Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis

Idiopathic pulmonary fibrosis is a lethal lung fibroproliferative disease with limited therapeutic options. Differential expression profiling of affected sites has been instrumental for involved pathogenetic mechanisms dissection and therapeutic targets discovery. However, there have been limited efforts to comparatively analyse/mine the numerous related publicly available datasets, to fully exploit their potential on the validation/creation of novel research hypotheses. In this context and towards that goal, we present Fibromine, an integrated database and exploration environment comprising of consistently re-analysed, manually curated transcriptomic and proteomic pulmonary fibrosis datasets covering a wide range of experimental designs in both patients and animal models. Fibromine can be accessed via an R Shiny application (http://www.fibromine.com/Fibromine) which offers dynamic data exploration and real-time integration functionalities. Moreover, we introduce a novel benchmarking system based on transcriptomic datasets underlying characteristics, resulting to dataset accreditation aiming to aid the user on dataset selection. Cell specificity of gene expression can be visualised and/or explored in several scRNA-seq datasets, in an effort to link legacy data with this cutting-edge methodology and paving the way to their integration. Several use case examples are presented, that, importantly, can be reproduced on-the-fly by a non-specialist user, the primary target and potential user of this endeavour.

Differential expression profiling of defense related genes for Leaf Curl Virus (ChiLCV) in resistant and susceptible genotypes of Chiili

The present investigation was undertaken to study the expression of eight defense related genes in leaf curl resistant line DLS-Sel-10 and susceptible line Phule Mukta after different days post inoculation (dpi) with viruliferous white flies to understand their role in resistance to chilli leaf curl virus (ChiLCV). The expression level of Ca PPO, Ca AsPer, Ca ATP/ADP and CaTopoII was observed to be higher in resistant genotype DLS-Sel-10 than the susceptible Phule Mukta at all the time points studied. Expression of CaNBS-LRR increased up to 12 dpi while that of Ca Thionin, and Ca SKP1 increased up to 24 dpi in the resistant line, thereafter it started declining. The CaSPI expression did not show any specific pattern in both the test plants. The heat map clustered all the genes under study into two major clusters based on their expression profiles, one comprising CaAsPer, Ca-Thionin, CaATP/ADP transporter, CaPPO and CaTopoII while other group comprised CaSKPI, Ca NBS and CaSPI. The challenge inoculation of the test genotypes also revealed that viral titre increased at a much slower rate in DLS-Sel-10 than Phule Mukta, suggesting thereby that DLS-Sel-10 is resisting the accumulation of ChiLCV and has a more active defense machinery than Phule Mukta.

A Comprehensive Investigation of Potential Novel Marine Psychrotolerant Actinomycetes sp. Isolated from the Bay-of-Bengal

Background: This study was carried out to classify the diversity of the deep marine psychrotolerant actinomycetes sp. nov., in the Bay of Bengal and exploit the production of coldactive industrial and pharmaceutical biomolecules. Objective: 1) Characterization, optimum the growth conditions and classify the diversity of the novel isolated deep marine psychrotolerant actinomycetes sp from the Bay-of-Bengal. 2) Screening for industrially important biocatalysts and determine the antimicrobial activities against the five dreadful pathogens. 3) The differential expression profiling of the candidate genes to regulate the biosynthesis of selected enzymes. Methods: The cold-adapted actinomycetes were isolated from the deep marine water collections at 1200 mts below the surface in Bay-of-Bengal. The phenotypic and genotypic characterizations have been carried out to understand the persistent diversity of this novel marine psychrotolerant actinomycetes species. The production of cold-active enzymes, such as amylase, cellulase, lipase, pectinase, and L-asparaginase, were screened and the expression profiling genes were determined by using qRT PCR. The antibacterial and antifungal activities have also been investigated. Results: A total number of 37 novel actinomycetes were isolated and the phenotypic and genotypic characterizations identified the genus, dominated by Streptomyces (17 distinct sub-groups) as the major group, followed by Micromonospora, Actinopolyspora, Actinosynnema, Streptoverticillium, Saccharopolyspora, Nocardiopsis, and Nocardia. The optimum growth and abundant mycelium formation are observed at 15°C to 20°C and also capability for thriving at 4°C. All the isolates exhibited a significant role in the production of biocatalysts, and the antagonistic activities were also noted against five major selected pathogens. Conclusion: The Streptomyces from the Bay-of-Bengal have high biosynthetic potential and can serve as a good resource for the exploration of bioactive natural products

Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants

Targeted metagenomics using strand-specific libraries with target enrichment is a sensitive, generalized approach to pathogen sequencing and transcriptome profiling. Using this method, we recovered 13 (76%) complete human respiratory syncytial virus (RSV) genomes from 17 clinical respiratory samples, reconstructed the phylogeny of the infecting viruses, and detected differential gene expression between 2 RSV subgroups, specifically, a lower expression of the P gene and a higher expression of the M2 gene in RSV-A than in RSV-B. This methodology can help to relate viral genetics to clinical phenotype and facilitate ongoing population-level RSV surveillance and vaccine development. Clinical Trials Registration. NCT03627572 and NCT03756766.