| 21 |
IPD2524 |
Global proteomic profiling of meningioma cohort |
Dr Sanjeeva Srivastava |
Global proteomic profiling of meningiomas using LFQ approach to identify biomarkers in meningioma patients
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
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| 22 |
IPD3692 |
A proteomics investigation of cigarette smoke exposed Wistar rats revealed improved anti-inflammatory effects of the cysteamine nanoemulsions delivered via inhalation |
Dr Sanjeeva Srivastava |
Cigarette smoking is the major cause of chronic inflammatory diseases such as Chronic Obstructive Pulmonary Disease (COPD). It is paramount to develop pharmacological interventions and delivery strategies against the cigarette smoke (CS) associated oxidative stress in COPD. This study in Wistar rats examined cysteamine in nanoemulsions to counteract the cigarette...
Cigarette smoking is the major cause of chronic inflammatory diseases such as Chronic Obstructive Pulmonary Disease (COPD). It is paramount to develop pharmacological interventions and delivery strategies against the cigarette smoke (CS) associated oxidative stress in COPD. This study in Wistar rats examined cysteamine in nanoemulsions to counteract the cigarette smoke distressed microenvironment. In vivo, 28 days of cigarette smoke and 15 days of cysteamine nanoemulsions treatment starting on 29th day consisting of oral and inhalation routes were established in Wistar rats. Additionally, we conducted inflammatory and epithelial-to-mesenchymal transition (EMT) studies in vitro in human bronchial epithelial cell lines (BEAS2B) using 5% cigarette smoke extract. Inflammatory and anti-inflammatory markers such as TNF-α, IL-6, IL-1ß, IL-8, IL-10, IL-13, have been quantified in bronchoalveolar lavage fluid (BALF) to evaluate the effects of the cysteamine nanoemulsions in normalizing the diseased condition. Histopathological analysis of the alveoli and the trachea showed the distorted, lung parenchyma and ciliated epithelial barrier, respectively. To obtain mechanistic insights into the cigarette smoke COPD rat model, “shotgun” proteomics of the lung tissues have been carried out using high-resolution mass spectrometry wherein genes such as ABI1, PPP3CA, PSMA2, FBLN5, ACTG1, CSNK2A1, and ECM1 exhibited significant differences across all the groups. Pathway analysis showed autophagy, signaling by receptor tyrosine kinase, cytokine signaling in immune system, extracellular matrix organization, and hemostasis, as the major contributing pathways across all the studied groups. This work offers new preclinical findings on how cysteamine taken orally or inhaled can combat cigarette smoke-induced oxidative stress.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
37581495
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| 23 |
IPD6660 |
Elevated carbon dioxide levels lead to proteome-wide alterations for optimal growth of a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801 |
Dr Prof. Sanjeeva Srivastava |
Biological CO2 mitigation by photosynthetic microorganisms has emerged as a promising approach for generating biomass-based energy during the course of CO2 fixation. Additionally, cyanobacteria-based biofuels have also garnered immense attention lately because of the depleting fossil fuel reserves and the growing energy demands. Synechococcus elongatus PCC 11801, a fast-growing, high...
