Genetic variation and pesticide exposure influence blood DNA methylation signatures in females with early-stage Parkinson's disease.

Although sex, genetics, and exposures can individually influence risk for sporadic Parkinson's disease (PD), the joint contributions of these factors to the epigenetic etiology of PD have not been comprehensively assessed. Here, we profiled sex-stratified genome-wide blood DNAm patterns, SNP genotype, and pesticide exposure in agricultural workers (71 early-stage PD cases, 147 controls) and explored replication in three independent samples of varying demographics (n = 218, 222, and 872). Using a region-based approach, we found more associations of blood DNAm with PD in females (69 regions) than in males (2 regions, Δßadj| ≥0.03, padj ≤ 0.05). For 48 regions in females, models including genotype or genotype and pesticide exposure substantially improved in explaining interindividual variation in DNAm (padj ≤ 0.05), and accounting for these variables decreased the estimated effect of PD on DNAm. The results suggested that genotype, and to a lesser degree, genotype-exposure interactions contributed to variation in PD-associated DNAm. Our findings should be further explored in larger study populations and in experimental systems, preferably with precise measures of exposure.

Treatment of coronary in-stent restenosis with a novel paclitaxel urea coated balloon.

Randomized clinical trials investigating the treatment of coronary in-stent restenosis with paclitaxel iopromide coated balloon catheters have shown favorable results. The aim of the present clinical investigation was to assess the efficacy of a novel paclitaxel urea coated angioplasty balloon in the treatment of coronary in-stent restenosis. A total of 26 restenotic bare metal stents in 23 patients with a lesion length of 22.8 ± 11.1 mm and a reference vessel diameter of 2.64 ± 0.31 mm were treated. Up to six months and including the six-month angiographic control, only one target lesion revascularization was necessary; in total, the rate of major adverse cardiovascular events until six-month follow-up was 4.3 %. In-stent late lumen loss was 0.07 ± 0.37 mm, in-segment late lumen loss 0.02 ± 0.50 mm. Binary restenosis was present in one patient (4.3%). The results of this first-in-human series with a paclitaxel urea coated balloon are comparable to paclitaxel iopromide coated balloon catheters. Randomized, controlled clinical trials are warranted to further evaluate this promising approach.

Population genetic study of the brain-derived neurotrophic factor (BDNF) gene.

Genetic variants in the brain-derived neurotrophic factor (BDNF) gene, predominantly the functional Val66Met polymorphism, have been associated with risk of bipolar disorder and other psychiatric disorders. However, not all studies support these findings, and overall the evidence for the association of BDNF with disease risk is weak. As differences in population genetic structure between patient samples could cause discrepant or spurious association results, we investigated this possibility by carrying out population genetic analyses of the BDNF genomic region. Substantial variation was detected in BDNF coding region single-nucleotide polymorphism (SNP) allele and haplotype frequencies between 58 global populations, with the derived Met allele of Val66Met ranging in frequency from 0 to 72% across populations. F(ST) analyses to assess diversity in the HapMap populations determined that the Val66Met F(ST) value was at the 99.8th percentile among all SNPs in the genome. As the BDNF population genetic differences may be due to local selection, we performed the long-range haplotype test for selection using 68 SNPs spanning the BDNF genomic region in 12 European-derived pedigrees. Evidence for positive selection was found for a high-frequency Val-carrying haplotype, with a relative extended haplotype homozygosity value above the 99 th percentile compared with HapMap data (P=4.6 x 10(-4)). In conclusion, we observed considerable BDNF allele and haplotype diversity among global populations and evidence for positive selection at the BDNF locus. These phenomena can have a profound impact on the detection of disease susceptibility genes and must be considered in gene association studies of BDNF.

Positive natural selection in the human lineage.

Positive natural selection is the force that drives the increase in prevalence of advantageous traits, and it has played a central role in our development as a species. Until recently, the study of natural selection in humans has largely been restricted to comparing individual candidate genes to theoretical expectations. The advent of genome-wide sequence and polymorphism data brings fundamental new tools to the study of natural selection. It is now possible to identify new candidates for selection and to reevaluate previous claims by comparison with empirical distributions of DNA sequence variation across the human genome and among populations. The flood of data and analytical methods, however, raises many new challenges. Here, we review approaches to detect positive natural selection, describe results from recent analyses of genome-wide data, and discuss the prospects and challenges ahead as we expand our understanding of the role of natural selection in shaping the human genome.

