bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable number of tandem repeats polymorphism in parathyroid hormone-related protein as predictor of peak bone mass in young healthy Finnish males
Authors: Gupta Ajay , Välimäki Ville-Valtteri , J Välimäki Matti , Löyttyniemi Eliisa , Richard Marilyn , L Bukka Prasanna , Goltzman David , C Karaplis Andrew 
Published: April 2008

ObjectiveMice with osteoblast-specific deletion of parathyroid hormone-related protein (PTHrP) exhibit impaired recruitment and increased apoptosis of osteogenic cells resulting in decreased bone formation and premature osteoporosis. The PTHrP levels within the bone microenvironment are therefore critical in influencing bone mass acquisition. Whether this is applicable in humans has not been established. Here, we studied the association of a variable number of tandem repeats (VNTR) polymorphism in PTHrP with peak bone mass.MethodsEnrolled in the study were 234 young Finnish males, with median age of 19.6 years (range 18.3–20.6 years). Lifestyle factors, serum bone markers, osteodensitometric measurements (lumbar spine and hip) and calcaneal quantitative ultrasound readings were obtained. The PTHrP VNTR length was determined by the PCR amplification of genomic DNA extracted from peripheral blood and correlated to bone parameters by the multiple regression models.ResultsThe presence of at least one 252 bp allele was associated with increased lumbar spine bone mineral density (BMD; P<0.0034), broadband ultrasound attenuation (BUA; P<0.0012) and speed-of-sound (SOS; P<0.0023) measurements. The correlation with increased lumbar spine BMD (P=0.0008), BUA (P=0.005) and SOS (P=0.001) was further strengthened by the pairing of the 252 bp allele with a 460 bp allele in comparison with those without any 252 bp allele. Electrophoretic mobility shift assays were used to illustrate the potential transcriptional functionality of the VNTR sequence.ConclusionThe results indicate that the PTHrP VNTR sequence likely modulates local PTHrP expression within the skeletal microenvironment and could serve as a diagnostic predictor of peak bone mass acquisition.
The role of F-18-fluorodeoxyglucose positron emission tomography in the postoperative evaluation of differentiated thyroid cancer
Authors: Al-Zahrani Ali S , Abouzied Mohei-Eldin M , Salam Suzan Abdel , Mohamed Gamal , Rifai Ayman , Al Sugair Abdulaziz , Amin Tarik 
Published: April 2008

ObjectivesThe objective of the study was to compare F-18-fluorodeoxyglucose position emission tomography (FDG-PET) with diagnostic whole body scanning (DxWBS) and post-ablation radioiodine whole body scanning (TxWBS) and to assess its prognostic value in newly diagnosed differentiated thyroid cancer (DTC) patients, hypothesizing that FDG-PET is more likely to disclose locoregional and distant metastases.Patients and methodsDxWBS and FDG-PET scanning were performed in 26 newly diagnosed DTC patients who underwent thyroidectomy and TxWBS in 24 cases who had radioactive iodine ablation. The results of the FDG-PET scans were correlated with the stage of the disease and the long-term outcome of DTC.ResultsOverall, 18 FDG-PET scans (69.2%) were positive showing a total of 40 foci while 8 scans (30.8%) were negative. The corresponding 26 DxWBS were all positive and showed a total of 47 foci. DxWBS and TxWBS showed similar foci in the 24 patients who had ablation therapy. In contrast to the FDG-PET scans that showed uptake of 26 foci (65%) outside the thyroid bed, 45 foci (95.7%) on DxWBS were in the thyroid bed while 2 foci (4.3%) were in cervical lymph nodes and no focus was seen outside the neck area (P=0.000). There was a clear correlation between the FDG-PET results, the stage of the disease and long-term outcome; seven of the eight negative FDG-PET scans were in stage 1, while all patients with disease higher than stage 1 (six patients) had positive scans. Over a median of 30 months (10–48), seven out of eight patients (87.5%) with negative FDG-PET scans were in remission compared with only eight patients (44.4%) with positive FDG-PET (P=0.04).ConclusionsIn the postoperative evaluation of DTC, compared with DxWBS and TxWBS, FDG-PET scans are more likely to reveal uptake outside the thyroid bed and to correlate with the stage of the disease and long-term outcome.
The methylenetetrahydrofolate reductase C677T genotype and the risk of obesity in three large population-based cohorts.
Authors: Lewis Sarah J , Lawlor Debbie A , Nordestgaard Børge G , Tybjærg-Hansen Anne , Ebrahim Shah , Zacho Jeppe , Ness Andy , Leary Sam , Smith George Davey 
Published: April 2008

