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Shishir K Gupta

About Shishir K Gupta:
No description specified

SEEK ID: https://funginet.hki-jena.de/people/167

Location:  Germany

Expertise: Evolutionary Bioinformatics, Molecular Modeling, Immunoinformatics, Bioinformatics, Comparative Genomics, Simulations, Host-Pathogen Interaction, Docking, Signaling Networks

Tools: Systems biological modelling, Genomics, R, Transcriptomics, Perl

ORCID: https://orcid.org/0000-0002-2335-1597

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Aspergillus fumigatus versus Genus Aspergillus: Conservation, adaptive evolution and specific virulence genes
B1

This repository contains the data of the study "Aspergillus fumigatus versus Genus Aspergillus: Conservation, adaptive evolution and specific virulence genes"

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Quality filtered amino acid sequences of 18 Aspergilli
B1
No description specified

Creator: Shishir K Gupta

Contributor: Shishir K Gupta

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Quality filtered CDS sequences of 18 Aspergilli
B1
No description specified

Creator: Shishir K Gupta

Contributor: Shishir K Gupta

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Nucleotide alignment of single copy orthologs
B1
No description specified

Creators: None

Contributor: Shishir K Gupta

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Amino acid sequences
B1
No description specified

Creators: None

Contributor: Shishir K Gupta

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Ortholog clusters
FungiNet B - Bioinformatics projects, B1

This is the result of OrthoMCL analysis.

Creator: Shishir K Gupta

Contributor: Shishir K Gupta

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Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs.
B1

Abstract (Expand)

Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive … and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6% of the entire C. floridanus proteome.

Authors: Shishir K Gupta, Mugdha Srivastava, O. Osmanoglu, Thomas Dandekar

Date Published: 11th Feb 2020

Journal: Sci Rep

Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle.
B1

Abstract (Expand)

Dendritic cells (DCs) are antigen presenting cells which serve as a passage between the innate and the acquired immunity. Aspergillosis is a major lethal condition in immunocompromised patients caused … by the adaptable saprophytic fungus Aspergillus fumigatus. The healthy human immune system is capable to ward off A. fumigatus infections however immune-deficient patients are highly vulnerable to invasive aspergillosis. A. fumigatus can persist during infection due to its ability to survive the immune response of human DCs. Therefore, the study of the metabolism specific to the context of infection may allow us to gain insight into the adaptation strategies of both the pathogen and the immune cells. We established a metabolic model of A. fumigatus central metabolism during infection of DCs and calculated the metabolic pathway (elementary modes; EMs). Transcriptome data were used to identify pathways activated when A. fumigatus is challenged with DCs. In particular, amino acid metabolic pathways, alternative carbon metabolic pathways and stress regulating enzymes were found to be active. Metabolic flux modeling identified further active enzymes such as alcohol dehydrogenase, inositol oxygenase and GTP cyclohydrolase participating in different stress responses in A. fumigatus. These were further validated by qRT-PCR from RNA extracted under these different conditions. For DCs, we outlined the activation of metabolic pathways in response to the confrontation with A. fumigatus. We found the fatty acid metabolism plays a crucial role, along with other metabolic changes. The gene expression data and their analysis illuminate additional regulatory pathways activated in the DCs apart from interleukin regulation. In particular, Toll-like receptor signaling, NOD-like receptor signaling and RIG-I-like receptor signaling were active pathways. Moreover, we identified subnetworks and several novel key regulators such as UBC, EGFR, and CUL3 of DCs to be activated in response to A. fumigatus. In conclusion, we analyze the metabolic and regulatory responses of A. fumigatus and DCs when confronted with each other.

Authors: Mugdha Srivastava, E. Bencurova, Shishir K Gupta, Esther Weiß, Jürgen Löffler, Thomas Dandekar

Date Published: 14th Jun 2019

Journal: Front Cell Infect Microbiol

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