A hydrogen-bonded dimer of 13-hydroxy-13-[(triisopropylsilyl)ethynyl]pentacen-6(13H)-one.

The title compound, C33H34O2Si, has been obtained as a product in the synthesis of 6,13-bis[(triisopropylsilyl)ethynyl]-6,13-dihydropentacene-6,13-diol. The solid-state structure reveals a dimer, with strong hydrogen bonds holding the two molecules in a face-to-face arrangement [O...O = 2.746 (2) A and O-H...O = 173 (2) degrees ]. Within each dimer, the pentacene units are pi-stacked (the distance between the mean least-squares planes of 22 C atoms is 3.60 A).

Classical solutions of an electron in magnetized wedge billiards.

We have studied the classical solutions of a free electron constrained to move inside a circular wedge of angle theta(w), in the presence of a homogeneous constant magnetic field B. These billiards have broken rotational symmetry. As B and theta(w) are varied, the apex of the billiards affects the classical dynamics in an important way. We find that for billiards with angles (sqrt[5]-1)/2< or =theta(w)< or =pi/2, the dynamics exhibits a reentrant transition as the field increases. The transition is from regular-to-mixed-to-chaotic-to-mixed-to-chaotic regimes. The reentrance is connected to the appearance and disappearance of periodic orbits nucleated at the boundaries of these billiards as the field increases. There is no reentrance when theta(w)>pi/2. In the latter case as B increases the dynamics goes from quasiintegrable, to intermediate and then to chaotic whispering gallery Larmor modes.

Family-based association study of 76 candidate genes in bipolar disorder: BDNF is a potential risk locus. Brain-derived neutrophic factor.

Identification of the genetic bases for bipolar disorder remains a challenge for the understanding of this disease. Association between 76 candidate genes and bipolar disorder was tested by genotyping 90 single-nucleotide polymorphisms (SNPs) in these genes in 136 parent-proband trios. In this preliminary analysis, SNPs in two genes, brain-derived neurotrophic factor (BDNF) and the alpha subunit of the voltage-dependent calcium channel were associated with bipolar disorder at the P<0.05 level. In view of the large number of hypotheses tested, the two nominally positive associations were then tested in independent populations of bipolar patients and only BDNF remains a potential risk gene. In the replication samples, excess transmission of the valine allele of amino acid 66 of BDNF was observed in the direction of the original result in an additional sample of 334 parent-proband trios (T/U=108/87, P=0.066). Resequencing of 29 kb surrounding the BDNF gene identified 44 additional SNPs. Genotyping eight common SNPs identified three additional markers transmitted to bipolar probands at the P < 0.05 level. Strong LD was observed across this region and all adjacent pairwise haplotypes showed excess transmission to the bipolar proband. Analysis of these haplotypes using TRANSMIT revealed a global P value of 0.03. A single haplotype was identified that is shared by both the original dataset and the replication sample that is uniquely marked by both the rare A allele of the original SNP and a novel allele 11.5 kb 3'. Therefore, this study of 76 candidate genes has identified BDNF as a potential risk allele that will require additional study to confirm.

High-resolution haplotype structure in the human genome.

Linkage disequilibrium (LD) analysis is traditionally based on individual genetic markers and often yields an erratic, non-monotonic picture, because the power to detect allelic associations depends on specific properties of each marker, such as frequency and population history. Ideally, LD analysis should be based directly on the underlying haplotype structure of the human genome, but this structure has remained poorly understood. Here we report a high-resolution analysis of the haplotype structure across 500 kilobases on chromosome 5q31 using 103 single-nucleotide polymorphisms (SNPs) in a European-derived population. The results show a picture of discrete haplotype blocks (of tens to hundreds of kilobases), each with limited diversity punctuated by apparent sites of recombination. In addition, we develop an analytical model for LD mapping based on such haplotype blocks. If our observed structure is general (and published data suggest that it may be), it offers a coherent framework for creating a haplotype map of the human genome.

