David A. Ornelles
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View article: Opposite regulation of immune genes in blood and skin highlights tissue-specific dynamics of mpox virus
Opposite regulation of immune genes in blood and skin highlights tissue-specific dynamics of mpox virus Open
Mpox re-emerged globally in 2022 with atypical clinical features and efficient human-to-human transmission, which underscores the need to better understand host immune responses. We conducted an integrative transcriptomic analysis of mpox …
View article: Cross-modal predictive modeling of multi-omic data in 3D airway organ tissue equivalents during viral infection
Cross-modal predictive modeling of multi-omic data in 3D airway organ tissue equivalents during viral infection Open
Introduction Developing robust predictive models from multi-omics data is challenging because sample sizes are typically small (often fewer than 100) while the feature space is vast (over 20,000 molecular features such as genes, transcript…
View article: Tracing the evolutionary pathway of SARS-CoV-2 through RNA sequencing analysis
Tracing the evolutionary pathway of SARS-CoV-2 through RNA sequencing analysis Open
View article: Antibody function predicts viral control in newborn monkeys immunised with an influenza virus HA stem nanoparticle
Antibody function predicts viral control in newborn monkeys immunised with an influenza virus HA stem nanoparticle Open
View article: Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance
Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance Open
Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often…
View article: Exploring the host response in infected lung organoids using NanoString technology: A statistical analysis of gene expression data
Exploring the host response in infected lung organoids using NanoString technology: A statistical analysis of gene expression data Open
In this study, we used a three-dimensional airway “organ tissue equivalent” (OTE) model at an air-liquid interface (ALI) to mimic human airways. We investigated the effects of three viruses (Influenza A virus (IAV), Human metapneumovirus (…
View article: A comparative analysis of RNA-Seq and NanoString technologies in deciphering viral infection response in upper airway lung organoids
A comparative analysis of RNA-Seq and NanoString technologies in deciphering viral infection response in upper airway lung organoids Open
In this study, we delved into the comparative analysis of gene expression data across RNA-Seq and NanoString platforms. While RNA-Seq covered 19,671 genes and NanoString targeted 773 genes associated with immune responses to viruses, our p…
View article: Immunogenicity and Protective Efficacy of Psoralen-Inactivated SARS-CoV-2 Vaccine in Nonhuman Primates
Immunogenicity and Protective Efficacy of Psoralen-Inactivated SARS-CoV-2 Vaccine in Nonhuman Primates Open
COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly impacted public health and the economy worldwide. Most of the currently licensed COVID-19 vaccines act by inhibiting the receptor-binding fun…
View article: Analysis of gene expression dynamics and differential expression in viral infections using generalized linear models and quasi-likelihood methods
Analysis of gene expression dynamics and differential expression in viral infections using generalized linear models and quasi-likelihood methods Open
Introduction Our study undertakes a detailed exploration of gene expression dynamics within human lung organ tissue equivalents (OTEs) in response to Influenza A virus (IAV), Human metapneumovirus (MPV), and Parainfluenza virus type 3 (PIV…
View article: Dynamic Actin Filament Traps Mediate Active Diffusion of Vesicular Stomatitis Virus Ribonucleoproteins
Dynamic Actin Filament Traps Mediate Active Diffusion of Vesicular Stomatitis Virus Ribonucleoproteins Open
RNA virus ribonucleoproteins (RNPs) are too large to freely diffuse in the host cytoplasm, yet their dominant motions consist of movements in random directions that resemble diffusion. We show that vesicular stomatitis virus (VSV) RNPs ove…
View article: Klebsiella pneumoniae <scp>l-</scp> Fucose Metabolism Promotes Gastrointestinal Colonization and Modulates Its Virulence Determinants
Klebsiella pneumoniae <span>l-</span> Fucose Metabolism Promotes Gastrointestinal Colonization and Modulates Its Virulence Determinants Open
Colonization of the gastrointestinal (GI) tract by Klebsiella pneumoniae is generally considered asymptomatic. However, gut colonization allows K. pneumoniae to either translocate to sterile site within the same host or transmit through th…
View article: Assessing alternatives to HEPA air purification requirements to reduce viral pathogen transmission in healthcare HVAC systems
Assessing alternatives to HEPA air purification requirements to reduce viral pathogen transmission in healthcare HVAC systems Open
Background: High-efficiency particulate air (HEPA) filters are currently recommended when using recirculated air to eliminate the risk of pathogen transmission such as SARS-CoV-2 from one patient care area to the next. We tested the effica…
