| 51 |
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 |
|
| 52 |
IPD2655 |
Aggregation of respiratory complex subunits marks the onset of proteotoxicity in proteasome inhibited cells |
Dr Swasti Raychaudhuri |
Proteostasis is maintained by optimum expression, folding, transport, and clearance of proteins. Deregulation of any of these processes triggers protein aggregation and is implicated in many age-related pathologies. Here, using quantitative proteomics and microscopy we show that aggregation of many nuclear-encoded mitochondrial proteins is an early protein-destabilization event during short-term...
Proteostasis is maintained by optimum expression, folding, transport, and clearance of proteins. Deregulation of any of these processes triggers protein aggregation and is implicated in many age-related pathologies. Here, using quantitative proteomics and microscopy we show that aggregation of many nuclear-encoded mitochondrial proteins is an early protein-destabilization event during short-term proteasome inhibition. Among these, Respiratory Chain Complex (RCC) subunits represent a group of functionally related proteins consistently forming aggregates under multiple proteostasis-stresses with varying aggregation-propensities. Sequence analysis reveals that several RCC subunits, irrespective of cleavable mitochondrial targeting sequence (MTS), contain low complexity regions (LCR) at N-terminus. Using different chimeric and mutant constructs we show that these low complexity regions partially contribute to intrinsic instability of multiple RCC subunits. Taken together, we propose that physicochemically driven aggregation of unassembled RCC subunits destabilizes their functional assembly inside mitochondria. This deregulates the biogenesis of respiratory complexes and marks the onset of mitochondrial dysfunction.
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Centre for Cellular & Molecular Biology (CCMB |
Shotgun proteomics, Gel-based experiment |
2024-11-16 |
30682348
|
| 53 |
IPD3807 |
QUATERNARY AND QUINARY ORGANIZATION OF RESPIRATORY COMPLEX SUBUNITS TO ADAPT PROTEOSTASIS-STRESS |
Dr. Swasti Raychaudhuri |
Phase separation and reversible aggregation of proteins is a well-recognized adaptive strategy to survive stress. Here, we show that RCC subunits are engaged into improved super-quaternary organizations inside mitochondria during proteostasis stress. Assembly and oligomeric organizations of Complex II and V are consolidated while Complex I, III and IV are...
Phase separation and reversible aggregation of proteins is a well-recognized adaptive strategy to survive stress. Here, we show that RCC subunits are engaged into improved super-quaternary organizations inside mitochondria during proteostasis stress. Assembly and oligomeric organizations of Complex II and V are consolidated while Complex I, III and IV are increasingly incorporated into respiratory supercomplexes in multiple cell-lines with different proteostasis and metabolic demands. Further, our results suggest that improved supra-organization of respiratory complexes (iSRC) is an outcome of conformational optimization towards better enzyme activity and co-terminus to appearance of aggregates of RCC subunits in stressed cells. Simultaneous reversion of iSRC and disappearance of aggregates during stress-withdrawal indicates complementarity between these quaternary and quinary proteome-reorganization mechanisms. iSRC appears to be the pre-emptive and deterministic ensemble over stochastic aggregation as it offers direct fitness-benefit.
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Centre for Cellular & Molecular Biology (CCMB |
Shotgun proteomics |
2024-11-16 |
|
| 54 |
IPD1344 |
QUATERNARY AND QUINARY ORGANIZATION OF RESPIRATORY COMPLEX SUBUNITS TO ADAPT PROTEOSTASIS-STRESS |
Dr Swasti Raychaudhuri |
Phase separation and reversible aggregation of proteins is a well-recognized adaptive strategy to survive stress. Here, we show that RCC subunits are engaged into improved super-quaternary organizations inside mitochondria during proteostasis stress. Assembly and oligomeric organizations of Complex II and V are consolidated while Complex I, III and IV are...
Phase separation and reversible aggregation of proteins is a well-recognized adaptive strategy to survive stress. Here, we show that RCC subunits are engaged into improved super-quaternary organizations inside mitochondria during proteostasis stress. Assembly and oligomeric organizations of Complex II and V are consolidated while Complex I, III and IV are increasingly incorporated into respiratory supercomplexes in multiple cell-lines with different proteostasis and metabolic demands. Further, our results suggest that improved supra-organization of respiratory complexes (iSRC) is an outcome of conformational optimization towards better enzyme activity and co-terminus to appearance of aggregates of RCC subunits in stressed cells. Simultaneous reversion of iSRC and disappearance of the aggregates during stress-withdrawal indicates complementarity between these quaternary and quinary proteome-reorganization mechanisms. iSRC appears to be the pre-emptive and deterministic ensemble over stochastic aggregation as it offers direct fitness-benefit.
