| 41 |
IPD4495 |
B. subtilis, Totarol, LC-MS/MS |
Dr Sanjeeva Srivastava |
Comprehensive Proteomic Analysis of Totarol Induced Alterations in Bacillus subtilis by Multipronged Quantitative Proteomics.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-23 |
25464363
|
| 42 |
IPD4797 |
Quantitative Proteomics analysis of Plasmodium vivax induced alterations in human serum during the acute and convalescent phases of infection |
Dr Sanjeeva Srivastava |
Malaria is by far the world’s most significant tropical infectious disease and over the last a few decades large-scale malaria epidemics have happened in almost all continents. Plasmodium falciparum and Plasmodium vivax account for over 90% of the total malaria cases worldwide. The estimated number of annual clinical cases of...
Malaria is by far the world’s most significant tropical infectious disease and over the last a few decades large-scale malaria epidemics have happened in almost all continents. Plasmodium falciparum and Plasmodium vivax account for over 90% of the total malaria cases worldwide. The estimated number of annual clinical cases of vivax malaria is even higher than that of falciparum malaria, but yet the morbidity associated with this infection and its spectrum of disease is largely neglected. Identification of serum/plasma proteins, which exhibit altered abundance at the onset and during the acute phase of any infection, could be informative to understand the pathobiology of different infectious diseases and host responses against the invading pathogens. To this end, in recent years, quite a few research groups including us have investigated alterations in serum/plasma proteome in severe and non-severe falciparum malaria (and also vivax malaria) to study malaria pathogenesis. In all these studies, serum/plasma proteome of the malaria patients have been analyzed during the febrile stages of the infection, either at the onset of the disease or at the fastigium stage. However, temporal profiling of serum/plasma proteome during acute and remission stages in malaria, which can provide snapshots of the transient and enduring alterations in serum proteome during the febrile, defervescence and convalescent stages has not been reported hitherto. Here, we report, for the first time, serum proteomic alterations in a longitudinal cohort of P. vivax infected patients to elucidate host responses when fever is established (temperature of the body reaches above higher normal level), during the stage when the temperature comes down to normal, and also during the gradual recovery of health after the illness. The three stages discussed in our study have been categorically chosen depending upon the clinical course of uncomplicated vivax malaria. Analysis of the early febrile stage represents host proteome profile immediately after onset of the infection, without any effect of anti-malarial drugs. The second, defervescence stage, reflects any immediate change in blood proteome at early recovery phase, while the convalescent stage indicates a phase after administration of 14 days radical cure treatment with primaquine and a complete recovery, when none of the patients displayed any apparent symptoms of malaria. We have also performed an extensive quantitative proteomics analysis to compare the serum proteome profiles of vivax malaria patients with low and moderately-high parasitemia with healthy community controls. Isobaric tags for relative and absolute quantitation (iTRAQ) and 2-D fluorescence difference gel electrophoresis (2D-DIGE)-based quantitative proteomics approaches were used in the discovery-phase of the study, and some selected differentially abundant serum proteins were validated further by using ELISA. Interestingly, some of the serum proteins like Serum amyloid A, Apolipoprotein A1, C-reactive protein, Titin and Haptoglobin, were found to be sequentially altered with respect to increased parasite counts, while many of the quantified candidates such as Hemopexin, Vitronectin, Clusterin and Apolipoprotein E exhibited nearly equal levels of differential serum abundance in different parasitemic malaria patients. Analysis of a longitudinal cohort of malaria patients indicated reversible alterations in serum levels of some proteins such as Haptoglobin, Apolipoprotein E, Apolipoprotein A1, Carbonic anhydrase 1, and Hemoglobin subunit alpha upon treatment; however, the levels of a few other proteins did not return to the baseline even during the convalescent phase of the infection. Identification of the differentially abundant serum proteins and associated physiological pathways in vivax malaria along with phase-specific protein profiles during the acute and convalescent phases of the infection can effectively enhance our understanding of P. vivax disease biology and host immune responses.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-26 |
28667326
|
| 43 |
IPD6869 |
Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea, part 3 |
Dr Subhra Chakraborty |
To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, TiO2-based phosphoproteomics study in three sequential seed developmental phases in chickpea was performed.
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DBT-National Institute of Plant Genome Research, New Delhi, India |
Shotgun proteomics |
2024-10-30 |
32146728
|
| 44 |
IPD6899 |
Gel based extracellular matrix proteome of jute |
Dr. Subhra Chakraborty |
Extracellular matrix (ECM) is the first line of defense which is an inimitable organelle that perceives biotic and abiotic stresses and reprograms biological processes of host. It also activates innate immune responses in temporal and spatial manner and acts as physical scaffold that prevents the entry of pathogen and microbes...
