A5028654360- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Cancer-related gene regulation
- Cancer-related molecular mechanisms research
- Bacterial Genetics and Biotechnology
- Viral Infectious Diseases and Gene Expression in Insects
- HIV-related health complications and treatments
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Neural Networks and Applications
- Single-cell and spatial transcriptomics
- Industrial Vision Systems and Defect Detection
- HIV Research and Treatment
- Fault Detection and Control Systems
- Metabolomics and Mass Spectrometry Studies
- Cell Image Analysis Techniques
- Cardiomyopathy and Myosin Studies
- Antimicrobial Resistance in Staphylococcus
- Bacterial biofilms and quorum sensing
- dental development and anomalies
- Gastrointestinal motility and disorders
- Glycosylation and Glycoproteins Research
University of Nebraska Medical Center
2013-2023
Fred and Pamela Buffett Cancer Center
2015
Nebraska Medical Center
2013
A hallmark of human cancer is global DNA hypomethylation (GDHO), but the mechanisms accounting for this defect and its pathological consequences have not been investigated in epithelial ovarian (EOC). In EOC, GDHO was associated with advanced disease reduced overall disease-free survival. (+) EOC tumors displayed a proliferative gene expression signature, including FOXM1 CCNE1 overexpression. Furthermore, these enriched within genomic blocks (hypomethylated blocks) that overlapped...
The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another assembly, CR_1.0, also available but substantially more fragmented than rheMac2 with smaller contigs scaffolds. Annotations these two assemblies are limited in completeness accuracy. High quality files required wide...
Abstract A hallmark of human cancer is global DNA hypomethylation (GDHO), but the mechanisms accounting for this defect and its pathological consequences have not been defined in epithelial ovarian (EOC). In EOC, GDHO was associated with advanced disease reduced overall disease-free survival. GDHO(+) EOC enriched a proliferative gene expression signature, including CCNE1 FOXM1 overexpression. preferentially occurred within genomic blocks (hypomethylated blocks) overlapping late-replicating,...
The focus of radiation biodosimetry has changed recently, and a paradigm shift for using molecular technologies omic platforms in addition to cytogenetic techniques been observed. In our study, we have used nonhuman primate model investigate the impact supralethal dose 12 Gy on alterations lung transcriptome. We 6 healthy 32 irradiated animal samples delineate radiation-induced changes. also medical countermeasure, γ-tocotrienol (GT3), observe any demonstrate significant changes...
Abstract Background Understanding protein subcellular localization is a necessary component toward understanding the overall function of protein. Numerous computational methods have been published over past decade, with varying degrees success. Despite large number in this area, only small fraction them are available for researchers to use their own studies. Of those that available, many limited by predicting organelles cell. Additionally, majority predict single location sequence, even...
LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in eukaryotic cell with brief coverage bacterial proteins. Proteins must be localized at their appropriate compartment to perform desired function. Mislocalization proteins unintended locations causative factor many human diseases; therefore, collection known sorting will help support important areas biomedical research....
Staphylococcus aureus is a medically important pathogen with high metabolic versatility allowing it to infect various niches within host. S. utilizes two major transcriptional regulators, namely, CodY and CcpA, remodel virulence gene expression in response changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has pronounced impact on different aspects staphylococcal physiology pathogenesis. To determine the contribution interplay these...
Ada3 protein is an essential component of histone acetyl transferase containing coactivator complexes conserved from yeast to human. We show here that germline deletion in mouse embryonic lethal, and adenovirus-Cre mediated conditional Ada3FL/FL fibroblasts leads a severe proliferation defect which was rescued by ectopic expression human Ada3. A delay G1 S phase cell cycle also seen due accumulation Cdk inhibitor p27 indirect effect c-myc gene transcription control further showed this could...
Gut microbiota plays a crucial role in inflammatory bowel diseases (IBD) and can potentially prevent IBD through microbial-derived metabolites, making it promising therapeutic avenue. Recent evidence suggests that despite an unclear underlying mechanism, red cabbage juice (RCJ) alleviates Dextran Sodium Sulfate (DSS)-induced colitis mice. Thus, the study aims to unravel molecular mechanism by which RCJ modulates gut alleviate DSS-induced Using C57BL/6J mice, we evaluated RCJ’s protective two...
Development of the palate comprises sequential stages growth, elevation, and fusion palatal shelves. The mesenchymal component palates plays a major role in early phases palatogenesis, such as growth elevation. Failure these steps may result cleft palate, second most common birth defect world. These palatogenesis require precise chronological orchestration key physiological processes, proliferation, differentiation, migration, apoptosis. There is compelling evidence for vital TGFβ-mediated...
Herein we present major updates to the National NeuroAIDS Tissue Consortium (NNTC) database. The NNTC's ongoing multisite clinical research study was established facilitate access ante-mortem and post-mortem data, tissues biofluids for neurohuman immunodeficiency virus (HIV) community. Recently, NNTC has expanded include data from central nervous system HIV Antiretroviral Therapy Effects Research (CHARTER) study. biospecimens CHARTER cohorts are available qualified researchers upon request....
This article reports changes in the striatal non-synaptic mitochondrial proteome of DJ-1, Parkin, and PINK1 knockout (KO) rats at 3 months age. mutations cause autosomal-recessive parkinsonism. It is thought that loss function these proteins contributes to onset pathogenesis Parkinson׳s disease (PD). As have functions regulation mitochondria, dataset generated here highlights protein expression changes, which can be helpful for understanding pathological alterations. In total, 1281 were...
We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is only available database for neuroAIDS studies that contains data in an integrated, standardized form. This has been created conjunction with NNTC, provides human tissue and biofluid samples to individual researchers conduct focused on neuroAIDS. The experimental datasets from 1206 subjects following categories (which are further broken down into subcategories): gene expression,...
The emergence of next-generation sequencing (NGS) technology has greatly influenced microbiome research and led to the development novel bioinformatics tools deeply analyze metagenomics datasets. Identifying strain-level variations in microbial communities is important understanding onset progression diseases, host–pathogen interrelationships, drug resistance, addition designing new therapeutic regimens. In this study, we developed a tool called StrainIQ (strain identification...
Gut microbiota plays a crucial role in inflammatory bowel disease (IBD) and has therapeutic benefits. Thus, targeting the gut is promising approach for IBD treatment. We recently found that red cabbage juice (RCJ) ameliorates dextran sulfate sodium (DSS)-induced colitis mice. However, underlying mechanisms remain unknown. The current study investigated modulation of response to treatment with RCJ ameliorate DSS colitis. initial results demonstrated mice treated + showed increased body weight...
NHE3 plays an important role in intestinal Na+ absorption and its down-regulation has been implicated inflammatory diarrhea. Recent evidence also indicates a novel of epigenetic mechanisms, such as DNA methylation the pathophysiology IBD. Whether changes are involved modulating gene expression is not known. To address this, methyl-CpG binding domain-based capture assay was performed Caco2 cells treated with pro-inflammatory cytokines. IL6 (100 ng/ml) or IL1β (50 for 48h increased at...