A5000404176- Genomics and Phylogenetic Studies
- Multiple Myeloma Research and Treatments
- RNA modifications and cancer
- Protein Degradation and Inhibitors
- T-cell and B-cell Immunology
- RNA Research and Splicing
- Gut microbiota and health
- CAR-T cell therapy research
- Cancer-related molecular mechanisms research
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- SARS-CoV-2 and COVID-19 Research
- Mosquito-borne diseases and control
- Cancer Genomics and Diagnostics
- Immune Cell Function and Interaction
- Chemokine receptors and signaling
- Probiotics and Fermented Foods
- Bacterial Identification and Susceptibility Testing
- Bacteriophages and microbial interactions
- Legume Nitrogen Fixing Symbiosis
- Esophageal Cancer Research and Treatment
- Peptidase Inhibition and Analysis
- Viral Infections and Outbreaks Research
- Advanced Proteomics Techniques and Applications
- Biological Research and Disease Studies
University of Arkansas for Medical Sciences
2017-2024
Winthrop Rockefeller Foundation
2022-2024
Oak Ridge National Laboratory
2015-2017
Molecular Microbiology and Genomics Consultants (Germany)
2017
Abstract Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct of native using Oxford Nanopore Technologies (ONT) can allow for directly detecting the base modifications, although these modifications might appear as errors. The percent Error Specific Bases (%ESB) was higher than...
Abstract Anti-multiple myeloma B cell maturation antigen (BCMA)-specific chimeric receptor (CAR) T-cell therapies represent a promising treatment strategy with high response rates in myeloma. However, durable cures following anti-BCMA CAR-T of are rare. One potential reason is that small subset minimal residual cells seeds relapse. Residual BCMA-CAR-T-mediated show less-differentiated features and express stem-like genes, including CD24. CD24-positive large fraction after BCMA-CAR-T therapy....
Abstract In this study, more than one hundred thousand Escherichia coli and Shigella genomes were examined classified. This is, to our knowledge, the largest E. genome dataset analyzed date. A Mash-based analysis of a cleaned set 10,667 from GenBank revealed 14 distinct phylogroups. representative or medoid identified for each phylogroup was used as proxy classify 95,525 unassembled Sequence Read Archive (SRA). We find that most sequenced belong four phylogroups (A, C, B1 E2(O157))....
Single-cell RNA sequencing has led to novel designations for mesenchymal cells associated with bone as well multiple what appear be the same cell type. The main goals of this study were increase amount single sequence data osteoblasts and osteocytes, compare from periosteum those inside bone, clarify major categories types murine bone. We created an atlas bone-associated by harmonizing published datasets in-house targeted Osx1-Cre Dmp1-Cre driver strains. Cells periosteal analyzed separately...
ABSTRACT The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere many plants. Their diversity influences phylogenetic heterogeneity these communities. On basis average amino acid identity, comparative genome analysis >1,000 genomes, 21 strains isolated from roots native Populus deltoides (eastern cottonwood) trees resulted in consistent robust genomic clusters with...
The genomic diversity of SARS-CoV-2 is the result a relatively low level spontaneous mutations introduced during viral replication. With millions genome sequences now available, we can begin to assess overall genetic repertoire this virus. We find that 2020, there was global wave one variant went largely unnoticed, possibly because its members were divided over several sublineages (B.1.177 and B.1.177.XX). collectively call Janus, it eventually replaced by Alpha (B.1.1.7) concern (VoC), next...
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies eccDNA employ short-read sequencing for their identification. However, cannot resolve the complexity genomic repeats, which can lead to missing products. Long-read technologies provide an alternative constructing complete maps. We present a software suite, Construction-based...
Multiple myeloma (MM) growth is supported by an immune-tolerant bone marrow microenvironment. Here, we find that loss of Never in mitosis gene A (NIMA)-related kinase 2 (NEK2) tumor microenvironmental cells associated with MM suppression. The absence NEK2 leads to both fewer tumor-associated macrophages (TAMs) and inhibitory T cells. expression myeloid progenitor promotes the generation functional TAMs when stimulated conditional medium. Clinically, high increased CD8+ effector memory cells,...
