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At least 253 records · Page 14Linked to original sources
PubMed2004

BioMercator: integrating genetic maps and QTL towards discovery of candidate genes.

SUMMARY: Breeding programs face the challenge of integrating information from genomics and from quantitative trait loci (QTL) analysis in order to identify genomic sequences controlling the variation of important traits. Despite the development of integrative databases, building a consensus map of genes, QTL and other loci gathered from multiple maps remains a manual and tedious task. Nevertheless, this is a critical step to reveal co-locations between genes and QTL. Another important matter is to determine whether QTL linked to same traits or related ones is detected in independent experiments and located in the same region, and represents a single locus or not. Statistical tools such as meta-analysis can be used to answer this question. BioMercator has been developed to automate map compilation and QTL meta-analysis, and to visualize co-locations between genes and QTL through a graphical interface. AVAILABILITY: Available upon request (http://moulon/~bioinfo/BioMercator/). Free of charge for academic use.

Algorithms↗
PubMedDate not supplied

Evolution with material symbol systems.

Pattee's semantic closure principle is used to study the characteristics and requirements of evolving material symbols systems. By contrasting agents that reproduce via genetic variation with agents that reproduce via self-inspection, we reach the conclusion that symbols are necessary to attain open-ended evolution, but only if the phenotypes of agents are the result of a material, self-organization process. This way, a study of the inter-dependencies of symbol and matter is presented. This study is based first on a theoretical treatment of symbolic representations, and secondly on simulations of simple agents with matter-symbol inter-dependencies. The agent-based simulations use evolutionary algorithms with indirectly encoded phenotypes. The indirect encoding is based on Fuzzy Development programs, which are procedures for combining fuzzy sets in such a way as to model self-organizing development processes.

Algorithms↗
PubMed2006

LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage.

UNLABELLED: The scale of genetic-variation datasets has increased enormously and the linkage equilibrium (LD) structure of these polymorphisms, particularly in whole-genome association studies, is of great interest. The significant computational complexity of calculating single- and multiple-marker correlations at a genome-wide scale remains challenging. We have developed a program that efficiently characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations. AVAILABILITY: LdCompare is licensed under the GNU General Public License (GPL). Source code, documentation, testing datasets and precompiled executables are available for download at: http://www.affymetrix.com/support/developer/tools/devnettools.affx

Algorithms↗
PubMed2004

SNAP: workbench management tool for evolutionary population genetic analysis.

UNLABELLED: The reconstruction of population processes from DNA sequence variation requires the coordinated implementation of several coalescent-based methods, each bound by specific assumptions and limitations. In practice, the application of these coalescent-based methods for parameter estimation is difficult because they make strict assumptions that must be verified a priori and their parameter-rich nature makes the estimation of all model parameters very complex and computationally intensive. A further complication is their distribution as console applications that require the user to navigate through console menus or specify complex command-line arguments. To facilitate the implementation of these coalescent-based tools we developed SNAP Workbench, a Java program that manages and coordinates a series of programs. The workbench enhances population parameter estimation by ensuring that the assumptions and program limitations of each method are met and by providing a step-by-step methodology for examining population processes that integrates both summary-statistic methods and coalescent-based population genetic models. AVAILABILITY: SNAP Workbench is freely available at http://snap.cifr.ncsu.edu. The workbench and tools can be downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset. SUPPLEMENTARY INFORMATION: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu.

Computer Simulation↗
PubMed2025

Landscape genomics analysis reveals the genetic basis underlying cashmere goats and dairy goats adaptation to frigid environments.

Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance. The purpose of this study was to comprehensively analyze the genetic basis of goat adaptation to cold environments, clarify the impact of environmental factors on genome diversity, and lay the foundation for breeding goat breeds to adapt to climate change. A total of 240 dairy goats were subjected to genome resequencing, and the whole genome sequencing data of 57 individuals from 6 published breeds were incorporated. By integrating multiple approaches such as phylogenetic analysis, population structure analysis, gene flow and population history exploration, selection signal analysis, and genome-environment association analysis, an in-depth investigation was carried out. Phylogenetic analysis unraveled the genetic relationships and differentiation patterns among dairy goats and other goat breeds. Through signal analysis (θπ, FST, XP-CLR), we identified numerous candidate genes associated with cold adaptation in dairy goats (STRIP1, ALX3, HTR4, NTRK2, MRPL11, PELI3, DPP3, BBS1) and cashmere goats (MED12L, MARC2, MARC1, DSG3, C6H4orf22, CHD7, MYPN, KIAA0825, MITF). Genome-environment association (GEA) analysis confirmed the link between these genes and environmental factors. Moreover, a detailed analysis of the critical genes C6H4orf22 and STRIP1 demonstrated their significant roles in the geographical variations of cold adaptation and allele frequency differences among different breeds. This study contributes to understanding the genetic basis of cold adaptation, providing crucial theoretical support for precision breeding programs aimed at improving production performance in cold regions by leveraging adaptive alleles, thereby ensuring sustainable animal husbandry.

Environmental adaptation↗
PubMed2002

Hypothalamic-pituitary-adrenal function.

Basal hypothalamic-pituitary-adrenal (HPA) function is characterised by pulses of corticosterone secretion followed by a transient refractory period when the axis appears to be inhibited. In females pulses of corticosterone secretion occur approximately once per hour with variation in pulse amplitude underlying a diurnal rhythm. Males show smaller pulses of secretion which become widely spaced during the early light phase nadir. Pulsatility is altered by genetic programming, early life experiences and reproductive status. Activation of the HPA axis during adjuvant induced arthritis results in an increase in the pulse frequency. This is associated with a marked change in hypothalamic gene expression with a diminution of CRH mRNA and a marked increase of AVP mRNA which becomes the predominant HPA secretagogue.

Adrenal Glands↗
PubMed2004

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

Databases, Genetic↗
PubMed2002

Oct4 distribution and level in mouse clones: consequences for pluripotency.

Somatic cell clones often fail at a developmental stage coincident with commencement of differentiation. The transcription factor Oct4 is expressed during cleavage stages and is essential for the differentiation of the blastocyst. Oct4 expression becomes restricted to the inner cell mass and epiblast. After gastrulation Oct4 is active only in germ cells and is silent in somatic cells. Here, Oct4 and an Oct4-GFP transgene were used as markers for which gene reprogramming could be directly related to the developmental potential of somatic cell clones. Cumulus cell clones initiated Oct4 expression at the correct stage but showed an incorrect spatial expression in the majority of blastocysts. The ability of clones to form outgrowths was reduced, and the outgrowths had low or even undetectable levels of Oct4 RNA or GFP. The quality of GFP signals in blastocysts correlated with the ability to generate outgrowths that maintain GFP expression and the frequency of embryonic stem (ES) cell derivation. Abnormal Oct4 expression in clones is either directly or indirectly caused by reprogramming errors and is indicative of a general failure to reset the genetic program. The abnormal Oct4 expression may be associated with aberrant expression of other crucial developmental genes, leading to abnormalities at various embryonic stages. Regardless of other genes, the variations observed in Oct4 levels alone account for the majority of failures currently observed for somatic cell cloning.

Animals↗
PubMed2002

Genetic diversity in european and Argentinian cultivated potatoes (Solanum tuberosum subsp. tuberosum) detected by inter-simple sequence repeats (ISSRs).

In this study, the use of inter-simple sequence repeats (ISSR) to assess genetic diversity between cultivated potatoes (Solanum tuberosum subsp. tuberosum) is reported. ISSR technology rapidly reveals high polymorphic fingerprints and thus determines the genetic diversity among potato cultivars. Nine primers were selected according to the number of amplified markers and the level of polymorphism detected. Three primers (GAG(CAA)5, CTG(AG)8, and (AG)8) were used to cluster the 28 potato accessions and 77 polymorphic markers were sufficient to identify all of the accessions. Among the 15 simple sequence repeat (SSR) motifs tested, the most abundant were CAA and AG. Argentinian- and European-grown potatoes were easily distinguished, with a higher level of genetic diversity among potatoes from Argentina. An ISSR study using a limited number of cultivars and very few primers clearly differentiated between all cultivars, thus ISSR was revealed to be a good tool for the genetic identification of potato and for future germplasm-management programs.

