| 11 |
IPD2865 |
Assessment of host hemoglobin accumulation in P. berghei heme pathway ferrochelatase knockout parasite food vacuole by iTRAQ |
Dr Arun Nagaraj |
Two independent sets of fourplex iTRAQ labelling were carried out to assess the accumulation of host Hb in PbFCKO FVs. The results obtained have suggested that there is a ~3-4 -fold increase in Hb ï¡ and ï¢ chains in FCKO FVs as quantified by iTRAQ.
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Institute of Life Sciences, Bhubaneswar, India. |
Top-down |
2025-01-31 |
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| 12 |
IPD4298 |
Food vacuole proteome of P. berghei heme pathway ferrochelatase knockout parasite by LC-MS/MS |
Dr Arun Nagaraj |
LC-MS/MS of in-solution trypsin digested FV protein extracts was carried out for the FVs isolated from PbWT and PbFCKO parasites. The FV preparations had signature FV proteins such as plasmepsin IV, berghepain, aminopeptidases, subunits of vacuolar-type H+ATPase (V-type H ATPase), together with parasitophorous vacuolar (PV) proteins including exported protein 1...
LC-MS/MS of in-solution trypsin digested FV protein extracts was carried out for the FVs isolated from PbWT and PbFCKO parasites. The FV preparations had signature FV proteins such as plasmepsin IV, berghepain, aminopeptidases, subunits of vacuolar-type H+ATPase (V-type H ATPase), together with parasitophorous vacuolar (PV) proteins including exported protein 1 (Exp1), Exp2, early transcribed membrane protein, PV1, PV5 (lipocalin) etc., and Rab GTPases associated with cytostome-FV trafficking. A total number of 251 and 201 proteins could be identified for WT (P1) and FCKO (P2) FVs, respectively, and 175 proteins were common between them suggesting an overall consistency in the preparations. The results obtained have suggested that the FV proteome in FCKO parasites is compromised. None of the subunits of V-type H+ATPase - a proton pump maintaining the acidic pH of FV could be detected in FCKO FVs indicating the lower abundance of these proteins. In addition, berghepain-2 - a cysteine protease involved in Hb degradation could not be detected in FCKO FVs.
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Institute of Life Sciences, Bhubaneswar, India. |
Top-down |
2025-01-31 |
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| 13 |
IPD8541 |
Proteomic analysis of L-Methionine Sulfoximine (MSO)-treated Plasmodium falciparum by LC-MS/MS |
Dr Arun Nagaraj |
LC-MS/MS of in-solution trypsin digested parasite protein extracts was carried out to examine the proteome of MSO-treated Pf parasites. Proteins were extracted from the untreated and MSO-treated parasite pellets of two independent experiments (Exp1: T7_R Vs T8; Exp2: T3_R Vs T4_R). For each experiment, two different sets of untreated and...
LC-MS/MS of in-solution trypsin digested parasite protein extracts was carried out to examine the proteome of MSO-treated Pf parasites. Proteins were extracted from the untreated and MSO-treated parasite pellets of two independent experiments (Exp1: T7_R Vs T8; Exp2: T3_R Vs T4_R). For each experiment, two different sets of untreated and MSO-treated cultures synchronized for ring stages and early trophozoites were used. MSO treatment was carried out at 50 ïM concentration for 12 h. A total number of 149 proteins associated with various metabolic and cellular functions, cytoadherence and host invasion, Hb degradation, etc., were downregulated in MSO-treated parasites. This also included important asparagine-rich proteins such as tRNA ligases, components of RNA processing and protein degradation pathways, lipocalin associated with hemozoin formation and antimalarial drug sensitivity, heat shock protein 110c essential for stabilizing the asparagine repeat-rich parasite proteins etc. Only ten proteins were found to be upregulated in MSO-treated Pf3D7 parasites. For downregulated proteins, proteins identified in both the untreated controls of two independent experiments and either undetectable or significantly downregulated (>1.5 fold) in MSO-treated Pf3D7 parasites were considered. For upregulated proteins, proteins significantly upregulated (>1.5 fold) in both the MSO-treated parasites of two independent experiments and/or undetectable in the untreated controls but detectable in the MSO-treated parasites were considered.
