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IPD9067 |
Identification of the host proteins binding to the CHIKV genomic RNA |
Prof. Sudhanshu Vrati |
RNA-binding proteins (RBPs) play a crucial role in RNA regulation. The RBPs are involved in a variety of functions, including viral RNA stabilisation, translation regulation, and controlling the synthesis of the complementary replication intermediate RNA. In several alphaviruses, Sindbis virus, Ross River virus, and Chikungunya virus (CHIKV), host RBPs are...
RNA-binding proteins (RBPs) play a crucial role in RNA regulation. The RBPs are involved in a variety of functions, including viral RNA stabilisation, translation regulation, and controlling the synthesis of the complementary replication intermediate RNA. In several alphaviruses, Sindbis virus, Ross River virus, and Chikungunya virus (CHIKV), host RBPs are the key replication regulators, thereby controlling the viral life cycle.
Though the coding region of alphaviruses exhibits sequence diversity, their non-coding regions are highly conserved at both sequence and structural levels. This conservation suggests that these sequences are crucial for the virus replication. Also, numerous reports have demonstrated that various RBPs bind to the conserved non-coding regions (NCRs) of the viral genome, thereby modulating its replication.
We, therefore, hypothesised that host RBPs binding to the conserved sequences within the NCRs of CHIKV may have a role in the viral replication. To validate the hypothesis, we used an RNA pull-down-based approach to identify the host proteins binding to the conserved RNAs specifically. To this end, biotinylated RNA, representing the conserved NCR sequence, was used as a bait to pull down the RBPs from the host cell lysates. The bound proteins were then eluted and analysed by mass spectrometry.
The identified RBPs were potential regulators of viral genome replication, providing insights into the host-virus interactions. Overall, this study aims to identify the host RBPs interacting with the CHIKV genome and understand their role in CHIKV replication.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
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2026-01-14 |
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| 2 |
IPD7164 |
Delineating the role of human β-microseminoprotein in male reproduction |
Dr. Dhanashree Jagtap |
Background: Beta-microseminoprotein (MSMB, β-MSP) is a non-glycosylated, cysteine
rich protein secreted by the epithelial cells of the prostate. β-MSP is found in abundance in
human seminal plasma and is also present on the spermatozoa. It is introduced into the semen during ejaculation and found to be absent in post-capacitated spermatozoa. Its abundance...
Background: Beta-microseminoprotein (MSMB, β-MSP) is a non-glycosylated, cysteine
rich protein secreted by the epithelial cells of the prostate. β-MSP is found in abundance in
human seminal plasma and is also present on the spermatozoa. It is introduced into the semen during ejaculation and found to be absent in post-capacitated spermatozoa. Its abundance in semen along with the fact that it is present on the pre-capacitated spermatozoa suggests that it may have a function which has not yet been elucidated.
b) Novelty: Many functions have been attributed to β-MSP but its exact role in human
reproduction is unclear. The difference between β-MSP levels of fertile and infertile
individuals will be delineated. Identification and characterization of novel binding partners of
β-MSP on spermatozoa of fertile versus infertile men will be accomplished. The mechanism
by which β-MSP exerts its action will be elucidated. Sperm capacitation which is essential for successful fertilization is associated with modification of protein composition of spermatozoa. The mechanism by which β-MSP is lost during this process will be deciphered.
c) Objectives: To investigate the difference in β-MSP levels and identify its novel binding
partners in fertile.
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ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, Maharashtra, India |
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2026-02-21 |
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| 3 |
IPD5407 |
Proteomic profiling of Klebsiella pneumoniae resistant against gradual increasing dose of colistin and meropenem |
Dr. Niraj Kumar |
Klebsiella pneumoniae (K. pneumoniae) rapidly acquires resistance to antibiotics, posing a major challenge to effective clinical management. In contrast, the discovery and development of new antibiotics are time-consuming, resource-intensive, and costly, highlighting the need for alternative therapeutic strategies. One promising approach to identify novel and/or alternative therapeutic strategies is to...
