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At least 235 records · Page 13Linked to original sources
PubMed1984

Traits for sire selection related to udder health and management.

Traits related to udder health were discussed: bacteriological measures, clinical frequency, and milk properties (somatic cell count, enzymes, etc.). Bacteriological testing of quarters maximizes information on infection but is impractical on a population scale. Clinical recording is an objective measure but fails to indicate subclinical cases and is not available in most countries. Cell counts are economical to obtain but are highly variable, difficult to interpret, and not sensitive indicators of subclinical infections. Several milk enzymes are possible indicators of tissue damage. Heritabilities are about .2 for cell counts and .1 for other measures, reflecting genetic variation in teat defenses, phagocytosis, or immune response. There appears to be genetic antagonism between cell count and milk yield (positive gentic correlation of .1 to .2) in contrast to the negative phenotypic relationship between milk yield and cell count. A program to select sires whose progeny have lowest cell counts should be formulated carefully; more needs to be known about interpretation of cell count as a defense mechanism. Heightened cell counts decrease the probability of infection upon subsequent challenge with pathogens. Is there heritable variation in cell count of cows before exposure? A combined criterion of cell count, lactose, and enzyme concentration should be studied.

Animals↗
PubMed2004

Distribution of Activator (Ac) throughout the maize genome for use in regional mutagenesis.

A collection of Activator (Ac)-containing, near-isogenic W22 inbred lines has been generated for use in regional mutagenesis experiments. Each line is homozygous for a single, precisely positioned Ac element and the Ds reporter, r1-sc:m3. Through classical and molecular genetic techniques, 158 transposed Ac elements (tr-Acs) were distributed throughout the maize genome and 41 were precisely placed on the linkage map utilizing multiple recombinant inbred populations. Several PCR techniques were utilized to amplify DNA fragments flanking tr-Ac insertions up to 8 kb in length. Sequencing and database searches of flanking DNA revealed that the majority of insertions are in hypomethylated, low- or single-copy sequences, indicating an insertion site preference for genic sequences in the genome. However, a number of Ac transposition events were to highly repetitive sequences in the genome. We present evidence that suggests Ac expression is regulated by genomic context resulting in subtle variations in Ac-mediated excision patterns. These tr-Ac lines can be utilized to isolate genes with unknown function, to conduct fine-scale genetic mapping experiments, and to generate novel allelic diversity in applied breeding programs.

Chromosome Mapping↗
PubMed2006

Temporal changes in the inequality of early growth of Cunninghamia lanceolata (Lamb.) Hook.: a novel application of the Gini coefficient and Lorenz asymmetry.

Growth within tree populations varies among individuals due to changes in biotic and abiotic factors. The degree of such variation, defined as growth inequality, serves as a useful indicator of the uniformity of growth within a population in response to the prevalent environmental conditions. By application of the Gini coefficient (G), an index for inequality, we characterized the early growth inequality of ninety crosses of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) and their open-pollinated parental lines. Tree cumulative height was measured annually for 8 consecutive years. Both the crosses and parental lines exhibited temporal changes in growth inequality. The inequality of total height among the crosses decreased logarithmically with age by nearly 3-fold after 13 growing seasons, suggesting that tree height became less variable among the crosses as trees grew larger. Interestingly, the Lorenz asymmetry, an index reflecting the shape of the Lorenze curve from which G is derived, revealed that the inequality of annual height increment among the crosses resulted from an alternate contribution of the fast-growing and slow-growing trees. Among parental lines, two provenances with the smallest and the largest overall inequality in total height showed a similar pattern of changes in annual growth inequality, and the provenance differences were consistent over time. Compared to the other provinces, a local provenance exhibited less variation in total height among individual trees as reflected by a smaller value of inequality, and was better adapted to the field conditions. Our results demonstrated the sensitivity and usefulness of the Gini coefficient and Lorenz asymmetry for the analysis of growth inequality in non-natural populations. Growth inequality is a potentially useful evaluation criterion for early selection. Given comparable initial growth, provenances/families with lower growth inequality values would likely outperform those with higher growth inequality, and eventually tree size of the latter would be more variable due to greater variations among individual trees. Assessment of growth inequality at early ages will advance our understanding of variability of tree growth within a population, facilitate forest genetics improvement programs, and enhance the efficiency of tree breeding.

