| 1 |
IPD8622 |
Hepatitis C virus induces HuR relocalization by coordinating PKC-δ and AMPK-α function |
Dr. Tushar Kanti Maiti |
Huh7.5 cells were transfected with HCV-JFH1 RNAand harvested after 48h of transfection. Total proteins were extracted in IP lysis buffer (Pierce, Thermo Scientific) containing 1× halt-protease and phosphatase inhibitor cocktail (Thermo Fisher Scientific, USA) with intermediate vortexing followed by mild sonication. The lysate was centrifuged at 14,000 × g for...
Huh7.5 cells were transfected with HCV-JFH1 RNAand harvested after 48h of transfection. Total proteins were extracted in IP lysis buffer (Pierce, Thermo Scientific) containing 1× halt-protease and phosphatase inhibitor cocktail (Thermo Fisher Scientific, USA) with intermediate vortexing followed by mild sonication. The lysate was centrifuged at 14,000 × g for 30 min at 4 °C. The supernatant was quantified by the BCA method (Thermo Fisher Scientific, USA). An equivalent amount (4 mg) of proteins from each condition was incubated with 3g of anti-HuR antibody for overnight at 4 °C. The immunocomplex was captured by using protein G Sepharose 4 fast flow beads (17-0618-01/ GE Healthcare). The immunoprecipitated complex was washed two times with IP lysis buffer and one time with mili-Q. Bound protein complexes were eluted in 50 µl SDS-PAGE 2X Laemmli sample buffer. The samples were resolved on 12% SDS–PAGE and stained with Coomassie stain (0.1% w/v). The gel was subjected to further in-gel mass spectrometry analysis.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Gel-based experiment, Affinity purification coupled with mass spectrometry proteomics |
2024-08-29 |
37540723
|
| 2 |
IPD1935 |
Dehydration-induced mitochondrial proteome dynamics and defense response in rice |
Dr. Tushar Kanti Maiti |
Water-deficit or dehydration greatly influences plant development and reduces crop productivity, particularly in rain-fed areas across the world. Despite extensive research over the past several decades, little is known about dehydration management of mitochondria and cellular energy metabolism. We, for the first time, mapped dehydration-induced global changes in protein expression...
Water-deficit or dehydration greatly influences plant development and reduces crop productivity, particularly in rain-fed areas across the world. Despite extensive research over the past several decades, little is known about dehydration management of mitochondria and cellular energy metabolism. We, for the first time, mapped dehydration-induced global changes in protein expression of the mitochondrial landscape to dissect the molecular mechanism, which might enable crop species to survive. Toward this, four-week-old rice seedlings were subjected to progressive dehydration by withholding water, and the stress severity was assessed by physicochemical reactions and mitochondrial architecture. The comparative mitochondrial proteomics analysis led to the identification of an array of stress-responsive proteins, presumably involved in a variety of cellular functions that includes energy production, organelle protein transportation and ROS detoxification, among others. The proteomics profile demonstrated that the alteration of tricarboxylic acid cycle intermediates is crucial for fuelling ATP production. Collectively, our results demonstrate that the global regulation of mitochondrial proteins is linked to dehydration response, which would favour genetic manipulation of crop species for better adaptation.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Shotgun proteomics |
2024-08-30 |
|
| 3 |
IPD9699 |
Molecular insight into palmitic acid-induced hepatocellular carcinoma cell death. |
Dr. Tushar Kanti Maiti |
The accumulation of lipid is a histological and biochemical hallmark of obesity-associated hepato-steatosis.Moreover, growing evidenceindicatesthathigher free fatty acids (FFAs) level in hepatocytes affects a myriad of biological processes leading to excessive metabolic imbalance, increased reactive oxygen species (ROS), deregulated autophagy, and impairment of mitochondrial and ER stress, that collectively drives...
The accumulation of lipid is a histological and biochemical hallmark of obesity-associated hepato-steatosis.Moreover, growing evidenceindicatesthathigher free fatty acids (FFAs) level in hepatocytes affects a myriad of biological processes leading to excessive metabolic imbalance, increased reactive oxygen species (ROS), deregulated autophagy, and impairment of mitochondrial and ER stress, that collectively drives cell death. Lipotoxicity and cell death mechanisms have been studied for many years. However, the molecular signals that link these two events during lipid stress remain poorly understood. From the very beginning, to systematically study hepato-lipotoxicity, HepG2 treated with PA providentially recapitulates the global lipotoxic responses, including insulin resistance to hepatocyte death. Therefore, using this cell-based model system, we pursued a comprehensive, differential quantitative approach where measurements of protein dynamics are analysed by mass spectrometry. Given that indispensable information, successive temporal phosphoproteomics dynamics are allowed us to in-depth analysis of lipotoxicity associated mechanistic network of cell death more precisely.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Shotgun proteomics |
2024-08-30 |
35732625
|
| 4 |
IPD6641 |
Deciphering the function of Angiomotin in trophoblast cells |
Dr Tushar Kanti Maiti |
Trophectoderm-specific expression of Angiomotin (AMOT) in pre-implantation embryos followed by its unique expression in the post-implantation ectoplacental cone that harbors the trophoblast stem cell niche prompted our investigation on the function of AMOT in trophoblast cells. Using the in vitro trophoblast stem cell culture model, we established differentiation dependent up-regulation...