Extracellular matrix (ECM) is the first line of defense which is an inimitable organelle that perceives biotic and abiotic stresses and reprograms biological processes of host. It also activates innate immune responses in temporal and spatial manner and acts as physical scaffold that prevents the entry of pathogen and microbes in response to stress and hormonal signals. Stem rot, caused by Macrophomina phaseolina adversely affects fiber production in jute. However, how wall related susceptibility affects ECM proteome remains undetermined in bast fiber crops. In order to develop ECM proteome of C. olitorius var. O-4, ECM fraction was isolated by mechanical disruption, CaCl2 extraction and enrichment. ECM fraction purity was assessed by 1-DE profiling in which the ECM fraction was found to be discrete from the crude extract and supernatant recovered during purification steps. Three biological replicates were performed for gel-based jute ECM proteomic analysis. MS/MS analysis of total extract and supernatants were identified as Rubisco or other chloroplastic proteins which were depleted in consecutive steps of purification depicting high degree of ECM purity. Fourteen bands of ECM enriched fraction were identified as canonical ECM localized proteins, e.g., beta-glucosidase, beta-d xylosidase, peroxidase, glycoside hydrolase and peroxiredoxin, confirming jute ECM protein purity and enrichment.
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DBT-National Institute of Plant Genome Research, New Delhi, India |
Gel-based experiment, Bottom-up proteomics |
2024-10-30 |
38572503
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| 45 |
IPD3847 |
Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea, part 1 |
Dr Subhra Chakraborty |
To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, 2-DE based proteomics study in six sequential seed developmental stages in chickpea was performed.
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DBT-National Institute of Plant Genome Research, New Delhi, India |
Gel-based experiment |
2024-10-30 |
32146728
|
| 46 |
IPD2566 |
iTRAQ based disease responsive extracellular matrix proteome of jute infected with Macrophomina Phaseolina |
Dr. Subhra Chakraborty |
Extracellular matrix (ECM) is the first line of defense which is an inimitable organelle that perceives biotic and abiotic stresses and reprograms biological processes of host. It also activates innate immune responses in temporal and spatial manner and acts as physical scaffold that prevents the entry of pathogen and microbes...
Extracellular matrix (ECM) is the first line of defense which is an inimitable organelle that perceives biotic and abiotic stresses and reprograms biological processes of host. It also activates innate immune responses in temporal and spatial manner and acts as physical scaffold that prevents the entry of pathogen and microbes in response to stress and hormonal signals. Stem rot, caused by Macrophomina phaseolina adversely affects fiber production in jute. However, how wall related susceptibility affects ECM proteome remains undetermined in bast fiber crops. Here, stem rot responsive quantitative temporal ECM proteome was developed in jute upon M. phaseolina infection. Using isobaric tags for relative and absolute quantitative proteomics and MS/MS analysis, we identified 415 disease responsive proteins (DRPs), involved in wall integrity, acidification, proteostasis, hydration and redox homeostasis. Disease-related correlation network identified functional hubs related to wall degrading enzymes, structural carbohydrates and signaling govern rot responsive wall-susceptibility.
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DBT-National Institute of Plant Genome Research, New Delhi, India |
Bottom-up |
2024-10-30 |
38572503
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| 47 |
IPD1218 |
Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea, part 2 |
Dr Subhra Chakraborty |
To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, 2-DE based phosphoproteomics study in six sequential seed developmental stages in chickpea was performed.
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DBT-National Institute of Plant Genome Research, New Delhi, India |
Gel-based experiment |
2024-10-30 |
32146728
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| 48 |
IPD8258 |
Cell membrane proteome analysis in HEK293T cells challenged with α-Synuclein amyloids |
Dr Swasti Raychaudhuri |
Amyloids interact with plasma membranes. Extracellular amyloids cross the plasma membrane barrier. Internalized extracellular amyloids are reported to trigger amyloidogenesis of endogenous proteins in recipient cells. To what extent these extracellular and intracellular amyloids perturb the plasma membrane proteome is not investigated. Using α-Synuclein as a model amyloid protein, we...