China↗
PubMed2006

Inbreeding reduces power-law scaling in the distribution of fluctuating asymmetry: an explanation of the basis of developmental instability.

The study of fluctuating asymmetry has been controversial because of conflicting results found in much of the primary literature. It has been suggested that the source of this conflict is the fact that the basis of fluctuating asymmetry is poorly understood and that, as a consequence, methodology of fluctuating asymmetry studies may be flawed. A new model for the phenomenological basis of fluctuating asymmetry, that variation in fluctuating asymmetry is in large part due to the random exponential growth of cell populations (geometric Brownian motion) that are terminated randomly around a genetically programmed development time, is presented here. If termination of development has a genetic component, then scaling effects and kurtosis in the distribution of fluctuating asymmetry should increase with genetic redundancy of the population. This model prediction was tested by comparing the distribution of multivariate size and shape fluctuating asymmetry in large samples collected from both wild populations and four moderately inbred lines of Drosophila simulans. It was found that while wild populations were best described by a lognormal distribution with power-law scaled tails, the inbred lines derived from the wild stock were dramatically normalized (half-normal) in three of four cases. As predicted, the scaling exponent of the upper tail of the distribution of fluctuating asymmetry increased with inbreeding while the kurtosis and mean fluctuating asymmetry decreased with inbreeding. The model suggests an additional explanation of leptokurtosis in fluctuating asymmetry. Kurtosis and scaling of the statistical distribution of fluctuating asymmetry in a population is related directly to genetic differences between individuals and these differences affect their ability to buffer the process of development against random perturbations.

Animals↗
PubMed2003

Efficient clustering of large EST data sets on parallel computers.

Clustering expressed sequence tags (ESTs) is a powerful strategy for gene identification, gene expression studies and identifying important genetic variations such as single nucleotide polymorphisms. To enable fast clustering of large-scale EST data, we developed PaCE (for Parallel Clustering of ESTs), a software program for EST clustering on parallel computers. In this paper, we report on the design and development of PaCE and its evaluation using Arabidopsis ESTs. The novel features of our approach include: (i) design of memory efficient algorithms to reduce the memory required to linear in the size of the input, (ii) a combination of algorithmic techniques to reduce the computational work without sacrificing the quality of clustering, and (iii) use of parallel processing to reduce run-time and facilitate clustering of larger data sets. Using a combination of these techniques, we report the clustering of 168 200 Arabidopsis ESTs in 15 min on an IBM xSeries cluster with 30 dual-processor nodes. We also clustered 327 632 rat ESTs in 47 min and 420 694 Triticum aestivum ESTs in 3 h and 15 min. We demonstrate the quality of our software using benchmark Arabidopsis EST data, and by comparing it with CAP3, a software widely used for EST assembly. Our software allows clustering of much larger EST data sets than is possible with current software. Because of its speed, it also facilitates multiple runs with different parameters, providing biologists a tool to better analyze EST sequence data. Using PaCE, we clustered EST data from 23 plant species and the results are available at the PlantGDB website.

Algorithms↗
PubMed1997

Mapping of 34 minisatellite loci resolved by two-dimensional DNA typing.

Two-dimensional (2-D) DNA typing is based on electrophoretic separation of genomic DNA fragments in two dimensions according to independent criteria (size and base-pair sequence), followed by hybridization analysis using multilocus probes. The technique allows simultaneous visualization of several hundred loci as spots in a 2-D pattern. The majority of the loci resolved are polymorphic. Using linkage analysis in a large CEPH family, this study reports the mapping of 34 loci detected by the minisatellite core probe 33.6. By multipoint linkage analysis, regional chromosome positions of the 33.6 loci could be deduced, showing no evidence of clustering. In the analysis of spot patterns, use was made of a computerized image analysis system specifically designed for 2-D DNA typing. Since experimental variations between different separation patterns were automatically corrected for with this program, rapid and reliable scorings could be obtained. The results presented demonstrate the availability of reliable genetic information throughout the 2-D separation pattern. Adding the use of semiautomated computerized pattern analysis, this study further substantiates the applicability of 2-D DNA typing in genome scanning, not only in theoretical but also in practical terms. Moreover, it can be anticipated that this method will have a specific advantage in studies that scan for trinucleotide repeat expansions and somatic instability, where the repeat sequences detected by appropriate core probes are of particular interest.