Argentina↗
PubMed2000

Identifying conservation units within captive chimpanzee populations.

One of the primary objectives in the captive management of any endangered primate is to preserve as much as possible the genetic diversity that has evolved and still exists in wild gene pools. The rationale for this is based on the theoretical understanding of the relationship between genetic diversity and fitness in response to selection. There remains little consensus, however, as to the type of genetic data that should be used to monitor captive populations. In order to develop a deeper understanding of the degree and nature of genetic diversity among "wild" chimpanzee gene pools, as well as to determine if one type of genetic data is more useful than others, DNA sequence data were generated at three unlinked, nonrepetitive nuclear loci, one polymorphic microsatellite, and the mitochondrial D-loop for 59 unrelated common and pygmy chimpanzees. The results suggest that: 1) data from nuclear loci can be used to differentiate common chimpanzee subspecies; 2) pygmy chimpanzees may have less genetic diversity than common chimpanzees; 3) shared microsatellite alleles do not always indicate identity by descent; and 4) nonrepetitive loci provide unique insights into evolutionary relationships and provide useful information for captive management programs.

Animals↗
PubMed1997

Changing expectations in the control of Mycoplasma gallisepticum.

Mycoplasma gallisepticum (MG) is traditionally controlled by maintaining MG-free flocks on single-age production sites and maintaining them MG-free utilizing good biosecurity and a consistent serological monitoring program. In recent years, several changes have taken place which have changed our ways about thinking about MG control. There have been significant improvements in detection methods. For example, polymerase chain reaction now represents a rapid and sensitive method for detecting the organism. ELISA kits are now much improved. DNA technology now allows rapid identification of specific strains (DNA finger-printing) for epidemiological studies. On the other hand, the industry world-wide is growing rapidly, and there are huge populations of poultry in small geographic areas, making control utilizing biosecurity more and more difficult. Also, multi-age production sites are becoming more common, especially in commercial egg production. This has led to increased usage of live MG vaccines, which are effective in controlling economic losses and may be used as tools in eradication programs.

Animals↗
PubMed2006

Analysis and validation of genome-specific DNA variations in 5' flanking conserved sequences of wheat low-molecular-weight glutenin subunit gene.

The thirty-three 5' flanking conserved sequences of the known low-molecular-weight subunit (LMW-GS) genes have been divided into eight clusters, which was in agreement with the classification based on the deduced N-terminal protein sequences. The DNA polymorphism between the eight clusters was obtained by sequence alignment, and a total of 34 polymorphic positions were observed in the approximately 200 bp regions, among which 18 polymorphic positions were candidate SNPs. Seven cluster-specific primer sets were designed for seven out of eight clusters containing cluster-specific bases, with which the genomic DNA of the ditelosomic lines of group 1 chromosomes of a wheat variety 'Chinese Spring' was employed to carry out chromosome assignment. The subsequent cloning and DNA sequencing of PCR fragments validated the sequences specificity of the 5' flanking conserved sequences between LMW-GS gene groups in different genomes. These results suggested that the coding and 5' flanking regions of LMW-GS genes are likely to have evolved in concerted fashion. The seven primer sets developed in this study could be used to isolate the complete ORFs of seven groups of LMW-GS genes, respectively, and therefore possess great value for further research in the contributions of a single LMW-GS gene to wheat quality in the complex genetic background and the efficient selections of quality-related components in breeding programs.

5' Flanking Region↗
PubMed1981

[Characterization of genetic EEG variables with the amplitude-interval-analysis. II. Variations of the beta-activity and controls (author's transl)].

In 165 adult male probands with different variants of beta-Activity (fronto-percentral beta-wave-groups; diffuse beta-waves) including 76 controls from the same proband population but with inconspicuous EEG patterns, a quantitative description of unipolar leads was carried out using a program for amplitude-interval (time-domain) analysis. Statistically significant differences between some means of the examined parameters were found between the various EEG variants. No single parameter, however, separates these variants reliably. For such a separation, methods of multivariate statistics will have to be used. Significant differences between left and right hemispheres (especially lower average alpha-activity together with higher beta-activity on the left-hand side) were found in all examined EEG types including the controls. Hence, the lack of a significant side difference in the variant with monotonous alpha-waves as described in the first report of this series remains unique.