Biological CO2 mitigation by photosynthetic microorganisms has emerged as a promising approach for generating biomass-based energy during the course of CO2 fixation. Additionally, cyanobacteria-based biofuels have also garnered immense attention lately because of the depleting fossil fuel reserves and the growing energy demands. Synechococcus elongatus PCC 11801, a fast-growing, high CO2 tolerant, novel isolate of cyanobacteria, is an interesting candidate for metabolic engineering applications. Since under laboratory conditions, it exhibited a high level of tolerance to different environmental stresses (CO2, light, temperature, salts and butanol), it seemed like an encouraging prospect for the production of fuels and other industrially relevant chemicals. This is the first-ever functional global proteomics investigation of Synechococcus elongatus PCC 11801 isolate grown at elevated CO2 levels using high-throughput iTRAQ approach. Three independent biological replicates were analyzed and a total of 861 proteins were identified, out of which 492 proteins were found to be present in all the three replicates. Of these, 248 proteins showing the same trend across the three replicates (≥1.5 fold up-regulation or ≤0.66 fold down-regulation) were chosen for pathway analysis. The metabolic responses were marked with a down-regulation of inorganic carbon transporters alongside an induction of nitrogen transport and absorption proteins in order to uphold the apposite carbon-nitrogen equilibrium. Further acclimation progression exposed an increased expression of proteins taking part in photosynthesis and generation of light harvesting pigments such as chlorophyll. Similarly, a downshift of proteins involved in photoprotection and defense against ROS (reactive oxygen species) was observed. Another principal discovery was the perturbation in expression of proteins belonging to central metabolic pathways like glycolysis, TCA cycle, pentose phosphate pathway as a coping mechanism to high CO2 stress. Further, validation studies were carried out using MRM assays and western blotting of key altered proteins.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
31000743
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| 24 |
IPD4039 |
Chlorella sp. FC2 IITG temporal nitrogen-starvation LC-MSMS |
Dr Sanjeeva Srivastava |
Proteomics study in non-model alga Chlorella FC2 IITG (FC2) challenged with nitrogen starvation for 120 h. Three different nitrogen starvation time-points 40 h, 88 h and 120 h was compared with 0 h (nitrogen sufficient condition). Comparative proteomics analysis was performed using 4-plex isobaric tags for relative and absolute quantification...
Proteomics study in non-model alga Chlorella FC2 IITG (FC2) challenged with nitrogen starvation for 120 h. Three different nitrogen starvation time-points 40 h, 88 h and 120 h was compared with 0 h (nitrogen sufficient condition). Comparative proteomics analysis was performed using 4-plex isobaric tags for relative and absolute quantification (iTRAQ) labelling strategy, followed by chromatographic separation and final generation of tandem mass spectrometry (MS/MS) spectra of tryptic digested peptides on Q-TOF mass spectrometer.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
28378827
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| 25 |
IPD5452 |
Multiplexed Quantitative Proteomics Provides Mechanistic Cues for Malaria Severity and Complexity |
Dr Sanjeeva Srivastava |
Management of severe malaria remains a critical global challenge. In this study, using a multiplexed quantitative proteomics pipeline we systematically investigated the plasma proteome alterations in non-severe and severe malaria patients. We identified a few parasite proteins in severe malaria patients, which could be promising from a diagnostic perspective. Further,...
Management of severe malaria remains a critical global challenge. In this study, using a multiplexed quantitative proteomics pipeline we systematically investigated the plasma proteome alterations in non-severe and severe malaria patients. We identified a few parasite proteins in severe malaria patients, which could be promising from a diagnostic perspective. Further, from host proteome analysis we observed substantial modulations in many crucial physiological pathways, including lipid metabolism, cytokine signaling, complement, and coagulation cascades in severe malaria. We propose that severe manifestations of malaria are possibly underpinned by modulations of the host physiology and defense machinery, which is evidently reflected in the plasma proteome alterations. Importantly, we identified multiple blood markers that can effectively define different complications of severe falciparum malaria, including cerebral syndromes and severe anemia. The ability of our identified blood markers to distinguish different severe complications of malaria may aid in developing new clinical tests for monitoring malaria severity.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
33204009
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| 26 |
IPD3343 |
Semen proteome analysis comparing the persistent effects of different SARS-COV-2 variants on male reproductive system in recovered men |
Dr sanjeeva srivastava |
After the initial COVID-19 wave, India experienced a second COVID-19 wave in March 2021, which was driven by the delta variant. By January 2021, India has also begun its vaccine campaign. Therefore, semen samples from recovered patients who were infected during the two waves of COVID-19 in India were obtained...
After the initial COVID-19 wave, India experienced a second COVID-19 wave in March 2021, which was driven by the delta variant. By January 2021, India has also begun its vaccine campaign. Therefore, semen samples from recovered patients who were infected during the two waves of COVID-19 in India were obtained to study the impact of variants on the male reproductive system. We compared samples from the second wave with those of first wave in India. We also included control samples to the comparison.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
38028760
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| 27 |
IPD5599 |
Detection of mutated peptides of SARS-CoV-2 from COVID-19-infected patients |
Dr Sanjeeva Srivastava |
This project involves the identification of mutated peptides from swab and plasma samples using an in-house developed Mutant Peptide Database (MPD)
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
37093804
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| 28 |
IPD2981 |
PROTEOMIC ALTERATIONS IN COLON ADENOCARCINOMA TISSUE LYSATES |
Dr Sanjeeva Srivastava |
Colorectal cancer is the third most common cancer worldwide, with 1.4 million people diagnosed in 2012 according to GLOBOCAN 2012. 95% of the colon cancer cases are that of adenocarcinomas. Removal of high-risk adenomas and tumors at early stage of colorectal cancer (CRC) can prevent its onset/progression into higher grades...