Klebsiella pneumoniae (K. pneumoniae) rapidly acquires resistance to antibiotics, posing a major challenge to effective clinical management. In contrast, the discovery and development of new antibiotics are time-consuming, resource-intensive, and costly, highlighting the need for alternative therapeutic strategies. One promising approach to identify novel and/or alternative therapeutic strategies is to exploit collateral sensitivity, whereby the evolution of resistance to one antibiotic results in increased susceptibility to another. In this study, we established adaptive laboratory evolution models by exposing K. pneumoniae (ATCC and clinical isolates) to sequentially increasing concentrations of colistin and meropenem, as well as by subjecting colistin-resistant (1× MIC) K. pneumoniae to stepwise meropenem exposure over a cumulative period of approximately 250 days. The evolved strains were subsequently characterized using label-free LC-MS/MS proteomic profiling to investigate the emergence of antibiotic-resistance and collateral responses between colistin and meropenem at both phenotypic and molecular levels. In total, 3,126 proteins were identified across all experimental conditions.
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DBT-Translational Health Science and Technology Institute, Faridabad, Haryana, India |
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2026-07-15 |
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| 4 |
IPD4939 |
LC-MS/MS Proteomic Dataset of Klebsiella pneumoniae 4 clinical isolates Grown in Human Plasma and Mueller Hinton Broth at 0 and 2 Hours |
Dr. Niraj Kumar |
This dataset presents a comprehensive LC-MS/MS-based proteomic profile of Klebsiella pneumoniae 4 clinical isolates cultured under two distinct environmental conditions: human plasma and Mueller-Hinton Broth (MHB). The study design incorporates two early time points, 0 hours (baseline) and 2 hours post-incubation, to capture immediate and early-stage proteomic adaptations. These conditions...
This dataset presents a comprehensive LC-MS/MS-based proteomic profile of Klebsiella pneumoniae 4 clinical isolates cultured under two distinct environmental conditions: human plasma and Mueller-Hinton Broth (MHB). The study design incorporates two early time points, 0 hours (baseline) and 2 hours post-incubation, to capture immediate and early-stage proteomic adaptations. These conditions were selected to enable direct comparison between a physiologically relevant host-mimicking environment and a standard nutrient-rich laboratory medium.
The dataset comprises a total of 12 LC-MS/MS files, including 4 biological replicates at 0 hours in Mueller-Hinton Broth (MHB), 4 replicates at 2 hours in human plasma, and 4 replicates at 2 hours in MHB. Protein identification was performed using a reference Klebsiella pneumoniae proteome database from UniProt, and standard proteomics workflows were applied for peptide matching, false discovery rate (FDR) control, and protein inference.
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DBT-Translational Health Science and Technology Institute, Faridabad, Haryana, India |
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2026-07-18 |
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| 5 |
IPD3489 |
Proteomic profiling of Klebsiella pneumoniae resistant against short-duration exposure (SDE) dose of colistin and meropenem. |
Dr. Niraj Kumar |
Short-duration exposure (SDE) of antibiotics is among the major drivers of the emergence of antimicrobial resistance (AMR) among bacterial pathogens. Klebsiella pneumoniae is a priority-1 (critical) bacterial pathogen rapidly acquiring MDR/XDR traits, even against next-generation antibiotics. Since meropenem (latest generation) and colistin (last-resort) antibiotics for treating K. pneumoniae infections and...
Short-duration exposure (SDE) of antibiotics is among the major drivers of the emergence of antimicrobial resistance (AMR) among bacterial pathogens. Klebsiella pneumoniae is a priority-1 (critical) bacterial pathogen rapidly acquiring MDR/XDR traits, even against next-generation antibiotics. Since meropenem (latest generation) and colistin (last-resort) antibiotics for treating K. pneumoniae infections and new antibiotic development is resource-intensive, understanding how resistance emerges following SDE is crucial for devising strategies to preserve antibiotics for long-term/future use. With this aim, we developed colistin-resistant and meropenem-resistant K. pneumoniae using SDE of antibiotics (1x, 2x, and 4x MICs) and proteome profiled. A total of 1379 proteins were identified using LC-MS.