Chromosome Mapping↗
PubMed2026

Genomic early growth mechanisms of two endangered Mexican spruces.

This study elucidated the genomic basis of family-level growth variance in the critically endangered endemic Mexican spruces Picea martinezii and P. mexicana by: (i) analyzing family- and population-level variations in seedling basal diameter and height after 12 months of growth under common garden conditions and seed weight as maternal provisioning trait; and (ii) identifying genomic loci (SNPs) associated with these traits. Despite limited sample sizes (77 and 74 families representing all known populations of both species), 32 and 10 outlier SNPs were identified yielding 17 and six annotated candidate genes in P. martinezii and P. mexicana, respectively. These genes showed contrasting multivariate associations suggesting species-specific hypothesized growth strategies at the family level: defense-oriented framework in P. martinezii and plasticity-driven response in P. mexicana. Notably, several candidate genes encode key components of growth hormone pathways, including a gibberellin-regulated protein, a cytokinin hydroxylase and the AP2-like transcription factor ANT, providing valuable insights into how maternal genetic variation corresponds to the hormonal pathways that govern cell proliferation and organ size in the progeny. Integration of these findings with the contrasting demographic histories of both species revealed that population bottlenecks enhance the detectability of growth-associated variants by reducing background genetic variation. These genomic resources provide actionable information for prioritizing conservation measures, implementing assisted gene flow to maintain adaptive potential under climate change and designing future breeding programs. With 80.9-99.6% sequence identity to conserved Picea abies homologs, these findings may extend across the genus.

Picea↗
PubMed2006

Surveillance of the genetic variation in incident HIV, HCV, and HBV infections in blood and plasma donors: implications for blood safety, diagnostics, treatment, and molecular epidemiology.

Surveillance for molecular variants in blood donors is vital to assuring that blood screening and supplemental assays are sensitive to circulating strains of blood-borne viruses. Blood screening and diagnostic assays licensed in the United States are largely based on prototype viral strains. Documentation of divergent viral strains in the donor pool can lead to accelerated development and licensure of robust serologic and nucleic acid amplification (NAT) assays for donor screening and diagnostic applications. In addition, surveillance for viral variants among donors has implications for assessing the prevalence of drug and vaccine escape mutants and for detecting and monitoring rare variants that may be newly introduced or increasing in the United States donor population. Combined NAT and serologic screening, supplemented by novel serologic testing strategies, can be used to identify donors with incident infections, which are of particular interest with respect to blood safety and public health implications. A systematic program is proposed for the genetic characterization of viral genomes in donors with incident HIV, HCV, or HBV infections.

Blood Donors↗
PubMed2006

Genetic variability affects the development of brown adipocytes in white fat but not in interscapular brown fat.

Cold exposure induces brown adipocytes in retroperitoneal fat (RP) of adult A/J mice but not in C57BL/6J (B6) mice. In contrast, induction of the mitochondrial uncoupling protein 1 gene (Ucp1) in interscapular brown adipose tissue (iBAT) shows no strain dependence. We now show that unlike iBAT, in which Ucp1 was expressed in the fetus and continued throughout life, in RP, Ucp1 was transiently expressed between 10 and 30 days of age and then disappeared. Similar to the lack of genetic variation in the expression of Ucp1 in iBAT during cold induction of adult mice, no genetic variation in Ucp1 expression in iBAT was detected during development. In contrast, UCP1-positive multilocular adipocytes, together with corresponding increases in Ucp1 expression, appeared in RP at 10 days of age in A/J and B6 mice, but with much higher expression in A/J mice. At 20 days of age, brown adipocytes represent the major adipocyte present in RP of A/J mice. The disappearance of brown adipocytes by 30 days of age suggested that tissue remodeling occurred in RP. Genetic variability in Ucp1 expression could not be explained by variation in the expression of selective transcription factors and signaling molecules of adipogenesis. In summary, the existence of genetic variability between A/J and B6 mice during the development of brown adipocyte expression in RP, but not in iBAT, suggests that developmental mechanisms for the brown adipocyte differentiation program are different in these adipose tissues.

