A5085970204- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Metabolomics and Mass Spectrometry Studies
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Cancer-related gene regulation
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Carcinogens and Genotoxicity Assessment
- Per- and polyfluoroalkyl substances research
- Biomedical Text Mining and Ontologies
- Cancer, Lipids, and Metabolism
- Colorectal Cancer Screening and Detection
- Folate and B Vitamins Research
- DNA Repair Mechanisms
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Cancer Cells and Metastasis
- Genetic factors in colorectal cancer
- Mycotoxins in Agriculture and Food
- Animal testing and alternatives
- Machine Learning and Data Classification
- Indoor Air Quality and Microbial Exposure
Research Triangle Park Foundation
2014-2025
Scio Diamond Technology Corporation (United States)
2023
National Institute of Environmental Health Sciences
2022
Scion
2018
SRA International (United States)
2009-2014
Triangle
2010
A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses increasing use transcriptomic data in toxicology, drug design, risk assessment and translational research. In this version, we have implemented additional statistical filtering options (e.g. Williams' trend test), curve fitting models, Linux Macintosh compatibility support for platforms with up-to-date gene annotations. Furthermore, extensive visualizations,...
The transcriptional repressors Snail and Slug are situated at the core of several signaling pathways proposed to mediate epithelial mesenchymal transition or EMT, which has been implicated in tumor metastasis. EMT involves an alteration from organized, cell structure a mesenchymal, invasive migratory phenotype. In order obtain global view impact expression, we performed microarray experiment using MCF-7 breast cancer line, does not express detectable levels Slug. cells were infected with...
There is growing interest in using machine learning approaches to priority rank studies and reduce human burden screening literature when conducting systematic reviews. In addition, identifying addressable questions during the problem formulation phase of review can be challenging, especially for topics having a large base. Here, we assess performance SWIFT-Review ranking algorithm relevant given research question. We also explore use identify, categorize, visualize areas that are data...
Prostate cancer (PCa) cells preferentially metastasize to bone at least in part by acquiring osteomimetic properties. Runx2, an osteoblast master transcription factor, is aberrantly expressed PCa cells, and promotes their metastatic phenotype. The transcriptional programs regulated Runx2 have been extensively studied during osteoblastogenesis, where it activates or represses target genes a context-dependent manner. However, little known about the gene regulatory networks influenced cells. We...
Changes in gene expression can help reveal the mechanisms of disease processes and mode action for toxicities adverse effects on cellular responses induced by exposures to chemicals, drugs environment agents. The U.S. Tox21 Federal collaboration, which currently quantifies biological nearly 10,000 chemicals via quantitative high-throughput screening(qHTS) vitro model systems, is now making an effort incorporate profiling into existing battery assays. Whole transcriptome analyses performed...
In the screening phase of systematic review, researchers use detailed inclusion/exclusion criteria to decide whether each article in a set candidate articles is relevant research question under consideration. A typical review may require thousands or tens and can utilize hundreds person-hours labor. Here we introduce SWIFT-Active Screener, web-based, collaborative software application, designed reduce overall burden required during this resource-intensive process. To prioritize for Screener...
BackgroundThe relationship of domestic endotoxin exposure to allergy and asthma has been widely investigated. However, few studies have evaluated predictors household endotoxin, none done so for multiple locations within homes on a national scale.ObjectivesWe assayed 2,552 house dust samples in nationwide study understand the bedroom floors, family room beds, kitchen sofas.MethodsReservoir from five was demographic housing information assessed through questionnaire onsite evaluation 2,456...
The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome deacetylation activities. Recent reports describing localization of NuRD provide new insights that question previous models on action, but are not in complete agreement. Here, we location analysis endogenous MBD3, component complex, two human breast cancer cell lines (MCF-7 MDA-MB-231) using independent genomic techniques: DNA adenine...
Memory is a hallmark of adaptive immunity, wherein lymphocytes mount superior response to previously encountered antigen. It has been speculated that epigenetic alterations in memory contribute their functional distinction from naive counterparts. However, the nature and extent compartments remain poorly characterized. Here we profile DNA methylome transcriptome B-lymphocyte subsets representing stages humoral immune before after antigen exposure vivo multiple humans. A significant...
Aberrant DNA methylation commonly occurs in cancer cells where it has been implicated the epigenetic silencing of tumor suppressor genes. Additional roles for methylation, such as transcriptional activation, have predicted but yet to be clearly demonstrated. The BCL6 oncogene is pathogenesis germinal center-derived B cell lymphomas. We demonstrate that intragenic CpG islands within first intron human locus were hypermethylated lymphoma expressed high amounts messenger RNA (mRNA). Inhibition...
Abstract A 5-day in vivo rat model was evaluated as an approach to estimate chemical exposures that may pose minimal risk by comparing benchmark dose (BMD) values for transcriptional changes the liver and kidney BMD toxicological endpoints from traditional toxicity studies. Eighteen chemicals, most having been tested National Toxicology Program 2-year bioassays, were evaluated. Some of these chemicals are potent hepatotoxicants (eg, DE71, PFOA, furan) rodents, some exhibit but have hepatic...