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DBT-Translational Health Science and Technology Institute, Faridabad, Haryana, India |
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2026-07-23 |
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| 6 |
IPD9272 |
From Omics to Function: NCU05627 Emerges as a Pivotal Sugar Transporter for Cellulase Secretion in Neurospora crassa |
Dr. Nidhi Adlakha |
This study investigates the role of sugar transporters in cellulase secretion and polysaccharide utilization in Neurospora crassa using an LC–MS/MS-based proteomics approach. Comparative proteomic profiling identified 2480 proteins shared between the experimental conditions, including several upregulated sugar transporters and carbohydrate-active enzymes (CAZymes) associated with biomass degradation. Functional annotation through Gene...
This study investigates the role of sugar transporters in cellulase secretion and polysaccharide utilization in Neurospora crassa using an LC–MS/MS-based proteomics approach. Comparative proteomic profiling identified 2480 proteins shared between the experimental conditions, including several upregulated sugar transporters and carbohydrate-active enzymes (CAZymes) associated with biomass degradation. Functional annotation through Gene Ontology analysis revealed enrichment of proteins involved in catalytic activity and metabolic processes. Among the identified sugar transporters, the putative xylose transporter NCU05627 was selected for further characterization due to its previously uncharacterized role in cellulase induction. Phylogenetic analysis grouped NCU05627 within the hexose transporter-enriched clade, suggesting a conserved role in sugar uptake. Functional studies demonstrated that deletion of NCU05627 reduced the secretion of plant cell wall-degrading enzymes. This dataset provides comprehensive insight into the sugar transportome of N. crassa and identifies transporter proteins potentially involved in cellulose degradation and fungal biomass conversion.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
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2026-10-29 |
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| 7 |
IPD3121 |
Proteomic characterization of the Plasmodium falciparum PCNA2 interactome |
Suman Kumar Dhar |
This project investigates the PCNA2 interactome in *Plasmodium falciparum* using LC-MS/MS. Samples were analysed using a Thermo Scientific Orbitrap Velos Pro mass spectrometer with data-dependent acquisition (DDA) and collision-induced dissociation (CID). Protein identification was performed using Proteome Discoverer 1.4 with SEQUEST HT against a *P. falciparum* protein database downloaded from...
This project investigates the PCNA2 interactome in *Plasmodium falciparum* using LC-MS/MS. Samples were analysed using a Thermo Scientific Orbitrap Velos Pro mass spectrometer with data-dependent acquisition (DDA) and collision-induced dissociation (CID). Protein identification was performed using Proteome Discoverer 1.4 with SEQUEST HT against a *P. falciparum* protein database downloaded from PlasmoDB. Trypsin was used as the protease, with precursor and fragment ion mass tolerances of 20 ppm and 0.6 Da, respectively. Percolator was used for post-search validation.
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Jawaharlal Nehru University, JNU Ring Rd, Delhi, India |
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2026-11-06 |
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| 8 |
IPD2983 |
Comparative quantitative proteomic analysis of Mycobacterium tuberculosis H37Rv cultured under metal-limited (Chelated Sauton's medium) and metal-rich (7H9) conditions |
Debasisa Mohanty |
Wild-type Mycobacterium tuberculosis H37Rv was cultured under two nutritional conditions representing metal limitation and metal sufficiency. Cells grown in chelated Sauton's medium (metal-limited) and Middlebrook 7H9 medium (metal-rich) were harvested during logarithmic growth, and total cellular proteins were extracted for label-free quantitative proteomic analysis. LC-MS/MS was performed to identify and...
Wild-type Mycobacterium tuberculosis H37Rv was cultured under two nutritional conditions representing metal limitation and metal sufficiency. Cells grown in chelated Sauton's medium (metal-limited) and Middlebrook 7H9 medium (metal-rich) were harvested during logarithmic growth, and total cellular proteins were extracted for label-free quantitative proteomic analysis. LC-MS/MS was performed to identify and quantify changes in protein abundance associated with adaptation to metal availability. The dataset provides a comprehensive comparison of the intracellular proteome of M. tuberculosis under metal-limited and metal-rich growth conditions and identifies proteins involved in metal acquisition, transport, metabolism, and stress adaptation
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No record found |
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2026-11-08 |
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