HUGIn: Hi-C Unifying Genomic Interrogator

Motivation: High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability. Results: We developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell lines. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTL results and functional genomics data. Availability and implementation: HUGIn is available at http://yunliweb.its.unc.edu/HUGIn. Contact: [email protected] or [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online

Adaptive Graph Construction for Isomap Manifold Learning

Isomap is a classical manifold learning approach that preserves geodesic distance of nonlinear data sets. One of the main drawbacks of this method is that it is susceptible to leaking, where a shortcut appears between normally separated portions of a manifold. We propose an adaptive graph construction approach that is based upon the sparsity property of the ℓ1 norm. The ℓ1 enhanced graph construction method replaces k-nearest neighbors in the classical approach. The proposed algorithm is first tested on the data sets from the UCI data base repository which showed that the proposed approach performs better than the classical approach. Next, the proposed approach is applied to two image data sets and achieved improved performances over standard Isomap

eIF4A RNA Helicase Associates with Cyclin-Dependent Protein Kinase A in Proliferating Cells and is Modulated by Phosphorylation

Eukaryotic initiation factor 4A (eIF4A) is a highly conserved RNA-stimulated ATPase and helicase involved in the initiation of messenger RNA translation. Previously, we found that eIF4A interacts with cyclin-dependent kinase A (CDKA), the plant ortholog of mammalian CDK1. Here, we show that this interaction occurs only in proliferating cells where the two proteins coassociate with 5′-cap-binding protein complexes, eIF4F or the plant-specific eIFiso4F. CDKA phosphorylates eIF4A on a conserved threonine residue (threonine-164) within the RNA-binding motif 1b TPGR. In vivo, a phospho-null (APGR) variant of the Arabidopsis (Arabidopsis thaliana) eIF4A1 protein retains the ability to functionally complement a mutant (eif4a1) plant line lacking eIF4A1, whereas a phosphomimetic (EPGR) variant fails to complement. The phospho-null variant (APGR) rescues the slow growth rate of roots and rosettes, together with the ovule-abortion and late-flowering phenotypes. In vitro, wild-type recombinant eIF4A1 and its phospho-null variant both support translation in cell-free wheat germ extracts dependent upon eIF4A, but the phosphomimetic variant does not support translation and also was deficient in ATP hydrolysis and helicase activity. These observations suggest a mechanism whereby CDK phosphorylation has the potential to down-regulate eIF4A activity and thereby affect translation

Dynamics of a grain-scale intruder in a two-dimensional granular medium with and without basal friction

We report on a series of experiments in which a grain-sized intruder is pushed by a spring through a two-dimensional granular material composed of photoelastic disks in a Couette geometry. We study the intruder dynamics as a function of packing fraction for two types of supporting substrates: A frictional glass plate and a layer of water for which basal friction forces are negligible. We observe two dynamical regimes: Intermittent flow, in which the intruder moves freely most of the time but occasionally gets stuck, and stick-slip dynamics, in which the intruder advances via a sequence of distinct, rapid events. When basal friction is present, we observe a smooth crossover between the two regimes as a function of packing fraction, and we find that reducing the interparticle friction coefficient causes the stick-slip regime to shift to higher packing fractions. When basal friction is eliminated, we observe intermittent flow at all accessible packing fractions. For all cases, we present results for the statistics of stick events, the intruder velocity, and the force exerted on the intruder by the grains. Our results indicate the qualitative importance of basal friction at high packing fractions and suggest a possible connection between intruder dynamics in a static material and clogging dynamics in granular flows.Fil: Kozlowski, Ryan. University of Duke; Estados UnidosFil: Carlevaro, Carlos Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaFil: Daniels, Karen E.. North Carolina State University; Estados UnidosFil: Kondic, Lou. New Jersey Institute of Technology; Estados UnidosFil: Pugnaloni, Luis Ariel. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Socolar, Joshua E. S.. University of Duke; Estados UnidosFil: Zheng, Hu. University of Duke; Estados Unidos. Tongji University. College of Civil Engineering. Department of Geotechnical Engineering ; ChinaFil: Behringer, Robert P.. University of Duke; Estados Unido

An initial animal proof-of-concept study for central administration of clozapine to schizophrenia patients

While clozapine is the acknowledged superior pharmacotherapeutic for the treatment of schizophrenia, the side effect profile, which includes potentially fatal complications, limits its usefulness. Central administration of clozapine directly into the brain could circumvent many of the side effect issues due to the dramatic reduction in dose and the limitation of the drug primarily to the CNS. The present study demonstrates that clozapine can be formulated as a stable solution at physiological pH, which does not have in vitro neurotoxic effects at concentrations which may be effective at treating symptoms. Acute central administration improved auditory gating deficits in a mouse model of schizophrenia-like deficits. Assessment of behavioral alterations in rats receiving chronic central infusions of clozapine via osmotic minipump was performed with the open field and elevated plus mazes. Neither paradigm revealed any detrimental effects of the infusion. While these data represent only an initial investigation, they none-the-less suggest that central administration of clozapine may be a viable alternate therapeutic approach for schizophrenia patients which may be effective in symptom reduction without causing behavioral or neurotoxic effects

Knockdown of Amyloid Precursor Protein in Zebrafish Causes Defects in Motor Axon Outgrowth