Adipocytes↗
PubMed1998

Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome.

Diagnostic re-sequencing plays a central role in medical and evolutionary genetics. In this report we describe a process that applies fluorescence-based re-sequencing and an integrated set of analysis tools to automate and simplify the identification of DNA variations using the human mitochondrial genome as a model system. Two programs used in genome sequence analysis (Phred, a base-caller, and Phrap, a sequence assembler) are applied to assess the quality of each base call across the sequence. Potential DNA variants are automatically identified and 'tagged' by comparing the assembled sequence with a reference sequence. We also show that employing the Consed program to display a set of highly annotated reference sequences greatly simplifies data analysis by providing a visual database containing information on the location of the PCR primers, coding and regulatory sequences and previously known DNA variants. Among the 12 genomes sequenced 378 variants including 29 new variants were identified along with two heteroplasmic sites, automatically detected by the PolyPhred program. Overall we document the ease and speed of performing high quality and accurate fluorescence-based re-sequencing on long tracts of DNA as well as the application of new approaches to automatically find and view DNA variants among these sequences.

Base Sequence↗
PubMed1997

Genetic variation in Asiatic lions and Indian tigers.

Previous reports have suggested that Asiatic lions and tigers are highly inbred and exhibit very low levels of genetic variation. Our analyses on these species have shown much higher degrees of polymorphism than reported. Randomly amplified polymorphic DNA (RAPD) analysis of 38 Asiatic lions, which exist as a single population in the Gir Forest Sanctuary in India, shows an average heterozygosity of 25.82% with four primers. Sperm motility studies by our colleagues corroborate this data. In Indian tigers, microsatellite analysis of five CA repeat loci and multilocus fingerprinting using Bkm 2(8) probe on a population of 22 individuals revealed a heterozygosity of 22.65%. Microsatellite analysis of loci Fca 77 and Fca 126 revealed polymorphism amongst the Asiatic x African lion hybrids, which has enabled us to use these as markers to discriminate the pure Asiatic lions from the hybrids. A similar analysis was used to identify hybrids of Indian and Siberian tigers through polymerase chain reaction (PCR) amplification of hair samples. To ascertain the variation which existed before the population bottleneck at the turn of the present century, microsatellite analysis was performed on 50- to 125-year-old skin samples from museum specimens. Our results show similar levels of genetic variability as in the present population (21.01%). This suggests that low genetic variability may be the characteristic feature of these species and not the result of intensive inbreeding. DNA fingerprinting studies of Asiatic lions and tigers have helped in identifying individuals with high genetic variability which can be used for conservation breeding programs.

Animals↗
PubMedDate not supplied

Cytoplasmic male sterility in sunflower: origin, inheritance, and frequency in natural populations.

Cytoplasmic male sterility (CMS) in commercial sunflower hybrids is thought to be derived from a related wild species, Helianthus petiolaris, yet CMS lines are known to carry the chloroplast DNA genotype of H. annuus. To clarify the origin of sunflower CMS, we developed a polymerase chain reaction-based strategy for detecting CMS in sunflower and surveyed more than 1,200 plants representing 55 accessions of H. annuus and 26 accessions of H. petiolaris. We also tested 160 progeny from three crosses for strict maternal inheritance of organelle DNAs to determine if the apparent discrepancy in the species donor of the mitochondrial DNA and chloroplast DNA genotypes in CMS lines might result from low-frequency maternal or biparental inheritance of either organelle. No CMS cytotypes were observed in natural populations of either H. annuus or H. petiolaris, and strict maternal inheritance of organelle DNA was observed. These data provide little insight, therefore, into the origin and population genetics of CMS in natural populations of sunflower, except that the evidence for strict maternal inheritance of organelles in sunflower makes it unlikely that the mtDNA and cpDNA genotypes in CMS lines were derived from different species. Nonetheless, the primers developed for assaying organelle DNA variation in sunflower may be useful tools for plant breeding programs, cytotype identification, and systematic and evolutionary studies in the domesticated sunflower and its relatives.

Base Sequence↗
PubMed2005

Ontogeny of drug metabolizing enzymes in the neonate.