Trophectoderm-specific expression of Angiomotin (AMOT) in pre-implantation embryos followed by its unique expression in the post-implantation ectoplacental cone that harbors the trophoblast stem cell niche prompted our investigation on the function of AMOT in trophoblast cells. Using the in vitro trophoblast stem cell culture model, we established differentiation dependent up-regulation of AMOT expression in trophoblast cells. To understand the function of AMOT in trophoblast cells mass spectrometry-based proteomic analysis was employed to identify the AMOT interactome within the trophoblast proteome. This approach utilized immunoprecipitation of endogenous AMOT followed by fractionation on SDS-PAGE and subsequently subjecting the tryptic digested excised gel bands to mass spectrometry.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Shotgun proteomics |
2024-08-30 |
33237582
|
| 5 |
IPD2755 |
Vaginal secretory proteome dynamically changes across the early and mid-trimesters of pregnancy |
Dr Tushar Kanti Maiti |
This study investigates the dynamic alterations in high vaginal fluid (HVF) proteome and its correlation with physiological changes during progression of term pregnancy. The HVF samples were collected at three time points as defined as V1 (6-12 weeks), V2 (18-20 weeks) and V3 (26-28 weeks) and SWATH-MS strategy were applied...
This study investigates the dynamic alterations in high vaginal fluid (HVF) proteome and its correlation with physiological changes during progression of term pregnancy. The HVF samples were collected at three time points as defined as V1 (6-12 weeks), V2 (18-20 weeks) and V3 (26-28 weeks) and SWATH-MS strategy were applied to profile changes in protein expression at early and middle stage of pregnancy. Using in-house generated HVF-specific protein library, 61 proteins (>1.5 fold at V2/V1 or V3/V1, q-value <0.05) changed as a function of gestational age. The stage-specific expression pattern of these proteins was mainly associated with the biology of cervical remolding, fetal development and microbial defense.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
SWATH MS |
2024-08-30 |
33497241
|
| 6 |
IPD1838 |
Molecular insight into palmitic acid-induced hepatocellular carcinoma cell death. |
Dr. Tushar Kanti Maiti |
The accumulation of lipid is a histological and biochemical hallmark of obesity-associated hepato-steatosis.Moreover, growing evidenceindicatesthathigher free fatty acids (FFAs) level in hepatocytes affects a myriad of biological processes leading to excessive metabolic imbalance, increased reactive oxygen species (ROS), deregulated autophagy, and impairment of mitochondrial and ER stress, that collectively drives...
The accumulation of lipid is a histological and biochemical hallmark of obesity-associated hepato-steatosis.Moreover, growing evidenceindicatesthathigher free fatty acids (FFAs) level in hepatocytes affects a myriad of biological processes leading to excessive metabolic imbalance, increased reactive oxygen species (ROS), deregulated autophagy, and impairment of mitochondrial and ER stress, that collectively drives cell death. Lipotoxicity and cell death mechanisms have been studied for many years. However, the molecular signals that link these two events during lipid stress remain poorly understood. From the very beginning, to systematically study hepato-lipotoxicity, HepG2 treated with PA providentially recapitulates the global lipotoxic responses, including insulin resistance to hepatocyte death. Therefore, using this cell-based model system, we pursued a comprehensive, differential quantitative approach where measurements of protein dynamics are analysed by mass spectrometry. Given that indispensable information, successive temporal phosphoproteomics dynamics are allowed us to in-depth analysis of lipotoxicity associated mechanistic network of cell death more precisely.