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Institute of Life Sciences, Bhubaneswar, India. |
Top-down |
2025-01-31 |
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| 14 |
IPD2453 |
Placental proteomics identified elevated Aldo-keto Reductase 1-B1 level in spontaneous preterm birth |
Dr Tushar K. Maiti |
The prevalence of preterm birth along with its associated mortality and lifelong morbidity warrant a better understanding of the underlying signaling events for better diagnosis and management of the condition. Placenta is an important transient organ that acts as a conduit between the fetus and mother. Any physiological and pathological...
The prevalence of preterm birth along with its associated mortality and lifelong morbidity warrant a better understanding of the underlying signaling events for better diagnosis and management of the condition. Placenta is an important transient organ that acts as a conduit between the fetus and mother. Any physiological and pathological changes taking place in the feto-maternal system are directly reflected in the placenta, making it a fitting choice to study the altered signaling mechanisms that are play. We undertook independent data acquisition of clinical placenta samples (n=40), obtained from Garbh-Ini cohort, to study their comparative protein profiles in spontaneous preterm vs term birth condition. When label-free quantitation (LFQ) was carried out, it yielded 23 differentially expressed proteins (DEPs) in the case-control comparison.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Shotgun proteomics |
2025-03-07 |
39762117
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| 15 |
IPD6020 |
Proteomic analysis of gut tissue of Labeo rohita infected with Aeromonas hydrophila |
Dr Sanjeeva Srivastava |
This study aimed at performing the quantitative proteomics analysis of gut tissue, one of Labeo rohita, one of the important aquaculture fish species. Data was acquired using high resolution mass spectrometry followed by Label free quantification. After performing statistical analysis, a panel of differentially expressed proteins were identified which include...
This study aimed at performing the quantitative proteomics analysis of gut tissue, one of Labeo rohita, one of the important aquaculture fish species. Data was acquired using high resolution mass spectrometry followed by Label free quantification. After performing statistical analysis, a panel of differentially expressed proteins were identified which include extracellular matrix proteins, cytoskeletal proteins, immune related proteins and metabolic enzymes. This analysis revealed important signaling pathways and protein-protein interaction networks which could help in understanding disease pathogenesis. The data acquired in the study would provide a basis for further omics research and can help in elucidating biological processes in healthy or diseased fish.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2025-03-09 |
39292008
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| 16 |
IPD1063 |
Identifying alterations post ILK inhibition in Meningioma cell lines |
Dr Sanjeeva Srivastava |
The current study reports alterations in PI3-Akt and Focal adhesion pathway post ILK inhibition in meningioma cell lines. The inhibition is done using a pyrazole that specifically inhibits Integrin Link Kinase. The global proteomic profile was analysed post treatment (24 hours) in treated vs untreated cell line replicates.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2025-03-09 |
32974197
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| 17 |
IPD3725 |
A Data-Independent-Acquisition-based proteomic approach towards understanding the acclimation strategy of Microchloropsis gaditana CCMP526 in hypersaline conditions |
Dr Sanjeeva Srivastava |
Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipid as an energy storage molecule. We used proteomics to...
Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipid as an energy storage molecule. We used proteomics to understand the molecular basis for acclimation of M. gaditana to increased salinity levels (55 and 100 PSU). Correspondence analysis (CA) was used for identification of salinity-responsive proteins (SRPs). The highest number of altered proteins was observed in 100 PSU. Gene Ontology (GO) enrichment analysis revealed a separate path of acclimation for cells exposed to 55 and 100 PSU. Osmolyte and lipid biosynthesis was up-regulated in high saline conditions. However, concomitantly lipid oxidation pathways were also up-regulated at high saline conditions, providing acetyl-CoA for energy metabolism through the TCA cycle. Carbon fixation and photosynthesis were tightly regulated, while chlorophyll biosynthesis was affected under high salinity conditions. Importantly, temporal proteome analysis of salinity-challenged M. gaditana revealed vital salinity-responsive proteins which could be used for strain engineering for improved salinity resistance.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2025-03-09 |
8412934
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| 18 |
IPD3211 |
A Data-Independent-Acquisition-based proteomic approach towards understanding the acclimation strategy of Microchloropsis gaditana CCMP526 in hypersaline conditions |
Dr Sanjeeva Srivastava |
Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipid as an energy storage molecule. We used proteomics to...
Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipid as an energy storage molecule. We used proteomics to understand the molecular basis for acclimation of M. gaditana to increased salinity levels (55 and 100 PSU). Correspondence analysis (CA) was used for identification of salinity-responsive proteins (SRPs). The highest number of altered proteins was observed in 100 PSU. Gene Ontology (GO) enrichment analysis revealed a separate path of acclimation for cells exposed to 55 and 100 PSU. Osmolyte and lipid biosynthesis was up-regulated in high saline conditions. However, concomitantly lipid oxidation pathways were also up-regulated at high saline conditions, providing acetyl-CoA for energy metabolism through the TCA cycle. Carbon fixation and photosynthesis were tightly regulated, while chlorophyll biosynthesis was affected under high salinity conditions. Importantly, temporal proteome analysis of salinity-challenged M. gaditana revealed vital salinity-responsive proteins which could be used for strain engineering for improved salinity resistance.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
SWATH MS |
2025-03-09 |
34497906
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| 19 |
IPD4061 |
Mass-spectrometry based plasma proteomics identifies biomarkers for the detection of COVID-19 progression |
Dr Sanjeeva Srivastava |
COVID-19 manifests itself in an array of symptoms. While most patients experience very mild-to-moderate symptoms, around one in five patients develop pneumonia coupled with severe respiratory distress. These patients require treatment in the intensive care units (ICU), however, most of the times, it leads to multi-organ dysfunction and death. ...
COVID-19 manifests itself in an array of symptoms. While most patients experience very mild-to-moderate symptoms, around one in five patients develop pneumonia coupled with severe respiratory distress. These patients require treatment in the intensive care units (ICU), however, most of the times, it leads to multi-organ dysfunction and death. Mass spectrometry based proteomics can help us to identify the precise pathophysiological pathways that get perturbed during the course of the disease. Our study involved a comprehensive proteome-wide investigation of COVID negative (n=20), non-severe (n= 18) and severe (n= 36) COVID-19 patients plasma samples. We categorized patients into severe and non-severe groups and conducted LFQ based discovery proteomics for unraveling differentially expressed proteins followed by pathway enrichment studies and validation of targets by targeted studies on a batch of longitudinal samples.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2025-03-09 |
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| 20 |
IPD8171 |
Organ wise proteomic profiling of Indian major carp, Labeo rohita |
Dr Sanjeeva Srivastava |
The aim of this study was to develop an organ wise proteome map for Labeo rohita. Using LC-MS/MS, we have performed in-depth proteomics analysis of 19 different sample types, including 17 tissue samples, plasma from female fish and embryo 4-day post fertilization. Whole analysis resulted in the identification of more...
The aim of this study was to develop an organ wise proteome map for Labeo rohita. Using LC-MS/MS, we have performed in-depth proteomics analysis of 19 different sample types, including 17 tissue samples, plasma from female fish and embryo 4-day post fertilization. Whole analysis resulted in the identification of more than more than 8000 proteins with 1% FDR of which more than 76% were identified with two or more than two unique peptides. The dataset show organ wise pattern of protein expression along with extensive catalogue of orgsn wise Post translational modification. This proteomic information would complement the recently published genome to accelerate further research.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics, Gel-based experiment |
2025-03-09 |
34962809
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