bioRxiv Science⌕ Search

Biology subjects

Ravi, K.

Publications and source records attributed to Ravi, K..

3 recordsLinked to original sources

Lung Microbiome Intervention Attenuates Herpesvirus-Induced Post-HCT Pulmonary Fibrosis Through PD-L1 Upregulation on Dendritic Cells

Alterations in the lung microbiome frequently accompany adverse pulmonary outcomes. Hematopoietic cell transplantation (HCT) markedly affects the lung microbiome corresponding with a high incidence of post-HCT pulmonary complications. In a preclinical mouse model of HCT, we observed a reduction in Lactobacillus johnsonii within the lung microbiome following transplantation. Intranasal administration of live or heat-killed (HK) L. johnsonii at low doses reduced gammaherpesvirus-induced pulmonary fibrosis in HCT mice, in which IL-17A plays an essential role. HK L. johnsonii treatment of HCT mice suppressed inflammatory cytokine production by lung macrophages and decreased Il17a expression in T helper 17 (Th17) cells. HK L. johnsonii increased PD-L1 expression on the surface of type II conventional dendritic cells (cDC2) in HCT mice and in vitro in bone marrow-derived dendritic cells (BMDCs). HK L. johnsonii-exposed BMDCs also inhibited IL-17A secretion from co-cultured Th17 cells in a PD-1-dependent manner. Notably, when HK L. johnsonii was administered to HCT mice reconstituted with bone marrow cells from PD-1 knockout (KO) mice, which lack a PD-L1 mediated response, HK L. johnsonii-mediated reduction of pulmonary fibrosis was negated. Collectively, our findings demonstrate that HK L. johnsonii mitigates herpesvirus-induced pulmonary fibrosis in HCT mice by modulating cDC2 surface expression of PD-L1, which subsequently suppresses Il17a expression in Th17 cells, pointing towards a potential postbiotic-based strategy for immunomodulation to address pulmonary complications of HCT.

immunology↗

Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell

In eukaryotes, linear motor proteins govern intracellular transport and organization. In bacteria, where linear motors are absent, the ParA/MinD (A/D) family of ATPases spatially organize an array of genetic- and protein-based cellular cargos. ParA is well known to segregate plasmids and chromosomes, as is MinD for its role in divisome positioning. Less studied is the growing list of ParA/MinD-like ATPases found across prokaryotes and involved in the spatial organization of diverse protein-based organelles, such as Bacterial Microcompartments (BMCs), flagella, chemotaxis clusters, and conjugation machinery. Given the fundamental nature of these processes in both cell survival and pathogenesis, the positioning of these cargos has been independently investigated to varying degrees in several organisms. However, it remains unknown whether multiple A/D ATPases can coexist and coordinate the positioning of such a diverse set of fundamental cargos in the same cell. If so, what are the mechanistic commonalities, variation, and specificity determinants that govern the positioning reaction for each cargo? Here, we find that over a third of sequenced bacteria encode multiple A/D ATPases. Among these bacteria, we identified several human pathogens as well as the experimentally tractable organism, Halothiobacillus neapolitanus, which encodes seven A/D ATPases. We directly demonstrate that five of these A/D ATPases are each dedicated to the spatial regulation of a single cellular cargo: the chromosome, the divisome, the carboxysome BMC, the flagellum, and the chemotaxis cluster. We identify putative specificity determinants that allow each A/D ATPase to position its respective cargo. Finally, we show how the deletion of one A/D ATPase can have indirect effects on the inheritance of a cargo actively positioned by another A/D ATPase, stressing the importance of understanding how organelle trafficking, chromosome segregation, and cell division are coordinated in bacterial cells. Together, our data show how multiple A/D ATPases coexist and function to position a diverse set of fundamental cargos in the same bacterial cell. With this knowledge, we anticipate the design of minimal autonomous positioning systems for natural- and synthetic-cargos in bacteria for synthetic biology and biomedical applications.

microbiology↗

Single Cell Viewer (SCV): An interactive visualization data portal for single cell RNA sequence data

MotivationThanks to technological advances made in the last few years, we are now able to study transcriptomes from thousands of single cells. These have been applied widely to study various aspects of Biology. Nevertheless, comprehending and inferring meaningful biological insights from these large datasets is still a challenge. Although tools are being developed to deal with the data complexity and data volume, we do not have yet an effective visualizations and comparative analysis tools to realize the full value of these datasets.\n\nResultsIn order to address this gap, we implemented a single cell data visualization portal called Single Cell Viewer (SCV). SCV is an R shiny application that offers users rich visualization and exploratory data analysis options for single cell datasets.\n\nAvailabilitySource code for the application is available online at GitHub (http://www.github.com/neuhausi/single-cell-viewer) and there is a hosted exploration application using the same example dataset as this publication at http://periscopeapps.org/scv_tirosh.\n\nContactisaac.neuhaus@bms.com; kandasamy.ravi@bms.com

bioinformatics↗