The current Monkeypox virus (MPX) outbreak is not only the largest known to date caused by a strain belonging West-African clade, but also results in remarkably different clinical and epidemiological features compared previous outbreaks of this virus. Here, we consider possibility that mutations viral genome may be responsible for its changed characteristics.Six sequences isolates from were five genomes 2017 Nigeria two historic genomes, all clade. We report differences are consistently...
Direct sequencing of single molecules through nanopores allows for accurate quantification and full-length characterization native RNA or complementary DNA (cDNA) without amplification. Both nanopore-based cDNA approaches involve complex transcriptome procedures at a lower cost. However, there are several differences between the two approaches. In this study, we perform matched to enable relevant comparisons evaluation. Using Saccharomyces cerevisiae , eukaryotic model organism widely used...
Autologous stem cell transplantation (ASCT) has been a mainstay in myeloma treatment for over three decades, but patient prognosis post-ASCT varies significantly. In retrospective study of 5259 patients with multiple (MM) at the University Arkansas Medical Sciences undergoing ASCT median 57-month follow-up, we divided dataset into training (70%) and validation (30%) subsets. Employing univariable multivariable Cox analyses, systematically assessed 29 clinical variables, identifying crucial...
Abstract Tumor immune microenvironmental alterations occur early in multiple myeloma (MM) development. In this study, we aim to systematically characterize the tumor microenvironment (TME) and tumor-immune interactions from precursor stages, i.e., monoclonal gammopathy of undetermined significance (MGUS) smoldering MM (SMM), newly diagnosed MM, comparing these healthy donors. Using CIBERSORT, mass cytometry (CyTOF), single-cell RNA sequencing (scRNA-Seq), examined innate adaptive changes...
Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies developing fetuses. The mechanisms behind these teratogenic effects are unknown, although epidemiological evidence suggests that not associated with original, African lineage of ZIKV. sequences 196 published ZIKV genomes were used assess whether recently proposed mechanistic...
Abstract Sequencing of native RNA and corresponding cDNA was performed using Oxford Nanopore Technology. The % Error Specific Bases (%ESB) higher for than cDNA, which enabled detection ribonucleotide modification sites. Based on %ESB differences the two templates, a bioinformatic tool ELIGOS developed applied to rRNAs E. coli, yeast human cells. captured 91%, 95%, ∼75%, respectively, known variety methylation sites in these rRNAs. Yeast transcriptomes from different growth conditions were...
Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples two patients in Arkansas, the southeastern corner United States. The viral genome was using ARTIC Network protocol and Oxford Nanopore Technologies sequencing.
ABSTRACT The explosion of microbial genome sequences in public databases allows for large-scale population genomic studies bacterial species, such as Escherichia coli . In this study, we examine and classify more than one hundred thousand E. Shigella genomes. After removing outliers, a semi-automated Mash-based analysis 10,667 assembled genomes reveals 14 distinct phylogroups. A representative or medoid identified each phylogroup serves proxy to 95,000 unassembled This shows that most...
Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains well nosocomial spread. Whole genome sequences from clinical samples contain lot of information but that needs analyzed and compared such way the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete C. using average amino acid identity (AAI) scores. This analysis revealed...
It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in data public databases allows us to explore ever growing large collections sequences. However, it less known majority available sequenced sequences not complete, drafts varying qualities. We have calculated quality scores for around 100,000 bacterial genomes from all major repositories put them fast easy-to-use database. Prokaryotic genomic sources...
Barrett's esophagus (BE) is most commonly seen as the condition in which normal squamous epithelium lining of replaced by goblet cells. Many studies show that BE a predisposing factor for development esophageal adenocarcinoma (EAC), particularly lethal cancer. The use single nucleotide polymorphisms (SNPs) to map BE/EAC genes has previously provided insufficient genetic information fully characterize heterogeneous nature disease. We therefore hypothesize rigorous interrogation other types...
Bacterial DNA is subject to various modifications involved in gene regulation and defense against bacteriophage attacks. Phosphorothioate (PT) are protective which the non-bridging oxygen phosphate backbone replaced with a sulfur atom. Here, we expand third-generation sequencing techniques allow for sequence-specific mapping of by demonstrating application Oxford Nanopore Technologies (ONT) ELIGOS software package site-specific detection characterization PT modifications. The ONT/ELIGOS...