Read more
...Read less
|
DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Affinity purification coupled with mass spectrometry proteomics |
2024-08-30 |
35732625
|
| 7 |
IPD9042 |
p53 amyloid induced cellular transformation and tumor formation in the mouse xenograft model |
Dr. Tushar Kanti Maiti |
p53 amyloid formation is predicted to be involved in cancer initiation, but the direct evidence of how altered p53 acts as an oncogene is lacking. Cells with p53 amyloids show enhanced survival, apoptotic resistance with increased proliferation and migration rates. Proteomic profiling of cells containing p53 aggregates suggests that p53...
p53 amyloid formation is predicted to be involved in cancer initiation, but the direct evidence of how altered p53 acts as an oncogene is lacking. Cells with p53 amyloids show enhanced survival, apoptotic resistance with increased proliferation and migration rates. Proteomic profiling of cells containing p53 aggregates suggests that p53 amyloid formation triggers aberrant expression of pro-oncogenes while downregulating the tumor-suppressive genes. We propose that wild-type p53 amyloid formation can potentially contribute to the initiation of tumor development.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Shotgun proteomics |
2024-08-30 |
35796018
|
| 8 |
IPD4755 |
Molecular insight into palmitic acid-induced hepatocellular carcinoma cell death. |
Dr. Tushar Kanti Maiti |
The accumulation of lipid is a histological and biochemical hallmark of obesity-associated hepato-steatosis.Moreover, growing evidenceindicatesthathigher free fatty acids (FFAs) level in hepatocytes affects a myriad of biological processes leading to excessive metabolic imbalance, increased reactive oxygen species (ROS), deregulated autophagy, and impairment of mitochondrial and ER stress, that collectively drives...
The accumulation of lipid is a histological and biochemical hallmark of obesity-associated hepato-steatosis.Moreover, growing evidenceindicatesthathigher free fatty acids (FFAs) level in hepatocytes affects a myriad of biological processes leading to excessive metabolic imbalance, increased reactive oxygen species (ROS), deregulated autophagy, and impairment of mitochondrial and ER stress, that collectively drives cell death. Lipotoxicity and cell death mechanisms have been studied for many years. However, the molecular signals that link these two events during lipid stress remain poorly understood. From the very beginning, to systematically study hepato-lipotoxicity, HepG2 treated with PA providentially recapitulates the global lipotoxic responses, including insulin resistance to hepatocyte death. Therefore, using this cell-based model system, we pursued a comprehensive, differential quantitative approach where measurements of protein dynamics are analysed by mass spectrometry. Given that indispensable information, successive temporal phosphoproteomics dynamics are allowed us to in-depth analysis of lipotoxicity associated mechanistic network of cell death more precisely.
Read more
...Read less
|
DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Affinity purification coupled with mass spectrometry proteomics |
2024-08-31 |
35732625
|
| 9 |
IPD4034 |
Vaginal secretory proteome dynamically changes across the early and mid-trimesters of pregnancy |
Dr Tushar Kanti Maiti |
This study investigates the dynamic alterations in high vaginal fluid (HVF) proteome and its correlation with physiological changes during progression of term pregnancy. The HVF samples were collected at three time points as defined as V1 (6-12 weeks), V2 (18-20 weeks) and V3 (26-28 weeks) and SWATH-MS strategy were applied...
This study investigates the dynamic alterations in high vaginal fluid (HVF) proteome and its correlation with physiological changes during progression of term pregnancy. The HVF samples were collected at three time points as defined as V1 (6-12 weeks), V2 (18-20 weeks) and V3 (26-28 weeks) and SWATH-MS strategy were applied to profile changes in protein expression at early and middle stage of pregnancy. Using in-house generated HVF-specific protein library, 61 proteins (>1.5 fold at V2/V1 or V3/V1, q-value <0.05) changed as a function of gestational age. The stage-specific expression pattern of these proteins was mainly associated with the biology of cervical remolding, fetal development and microbial defense.
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...Read less
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
SRM/MRM |
2024-08-31 |
33497241
|
| 10 |
IPD9355 |
Salivary proteome signatures in the early and middle stages of human pregnancy with term birth outcome |
Dr Tushar Kanti Maiti |
This prospective study is to find changes in salivary protein expressions from first to early third trimester of pregnancy in normal term birth using SWATH-MS strategy. Saliva at three periods of gestation, 6-13 (V1), 18-21(V2), and 26-29 (V3) weeks from 20 singleton pregnant women were used in a discovery phase....
This prospective study is to find changes in salivary protein expressions from first to early third trimester of pregnancy in normal term birth using SWATH-MS strategy. Saliva at three periods of gestation, 6-13 (V1), 18-21(V2), and 26-29 (V3) weeks from 20 singleton pregnant women were used in a discovery phase. Selected proteins from the discovery study were verified by targeted schedule-MRM (multiple reaction monitoring) experiments in a separate subset of subjects (N=14). Using in-house generated saliva-specific protein library, 65 proteins (q-value<0.1) changed as a function of gestational age.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
SWATH MS, SRM/MRM |
2024-08-31 |
32415095
|