Interlaboratory reproducibility of standard accelerated aging methods for oxidation of UHMWPE.

During accelerating aging, experimental uncertainty may arise due to variability in the oxidation process, or due to limitations in the technique that is ultimately used to measure oxidation. The purpose of the present interlaboratory study was to quantify the repeatability and reproducibility of standard accelerated aging methods for ultra-high molecular weight polyethylene (UHMWPE). Sections (200 microm thick) were microtomed from the center of an extruded rod of GUR 4150 HP, gamma irradiated in air or nitrogen, and circulated to 12 institutions in the United States and Europe for characterization of oxidation before and after accelerated aging. Specimens were aged for 3 weeks at 80 degrees C in an air circulating oven or for 2 weeks at 70 degrees C in an oxygen bomb (maintained at 503 kPa (5 atm.) of O2) in accordance with the two standard protocols described in ASTM F 2003-00. FTIR spectra were collected from each specimen within 24 h of the start and finish of accelerated aging, and oxidation indices were calculated by normalizing the peak area of the carbonyl region by the reference peak areas at 1370 or 2022 cm(-1). The mean relative interlaboratory uncertainty of the oxidation data was 78.5% after oven aging and 129.1% after bomb aging. The oxidation index measurement technique was not found to be a significant factor in the reproducibility. Comparable relative intrainstitutional uncertainty was observed after oven aging and bomb aging. For both aging methods, institutions successfully discriminated between air-irradiated and control specimens. However, the large interinstitutional variation suggests that absolute performance standards for the oxidation index of UHMWPE after accelerated aging may not be practical at the present time.

Genomewide linkage analysis of stature in multiple populations reveals several regions with evidence of linkage to adult height.

Genomewide linkage analysis has been extremely successful at identification of the genetic variation underlying single-gene disorders. However, linkage analysis has been less successful for common human diseases and other complex traits in which multiple genetic and environmental factors interact to influence disease risk. We hypothesized that a highly heritable complex trait, in which the contribution of environmental factors was relatively limited, might be more amenable to linkage analysis. We therefore chose to study stature (adult height), for which heritability is approximately 75%-90% (Phillips and Matheny 1990; Carmichael and McGue 1995; Preece 1996; Silventoinen et al. 2000). We reanalyzed genomewide scans from four populations for which genotype and height data were available, using a variance-components method implemented in GENEHUNTER 2.0 (Pratt et al. 2000). The populations consisted of 408 individuals in 58 families from the Botnia region of Finland, 753 individuals in 183 families from other parts of Finland, 746 individuals in 179 families from Southern Sweden, and 420 individuals in 63 families from the Saguenay-Lac-St.-Jean region of Quebec. Four regions showed evidence of linkage to stature: 6q24-25, multipoint LOD score 3.85 at marker D6S1007 in Botnia (genomewide P<.06), 7q31.3-36 (LOD 3.40 at marker D7S2195 in Sweden, P<.02), 12p11.2-q14 (LOD 3.35 at markers D12S10990-D12S398 in Finland, P<.05) and 13q32-33 (LOD 3.56 at markers D13S779-D13S797 in Finland, P<.05). In a companion article (Perola et al. 2001 [in this issue]), strong supporting evidence is obtained for linkage to the region on chromosome 7. These studies suggest that highly heritable complex traits such as stature may be genetically tractable and provide insight into the genetic architecture of complex traits.

Association analysis of NOTCH4 loci in schizophrenia using family and population-based controls.

A genetic association between NOTCH4 and schizophrenia has previously been proposed. Unsing all markers previously shown to be associated, we found no evidence for such in three independent family-based samples (n=519 parent-offspring trios), and a case-control sample derived from the same ethnic background as the original observation. These data strongly suggest that NOTCH4 is not a significant susceptibility allele for schizophrenia.

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.

We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.

SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping.