ObjectiveEpidemiological studies have shown that low folate levels are associated with a high body mass index (BMI). These findings have potentially important health implications and warrant further investigation to determine whether a causal relationship exists and the direction of this relationship. The methylenetetrahydrofolate reductase (MTHFR)C677T TTgenotype is associated with reduced folate availability and may be a surrogate for measuring folate levels. We sought to determine whetherMTHFR C677Tgenotype was associated with obesity.DesignWe carried out our study on four populations from three longitudinal studies based in the UK and Denmark in which DNA for genotyping was obtained along with measures of obesity.MethodsOur subjects were taken from the British Women's Heart and Health Study (BWHHS), the Avon Longitudinal Study of Parents and Children (two populations: mothers and children) and the Copenhagen City Heart Study. We performed analyses separately by population, and then carried out a meta-analysis, combining similar populations.ResultsInitial findings in the BWHHS suggested that theTTgenotype may be associated with an increased risk of obesity BMI≥30, however, no association was found with BMI or central adiposity in this cohort. This genotype was not associated with obesity in our other cohorts.ConclusionsOur results suggest that the initial positive finding with obesity in the BWHHS was a chance finding. Our findings do not support a causal effect of low folate on obesity.
The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements
Authors: Dolgin Elie S , Charlesworth Brian 
Published: April 2008

Abstract
Transposable elements (TEs) often accumulate in regions of the genome with suppressed recombination. But it is unclear whether this pattern reflects a reduction in the efficacy of selection against deleterious insertions or a relaxation of ectopic recombination. Discriminating between these two hypotheses has been difficult, because no formal model has investigated the effects of recombination under the deleterious insertion model. Here we take a simulation-based approach to analyze this scenario and determine the conditions under which element accumulation is expected in low recombination regions. We show that TEs become fixed as a result of Hill–Robertson effects in the form of Muller's ratchet, but only in regions of extremely low recombination when excision is effectively absent and synergism between elements is weak. These results have important implications for differentiating between the leading models of how selection acts on TEs and should help to interpret emerging population genetic and genomic data.
An Improved Method for Quantitative Trait Loci Detection and Identification of Within-Line Segregation in F2 Intercross Designs
Authors: Rönnegård Lars , Besnier Francois , Carlborg Örjan 
Published: April 2008

Abstract
We present a new flexible, simple, and powerful genome-scan method (flexible intercross analysis, FIA) for detecting quantitative trait loci (QTL) in experimental line crosses. The method is based on a pure random-effects model that simultaneously models between- and within-line QTL variation for single as well as epistatic QTL. It utilizes the score statistic and thereby facilitates computationally efficient significance testing based on empirical significance thresholds obtained by means of permutations. The properties of the method are explored using simulations and analyses of experimental data. The simulations showed that the power of FIA was as good as, or better than, Haley–Knott regression and that FIA was rather insensitive to the level of allelic fixation in the founders, especially for pedigrees with few founders. A chromosome scan was conducted for a meat quality trait in an F2 intercross in pigs where a mutation in the halothane (Ryanodine receptor, RYR1) gene with a large effect on meat quality was known to segregate in one founder line. FIA obtained significant support for the halothane-associated QTL and identified the base generation allele with the mutated allele. A genome scan was also performed in a previously analyzed chicken F2 intercross. In the chicken intercross analysis, four previously detected QTL were confirmed at a 5% genomewide significance level, and FIA gave strong evidence (P &lt; 0.01) for two of these QTL to be segregating within the founder lines. FIA was also extended to account for epistasis and using simulations we show that the method provides good estimates of epistatic QTL variance even for segregating QTL. Extensions of FIA and its applications on other intercross populations including backcrosses, advanced intercross lines, and heterogeneous stocks are also discussed.
Molecular Characterization of Lal2, an SRK-Like Gene Linked to the S-Locus in the Wild Mustard Leavenworthia alabamica
Authors: Busch Jeremiah W , Sharma Julia , Schoen Daniel J 
Published: April 2008