Adult↗
PubMed1991

Programming of cholesterol metabolism by breast or formula feeding.

We tested the hypothesis that breast or formula feeding and cholesterol intake during the neonatal period influence cholesterol metabolism and arterial fatty streaks in young adult baboons. Genetic variation was controlled by randomly assigning half-sib sire progeny to a factorial dietary design. We measured serum cholesterol and lipoprotein cholesterol concentrations enzymically and cholesterol production and bile acid excretion rates isotopically. The bile cholesterol saturation index was calculated from enzymic analyses of cholesterol, bile salt and phospholipid concentrations in gallbladder bile. Breast-fed baboons had higher serum VLDL + LDL cholesterol/HDL cholesterol ratios in the early postweaning period (six months) until adulthood (7-8 years) than formula-fed baboons. In adulthood a high cholesterol diet increased bile acid excretion by approximately 40% in formula-fed baboons but did not significantly increase the bile acid excretion rate among breast-fed animals. Adult baboons breast fed as infants also had an approximately 8% lower cholesterol production rate than formula-fed animals and a 20% higher bile cholesterol saturation index. The level of cholesterol in the infant formulas influenced cholesterol metabolism in adulthood but not serum lipoprotein concentrations. As young adults, breast-fed baboons had more extensive arterial fatty streaks than formula-fed baboons. This difference could be accounted for by differences in the lipoprotein ratios. These results demonstrate that breast and formula feeding differentially modify cholesterol metabolism. This may influence the development of chronic diseases.

Adult↗
PubMed2003

The genetic diversity of cultivated soybean grown in China.

Cultivated soybean ( Glycine max) is an economically important crop that is grown for its oil and protein products. A better knowledge of its genetic diversity will be valuable for the utilization, conservation, and management of germplasm collections. Using the database of the National Germplasm Evaluation Program of China (NGEPC), we studied the geographical distribution of accessions, the genetic diversity of 15 qualitative and quantitative characters, and the genetic diversity centers of cultivated soybean in China using variation in these 15 traits and genetic diversity indexes (Shannon index). Cultivated soybean is widely distributed throughout China. As an indication of its distribution, a line can be roughly drawn from the Daxinganling mountains in northeastern China to the Qingzang plateaus in southwestern China based on the abundance of accessions and locations of the collections. Of the 22,637 known accessions in China, the 20,570 collected over a vast area between latitudes 18 degrees and 53 degrees N and longitudes 80 degrees and 136 degrees E were used in this study. The Shannon indexes of various morphological traits were calculated. Cultivated soybean accessions were found to exhibit a higher genetic diversity in the area between 34 degrees -41 degrees N and 110 degrees -115 degrees E. On the basis of the geographical distribution of a number of accessions, and their genetic diversity, one genetic diversity center-downstream of the Yellow River Valley-is proposed. Based on these results and on Vavilov's theory on crop origins, one possible diversity center was proposed.

China↗
PubMed2005

Cholesterol ester transfer protein (CETP) Taq1B polymorphism influences the effect of a standardized cardiac rehabilitation program on lipid risk markers.

Cardiac rehabilitation programs (CR) are standard treatment for patients with coronary artery disease (CAD), yet a large variation in risk factor and lipoprotein changes exists. We investigated the role of three common genetic polymorphisms (CETP Taq1B, LIPC -514 and apo E) associated with alterations of lipoprotein metabolism, in patients before and after standardized CR. Three-hundred and seven patients were recruited for this study. DNA samples were collected and all three genotypes were determined for every patient. While the hepatic lipase LIPC promoter polymorphism and apo E genotype showed little or no correlation with response to CR, CETP Taq1B showed significant association with changes in plasma lipid and lipoproteins. The B1 homozygotes for CETP Taq1B genotype showed significant reduction in TC (-0.25+/-0.07, p < 0.01), LDL-C (-0.15+/-0.06, p < 0.050) and TG (-0.20+/-0.08, p < 0.05). B2 carriers showed no significant change in these parameters. HDL-C, exercise capacity and BMI improved independent of genotype. Individuals with the B1B1 genotype appear to respond well to CR, whereas B2 carriers exhibit marginal gains in lipoprotein risk factors. Although the B2 carriers had similar benefits in exercise capacity and weight reduction, long-term consequences of little or no change in lipoprotein risk factors require further investigation to establish appropriate management strategies.