Colorectal cancer (CRC) tends to occur at older age; however, CRC incidence rates have been rising sharply among young age groups. The increasing prevalence of obesity is recognized as a major risk, yet the mechanistic underpinnings remain poorly understood. Using diet-induced mouse model, we identified obesity-associated molecular changes in colonic epithelium and aged mice, further investigated whether were reversed after weight loss. Transcriptome analysis indicated that obesity-related...
Per- and polyfluoroalkyl substances (PFAS) comprise a diverse class of chemicals used in industrial processes, consumer products, fire-fighting foams which have become environmental pollutants concern due to their persistence, ubiquity, associations with adverse human health outcomes, including pregnant persons offspring. Multiple PFAS are associated liver outcomes adult humans toxicological models, but effects on the developing not fully described. Here we performed transcriptomic analyses...
Deep sequencing was used to investigate the subchronic effects of 1 ppm aflatoxin B1 (AFB1), a potent hepatocarcinogen, on male rat liver transcriptome prior onset histopathological lesions or tumors. We hypothesized RNA-Seq would reveal more differentially expressed genes (DEG) than microarray analysis, including low copy and novel transcripts related AFB1's carcinogenic activity compared feed controls (CTRL). Paired-end reads were mapped genome (Rn4) with TopHat further analyzed by DESeq...
Abstract Because the liver plays a vital role in clearance of exogenous chemical compounds, it is susceptible to chemical-induced toxicity. Animal-based testing routinely used assess hepatotoxic potential chemicals. While large-scale high-throughput sequencing data can indicate genes affected by exposures, we need system-level approaches interpret these changes. To this end, developed an updated rat genome-scale metabolic model integrate transcriptomics and utilized structure...
Aqueous film-forming foams (AFFFs) are complex product mixtures that often contain per- and polyfluorinated alkyl substances (PFAS) to enhance fire suppression protect firefighters. However, PFAS have been associated with a range of adverse health effects (e.g., liver thyroid disease cancer), innovative approach methods better understand their toxicity potential identify safer alternatives needed. In this study, we investigated set 30 AFFF, PFAS, clinical drugs) using differentiated cultures...
Abstract Introduction The objective of this study is to determine if multiple systemic autoimmune diseases (SAID) share gene expression pathways that could provide insights into pathogenic mechanisms common these disorders. Methods RNA microarray analyses (Agilent Human 1A(V2) 20K oligo arrays) were used quantify in peripheral blood cells from 20 monozygotic (MZ) twin pairs discordant for SAID. Six affected probands with lupus erythematosus (SLE), six rheumatoid arthritis (RA), eight...
Toxicants with the potential to bioaccumulate in humans and animals have long been a cause for concern, particularly due their association multiple diseases organ injuries. Per- polyfluoro alkyl substances (PFAS) polycyclic aromatic hydrocarbons (PAH) are two such classes of chemicals that associated steatosis liver. Although PFAS PAH classified as molecular mechanisms toxicity remain be explored detail. In this study, we aimed identify by which an acute exposure can induce lipid...
Abstract Formalin‐fixed, paraffin‐embedded (FFPE) pathology specimens represent a potentially vast resource for transcriptomic‐based biomarker discovery. We present here comparison of results from whole transcriptome RNA‐Seq analysis RNA extracted fresh frozen and FFPE livers. The samples were derived rats exposed to aflatoxin B 1 (AFB ) corresponding set control animals. Principal components indicated that separated in the two groups representing presence or absence chemical exposure, both...
Animal models have historically been poor preclinical predictors of gastrointestinal (GI) directed therapeutic efficacy and drug-induced GI toxicity. Human stem primary cell-derived culture systems are a major focus efforts to create biologically relevant that enhance predictive value intestinal The inherent variability in cell-based cultures makes development useful challenge; the stochastic nature cell differentiation interferes with ability build validate reproducible assays query drug...
Apoptosis of lymphocytes governs the response immune system to environmental stress and toxic insult. Signaling through ubiquitously expressed glucocorticoid receptor, stress-induced hormones induce apoptosis via mechanisms requiring altered gene expression. Several reports have detailed changes in expression mediating glucocorticoid-induced lymphocytes. However, few studies examined role non-coding miRNAs this essential physiological process. Previously, using hybridization-based analysis...
Abstract Background Home care/hospice nurses may be at elevated risk of blood exposure because the nature their work and environment. However, little is known about incidence in this population. Methods A mail survey (n = 1,473) was conducted among home North Carolina 2006. Results The adjusted response rate 69%. Nine percent had least one exposure/year. Overall 27.4 (95% confidence interval: 20.2, 34.6)/100,000 visits. Nurses who worked care ≤5 years higher rates than other nurses—seven...