Abstract
Single-locus sporophytic self-incompatibility inhibits inbreeding in many members of the mustard family (Brassicaceae). To investigate the genetics of self-incompatibility in the wild mustard Leavenworthia alabamica, diallel crosses were conducted between full siblings. Patterns of incompatibility were consistent with the action of single-locus sporophytic self-incompatibility. DNA sequences related to S-locus receptor kinase (SRK), the gene involved in self-pollen recognition in mustards, were cloned and sequenced. A single sequence with high identity to SRK and several other groups of sequences (Lal1, Lal2, Lal3, Lal8, and Lal14) were isolated from L. alabamica. We propose that either Lal2 sequences are divergent alleles of SRK or Lal2 is in tight linkage with SRK because (1) Lal2 alleles cosegregate with S-alleles inferred from dialleles in all 97 cases tested in five families; (2) Lal2 sequences are highly diverse at both synonymous and nonsynonymous sites and exhibit patterns of selective constraint similar to those observed at SRK in Brassica and Arabidopsis; and (3) transcripts of one Lal2 allele were detected in leaves and the styles of open flowers, but were most abundant in the stigmas of maturing buds. We discuss the utility of the S-linked polymorphism at Lal2 for studying the evolutionary forces acting on self-incompatibility in Leavenworthia.
Reproducing Kernel Hilbert Spaces Regression Methods for Genomic Assisted Prediction of Quantitative Traits
Authors: Gianola Daniel , van Kaam Johannes B C H M 
Published: April 2008

Abstract
Reproducing kernel Hilbert spaces regression procedures for prediction of total genetic value for quantitative traits, which make use of phenotypic and genomic data simultaneously, are discussed from a theoretical perspective. It is argued that a nonparametric treatment may be needed for capturing the multiple and complex interactions potentially arising in whole-genome models, i.e., those based on thousands of single-nucleotide polymorphism (SNP) markers. After a review of reproducing kernel Hilbert spaces regression, it is shown that the statistical specification admits a standard mixed-effects linear model representation, with smoothing parameters treated as variance components. Models for capturing different forms of interaction, e.g., chromosome-specific, are presented. Implementations can be carried out using software for likelihood-based or Bayesian inference.
Nonparametric Methods for Incorporating Genomic Information Into Genetic Evaluations: An Application to Mortality in Broilers
Authors: González-Recio Oscar , Gianola Daniel , Long Nanye , Weigel Kent A , Rosa Guilherme J M , Avendaño Santiago 
Published: April 2008

Abstract
Four approaches using single-nucleotide polymorphism (SNP) information (F∞-metric model, kernel regression, reproducing kernel Hilbert spaces (RKHS) regression, and a Bayesian regression) were compared with a standard procedure of genetic evaluation (E-BLUP) of sires using mortality rates in broilers as a response variable, working in a Bayesian framework. Late mortality (14–42 days of age) records on 12,167 progeny of 200 sires were precorrected for fixed and random (nongenetic) effects used in the model for genetic evaluation and for the mate effect. The average of the corrected records was computed for each sire. Twenty-four SNPs seemingly associated with late mortality were included in three methods used for genomic assisted evaluations. One thousand SNPs were included in the Bayesian regression, to account for markers along the whole genome. The posterior mean of heritability of mortality was 0.02 in the E-BLUP approach, suggesting that genetic evaluation could be improved if suitable molecular markers were available. Estimates of posterior means and standard deviations of the residual variance were 24.38 (3.88), 29.97 (3.22), 17.07 (3.02), and 20.74 (2.87) for E-BLUP, the linear model on SNPs, RKHS regression, and the Bayesian regression, respectively, suggesting that RKHS accounted for more variance in the data. The two nonparametric methods (kernel and RKHS regression) fitted the data better, having a lower residual sum of squares. Predictive ability, assessed by cross-validation, indicated advantages of the RKHS approach, where accuracy was increased from 25 to 150%, relative to other methods.
Pleiotropic Patterns of Quantitative Trait Loci for 70 Murine Skeletal Traits
Authors: Kenney-Hunt Jane P , Wang Bing , Norgard Elizabeth A , Fawcett Gloria , Falk Doug , Pletscher L Susan , Jarvis Joseph P , Roseman Charles , Wolf Jason , Cheverud James M 
Published: April 2008