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...Read less
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Centre for Cellular & Molecular Biology (CCMB |
Shotgun proteomics |
2024-11-16 |
32878939
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| 55 |
IPD3822 |
Fangs in the ghats: preclinical insights into the medical importance of endemic pit vipers from the Western Ghats |
Dr. Kartik Sunagar |
The socioeconomic burden of snakebite in India is largely attributed to the ‘big four’ snakes, completely neglecting the considerable impact of envenoming by many other snake species. Bites from the so-called ‘neglected many’ are often treated with a polyvalent antivenom that is manufactured against the ‘big four’ snakes - a...
The socioeconomic burden of snakebite in India is largely attributed to the ‘big four’ snakes, completely neglecting the considerable impact of envenoming by many other snake species. Bites from the so-called ‘neglected many’ are often treated with a polyvalent antivenom that is manufactured against the ‘big four’ snakes - a strategy that has been widely documented to fail. Yet, specific antivenoms are not commercially manufactured against these snakes. While the medical importance of various species of cobras, saw-scaled vipers, and kraits is very well-known, the clinical impact of pit vipers from the rainforests of the Western Ghats, northeastern India, and Andaman and Nicobar islands has remained elusive. Amongst the 90+ species of snakes found in the Western Ghats, the hump-nosed (Hypnale hypnale), Malabar (Craspedocephalus malabaricus) and bamboo (Craspedocephalus gramineus) pit vipers can potentially inflict clinically severe envenoming in humans. To evaluate the severity of toxicity inflicted by these snakes, we characterised their venom composition, biochemical and pharmacological activities, and toxicity- and morbidity-inducing potentials. Our findings highlight the therapeutic inadequacies of the generic Indian and Hypnale-specific Sri Lankan polyvalent antivenoms in neutralising morbidity and mortality resulting from pit viper envenomings and underscore the need for a regional antivenom therapy in India.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
37298463
|
| 56 |
IPD8910 |
A wolf in another wolf’s clothing: Post-genomic regulation dictates venom profiles of medically-important cryptic kraits in India |
Dr. Kartik Sunagar |
This study investigates the widespread cryptic Bungarus caeruleus (Comman krait) in India and clinical repercussions of their bits by implementing multidisciplinary approach involving proteomics, transcripomics, and assessment of toxicity and efficacy of currently marketed anivenoms. The study also aims at understanding the evolutionary relationships between these phenotypically simillar kraits.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
33477742
|
| 57 |
IPD3987 |
The preclinical evaluation of a second-generation antivenom for treating snake envenoming in India |
Dr. Kartik Sunagar |
In this study, by employing chromatographic purification of the bulk, we have significantly enhanced the preclinical performance of the conventional Indian antivenom product. The effectiveness of the test batches of this ‘second-generation’ antivenom was evaluated using a variety of in vitro and in vivo preclinical assays, including venom recognition and...
In this study, by employing chromatographic purification of the bulk, we have significantly enhanced the preclinical performance of the conventional Indian antivenom product. The effectiveness of the test batches of this ‘second-generation’ antivenom was evaluated using a variety of in vitro and in vivo preclinical assays, including venom recognition and toxicity and pathology neutralisation. The outcomes of these experiments demonstrated the significantly superior performance of the purified product over all other major commercial Indian antivenoms.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
35324665
|
| 58 |
IPD6128 |
Stings on wings: venom proteomics and tissue transcriptomics of the lesser banded hornet, Vespa affinis |
Dr Kartik Sunagar |
The project aims at unraveling the venom repertoire of the lesser banded hornet (Vespa affinis) and investigate the regimes of natural selection underpinning their venom evolution. The study also sheds light on the clinical repercussions of the V. affinis venom.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
36601583
|
| 59 |
IPD7258 |
The Arabian cousin: Comparative venomics of Daboia palaestinae and Daboia russelii |
Dr. Kartik Sunagar |
In this study, to unravel the influence of phylogenetic divergence and biogeography in shaping the composition and activity of Daboia venoms, we comparatively investigated the venoms of D. russelii from western India and D. palaestinae from Israel.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
36355975
|
| 60 |
IPD3551 |
Hiss of death - Biogeographical venom variation in the Indian spectacled cobra (Naja naja) underscores the pressing need for pan-India efficacious snakebite therapy |
Dr. Kartik Sunagar |
The project aims at investigating the snake venom variability of Naja naja populations from six different biogeographic zones across India.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
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