Apolipoproteins E↗
PubMed2004

New lipids in enteral feeding.

PURPOSE OF REVIEW: Lipid sources for enteral nutrition continue to be an exciting area of investigation. It is timely to review recent developments which have largely contributed to thrust enteral feeding into a new era. RECENT FINDINGS: Although much more research needs to be done, there is a better understanding of the competitive relationships between n-6/n-3 fatty acids in conditions of metabolic and immune stress as well as in autoimmune and degenerative diseases. Although structured lipids are more completely absorbed and cleared, other more important clinical benefits need to be documented before they can be considered cost-effective. Immune enhancing formulas are the subject of controversy and some have been shown to be more effective than others. Enteral formulations with short-chain fatty acids are promising but more experimental work on the normal, and the sick colon is needed. Finally, there are a few isolated studies suggesting that enteral feeding with liposomes and with lipolytic products may have advantages when the digestive phase needs to be circumvented. The era of nutrigenomics, in which the effect of specific lipids on genes and proteins is being explored, is with us. We can look forward to nutrigenetics when the effect of genetic variation on the interaction between diet and disease will guide our practice. SUMMARY: Clinicians already have access to lipid sources and formulations which allow them to individualize enteral feeding programs. More clinical and technological research needs to be carried out, however, before products can be tailored to produce optimal effects in specific conditions.

Digestion↗
PubMedDate not supplied

Early adoption of BRCA1/2 testing: who and why.

PURPOSE: Relatively little is known about the characteristics of women who chose to undergo BRCA1/2 testing soon after testing became available, including how they became aware of and chose to pursue testing. Diffusion of innovation theory states that acceptance of an innovation is a function of the potential adopter's value for innovation and perceptions of the compatibility, complexity, and relative advantage of the innovation. These factors may contribute to early uptake of BRCA1/2 testing. The purpose of this study was to describe the characteristics of women who were "early adopters" of clinical BRCA1/2 testing and to determine whether diffusion theory explains variation in uptake of testing after participation in genetic counseling for BRCA1/2 testing. METHODS: A retrospective cohort study of participants in genetic counseling for BRCA1/2 testing was conducted at a clinical program in a large academic health system. Measures included components of diffusion of innovation theory (participant's value for innovation, i.e., "innovativeness," and perceptions of the compatibility, complexity, and relative advantage of BRCA1/2 testing), characteristics of how the participant became aware of and sought BRCA1/2 testing, and decisions about testing after counseling. RESULTS: From the 229 respondents, 71 (31%) had undergone testing at the time of the survey. Fifty-seven women (25%) had sought BRCA1/2 testing because a family member had breast or ovarian cancer and 37 (16%) because they had breast or ovarian cancer. Only 15 women (7%) reported seeking testing because of a physician's recommendation. After multivariate adjustment, higher innovativeness and higher ratings of the compatibility of BRCA1/2 testing were associated with undergoing testing after counseling [relative risk (RR) 1.76, 95% confidence interval (CI) 1.2-2.6]. However, ratings of the complexity or relative advantage of testing were not associated with testing decisions. Higher innovativeness was associated with being the first in the family to undergo testing (RR 4.85, 95% CI 1.6-14.9), becoming aware of BRCA1/2 testing through the media (RR 1.50, 95% CI 1.0-2.4), and being aware of BRCA1/2 testing prior to counseling (RR 1.25, 95% CI 1.1-1.4). CONCLUSIONS: The uptake of BRCA1/2 testing among women undergoing genetic counseling was associated with innovative characteristics of the participant and the perceived compatibility of the test with existing values and needs, but not with the complexity or relative advantage of the test. Most "early adopters" had heard of BRCA1/2 testing from a source other than their physician and had sought testing because of a personal or family member's cancer diagnosis. These findings can inform predictions surrounding the introduction of future genetic susceptibility tests and strategies for guiding the further diffusion of BRCA1/2 testing.

Decision Making↗