Generating human single-nucleotide polymorphisms (SNPs) is no longer a rate-limiting step for genetic studies of disease. The number of SNPs in public databases already exceeds 200,000, and the total is expected to exceed 1,000,000 within a year. Rather, progress is limited by the inability to genotype large numbers of SNPs. Current genotyping methods are suitable for studying individual loci or at most a handful at a time. Here, we describe a method for parallel genotyping of SNPs, called single base extension-tag array on glass slides, SBE-TAGS. The principle is as follows. SNPs are genotyped by single base extension (SBE), using bifunctional primers carrying a unique sequence tag in addition to a locus-specific sequence. Because each locus has a distinct tag, the genotyping reactions can be performed in a highly multiplexed fashion, and the resulting product can then be "demultiplexed" by hybridization to the reverse complements of the sequence tags arrayed on a glass slide. SBE-TAGS is simple and inexpensive because of the high degree of multiplexing and the use of an easily generated, generic tag array. The method is also highly accurate: we genotyped over 100 SNPs, obtaining over 5, 000 genotypes, with approximately 99% accuracy.

The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes.

Genetic association studies are viewed as problematic and plagued by irreproducibility. Many associations have been reported for type 2 diabetes, but none have been confirmed in multiple samples and with comprehensive controls. We evaluated 16 published genetic associations to type 2 diabetes and related sub-phenotypes using a family-based design to control for population stratification, and replication samples to increase power. We were able to confirm only one association, that of the common Pro12Ala polymorphism in peroxisome proliferator-activated receptor-gamma(PPARgamma) with type 2 diabetes. By analysing over 3,000 individuals, we found a modest (1.25-fold) but significant (P=0.002) increase in diabetes risk associated with the more common proline allele (85% frequency). Moreover, our results resolve a controversy about common variation in PPARgamma. An initial study found a threefold effect, but four of five subsequent publications failed to confirm the association. All six studies are consistent with the odds ratio we describe. The data implicate inherited variation in PPARgamma in the pathogenesis of type 2 diabetes. Because the risk allele occurs at such high frequency, its modest effect translates into a large population attributable risk-influencing as much as 25% of type 2 diabetes in the general population.

Wear behavior and histopathology of classic cemented metal on metal hip endoprostheses.

The authors reviewed their collection of retrieved all metal hip joints (9 McKee-Farrar, 7 Müller, and 3 Huggler type prostheses) and tissues from the joint capsules and implant beds. The amount of wear was measured, and the total volume was calculated. The tissues were analyzed by atomic absorption spectral analysis or inductively coupled plasma mass spectrometry and examined by light and scanning electron microscopy. The size of particles was measured with a texture analysis system. The articulating surfaces showed many delicate scratches which represent normal wear. The calculated annual wear averaged approximately 5 mm3 per year, which is low compared with polyethylene. The cellular reaction to metal wear particles was regarded as mild. The cellular reaction to scattered and worn bone cement was always more pronounced than to metallic debris. Scanning electron microscopy confirmed the irregular shapes and mostly submicron size of the metal particles. The analytically detected metal content of the periarticular tissue was relatively low and in accordance with the wear measurements from the articulating surfaces. The excess of chromium in the tissues is discussed in the light of the elimination of cobalt as well as the relation between elements representing either corrosion products or elements still bound in wear particles.

Endobronchial electrocautery. A role in bronchogenic carcinoma?

Progressive respiratory failure due to massive endobronchial involvement causes death in some patients with bronchogenic carcinoma. The absence of satisfactory therapeutic modalities directed specifically at masses of endobronchial tumor has limited our ability to effectively palliate these patients. Electro-cautery is a technique which has the potential for removing large quantities of endobronchial tumor safely, painlessly , and without measurable blood loss. It is especially well suited to the patient requiring local palliation with immediate relief of airway obstruction and without a prolonged hospital stay. The report reviews: a) its use in an individual with tracheal obstruction; b) the effect of electrocautery current changes and probe type on canine trachea; and, c) the technical problems which must be considered in using endobronchial electrocautery. In the individual with tracheal obstruction, large amounts of tumor were cleared with excellent hemostasis. The canine trachea demonstrates that the amount and duration of current used are extremely important. Equipment available of gastrointestinal electrocautery can produce significant tracheal damage and must be used with great caution. Finally, fiberoptic bronchoscopes are not designed for electrocautery work, and care must be employed when performing such procedures through these instruments.