Project description:JC polyomavirus (circular genome) contains two opposite coding regions separated by the regulator non-coding control region (NCCR). NCCR rearrangements and missense mutations in the viral capsid protein VP1 gene differentiate JCV prototype genomes recovered from PML lesions from archetype urine strains. To further investigate the emerging variability of JCV populations in PML, we deep sequenced JCV whole genome recovered from CNS and/or urine samples from HIV- and non HIV-infected PML patients, using single-molecule real-time sequencing (PacBio, Paciﬁc Biosciences). Phylogenetic analysis showed that PML strains distributed among 6 of 7 known genotypes. Whole genome single molecule sequencing provides insight in the genesis of JCV neurotropic populations.

2022-01-12 | E-MTAB-11077 | biostudies-arrayexpress

JC Polyomavirus Infection of Primary Human Renal Epithelial Cells Is Controlled by a Type I IFN-Induced Response

Project description:JC polyomavirus (JCPyV) established a persistent infection, but BK polyomavirus (BKPyV) killed the cells in 15 days. To identify the cellular factors responsible for controlling JCPyV infection and promoting viral persistence, we profiled the transcriptomes of JCPyV- and BKPyV-infected cells at several time points postinfection. We found that interferon-stimulated genes (ISGs) were only activated in the JCPyV and not in the BKPyV-infected cells.

2019-08-15 | GSE135833 | GEO

Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels

Project description:The microarrays experiments was performed with the purpose of identify transcriptional networks activated by copper. This experiment correspond the work tituled Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels (work in preparation).Mauricio Latorrea,b, Jessica Galloway-PeM-CM-1ac,d,e, Jung Hyeo Rhoc,d, Marko Budinichf, Barbara E. Murrayc,d,e, Alejandro Maassb,f, Mauricio GonzM-CM-!leza,b,f*. a INTA, Laboratorio de BioinformM-CM-!tica y ExpresiM-CM-3n GM-CM-)nica, INTA, Universidad de Chile, Santiago, Chile. b Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile. c Division of Infectious Disease, Department of Medicine, University of Texas Medical School, Houston, Texas, United States of America. d Center for the Study of Emerging and Reemerging Pathogens, University of Texas Medical School, Houston, Texas, United States of America. e Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America f Mathomics, Center for Mathematical Modeling (UMI2807CNRS), Santiago, Chile. * Corresponding author. Address: El LM-CM--bano 5524, Santiago 11, Chile. Fax: +56 (2) 2214030. A eight chip study (two technical replicates) using total RNA recovered from four separate cultures of: Enterococcus faecalis OG1RF (N medium growth), Enterococcus faecalis OG1RF copM-NM-^T mutant strain (N medium growth), Enterococcus faecalis OG1RF copM-NM-^T mutant low copper treatment (N medium growth + 0.05 mM CuSO4) and Enterococcus faecalis OG1RF copM-NM-^T mutant low copper treatment (N medium growth + 0.5 mM CuSO4). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).

2013-11-12 | E-GEOD-45131 | biostudies-arrayexpress

JC polyomavirus strains in PML

Project description:Distinct JC polyomavirus strains in patients with progressive multifocal leukoencephalopathy

| PRJEB15261 | ENA

Complete genome sequences of JC Polyomaviruses

Project description:Complete JC Polyomavirus genome sequences derived by next-generation sequencing in Vietnamese renal transplant recipients

| PRJEB29754 | ENA

Comprehensive proteomic analysis of JC polyomavirus-infected human astrocytes and their extracellular vesicles

Project description:JC polyomavirus (JCPyV) is the causative agent of progressive multifocal leukoencephalopathy (PML), a devastating demyelinating disease of the central nervous system that results in the widespread formation of lesions across the brain parenchyma. The virus is opportunistic and remains in a benign state in the kidneys and lymphoid organs of more than half of the global human adult population. However, in rare cases of severe or selective immune suppression, JCPyV can establish a lytic infection of glial cells in the brain. While PML has traditionally been characterized as a lytic infection of oligodendrocytes, more recent findings suggest an important role for astrocytes during the initial stages of disease. Because of the exceptional species and tissue specificity of the virus, appropriate models of JCPyV infection in the brain are lacking, thus hampering progress towards the development of novel antiviral strategies and biomarkers of disease activity. Here, using iPSC-derived astrocytes infected with JCPyV and analyzed by LC-MS/MS, we show that the virus strongly influences the cell biology, inducing an unique proteomic signature that sharply contrasts with mock-infected cells.

2023-08-28 | PXD044144 | Pride

Salmonella enterica subsp. enterica serovar Typhi

Project description:Epidemiological and phylogenetic investigation of Salmonella Typhi infection in Santiago Chile 2017-2019

| PRJNA935358 | ENA