Non-Game Bird habitat Associated With Haul Roads and Surface Mining for Bentonite Clay

A 2 year study was conducted to investigate possible differences in density and diversity of birds in relation to distance from mining haul roads and various aged mine spoils. Winter bird surveys and breeding bird counts were conducted during 1977 and 1978. Bird density and diversity were estimated and compared between the following habitat areas: old spoils (mined ≥20 years ago, unreclaimed), new spoils (mined ≤20 years ago, reclaimed) and unmined areas. Within unmined areas density and diversity of birds 100m, 300m, 500m, and 900m from a mining haul road were compared to detect differences in density and diversity with distance from the haul road. Density of common bird species within mined and unmined areas was compared. Forward stepwise multiple regression was used to identify groups of physical and/or vegetation variables that accounted for variation in bird density and diversity indices. Management suggestions for reclamation of strip mined areas are given. Horned larks (Eremophila alpestres) was the only species observed during the 1977 winter survey within the old spoils, new spoils and unmined areas. Highest horned lark density occurred in new spoils. Horned larks, common redpolls (Acanthis flammea) and snow buntings (Plectrophenax nivalis) were observed during the 1978 winter survey. All 3 species were observed in new spoils and snow huntings were the most abundant. Horned larks and common redpolls were observed in old spoils with common redpolls most abundant. Snow buntings and horned larks were observed in unmined areas. Snow buntings were the most common species in unmined areas. Breeding bird counts indicated that the highest bird diversity occurred on reclaimed mine spoils both years. The highest bird density occurred on reclaimed areas in 1977. Bird densities in unmined areas and reclaimed spoils were similar in 1978. The lowest bird density and diversity consistently occurred in the old unreclaimed mine spoils. Vesper sparrows (Pooecetes graminius) were the most common bird species in unmined areas but were less numerous in reclaimed areas because of the absence of shrub cover. Orthogonal T-tests were used to test for differences in bird density and diversity at 100m, 300m, 500m, and 900m interval from a mining haul road. Differences in bird diversity were not significant at the 10% level except in 1978 between the 900m interval and the pooled 100m, 300m, and 500m intervals. Bird density increased with distance from the haul road in 1978 but not in 1977. Horned larks and brewer’s sparrows (Spizella breweri) showed significant (p≤.10) increases in density with distance from the haul road. Reclamation of strip mined land resulted in bird densities similar to bird densities in unmined areas. Diversity in reclaimed areas was higher than in unmined areas. Vesper and brewer’s sparrows were uncommon on reclaimed land because of the absence of shrubs. Birds did not appear to be affected by presence of mining haul roads with the exception of horned larks and brewer’s sparrows

Genome-wide linkage scan for prostate cancer susceptibility from the university of michigan prostate cancer genetics project: Suggestive evidence for linkage at 16q23

BACKGROUND Prostate cancer linkage studies have been used to localize rare and presumably highly penetrant cancer susceptibility genes. Underlying genetic heterogeneity, as well as the high sporadic background of the disease, has resulted in many signals that are often not reproducible between research studies. METHODS We conducted a SNP-based genome wide linkage scan on 131 Caucasian prostate cancer families participating in the University of Michigan Prostate Cancer Genetics Project (PCGP). RESULTS The strongest evidence for linkage was detected at 16q23 (LOD = 2.70 at rs1079635). Prostate cancer linkage to the same region of 16q23 has been observed by others and the region contains several strong candidate genes including the known prostate cancer tumor suppressor genes ATBF1 and WWOX . This linkage signal was not detected in our prior linkage study on 175 PCGP families, illustrating the genetic heterogeneity underlying prostate cancer susceptibility. CONCLUSIONS Further linkage studies in combination with tumor analyses from linked families are in progress to identify the putative hereditary prostate cancer gene at 16q23. Prostate 69:385–391, 2009. © 2008 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61534/1/20891_ftp.pd

Lung Injury Pathways: Adenosine Receptor 2B Signaling Limits Development of Ischemic Bronchiolitis Obliterans Organizing Pneumonia