AbstractQuantitative trait locus (QTL) studies of a skeletal trait or a few related skeletal components are becoming commonplace, but as yet there has been no investigation of pleiotropic patterns throughout the skeleton. We present a comprehensive survey of pleiotropic patterns affecting mouse skeletal morphology in an intercross of LG/J and SM/J inbred strains (N = 1040), using QTL analysis on 70 skeletal traits. We identify 798 single-trait QTL, coalescing to 105 loci that affect on average 7–8 traits each. The number of traits affected per locus ranges from only 1 trait to 30 traits. Individual traits average 11 QTL each, ranging from 4 to 20. Skeletal traits are affected by many, small-effect loci. Significant additive genotypic values average 0.23 standard deviation (SD) units. Fifty percent of loci show codominance with heterozygotes having intermediate phenotypic values. When dominance does occur, the LG/J allele tends to be dominant to the SM/J allele (30% vs. 8%). Over- and underdominance are relatively rare (12%). Approximately one-fifth of QTL are sex specific, including many for pelvic traits. Evaluating the pleiotropic relationships of skeletal traits is important in understanding the role of genetic variation in the growth and development of the skeleton.
Wispy, the Drosophila Homolog of GLD-2, Is Required During Oogenesis and Egg Activation
Authors: Cui Jun , Sackton Katharine L , Horner Vanessa L , Kumar Kritika E , Wolfner Mariana F 
Published: April 2008

AbstractEgg activation is the process that modifies mature, arrested oocytes so that embryo development can proceed. One key aspect of egg activation is the cytoplasmic polyadenylation of certain maternal mRNAs to permit or enhance their translation. wispy (wisp) maternal-effect mutations in Drosophila block development during the egg-to-embryo transition. We show here that the wisp gene encodes a member of the GLD-2 family of cytoplasmic poly(A) polymerases (PAPs). The WISP protein is required for poly(A) tail elongation of bicoid, Toll, and torso mRNAs upon egg activation. In Drosophila, WISP and Smaug (SMG) have previously been reported to be required to trigger the destabilization of maternal mRNAs during egg activation. SMG is the major regulator of this activity. We report here that SMG is still translated in activated eggs from wisp mutant mothers, indicating that WISP does not regulate mRNA stability by controlling the translation of smg mRNA. We have also analyzed in detail the very early developmental arrest associated with wisp mutations. Pronuclear migration does not occur in activated eggs laid by wisp mutant females. Finally, we find that WISP function is also needed during oogenesis to regulate the poly(A) tail length of dmos during oocyte maturation and to maintain a high level of active (phospho-) mitogen-activated protein kinases (MAPKs).
Genetic Dissociation of Ethanol Sensitivity and Memory Formation in Drosophila melanogaster
Authors: LaFerriere Holly , Guarnieri Douglas J , Sitaraman Divya , Diegelmann Soeren , Heberlein Ulrike , Zars Troy 
Published: April 2008

Abstract
The ad hoc genetic correlation between ethanol sensitivity and learning mechanisms in Drosophila could overemphasize a common process supporting both behaviors. To challenge directly the hypothesis that these mechanisms are singular, we examined the learning phenotypes of 10 new strains. Five of these have increased ethanol sensitivity, and the other 5 do not. We tested place and olfactory memory in each of these lines and found two new learning mutations. In one case, altering the tribbles gene, flies have a significantly reduced place memory, elevated olfactory memory, and normal ethanol response. In the second case, mutation of a gene we name ethanol sensitive with low memory (elm), place memory was not altered, olfactory memory was sharply reduced, and sensitivity to ethanol was increased. In sum, however, we found no overall correlation between ethanol sensitivity and place memory in the 10 lines tested. Furthermore, there was a weak but nonsignificant correlation between ethanol sensitivity and olfactory learning. Thus, mutations that alter learning and sensitivity to ethanol can occur independently of each other and this implies that the set of genes important for both ethanol sensitivity and learning is likely a subset of the genes important for either process.
Estimation of Pairwise Identity by Descent From Dense Genetic Marker Data in a Population Sample of Haplotypes
Authors: Browning Sharon R 
Published: April 2008

