Holly Coleman
A5063982700- Epigenetics and DNA Methylation
- HIV Research and Treatment
- Genomics and Chromatin Dynamics
- Glycosylation and Glycoproteins Research
- T-cell and B-cell Immunology
- Monoclonal and Polyclonal Antibodies Research
- 3D Printing in Biomedical Research
- Protein purification and stability
- RNA modifications and cancer
- Vibrio bacteria research studies
- Collagen: Extraction and Characterization
- Antibiotic Resistance in Bacteria
- Melanoma and MAPK Pathways
- Nanomaterials and Printing Technologies
- Ultrasound and Hyperthermia Applications
- Cancer-related Molecular Pathways
- Pressure Ulcer Prevention and Management
- Cell death mechanisms and regulation
- Health Policy Implementation Science
- Escherichia coli research studies
- Neurogenetic and Muscular Disorders Research
- Genetics and Neurodevelopmental Disorders
- Electrochemical Analysis and Applications
- Genetic Syndromes and Imprinting
- Congenital Anomalies and Fetal Surgery
University of Colorado Boulder
2023-2024
National Institutes of Health
2010-2020
Missouri University of Science and Technology
2018-2020
University of Rochester
2019-2020
State Street (United States)
2020
National Human Genome Research Institute
2010-2019
Office of Extramural Research
2012
Significance Using high-throughput experiments, we determined the functional epigenomic landscape in pancreatic islet cells. Computational integration of these data along with similar from ENCODE project revealed presence large gene control elements across diverse cell types that refer to as “stretch enhancers.” Stretch enhancers are type specific and associated increased expression genes involved cell-specific processes. We find genetic variations common disease highly enriched stretch...
Genome-wide association studies (GWAS) have identified >100 independent SNPs that modulate the risk of type 2 diabetes (T2D) and related traits. However, pathogenic mechanisms most these remain elusive. Here, we examined genomic, epigenomic, transcriptomic profiles in human pancreatic islets to understand links between genetic variation, chromatin landscape, gene expression context T2D. We first integrated genome transcriptome variation across 112 islet samples produce dense cis-expression...
Diabetics frequently suffer from chronic, nonhealing wounds. Although bacterial colonization and/or infection are generally acknowledged to negatively impact wound healing, the precise relationship between microbial community and impaired healing remains unclear. Because host cutaneous defense response is proposed play a key role in modulating colonization, we longitudinally examined diabetic microbiome tandem with tissue gene expression. By sequencing 16S ribosomal RNA genes, show that...
While Staphylococcus epidermidis is commonly isolated from healthy human skin, it also the most frequent cause of nosocomial infections on indwelling medical devices. Despite its importance, few genome sequences existed and hospital-associated lineage, ST2, had not been fully sequenced.We cultivated 71 commensal S. isolates 15 skin sites compared them with 28 venous catheters blood cultures. We produced 21 9 draft genomes, annotated their gene content, phylogenetic relatedness biochemical...
Synonymous mutations, which do not alter the protein sequence, have been shown to affect function [Sauna ZE, Kimchi-Sarfaty C (2011) Nat Rev Genet 12(10):683–691]. However, synonymous mutations are rarely investigated in cancer genomics field. We used whole-genome and -exome sequencing identify somatic 29 melanoma samples. Validation of one mutation BCL2L12 285 samples identified 12 cases that harbored recurrent F17F mutation. This led increased mRNA levels because differential targeting WT...
Acinetobacter baumannii is an emerging human pathogen and a significant cause of nosocomial infections among hospital patients worldwide. The enormous increase in multidrug resistance isolates the recent emergence pan-drug–resistant strains underscores urgency to understand how A. evolves environments. To this end, we undertook genomic study polyclonal outbreak multidrug-resistant at research-based National Institutes Health Clinical Center. Comparing complete genome sequences three dominant...
Next-generation sequencing of antibody transcripts from HIV-1-infected individuals with broadly neutralizing antibodies could provide an efficient means for identifying somatic variants and characterizing their lineages. Here, we used 454 pyrosequencing identity/divergence grid sampling to analyze heavy- light-chain sequences donor N152, the source 10E8. We identified up 28% difference in amino acid sequence. Heavy- phylogenetic trees 10E8 displayed similar architectures, reconstituted...