View article: COVID-19 vaccination and HIV-1 acquisition
COVID-19 vaccination and HIV-1 acquisition Open
View article: SAMHD1 Phosphorylation at T592 Regulates Cellular Localization and S-phase Progression
SAMHD1 Phosphorylation at T592 Regulates Cellular Localization and S-phase Progression Open
SAMHD1 activity is regulated by a network of mechanisms including phosphorylation, oxidation, oligomerization, and others. Significant questions remain about the effects of phosphorylation on SAMHD1 function and activity. We investigated t…
View article: Diversity in responses to oncolytic Lassa-vesicular stomatitis virus in patient-derived glioblastoma cells
Diversity in responses to oncolytic Lassa-vesicular stomatitis virus in patient-derived glioblastoma cells Open
View article: Detection of Environmental Spread of SARS-CoV-2 and Associated Patient Characteristics
Detection of Environmental Spread of SARS-CoV-2 and Associated Patient Characteristics Open
Understanding transmission of severe acute respiratory syndrome coronavirus 2 informs infection prevention practices. Air sampling devices were placed in patient hospital rooms for consecutive collections with and without masks. With patie…
View article: Vesicular stomatitis virus nucleocapsids diffuse through cytoplasm by hopping from trap to trap in random directions
Vesicular stomatitis virus nucleocapsids diffuse through cytoplasm by hopping from trap to trap in random directions Open
Within 2–6 hours after infection by vesicular stomatitis virus (VSV), newly assembled VSV particles are released from the surface of infected cells. In that time, viral ribonucleoprotein (RNP) particles (nucleocapsids) travel from their in…
View article: MAP3K7 and CHD1 Are Novel Mediators of Resistance to Oncolytic Vesicular Stomatitis Virus in Prostate Cancer Cells
MAP3K7 and CHD1 Are Novel Mediators of Resistance to Oncolytic Vesicular Stomatitis Virus in Prostate Cancer Cells Open
A key principle of oncolytic viral therapy is that many cancers develop defects in their antiviral responses, making them more susceptible to virus infection. However, some cancers display resistance to viral infection. Many of these resis…
View article: TCR Dependent Metabolic Programming Regulates Autocrine IL-4 Production Resulting in Self-Tuning of the CD8+ T Cell Activation Setpoint
TCR Dependent Metabolic Programming Regulates Autocrine IL-4 Production Resulting in Self-Tuning of the CD8+ T Cell Activation Setpoint Open
The ability of T cells to sense and respond to environmental cues by altering their functional capabilities is critical for a safe and optimally protective immune response. One of the important properties that contributes to this goal is t…
View article: Epigenetics and the dynamics of chromatin during adenovirus infections
Epigenetics and the dynamics of chromatin during adenovirus infections Open
The DNA genome of eukaryotic cells is compacted by histone proteins within the nucleus to form chromatin. Nuclear‐replicating viruses such as adenovirus have evolved mechanisms of chromatin manipulation to promote infection and subvert hos…
View article: Transport Modes of Viral Nucleoproteins in Live Cells
Transport Modes of Viral Nucleoproteins in Live Cells Open
View article: Activation-dependent modulation of Streptococcus pneumoniae-mediated death in human lymphocytes
Activation-dependent modulation of Streptococcus pneumoniae-mediated death in human lymphocytes Open
Streptococcus pneumoniae (Spn) is a leading cause of community-acquired pneumonia, with infants and the elderly exhibiting significant susceptibility to the development of severe disease. A growing body of evidence supports the ability of …
View article: Migration of Nucleocapsids in Vesicular Stomatitis Virus-Infected Cells Is Dependent on both Microtubules and Actin Filaments
Migration of Nucleocapsids in Vesicular Stomatitis Virus-Infected Cells Is Dependent on both Microtubules and Actin Filaments Open
The distribution of vesicular stomatitis virus (VSV) nucleocapsids in the cytoplasm of infected cells was analyzed by scanning confocal fluorescence microscopy using a newly developed quantitative approach called the border-to-border distr…
View article: Neonatal Infection with Species C Adenoviruses Confirmed in Viable Cord Blood Lymphocytes
Neonatal Infection with Species C Adenoviruses Confirmed in Viable Cord Blood Lymphocytes Open
Credible but conflicting reports address the frequency of prenatal infection by species C adenovirus. This question is important because these viruses persist in lymphoid cells and suppress double-stranded DNA-break repair. Consequently, p…
View article: Adenovirus Replaces Mitotic Checkpoint Controls
Adenovirus Replaces Mitotic Checkpoint Controls Open
Infection with adenovirus triggers the cellular DNA damage response, elements of which include cell death and cell cycle arrest. Early adenoviral proteins, including the E1B-55K and E4orf3 proteins, inhibit signaling in response to DNA dam…