University of Utah

About: University of Utah is a education organization based out in Salt Lake City, Utah, United States. It is known for research contribution in the topics: Population & Medicine. The organization has 52894 authors who have published 124076 publications receiving 5265834 citations. The organization is also known as: The U & The University of Utah.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Abstract: The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.

Gene for von Recklinghausen neurofibromatosis is in the pericentromeric region of chromosome 17

Abstract: Linkage analysis of 15 Utah kindreds demonstrated that a gene responsible for von Recklinghausen neurofibromatosis (NF) is located near the centromere on chromosome 17. The families also gave no evidence for heterogeneity, indicating that a significant proportion of NF cases are due to mutations at a single locus. Further genetic analysis can now refine this localization and may lead to the eventual identification and cloning of the defective gene responsible for this disorder.

A beginner's guide to eukaryotic genome annotation

Abstract: The falling cost of genome sequencing is having a marked impact on the research community with respect to which genomes are sequenced and how and where they are annotated. Genome annotation projects have generally become small-scale affairs that are often carried out by an individual laboratory. Although annotating a eukaryotic genome assembly is now within the reach of non-experts, it remains a challenging task. Here we provide an overview of the genome annotation process and the available tools and describe some best-practice approaches.

Polarizable Force Field Development and Molecular Dynamics Simulations of Ionic Liquids

Abstract: A many-body polarizable force field has been developed and validated for ionic liquids (ILs) containing 1-methyl-3-alkylimidazolium, 1-alkyl-2-methyl-3-alkylimidazolium, N-methyl-N-alkylpyrrolidinium, N-alkylpyridinium, N-alkyl-N-alkylpiperidinium, N-alkyl-N-alkylmorpholinium, tetraalkylammonium, tetraalkylphosphonium, N-methyl-N-oligoetherpyrrolidinium cations and BF4−, CF3BF3−, CH3BF3−, CF3SO3−, PF6−, dicyanamide, tricyanomethanide, tetracyanoborate, bis(trifluoromethane sulfonyl)imide (Ntf2− or TFSI−), bis(fluorosulfonyl)imide (FSI−) and nitrate anions. Classical molecular dynamics (MD) simulations have been performed on 30 ionic liquids at 298, 333, and 393 K. The IL density, heat of vaporization, ion self-diffusion coefficient, conductivity, and viscosity were found in a good agreement with available experimental data. Ability of the developed force field to predict ionic crystal cell parameters has been tested on four ionic crystals containing Ntf2− anions. The influence of polarization on the struc...

Activated platelets signal chemokine synthesis by human monocytes.

Abstract: Human blood monocytes adhere rapidly and for prolonged periods to activated platelets that display P-selectin, an adhesion protein that recognizes a specific ligand on leukocytes, P-selectin glycoprotein-1. We previously demonstrated that P-selectin regulates expression and secretion of cytokines by stimulated monocytes when it is presented in a purified, immobilized form or by transfected cells. Here we show that thrombin-activated platelets induce the expression and secretion of monocyte chemotactic protein-1 and IL-8 by monocytes. Enhanced monokine synthesis requires engagement of P-selectin glycoprotein-1 on the leukocyte by P-selectin on the platelet. Secretion of the chemokines is not, however, directly signaled by P-selectin; instead, tethering of the monocytes by P-selectin is required for their activation by RANTES (regulated upon activation normal T cell expressed presumed secreted), a platelet chemokine not previously known to induce immediate-early gene products in monocytes. Adhesion of monocytes to activated platelets results in nuclear translocation of p65 (RelA), a component of the NF-kappaB family of transcription factors that binds kappaB sequences in the regulatory regions of monocyte chemotactic protein-1, IL-8, and other immediate-early genes. However, expression of tissue factor, a coagulation protein that also has a kappaB sequence in the 5' regulatory region of its gene, is not induced in monocytes adherent to activated platelets. Thus, contact of monocytes with activated platelets differentially affects the expression of monocyte products. These experiments suggest that activated platelets regulate chemokine secretion by monocytes in inflammatory lesions in vivo and provide a model for the study of gene regulation in cell-cell interactions.