A comparison of human brain dissection by drill versus saw on nucleic acid quality

This study examined the effect of two dissection techniques on the quality of human brain specimens. Frozen cerebellar samples were obtained from postmortem brains of 10 subjects free from neurological and psychiatric disease. These tissues were tested for RNA and DNA concentration and quality after being dissected with either an electric dental drill or a small handsaw. RNA and DNA were extracted separately from each sample, and the concentrations and quality of each were measured. We found that dissection technique does not significantly affect RNA or DNA quality/yield. RNA and DNA yields, as well as RNA integrity showed no significant differences between the two dissection techniques. Therefore, these results support the use of a high-speed hand-held electric dental drill as an efficient and anatomically precise means of human brain dissection without compromising tissue quality. Published by Elsevier B.V

A Bibliometric Analysis of an International Research Ethics Trainee Program

We used bibliometric analysis to evaluate the citations associated with publications by trainees in the Fogarty International Center’s International Research Ethics Education and Curriculum Development program. Papers published between 2004 and 2008 were identified for analysis. The outcome measures were total citations, h-index, and i-10. A total of 328 manuscripts were identified, with a yearly average of 66 publications and 363 citations. The median number of citations per paper is 3 (IQR Q1–Q3:6). 12.6% (n = 53) of papers were cited over 10 times and the h-index is 22, indicating that 22 papers had been cited at least 22 times. The data indicate that trainees have been productive and contributed to the scholarly literature. Future studies to benchmark this performance with other bioethics education programs are required to make interpretation of citation analysis more meaningful

X-ray enabled MOCASSIN: a 3D code for photoionized media

We present a new version of the fully 3D photoionization and dust radiative transfer code, MOCASSIN, that uses a Monte Carlo approach for the transfer of radiation. The X-ray enabled MOCASSIN allows a fully geometry independent description of low-density gaseous environments strongly photoionized by a radiation field extending from radio to gamma rays. The code has been thoroughly benchmarked against other established codes routinely used in the literature, using simple plane parallel models designed to test performance under standard conditions. We show the results of our benchmarking exercise and discuss applicability and limitations of the new code, which should be of guidance for future astrophysical studies with MOCASSIN.Comment: Accepted for publication in ApJS 9 pages, 5 figure

Relative Contributions of Genes, Environment, and Interactions to Blood Lipid Concentrations in a General Adult Population

The authors evaluated the contributions of nine genetic (G) variants (selected from 275 single nucleotide polymorphisms in 11 reverse cholesterol transport pathway genes), five environmental (E) factors (selected from 10), and G × G, E × E, and G × E interactions in explaining population variance of blood lipid concentrations. Total cholesterol, triglycerides, and high density lipoprotein (HDL) cholesterol were measured, and low density lipoprotein (LDL) cholesterol and HDL cholesterol/LDL cholesterol ratio were calculated in a population-based random sample of 1,543 men and women in Geneva, Switzerland, aged 35-74 years in 1999-2001. Explained variances (R2) for HDL cholesterol/LDL cholesterol ratio, HDL cholesterol, and LDL cholesterol, respectively, were 34%, 33%, and 19%, decomposed into main effects of G (6%, 4%, and 5%) and E (25%, 28%, and 11%), with just 3%, 2%, and 3% due to G × G, E × E, and G × E interactions, respectively. Risk factor clustering was only moderate: 70% of study subjects had ≤3 variants, 75% had ≤2 environmental exposures, and 69% had ≤5 of both types of factors. Multiple genes with weak associations, together with more dominating environmental factors, are involved in determining blood lipid concentrations. Interactions added little explained variance. Increasing trends in hypercholesterolemia are attributable to environmental changes affecting populations as a whole. Reducing obesity and smoking and moderating alcohol intake in entire populations should remain the primary strategies for lipid contro