Amyloids interact with plasma membranes. Extracellular amyloids cross the plasma membrane barrier. Internalized extracellular amyloids are reported to trigger amyloidogenesis of endogenous proteins in recipient cells. To what extent these extracellular and intracellular amyloids perturb the plasma membrane proteome is not investigated. Using α-Synuclein as a model amyloid protein, we performed membrane shaving followed by mass spectrometry experiment to identify the conformational changes in the cell surface proteins after extracellular amyloid challenge. We also performed membrane proteomics after the biogenesis of intracellular α-Synuclein amyloids. Our results suggest that promiscuous interaction with extracellular amyloids stochastically alter the conformation of plasma membrane proteins. This affects the biological process through the plasma membrane and result in loss in cell viability. Cells that survive the extracellular amyloid shock can grow normally and gradually develop intracellular amyloids which do not directly impact the plasma membrane proteome and associated biological processes. Thus, α-Synuclein amyloids can damage the plasma membrane and related processes only during cell to cell transfer and not during their intracellular biogenesis.
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Centre for Cellular & Molecular Biology (CCMB |
Shotgun proteomics, Gel-based experiment |
2024-11-16 |
38973669
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| 49 |
IPD4200 |
A comprehensive comparison of Rapid and Deep Plasma Proteomics workflows to identify and quantify biomarkers of Sickle Cell Anaemia |
Dr. Swasti Raychaudhuri |
Plasma serves as a rich source of protein biomarkers but in-depth proteomic analysis is challenging due to the vast dynamic range of protein abundance. Pre-fractionation of plasma proteins is commonly practiced to improve the proteome coverage but the protocols are time-expensive, suffer from flowchart complexity, and often less reproducible. Here,...
Plasma serves as a rich source of protein biomarkers but in-depth proteomic analysis is challenging due to the vast dynamic range of protein abundance. Pre-fractionation of plasma proteins is commonly practiced to improve the proteome coverage but the protocols are time-expensive, suffer from flowchart complexity, and often less reproducible. Here, we explore multiple strategies of shotgun proteomics to optimize biomarker discovery workflows for Sickle Cell Anaemia (SCA) patients from remote India. A deep proteomics workflow via off-line reverse phase Ultra High-Pressure Liquid Chromatography based fractionation of tryptic digested plasma peptides followed by optimized pooling of peptides based on charge and hydrophobicity yielded the best depth of plasma proteome with a trade-off of significantly long experimental time. Alternatively, a rapid analysis of tryptic digested plasma peptides via a shorter gradient mass spectrometry run saves time but quantifies only ~ 50% of the proteins than the deep workflow. Intriguingly, despite the difference in proteome coverage, more than 80% of known FDA and SCA biomarkers quantified in the deep workflow are also quantified in the rapid workflow. Given the practical difficulties of sample collection and plasma preservation in rural India, we propose the deep proteomics workflow for biomarker discovery in smaller cohorts and the rapid workflow for biomarker validations in larger cohorts. Additional targeted proteomics based strategies may be designed for the validation of missing biomarkers in the rapid workflow.
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Centre for Cellular & Molecular Biology (CCMB |
Shotgun proteomics |
2024-11-16 |
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| 50 |
IPD8972 |
Distinct Stress Response to Mitochondrial Inter-membrane Space and Matrix Proteotoxic Stress are Preferentially Modulated by TOM complex and Vms1, respectively |
Dr Swasti Raychaudhuri |
Double-membrane-bound architecture of mitochondria is essential for its ATP synthesis function; simultaneously such structure sub-divides the organelle into inter-membrane space (IMS) and matrix. IMS and matrix are inherently different in protein folding milieu due to their contrasting oxido-reductive environments and distinctly different protein quality control (PQC) machineries. By inducing proteotoxic...
Double-membrane-bound architecture of mitochondria is essential for its ATP synthesis function; simultaneously such structure sub-divides the organelle into inter-membrane space (IMS) and matrix. IMS and matrix are inherently different in protein folding milieu due to their contrasting oxido-reductive environments and distinctly different protein quality control (PQC) machineries. By inducing proteotoxic stress limited to IMS or matrix using varied stressor proteins, we decipher distinct cellular response to IMS and matrix stress. IMS stress leads to specific upregulation of IMS-resident chaperones and TOM complex components. In contrast, matrix stress leads to specific upregulation of matrix- chaperones and cytosolic PQC components. We report that cells respond to mitochondrial stress by an adaptive mechanism by adjourning mitochondrial respiration while upregulating glycolysis as a compensatory pathway. By systematic genetic interaction, we show that TOM complex components act as specific modulators of IMS-stress response while Vms1 preferentially modulates the matrix stress response
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Centre for Cellular & Molecular Biology (CCMB |
Top-down |
2024-11-16 |
35500842
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