Project description:Paramyxoviruses are negative sense single-stranded RNA viruses that comprise many important human and animal pathogens, including human parainfluenza viruses. These viruses bud from the plasma membrane of infected cells after the viral ribonucleoprotein complex (vRNP) is transported from the cytoplasm to the cell membrane via Rab11a marked recycling endosomes. The viral proteins that are critical for mediating this important initial step in viral assembly are unknown. Here we use the model paramyxovirus, murine parainfluenza virus 1, or Sendai virus (SeV), to investigate the roles of viral proteins in Rab11a-driven virion assembly. We previously reported that infection with SeV containing high levels of copy-back defective viral genomes (DVGs) generates heterogenous populations of cells, with cells enriched in full-length virus producing viral particles containing standard or defective viral genomes, while cells enriched in DVGs did not, despite high levels of defective viral genome replication. Here we take advantage of this heterogenous cell phenotype to identify proteins that mediate interaction of vRNPs with Rab11a. We examine the role of matrix protein and nucleoprotein and determine that they are not sufficient to drive interaction of vRNPs and recycling endosomes. Then, using a combination of mass spectrometry and comparative protein abundance and localization in DVG- and FL-high cells, we identify viral polymerase complex components L and, specifically, its cofactor C proteins as interactors with Rab11a. We find that accumulation of these proteins within the cell is the defining feature that differentiates cells that proceed to viral egress from cells which remain in replication phases. Paramyxoviruses are a family of viruses that include a number of pathogens with significant burdens on human health. Particularly, human parainfluenza viruses are an important cause of pneumonia and bronchiolitis in children and do not have any vaccines or direct acting antivirals. These cytoplasmic replicating viruses bud from the plasma membrane and coopt cellular endosomal recycling pathways to traffic viral ribonucleoprotein complexes from the cytoplasm to the membrane of infected cells, yet the viral proteins required for viral engagement with the recycling endosome pathway is not known. Here we use the model paramyxovirus Sendai virus, or murine parainfluenza virus 1, to investigate the role of viral proteins in this initial step in viral assembly. We find that viral polymerase components large protein L and accessory C proteins are necessary for engagement with recycling endosomes. These findings are important in identifying viral targets for the development of antivirals.
Project description:High-throughput small RNA sequencing (sRNA-seq) has facilitated many discoveries, but extracellular sRNA (ExRNA) present unique analytical challenges that are not met by current software. Therefore, we developed a novel data analysis pipeline entitled, “TIGER”, which caters to exRNA. To demonstrate the power of this tool, sRNA-seq was performed on high-density lipoproteins (HDL), apolipoprotein B particles (APOB), bile, urine, and liver samples. TIGER was able to characterize approximately 60% of lipoprotein, and >85% of liver, bile, and urine sRNA-seq depth, a significant advance compared to existing software. A key advance for the TIGER pipeline is the ability to analyze host and non-host sRNAs at genomic, parent RNA, and individual fragment levels. Results suggest that the majority of sRNAs on lipoproteins are derived from bacterial sources in the microbiome and environment. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of exRNA.
Project description:This series includes 1 microarray used to detect parainfluenza 4a from an endotracheal aspirate from a patient with acute respiratory failure Keywords: viral detection
Project description:This series includes 1 microarray used to detect parainfluenza 4a from an endotracheal aspirate from a patient with acute respiratory failure The series includes 1 microarray used for viral detection using Viro3 viral detection platform
Project description:This study was designed to identify differentially expressed (DE) genes between natural breastfeeding young South China tiger whole blood and artificial feeding young South China tiger whole blood through microarray and bioinformatics analysis, thus trying to identify modified metabolic pathways as a consequence of milk replacer during the suckling period.