Amyloid precursor protein (APP) plays a pivotal role in Alzheimer’s disease (AD) pathogenesis, but its normal physiological functions are less clear. Combined deletion of the APP and APP-like protein 2 (APLP2) genes in mice results in post-natal lethality, suggesting that APP performs an essential, if redundant, function during embryogenesis. We previously showed that injection of antisense morpholino to reduce APP levels in zebrafish embryos caused convergent-extension defects. Here we report that a reduction in APP levels causes defective axonal outgrowth of facial branchiomotor and spinal motor neurons, which involves disorganized axonal cytoskeletal elements. The defective outgrowth is caused in a cell-autonomous manner and both extracellular and intracellular domains of human APP are required to rescue the defective phenotype. Interestingly, wild-type human APP rescues the defective phenotype but APPswe mutation, which causes familial AD, does not. Our results show that the zebrafish model provides a powerful system to delineate APP functions in vivo and to study the biological effects of APP mutations

Tissue-specific patterns of gene expression in the epithelium and stroma of normal colon in healthy individuals in an aspirin intervention trial

AbstractRegular aspirin use reduces colon adenoma and carcinoma incidence. UDP-glucuronosyltransferases (UGT) are involved in aspirin metabolism and clearance, and variant alleles in UGT1A6 have been shown to alter salicylic acid metabolism and risk of colon neoplasia. In a randomized, cross-over, placebo-controlled trial of 44 healthy men and women, homozygous for UGT1A6*1 or UGT1A6*2, we explored differences between global epithelial and stromal expression, using Affymetrix U133+2.0 microarrays and tested effects of 60-day aspirin supplementation (325mg/d) on epithelial and stromal gene expression and colon prostaglandin E2 (PGE2) levels. We conducted a comprehensive study of differential gene expression between normal human colonic epithelium and stroma from healthy individuals. Although no statistically significant differences in gene expression were observed in response to aspirin or UGT1A6 genotype, we have identified the genes uniquely and reproducibly expressed in each tissue type and have analyzed the biologic processes they represent. Here we describe in detail how the data, deposited in the Gene Expression Omnibus (GEO) – accession number GSE71571 – was generated including the basic analysis as contained in the manuscript published in BMC Medical Genetics with the PMID 25927723 (Thomas et al., 2015 [9])

A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants.

Defects in USH2A cause both isolated retinal disease and Usher syndrome (ie, retinal disease and deafness). To gain insights into isolated/nonsyndromic USH2A retinopathy, we screened USH2A in 186 probands with recessive retinal disease and no hearing complaint in childhood (discovery cohort) and in 84 probands with recessive retinal disease (replication cohort). Detailed phenotyping, including retinal imaging and audiological assessment, was performed in individuals with two likely disease-causing USH2A variants. Further genetic testing, including screening for a deep-intronic disease-causing variant and large deletions/duplications, was performed in those with one likely disease-causing change. Overall, 23 of 186 probands (discovery cohort) were found to harbour two likely disease-causing variants in USH2A. Some of these variants were predominantly associated with nonsyndromic retinal degeneration ('retinal disease-specific'); these included the common c.2276 G>T, p.(Cys759Phe) mutation and five additional variants: c.2802 T>G, p.(Cys934Trp); c.10073 G>A, p.(Cys3358Tyr); c.11156 G>A, p.(Arg3719His); c.12295-3 T>A; and c.12575 G>A, p.(Arg4192His). An allelic hierarchy was observed in the discovery cohort and confirmed in the replication cohort. In nonsyndromic USH2A disease, retinopathy was consistent with retinitis pigmentosa and the audiological phenotype was variable. USH2A retinopathy is a common cause of nonsyndromic recessive retinal degeneration and has a different mutational spectrum to that observed in Usher syndrome. The following model is proposed: the presence of at least one 'retinal disease-specific' USH2A allele in a patient with USH2A-related disease results in the preservation of normal hearing. Careful genotype-phenotype studies such as this will become increasingly important, especially now that high-throughput sequencing is widely used in the clinical setting.European Journal of Human Genetics advance online publication, 4 February 2015; doi:10.1038/ejhg.2014.283

An Autoethnographic Study of Interprofessional Education Partnerships

Background: Thiis qualitative longitudinal study describes an Interprofessional Education (IPE) collaboration between a public university with medical and pharmacy schools and a private, non-affiliated university with a nursing school. The study explores the dynamics of the IPE partnership and lessons learned over a three-year period in which members of the collaborative directed three IPE simulations.Methods and Findings: An autoethnographic inquiry technique was used to interview eight collaborators who designed and implemented a large-scale IPE simulation for approximately 300 students and 100 faculty members annually for three years. Two, 90-minute group narrative interviews were conducted and audio recorded for transcription and analysis. Five themes emerged: Natural Collaboration, Shared Vision and Commitment, Integrations and Synergy, All Hands on Deck, and Lasting Foundations. Collaborators agreed the joint effort was a positive experience with multidimensional returns on investment. They applied teamwork competencies to build the partnership, develop the IPE simulation, and overcome implementation challenges.Conclusions: Thiis article provides readers with the opportunity to learn from those who have been intimately involved in the design and implementation of a large-scale IPE collaboration to enhance the shared learning process for health students and faculty. Findings highlight the complexity of building an IPE collaborative and the necessity to build partnerships with facilitators committed to communication