Purpose/Aim of the Study: Adenosine signaling was studied in bronchiolitis obliterans organizing pneumonia (BOOP) resulting from unilateral lung ischemia. Materials and Methods: Ischemia was achieved by either left main pulmonary artery or complete hilar ligation. Sprague–Dawley (SD) rats, Dahl salt sensitive (SS) rats and SS mutant rat strains containing a mutation in the A2B adenosine receptor gene (Adora2b) were studied. Adenosine concentrations were measured in bronchoalveolar lavage (BAL) by HPLC. A2A (A2AAR) and A2B adenosine receptor (A2BAR) mRNA and protein were quantified. Results: Twenty-four hours after unilateral PA ligation, BAL adenosine concentrations from ischemic lungs were increased relative to contralateral lungs in SD rats. A2BAR mRNA and protein concentrations were increased after PA ligation while miR27a, a negatively regulating microRNA, was decreased in ischemic lungs. A2AAR mRNA and protein concentrations remained unchanged following ischemia. A2BAR protein was increased in PA ligated lungs of SS rats after 7 days, and 4 h after complete hilar ligation in SD rats. SS-Adora2b mutants showed a greater extent of BOOP relative to SS rats, and greater inflammatory changes. Conclusion: Increased A2BAR and adenosine following unilateral lung ischemia as well as more BOOP in A2BAR mutant rats implicate a protective role for A2BAR signaling in countering ischemic lung injury

Quantitative trait association in parent offspring trios: Extension of case/pseudocontrol method and comparison of prospective and retrospective approaches

The case/pseudocontrol method provides a convenient framework for family-based association analysis of case-parent trios, incorporating several previously proposed methods such as the transmission/disequilibrium test and log-linear modelling of parent-of-origin effects. The method allows genotype and haplotype analysis at an arbitrary number of linked and unlinked multiallelic loci, as well as modelling of more complex effects such as epistasis, parent-of-origin effects, maternal genotype and mother-child interaction effects, and gene-environment interactions. Here we extend the method for analysis of quantitative as opposed to dichotomous (e.g. disease) traits. The resulting method can be thought of as a retrospective approach, modelling genotype given trait value, in contrast to prospective approaches that model trait given genotype. Through simulations and analytical derivations, we examine the power and properties of our proposed approach, and compare it to several previously proposed single-locus methods for quantitative trait association analysis. We investigate the performance of the different methods when extended to allow analysis of haplotype, maternal genotype and parent-of-origin effects. With randomly ascertained families, with or without population stratification, the prospective approach (modeling trait value given genotype) is found to be generally most effective, although the retrospective approach has some advantages with regard to estimation and interpretability of parameter estimates when applied to selected samples. Genet. Epidemiol. 31:833, 2007. © 2007 Wiley-Liss, Inc

A Weighted U Statistic for Genetic Association Analyses of Sequencing Data

With advancements in next generation sequencing technology, a massive amount of sequencing data are generated, offering a great opportunity to comprehensively investigate the role of rare variants in the genetic etiology of complex diseases. Nevertheless, this poses a great challenge for the statistical analysis of high-dimensional sequencing data. The association analyses based on traditional statistical methods suffer substantial power loss because of the low frequency of genetic variants and the extremely high dimensionality of the data. We developed a weighted U statistic, referred to as WU-seq, for the high-dimensional association analysis of sequencing data. Based on a non-parametric U statistic, WU-SEQ makes no assumption of the underlying disease model and phenotype distribution, and can be applied to a variety of phenotypes. Through simulation studies and an empirical study, we showed that WU-SEQ outperformed a commonly used SKAT method when the underlying assumptions were violated (e.g., the phenotype followed a heavy-tailed distribution). Even when the assumptions were satisfied, WU-SEQ still attained comparable performance to SKAT. Finally, we applied WU-seq to sequencing data from the Dallas Heart Study (DHS), and detected an association between ANGPTL 4 and very low density lipoprotein cholesterol

Haplotype association analysis for late onset diseases using nuclear family data

In haplotype-based association studies for late onset diseases, one attractive design is to use available unaffected spouses as controls (Valle et al. [1998] Diab. Care 21:949–958). Given cases and spouses only, the standard expectation-maximization (EM) algorithm (Dempster et al. [1977] J. R. Stat. Soc. B 39:1–38) for case-control data can be used to estimate haplotype frequencies. But often we will have offspring for at least some of the spouse pairs, and offspring genotypes provide additional information about the haplotypes of the parents. Existing methods may either ignore the offspring information, or reconstruct haplotypes for the subjects using offspring information and discard data from those whose haplotypes cannot be reconstructed with high confidence. Neither of these approaches is efficient, and the latter approach may also be biased. For case-control data with some subjects forming spouse pairs and offspring genotypes available for some spouse pairs or individuals, we propose a unified, likelihood-based method of haplotype inference. The method makes use of available offspring genotype information to apportion ambiguous haplotypes for the subjects. For subjects without offspring genotype information, haplotypes are apportioned as in the standard EM algorithm for case-control data. Our method enables efficient haplotype frequency estimation using an EM algorithm and supports probabilistic haplotype reconstruction with the probability calculated based on the whole sample. We describe likelihood ratio and permutation tests to test for disease-haplotype association, and describe three test statistics that are potentially useful for detecting such an association. Genet. Epidemiol. 2006. © 2006 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/50656/1/20139_ftp.pd