Fetal exposure to xenobiotics is modulated to a considerable degree by the metabolic capabilities of the mother and the placenta. However, once liberated from the uterine environment the neonate is instantly exposed to a wide array of new macromolecules in the form of byproducts of cellular metabolism, dietary constituents, environmental toxins and pharmacologic agents. The rapid and efficient biotransformation of these compounds by Phase I and Phase II drug-metabolizing enzymes is an essential process if the infant is to avoid the accumulation of reactive compounds that could produce cellular injury or tissue dysfunction. Genetic polymorphisms and environmental factors are known to contribute dramatically to individual variation in the activity of drug-metabolizing enzymes. More recently, it has become apparent that programmed, developmental, regulatory events occur - independent of genotype - which further add to individual variation in drug metabolism. An appreciation of the impact of ontogeny on the expression and functional activity of the major drug-metabolizing enzymes enables the practicing clinician to predict the ultimate consequence of drug administration in the neonate to help guide optimal drug therapy.

Biotransformation↗
PubMed2004

Single nucleotide polymorphisms associated with rat expressed sequences.

Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in populations and are thus most likely to account for the majority of phenotypic and behavioral differences between individuals or strains. Although the rat is extensively studied for the latter, data on naturally occurring polymorphisms are mostly lacking. We have used publicly available sequences consisting of whole-genome shotgun (WGS), expressed sequence tag (EST), and mRNA data as a source for the in silico identification of SNPs in gene-coding regions and have identified a large collection of 33,305 high-quality candidate SNPs. Experimental verification of 471 candidate SNPs using a limited set of rat isolates revealed a confirmation rate of approximately 50%. Although the majority of SNPs were identified between Sprague-Dawley (EST data) and Brown Norway (WGS data) strains, we found that 66% of the verified variations are common among different rat strains. All SNPs were extensively annotated, including chromosomal and genetic map information, and nonsynonymous SNPs were analyzed by SIFT and PolyPhen prediction programs for their potential deleterious effect on protein function. Interestingly, we retrieved three SNPs from the database that result in the introduction of a premature stop codon and that could be confirmed experimentally. Two of these "in silico-identified knockouts" reside in interesting QTL regions. Data are publicly available via a Web interface (http://cascad.niob.knaw.nl), allowing simple and advanced search queries.

Animals↗
PubMed1981

[Characterization of genetic EEG-variations with the amplitude-interval-analysis. I. Variations of alpha-activity; flat-EEG; borderline flat EEG, occipital slow beta-waves; monotonous alpha-rhythm (author's transl)].

In 121 healthy adult male probands with different variants of alpha-activity (monotonous alpha-waves; low voltage EEG, borderline low voltage EEG; occipital slow beta-waves) a quantitative description of unipolar leads was carried out using a program for amplitude-interval (time-domain) analysis. Statistically significant differences between means of the examined parameters were discovered 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 right and left hemispheres (primarily lower alpha-activity together with higher beta-activity on the left hemisphere) were found in all EEG types examined except the variant with monotonous alpha-waves.

Alpha Rhythm↗
PubMed2005

Patterns of Eurasian HSV-1 molecular diversity and inferences of human migrations.

Following our recent report of high levels of recombination and geographic structuring amongst isolates from two populations, we have investigated global patterns of herpes simplex virus type 1 (HSV-1) molecular diversity using population samples from six countries in Europe, Asia and Africa. Sequence comparisons show that HSV-1 from Kenya is both highly diverse and distinct from either European or Asian HSV-1. HSV-1 populations are much more highly differentiated than human populations at the same geographic scales, with 35% of total variation at the level of inter-population comparisons, a difference likely to be due to higher rates of both mutation and genetic drift in HSV-1 than in equivalent human data. There is substantial differentiation between northwestern European HSV-1 populations and those from East Asia, and while patterns of British and Swedish HSV-1 variation were indistinguishable, differentiation was detectable amongst Chinese, Korean and Japanese HSV-1 samples, in spite of their lower overall diversity. The program Structure was used to reconstruct ancestral Eurasian lineages, which we estimated to have originated approximately 60,000 years ago. A specific pattern detected amongst East Asian HSV-1 isolates is currently best explained by the two waves of migration responsible for the peopling of Japan.

Afghanistan↗
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↗