W. Evan Johnson
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View article: Defining the <i>Mycobacterium tuberculosis</i> Pangenome and Suggestions for a New Composite Reference Sequence
Defining the <i>Mycobacterium tuberculosis</i> Pangenome and Suggestions for a New Composite Reference Sequence Open
Mycobacterium tuberculosis (Mtb) causes tuberculosis (TB), a global disease with diverse clinical and microbiological manifestations. Studies into the biological causes of this phenotypic diversity have been largely limited to a few refere…
View article: Diet-mediated immunometabolic regulation promotes Klebisella pneumoniae airway clearance 2722
Diet-mediated immunometabolic regulation promotes Klebisella pneumoniae airway clearance 2722 Open
Description Antimicrobial-resistant and susceptible Klebsiella pneumoniae (Kp) are major causes of pneumonia and mortality in healthcare settings. One emerging immune evasion strategy of Kp involves its manipulation of the host metabolism,…
View article: Dysregulated of monocyte function prior to liver transplant is associated with increased risk of post-transplant mortality 3930
Dysregulated of monocyte function prior to liver transplant is associated with increased risk of post-transplant mortality 3930 Open
Description Cirrhosis induces progressively severe immune dysfunction, which persists early after liver transplant (LT) and increases risk of morbidity and mortality both prior to and following LT. We have previously identified the Liver I…
View article: Lipid peroxidation and type I interferon coupling fuels pathogenic macrophage activation causing tuberculosis susceptibility
Lipid peroxidation and type I interferon coupling fuels pathogenic macrophage activation causing tuberculosis susceptibility Open
A quarter of the human population is infected with Mycobacterium tuberculosis , but less than 10% of those infected develop pulmonary TB. We developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining f…
View article: Combining blood transcriptomic signatures improves the prediction of progression to tuberculosis among household contacts in Brazil
Combining blood transcriptomic signatures improves the prediction of progression to tuberculosis among household contacts in Brazil Open
Tuberculosis remains a major health threat, infecting nearly a third of the world’s population. Of those infected, 5-10% progress from latent infection to active tuberculosis (TB) disease and biomarkers to identify which individuals will p…
View article: MetaScope: A High-Resolution Framework for Species-Level 16S Metataxonomic Classification
MetaScope: A High-Resolution Framework for Species-Level 16S Metataxonomic Classification Open
Accurate species-level classification of microbial communities remains a major challenge in microbiome analysis, particularly when using traditional 16S rRNA amplicon sequencing pipelines such as QIIME2 and DADA2. These methods often fail …
View article: Synaptic transmission promotes brain metastatic outgrowth in breast cancer
Synaptic transmission promotes brain metastatic outgrowth in breast cancer Open
This work demonstrates that normal neuron-to-neuron signaling machinery is hijacked by metastasizing cancer cells during their outgrowth in the central nervous system.
View article: Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility
Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility Open
A quarter of human population is infected with Mycobacterium tuberculosis, but less than 10% of those infected develop pulmonary TB. We developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining featur…
View article: Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility
Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility Open
A quarter of human population is infected with Mycobacterium tuberculosis, but less than 10% of those infected develop pulmonary TB. We developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining featur…
View article: The impact of tuberculosis and its treatment on the lung and gut microbiota: A global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis
The impact of tuberculosis and its treatment on the lung and gut microbiota: A global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis Open
Background Tuberculosis (TB) remains the leading cause of bacterial disease-related deaths worldwide. Historically, the Koch’s single-causative-agent model has shaped diagnostics, treatment, and prevention. However, metagenomic studies hav…
View article: Sex specific correction of maternal inflammation-induced behavioral abnormalities by the inhibition of colony-stimulating factor 1 receptor
Sex specific correction of maternal inflammation-induced behavioral abnormalities by the inhibition of colony-stimulating factor 1 receptor Open
We have previously reported the therapeutic effect of depletion and regeneration of endogenous microglia on autism spectrum disorder-like behaviors in offspring from the dams under maternal immune activation (MIA) by dampening their neurit…
View article: Longitudinal Analysis of Nasopharyngeal Microbial Risk Markers for Fatal Acute Febrile Illness in a Zambian Birth Cohort
Longitudinal Analysis of Nasopharyngeal Microbial Risk Markers for Fatal Acute Febrile Illness in a Zambian Birth Cohort Open
Background Fatal acute febrile illness (fAFI) is a known predecessor of many infant mortality events in low-resource settings, but early risk markers for this condition remain poorly understood. Nasopharyngeal (NP) microbiome patterns may …
View article: Bridging the gap between R and Python in bulk transcriptomic data analysis with InMoose
Bridging the gap between R and Python in bulk transcriptomic data analysis with InMoose Open
