were explored by varying the genetic correlations between the three underlying traits. Challenge test designs varied in the number of groups, group sizes, and family distribution across groups. For comparison, a reference scenario with direct selection on the underlying traits was included. Genomic selection was applied over 10 discrete generations, and its impact on disease transmission was assessed using the basic reproductive ratio (R0). RESULTS: When selection was based on dead/alive status, R0 was highly sensitive to both the genetic correlations between the three underlying traits and the challenge test design. In contrast, selection based on time to death consistently reduced R0 across all scenarios (often to below 1 within four generations), regardless of trait correlations or test design. Selection on time to death primarily produced fish with reduced susceptibility to infection, while selection on dead/alive status produced fish with increased resistance and endurance to infection, delaying onset of infection or death without necessarily limiting transmission. Direct selection on the underlying epidemiological traits was the most efficient approach to reduce both mortality and transmission. CONCLUSIONS: Genomic selection for disease resistance, when measured as time to death in cohabitation or bath challenge tests conducted until mortality naturally levels off, reduces both mortality and disease spread. Breeding programs may benefit from challenge test designs that enable estimation of genetic parameters for the underlying traits affecting disease transmission and survival.

Animals↗