Abstract
I present a new approach for calculating probabilities of identity by descent for pairs of haplotypes. The approach is based on a joint hidden Markov model for haplotype frequencies and identity by descent (IBD). This model allows for linkage disequilibrium, and the method can be applied to very dense marker data. The method has high power for detecting IBD tracts of genetic length of 1 cM, with the use of sufficiently dense markers. This enables detection of pairwise IBD between haplotypes from individuals whose most recent common ancestor lived up to 50 generations ago.
Fine Mapping of Quantitative Trait Loci Affecting Female Fertility in Dairy Cattle on BTA03 Using a Dense Single-Nucleotide Polymorphism Map
Authors: Druet Tom , Fritz Sébastien , Boussaha Mekki , Ben-Jemaa Slim , Guillaume François , Derbala David , Zelenika Diana , Lechner Doris , Charon Céline , Boichard Didier , Gut Ivo G , Eggen André , Gautier Mathieu 
Published: April 2008

Abstract
Fertility quantitative trait loci (QTL) are of high interest in dairy cattle since insemination failure has dramatically increased in some breeds such as Holstein. High-throughput SNP analysis and SNP microarrays give the opportunity to genotype many animals for hundreds SNPs per chromosome. In this study, due to these techniques a dense SNP marker map was used to fine map a QTL underlying nonreturn rate measured 90 days after artificial insemination previously detected with a low-density microsatellite marker map. A granddaughter design with 17 Holstein half-sib families (926 offspring) was genotyped for a set of 437 SNPs mapping to BTA3. Linkage analysis was performed by both regression and variance components analysis. An additional analysis combining both linkage analysis and linkage-disequilibrium information was applied. This method first estimated identity-by-descent probabilities among base haplotypes. These probabilities were then used to group the base haplotypes in different clusters. A QTL explaining 14% of the genetic variance was found with high significance (P &lt; 0.001) at position 19 cM with the linkage analysis and four sires were estimated to be heterozygous (P &lt; 0.05). Addition of linkage-disequilibrium information refined the QTL position to a set of narrow peaks. The use of the haplotypes of heterozygous sires offered the possibility to give confidence in some peaks while others could be discarded. Two peaks with high likelihood-ratio test values in the region of which heterozygous sires shared a common haplotype appeared particularly interesting. Despite the fact that the analysis did not fine map the QTL in a unique narrow region, the method proved to be able to handle efficiently and automatically a large amount of information and to refine the QTL position to a small set of narrow intervals. In addition, the QTL identified was confirmed to have a large effect (explaining 13.8% of the genetic variance) on dairy cow fertility as estimated by nonreturn rate at 90 days.
Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing
Authors: Cutter Asher D , Wasmuth James D , Washington Nicole L 
Published: April 2008

Abstract
The evolution of self-fertilization can mediate pronounced changes in genomes as a by-product of a drastic reduction in effective population size and the concomitant accumulation of slightly deleterious mutations by genetic drift. In the nematode genus Caenorhabditis, a highly selfing lifestyle has evolved twice independently, thus permitting an opportunity to test for the effects of mode of reproduction on patterns of molecular evolution on a genomic scale. Here we contrast rates of nucleotide substitution and codon usage bias among thousands of orthologous groups of genes in six species of Caenorhabditis, including the classic model organism Caenorhabditis elegans. Despite evidence that weak selection on synonymous codon usage is pervasive in the history of all species in this genus, we find little difference among species in the patterns of codon usage bias and in replacement-site substitution. Applying a model of relaxed selection on codon usage to the C. elegans and C. briggsae lineages suggests that self-fertilization is unlikely to have evolved more than ∼4 million years ago, which is less than a quarter of the time since they shared a common ancestor with outcrossing species. We conclude that the profound changes in mating behavior, physiology, and developmental mechanisms that accompanied the transition from an obligately outcrossing to a primarily selfing mode of reproduction evolved in the not-too-distant past.