We introduce InMoose, an open-source Python environment aimed at omic data analysis. We illustrate its capabilities for bulk transcriptomic data analysis. Due to its wide adoption, Python has grown as a de facto standard in fields increasi…
View article: Helminth infection favors reprogramming and proliferation of lung neutrophils
Helminth infection favors reprogramming and proliferation of lung neutrophils Open
Summary Neutrophils are a granulocytic population of myeloid cells that have critical effector functions during infectious disease but are generally thought to be short-lived and nonproliferative with markedly limited activation states. In…
View article: <i>Atp1a2</i> and <i>Kcnj9</i> Are Candidate Genes Underlying Sensitivity to Oxycodone‐Induced Locomotor Activation and Withdrawal‐Induced Anxiety‐Like Behaviors in <scp>C57BL</scp> /6 Substrains
<i>Atp1a2</i> and <i>Kcnj9</i> Are Candidate Genes Underlying Sensitivity to Oxycodone‐Induced Locomotor Activation and Withdrawal‐Induced Anxiety‐Like Behaviors in <span>C57BL</span> /6 Substrains Open
Opioid use disorder is heritable, yet its genetic etiology is largely unknown. C57BL/6J and C57BL/6NJ mouse substrains exhibit phenotypic diversity in the context of limited genetic diversity which together can facilitate genetic discovery…
View article: Bulk Transcriptomic Analysis with InMoose, the Integrated Multi-Omic Open-Source Environment in Python
Bulk Transcriptomic Analysis with InMoose, the Integrated Multi-Omic Open-Source Environment in Python Open
We introduce InMoose, an open-source Python environment aimed at omic data analysis. We illustrate its capabilities for bulk transcriptomic data analysis. Due to its wide adoption, Python has grown as a de facto standard in fields increasi…
View article: G-quadruplex stabilizer CX-5461 effectively combines with radiotherapy to target α-thalassemia/mental retardation X-linked-deficient malignant glioma
G-quadruplex stabilizer CX-5461 effectively combines with radiotherapy to target α-thalassemia/mental retardation X-linked-deficient malignant glioma Open
Background Inactivation of α-thalassemia/mental retardation X-linked (ATRX) represents a defining molecular feature in large subsets of malignant glioma. ATRX deficiency gives rise to abnormal G-quadruplex (G4) DNA secondary structures, en…
View article: EPCO-13. HUMAN ENDOGENOUS RETROVIRUS (HERV) PLAYS A CRITICAL ROLE IN ONCOGENIC MECHANISM IN<i>IDH1</i>-WILD TYPE GLIOBLASTOMAS
EPCO-13. HUMAN ENDOGENOUS RETROVIRUS (HERV) PLAYS A CRITICAL ROLE IN ONCOGENIC MECHANISM IN<i>IDH1</i>-WILD TYPE GLIOBLASTOMAS Open
IDH1-wildtype (WT) GBMs are the most common and aggressive tumors of the central nervous system (CNS), with a median survival rate of 12-15 months, and are resistant to clinical therapies due to their heterogenous molecular phenotype. In t…
View article: EPCO-25. TRANSPOSABLE ELEMENTS INDUCE ONCO-EXAPTATION EVENTS IN MALIGNANT ATRX-DEFICIENT GLIOMAS
EPCO-25. TRANSPOSABLE ELEMENTS INDUCE ONCO-EXAPTATION EVENTS IN MALIGNANT ATRX-DEFICIENT GLIOMAS Open
Deficiency of ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-linked), a core member of SWI/SNF family chromatin regulator is altered in diffuse gliomas and coexist with IDH1/2 mutations in adults and histone G34R/V alterations in pe…
View article: Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants
Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants Open
Background Previous studies of infants born to HIV-positive mothers have linked HIV exposure to poor outcomes from gastrointestinal and respiratory illnesses, and to overall increased mortality rates. The mechanism behind this is unknown, …
View article: EPITHELIAL REMODELING AND MICROBIAL DYSBIOSIS IN THE LOWER RESPIRATORY TRACT OF VITAMIN A-DEFICIENT MOUSE LUNGS
EPITHELIAL REMODELING AND MICROBIAL DYSBIOSIS IN THE LOWER RESPIRATORY TRACT OF VITAMIN A-DEFICIENT MOUSE LUNGS Open
The World Health Organization identified vitamin A deficiency (VAD) as a major public health issue in low-income communities and developing countries, while additional studies have shown dietary VAD leads to various lung pathologies. Once …
View article: Hepatotoxicity of silver nanoparticles: Benchmark concentration modeling of an in vitro transcriptomics study in human iPSC-derived hepatocytes
Hepatotoxicity of silver nanoparticles: Benchmark concentration modeling of an in vitro transcriptomics study in human iPSC-derived hepatocytes Open
Despite two decades of research on silver nanoparticle (AgNP) toxicity, a safe threshold for exposure has not yet been established, albeit being critically needed for risk assessment and regulatory decision-making. Traditionally, a point-o…
View article: Atp1a2 and Kcnj9 are candidate genes underlying sensitivity to oxycodone-induced locomotor activation and withdrawal-induced anxiety-like behaviors in C57BL/6 substrains
Atp1a2 and Kcnj9 are candidate genes underlying sensitivity to oxycodone-induced locomotor activation and withdrawal-induced anxiety-like behaviors in C57BL/6 substrains Open
Opioid use disorder is heritable, yet its genetic etiology is largely unknown. C57BL/6J and C57BL/6NJ mouse substrains exhibit phenotypic diversity in the context of limited genetic diversity which together can facilitate genetic discovery…
View article: Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study
Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study Open
Background Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or are a consequence o…
View article: Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility
Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility Open
A quarter of human population is infected with Mycobacterium tuberculosis, but less than 10% of those infected develop pulmonary TB. We developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining featur…