Automated Telephone Monitoring for Relapse Risk among Recent Quitters Enrolled in Quitline Services

poster abstractThis study is part of a randomized controlled trial to test the efficacy of interactive voice response (IVR) technology for enhancing existing quitline services (Free & Clear’s Quit for Life® program) to prevent smoking relapse and achieve abstinence. The IVR system screens for six indicators of risk for relapse including smoking lapse, physical withdrawal symptoms, depressive symptoms, perceived stress, decreased self-efficacy for quitting, and decreased motivation to quit. Participants can screen positive on any one or more risks, resulting in a rollover call to a telephone counselor. There are two intervention arms that differ in timing and frequency of IVR screening. In the Technology Enhanced Quitline arm (TEQ-10), 10 automated calls are placed at decreasing frequency for 8 weeks post-quit (twice a week for the first two weeks, then weekly). The High Intensity Technology-Enhanced Quitline arm (TEQ-20) includes 20 IVR calls (daily for the first 2 weeks, then weekly). This preliminary analysis includes IVR data collected on calls from 4/12/2010 to 10/31/2010. 2620 calls were made to 98 participants in the two intervention arms, TEQ-10 (n=44) and TEQ-20 (n=54). The two arms did not differ significantly on demographics or comorbid conditions. Three outcomes were analyzed: completed screening assessments, positive screen for relapse risk, and smoking lapse (i.e., smoking even a puff since the last call). 136 of the 736 (18.5%) completed assessments were positive for relapse risk: 66 for smoking lapse (49%), 42 craving (31%), 32 depressive symptoms (24%), 27 lack of confidence (20%), 8 stress (6%), and 8 lack of motivation (6%). Logistic regression models (adjusted for age and gender), with GEE estimation to account for withinperson correlation, showed that compared to the TEQ-10 study group, participants in the TEQ-20 study group were more likely to complete assessments (OR=1.7; 95% CI=1.2-2.4), less likely to screen positive for relapse risk (OR=.3; 95% CI=.2-.6), and less likely to have smoked (OR=.2; 95% CI=.09-.4). These results indicate that frequent IVR monitoring during the immediate postquit period may have a positive effect on relapse risk

Association of extreme blood lipid profile phenotypic variation with 11 reverse cholesterol transport genes and 10 non-genetic cardiovascular disease risk factors

This study explored the genetic basis of the combination of extreme blood levels of HDL-C and LDL-C, a well-studied endophenotype for CVD, which has several attractive features as a target for genetic analysis: (1) the trait is moderately heritable; (2) non-genetic risk factors account for a significant but still limited portion of the phenotypic variance; (3) it is known to be moderated by a number of gene products. We exhaustively surveyed 11 candidate genes for allelic variation in a random population-based sample characterized for known CVD risk factors and blood lipid profiles. With the goal of generating specific etiological hypotheses, we compared two groups of subjects with extreme lipid phenotypes, from the same source population, using a case-control design. Cases (n=186) were subjects, within the total sample of 1708 people, who scored in the upper tertile of LDL-C and the lowest tertile of HDL-C, while controls (n=185) scored in the lowest tertile of LDL-C and the upper tertile of HDL-C. We used logistic regression and a four-tiered, systematic model building strategy with internal cross-validation and bootstrapping to investigate the relationships between the trait and 275 genetic variants in the presence of 10 non-genetic risk factors. Our results implicate a subset of nine genetic variants, spanning seven candidate genes, together with five environmental risk factors, in the etiology of extreme lipoprotein phenotypes. We propose a model involving these 14 genetic and non-genetic risk factors for evaluation in future independent studie