ABSTRACT Carbapenem-resistant Klebsiella pneumoniae strains are formidable hospital pathogens that pose a serious threat to patients around the globe due rising incidence in health care facilities, high mortality rates associated with infection, and potential spread antibiotic resistance other bacterial species, such as Escherichia coli . Over 6 months 2011, 17 at National Institutes of Health (NIH) Clinical Center became colonized highly virulent, transmissible carbapenem-resistant strain...
Significance An extraordinary influx of sequencing information is revolutionizing biological inquiry. While sequences entire antibody repertoires are straightforward to obtain, understanding function on the basis sequence alone has remained elusive. Can bioinformatics identify function-specific antibodies within ocean B cell transcripts representing unrelated specificities? We undertook challenge identifying VRC01 class. These individually neutralize up 90% HIV-1; although they share less...
Abstract Developing predictive animal models to assess how candidate vaccines and infection influence the ontogenies of Envelope (Env)-specific antibodies is critical for development an HIV vaccine. Here we use two nonhuman primate compare roles antigen persistence, diversity innate immunity. We perform longitudinal analyses Env-specific B-cell receptor responses SHIV AD8 Env protein vaccination with eight different adjuvants. A subset -infected animals higher viral loads greater show...
Long noncoding RNAs (lncRNAs) play a broad range of biological roles, including regulation expression genes and chromosomes. Here, we present evidence that lncRNAs are involved in vertebrate circadian biology. Differential night/day 112 (0.3 to >50 kb) occurs the rat pineal gland, which is source melatonin, hormone night. Approximately one-half these changes reflect nocturnal increases. Studies eight with 2- >100-fold daily rhythms indicate that, most cases, change results from neural...
Engineered inorganic nanoparticles (NPs) are essential components in the development of nanotechnologies. For applications nanomedicine, particles need to be functionalized ensure a good dispersibility biological fluids. In many cases however, functionalization is not sufficient: become either coated by corona serum proteins or precipitate out solvent. We show that changing coating magnetic iron oxide NPs using poly-L-lysine (PLL) polymer colloidal stability dispersion improved aqueous...
Sialic acid-recognizing Ig-like lectins (Siglecs) are signaling receptors that modulate immune responses, and targeted for interactions by certain pathogens. We describe two primate Siglecs were rendered nonfunctional single genetic events during hominin evolution after our common ancestor with the chimpanzee. SIGLEC13 was deleted an Alu-mediated recombination event, a base pair deletion disrupted ORF of SIGLEC17. Siglec-13 is expressed on chimpanzee monocytes, innate cells react to...
Abstract DNA methylation plays a key role in X-chromosome inactivation (XCI), process that achieves dosage compensation for X-encoded gene products between mammalian female and male cells. However, differential sex chromosome complicates genome-wide epigenomic assessments, the X is frequently excluded from female-to-male comparative analyses. Using sexually dimorphic mouse liver as model, we provide general framework comparing base-resolution patterns across samples have different numbers...
Abstract DNA methylation is an essential epigenetic process in mammals, intimately involved gene regulation. Here we address the extent to which genetics, sex, and pregnancy influence genomic by intercrossing 2 inbred mouse strains, C57BL/6N C3H/HeN, analyzing parents offspring using whole-genome bisulfite sequencing. Differential across genotype detected at thousands of loci preserved on parental alleles offspring. In comparison autosomal patterns hundreds differentially methylated regions...
Abstract Spinal muscular atrophy (SMA) is the most common genetic disease in children. SMA generally caused by mutations gene SMN1 . The survival of motor neurons (SMN) complex consists SMN1, Gemins (2–8), and Strap/Unrip. We previously demonstrated smn1 gemin5 inhibited tissue regeneration zebrafish. Here we investigated each individual SMN member identified gemin3 as another regeneration-essential gene. These three genes are likely pan-regenerative, since they affect hair cells, liver,...
The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation numerous draft whole-genome sequence assemblies. In contrast, process refining those assemblies to improve contiguity increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, expensive. As a result, vast majority genome sequences generated date remain at stage.To date, our efforts focused on comparative studies targeted genomic regions,...