Colorectal cancer is the third most common cancer worldwide, with 1.4 million people diagnosed in 2012 according to GLOBOCAN 2012. 95% of the colon cancer cases are that of adenocarcinomas. Removal of high-risk adenomas and tumors at early stage of colorectal cancer (CRC) can prevent its onset/progression into higher grades of cancer. The prognosis of colorectal cancer and the stage of diagnosis are closely correlated. 5-year survival rate is observed among 90% patients when diagnosed early and in less than 10% when the metastases develop. This makes the implementation of screening methods aimed at early detection paramount for reduced incidence and mortality rate. Adenocarcinomas are the cancers originating from the gland forming cells of the colon and rectal lining and are known to be the most common type of colorectal cancer. The current diagnosis options for colorectal cancers are limited to biopsy, stool tests and other laboratory tests, barium enema based imaging and other imaging techniques, colonoscopy and other endoscopic procedures which are time consuming. In this study, we used proteomics approach with an aim to identify protein biomarkers which can aid in early detection of colon adenocarcinomas to be precise. Proteins from tumor tissue of colon adenocarcinoma subjects (n=11) and their matched controls were subjected to 4-plex iTRAQ labelling followed by off-gel fractionation prior to LC-MS/MS run. The mass spectrometry data was analysed independently using two different analysis software - Spectrum Mill (SM) and Trans Proteome Pipeline (TPP). The proteins identified using either SM and/or TPP were subjected to pathway analysis using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8 and the proteins common between the two analyses were compared with the data from CPTAC portal and Human Protein Atlas. The expression level of the shortlisted panel of proteins was studied in brain cancers as a non-colon adenocarcinoma control group and validated using MRM approach. A list of 285 unique proteins was identified to be significantly dysregulated in colon adenocarcinoma as compared to its matched controls. These proteins were found to be involved in glycolysis, pentose phosphate pathway, biosynthesis of amino acids, protein processing, spliceosome, proteosome, focal adhesion and proteoglycans in cancer. 94 of the 285 proteins were identified by both- SM and TPP. 34 of these 94 proteins were found to be dysregulated with same trend as that in data reported on CPTAC portal and 9 of these 34 proteins were validated using MRM approach. The proteins identified from this study could be validated further to investigate the role of these proteins as potential biomarkers for early detection of colon adenocarcinoma.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
29568375
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| 29 |
IPD2593 |
Phosphoproteome profile of Human Brain Hemisphere |
Dr Sanjeeva Srivastava |
This project is a continuation of our previous study which resembles Interregional and Inter-hemisphere Proteome of the Human Brain. The current study aims to generate a multiregional phosphoproteome map of 12 neuroanatomical regions from both the hemisphere. The analysis of the raw data was done using MaxQuant and Perseus software....
This project is a continuation of our previous study which resembles Interregional and Inter-hemisphere Proteome of the Human Brain. The current study aims to generate a multiregional phosphoproteome map of 12 neuroanatomical regions from both the hemisphere. The analysis of the raw data was done using MaxQuant and Perseus software. In addition to this phosphopeptides showing equal to and more than 0.75 localization probability and intensities inall the replicates were selected for further analysis. The hemisphere and region specificphosphoproteome expression has also been studied further to understand the functional aspect using in-silico tools. Finally, the data has also been integrated with the previously published proteomic expression in the brainprot (http://www.brainprot.org/) to drive the scientific community in neurobiology research.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-18 |
36317652
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| 30 |
IPD2081 |
Bacillus subtilis under Curcumin treatment LC-MS/MS |
Dr Sanjeeva Srivastava |
Comprehensive Analysis of Temporal Alterations in Cellular Proteome of Bacillus subtilis under Curcumin Treatment
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Bottom-up |
2024-10-18 |
25874956
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