Sterol Carrier Protein-2 Directly Interacts with Caveolin-1 in Vitro and in Vivo

HDL-mediated reverse-cholesterol transport as well as phosphoinositide signaling are mediated through plasma membrane microdomains termed caveolae/lipid rafts. However, relatively little is known regarding mechanism(s) whereby these lipids traffic to or are targeted to caveolae/lipid rafts. Since sterol carrier protein-2 (SCP-2) binds both cholesterol and phosphatidylinositol, the possibility that SCP-2 might interact with caveolin-1 and caveolae was examined. Double immunolabeling and laser scanning fluorescence microscopy showed that a small but significant portion of SCP-2 colocalized with caveolin-1 primarily at the plasma membrane of L-cells and more so within intracellular punctuate structures in hepatoma cells. In SCP-2 overexpressing L-cells, SCP-2 was detected in close proximity to caveolin, 48 ± 4 Å, as determined by fluorescence resonance energy transfer (FRET) and immunogold electron microscopy. Cell fractionation of SCP-2 overexpressing L-cells and Western blotting detected SCP-2 in purified plasma membranes, especially in caveolae/ lipid rafts as compared to the nonraft fraction. SCP-2 and caveolin-1 were coimmunoprecipitated from cell lysates by anti-caveolin-1 and anti-SCP-2. Finally, a yeast two-hybrid assay demonstrated that SCP-2 directly interacts with caveolin-1 in vivo. These interactions of SCP-2 with caveolin-1 were specific since a functionally related protein, phosphatidyinositol transfer protein (PITP), colocalized much less well with caveolin-1, was not in close proximity to caveolin-1 (i.e., \u3e120 Å), and was not coimmunoprecipitated by anti-caveolin-1 from cell lysates. In summary, it was shown for the first time that SCP-2 (but not PITP) selectively interacted with caveolin-1, both within the cytoplasm and at the plasma membrane. These data contribute significantly to our understanding of the role of SCP-2 in cholesterol and phosphatidylinositol targeted from intracellular sites of synthesis in the endoplasmic reticulum to caveolae/lipid rafts at the cell surface plasma membrane

Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes

<p>Abstract</p> <p>Background</p> <p>Genes responsible for biosynthesis of fungal secondary metabolites are usually tightly clustered in the genome and co-regulated with metabolite production. Epipolythiodioxopiperazines (ETPs) are a class of secondary metabolite toxins produced by disparate ascomycete fungi and implicated in several animal and plant diseases. Gene clusters responsible for their production have previously been defined in only two fungi. Fungal genome sequence data have been surveyed for the presence of putative ETP clusters and cluster data have been generated from several fungal taxa where genome sequences are not available. Phylogenetic analysis of cluster genes has been used to investigate the assembly and heredity of these gene clusters.</p> <p>Results</p> <p>Putative ETP gene clusters are present in 14 ascomycete taxa, but absent in numerous other ascomycetes examined. These clusters are discontinuously distributed in ascomycete lineages. Gene content is not absolutely fixed, however, common genes are identified and phylogenies of six of these are separately inferred. In each phylogeny almost all cluster genes form monophyletic clades with non-cluster fungal paralogues being the nearest outgroups. This relatedness of cluster genes suggests that a progenitor ETP gene cluster assembled within an ancestral taxon. Within each of the cluster clades, the cluster genes group together in consistent subclades, however, these relationships do not always reflect the phylogeny of ascomycetes. Micro-synteny of several of the genes within the clusters provides further support for these subclades.</p> <p>Conclusion</p> <p>ETP gene clusters appear to have a single origin and have been inherited relatively intact rather than assembling independently in the different ascomycete lineages. This progenitor cluster has given rise to a small number of distinct phylogenetic classes of clusters that are represented in a discontinuous pattern throughout ascomycetes. The disjunct heredity of these clusters is discussed with consideration to multiple instances of independent cluster loss and lateral transfer of gene clusters between lineages.</p

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

We tested whether self-organizing maps (SOMs) could be used to effectively integrate, visualize, and mine diverse genomics data types, including complex chromatin signatures. A fine-grained SOM was trained on 72 ChIP-seq histone modifications and DNase-seq data sets from six biologically diverse cell lines studied by The ENCODE Project Consortium. We mined the resulting SOM to identify chromatin signatures related to sequence-specific transcription factor occupancy, sequence motif enrichment, and biological functions. To highlight clusters enriched for specific functions such as transcriptional promoters or enhancers, we overlaid onto the map additional data sets not used during training, such as ChIP-seq, RNA-seq, CAGE, and information on cis-acting regulatory modules from the literature. We used the SOM to parse known transcriptional enhancers according to the cell-type-specific chromatin signature, and we further corroborated this pattern on the map by EP300 (also known as p300) occupancy. New candidate cell-type-specific enhancers were identified for multiple ENCODE cell types in this way, along with new candidates for ubiquitous enhancer activity. An interactive web interface was developed to allow users to visualize and custom-mine the ENCODE SOM. We conclude that large SOMs trained on chromatin data from multiple cell types provide a powerful way to identify complex relationships in genomic data at user-selected levels of granularity