| 11 |
IPD3284 |
Exploiting Dynamics of Genomic Islands to Edit the Genome of Vibrio cholerae and Identify Novel Interactions Between Core and Acquired Genome |
Dr Tushar Kanti Maiti |
Horizontally acquired genetic elements (HGEs) plays a major for determination of virulence, antimicrobial resistance, adaptation and evolution in pathogenic bacteria. Conserved integrative mobile genetic elements (MGEs) of Vibrio cholerae contribute in the disease development, antimicrobial resistance and metabolic functions. To understand the dynamics of integrative MGEs and cross talk between...
Horizontally acquired genetic elements (HGEs) plays a major for determination of virulence, antimicrobial resistance, adaptation and evolution in pathogenic bacteria. Conserved integrative mobile genetic elements (MGEs) of Vibrio cholerae contribute in the disease development, antimicrobial resistance and metabolic functions. To understand the dynamics of integrative MGEs and cross talk between MGEs and core genome, engineered genome of V. cholerae was monitored in the presence and absence of horizontally acquired genetic elements. Deletion of more than 250 revealed that CTX contributes to the essentiality of SOS response master regulator LexA in V. cholerae. Also, he core genome encoded RecA helps CTX to bypass the host immunity and replicate in the host cell in the presence of similar prophage in the host chromosome. Finally, our multiomics data reveal importance of MGEs in modulating the level of cellular proteome and metabolome in V. cholerae. This study for the first time engineered the genome of V. cholerae strains to eliminate all the GIs, ICE and prophages from their genome and revealed new interactions between core and acquired genomes. The engineered strain could be a potential candidate for understanding evolution of cholera pathogen and development of therapeutics.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
SWATH MS |
2024-08-31 |
32873641
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| 12 |
IPD5484 |
“Trading virulence forsurvival”:Metabolic pathway switch is a key mechanism for survival of Macrophomina phaseolina upon Burkholderia contaminans challenge |
Dr Tushar K. Maiti |
Macrophominaphaseolina is attributed to infect a wide range of plants. There are not a successful strategies to eradicate the fungus from the soil. In this study, a jute endophytic bacteria, Burkholderiacontaminans has been found to have a promising effect in controlling M. phaseolinain in vitro culture. Using the iTRAQ LC-MS/MS...
Macrophominaphaseolina is attributed to infect a wide range of plants. There are not a successful strategies to eradicate the fungus from the soil. In this study, a jute endophytic bacteria, Burkholderiacontaminans has been found to have a promising effect in controlling M. phaseolinain in vitro culture. Using the iTRAQ LC-MS/MS method for quantitative proteomics study, a comparative analysis of the whole proteome of M.phaseolinaunder both Burkholderiachallenged and unchallenged conditions were made and analyzed. A tough battle appears to ensue between the fungus and the bacterium, where Burkholderia manages to arrest the growth of the fungus and decrease its pathogenicity but, the latter apparently survives under ‘hibernating’ conditions by up-regulating its energy metabolism.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Shotgun proteomics |
2024-09-01 |
32010805
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| 13 |
IPD1454 |
Comparative evaluation of the aqueous humor proteome of primary angle closure and primary open angle glaucomas and senile cataract eyes |
Dr. Inderjeet Kaur |
Comparative evaluation of the aqueous humor proteome of primary angle closure and primary open angle glaucomas and senile cataract eyes.
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Department of Biotechnology, Central University Of Haryana |
Shotgun proteomics |
2024-09-11 |
29332228
|
| 14 |
IPD6238 |
XPO1 is a critical player for Bortezomib resistance in Multiple Myeloma: A quantitative proteomic approach |
Dr Srikanth Rapole |
Among the blood cancers, 13% mortality is caused by Multiple myeloma (MM) type of haematological malignancy. In spite of therapeutic advances in chemotherapy treatment, still MM remains an incurable disease is mainly due to emergence of chemoresistance. At present time, FDA approved bortezomib is the first line drug for MM...
Among the blood cancers, 13% mortality is caused by Multiple myeloma (MM) type of haematological malignancy. In spite of therapeutic advances in chemotherapy treatment, still MM remains an incurable disease is mainly due to emergence of chemoresistance. At present time, FDA approved bortezomib is the first line drug for MM treatment. However, like other chemotherapy, MM patients are acquiring resistance against bortezomib. The present study aims to identify and validate bortezomib resistant protein targets in MM using iTRAQ and label free quantitative proteomic approaches. 125 differentially expressed proteins were commonly found in both approaches with similar differential expression pattern. XPO1 protein was selected for further validation as its significant high expression was observed in both iTRAQ and label free analysis. Bioinformatic analysis of these common differentially expressed proteins showed a clear cluster of proteins such as SMC1A, RCC2, CSE1, NUP88, NUP50, TPR, HSPA14, DYNLL1, RAD21 and RANBP2 being associated with XPO1. Functional studies like cell count assay, flow cytometry assay and soft agar assay proved that XPO1 knock down in RPMI 8226R cell line results in re-sensitization to bortezomib drug.
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National Centre for Biological Sciences, Bangalore, Karnataka, India |
Shotgun proteomics |
2024-09-22 |
31465861
|
| 15 |
IPD8192 |
Proteomic Alterations in Multiple Myeloma: A Comprehensive Study Using Bone Marrow Interstitial Fluid and Serum Samples |
Dr Srikanth Rapole |
Multiple myeloma (MM) is a plasma cell associated cancer and the second most common hematological malignancies. Although researchers have been working on MM, comprehensive quantitative proteomic analysis of Bone Marrow Interstitial Fluid (BMIF) and Blood Serum is not yet reported. Being a proximal biofluid for the hematological malignancies, BMIF could...
Multiple myeloma (MM) is a plasma cell associated cancer and the second most common hematological malignancies. Although researchers have been working on MM, comprehensive quantitative proteomic analysis of Bone Marrow Interstitial Fluid (BMIF) and Blood Serum is not yet reported. Being a proximal biofluid for the hematological malignancies, BMIF could serve as a potential source for identifying diagnostic, prognostic and therapeutic markers for various blood cancers including MM. Moreover, serum, being a minimal invasive biofluid, serves as a potential source for discovering diagnostic and prognostic markers for various cancers including MM as well. We employed multipronged quantitative proteomic approaches like iTRAQ and SWATH-MS for MM BMIF and serum where we identified 279 and 116 non-redundant differentially expressed proteins in MM BMIF and serum respectively. Additionally, the probable biological and functional roles of the differentially abundant proteins were probed in the manifestation of MM disease pathology by using various bioinformatic tools. Furthermore, a selected panel of statistically significant proteins was verified for their differential abundance by immunoblotting as well as MS-based SRM assays. The significant discrimination efficiency of the models generated through multivariate statistical analysis was decent to distinguish between the MM and controls. Moreover, potential candidate proteins were also validated in a fresh independent cohort of serum samples using Enzyme-linked immunosorbent assay (ELISA), as it is a minimal invasive fluid that could easily be used for the diagnostics applications. The significance of this study remains in the fact that the proteins which are observed in the BMIF and also reflected in the serum with similar expression profile are proposed as a potential candidate biomarker panel for MM diagnosis
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National Centre for Biological Sciences, Bangalore, Karnataka, India |
SWATH MS, SRM/MRM, Shotgun proteomics |
2024-09-22 |
33585190
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| 16 |
IPD5583 |
Multipronged quantitative proteomics reveals serum proteome alterations in breast cancer intrinsic subtypes |
Dr Srikanth Rapole |
Being molecularly heterogeneous, breast cancer tends to be a complicated oncological disease with high incidence rates throughout the world. The primary aim of this study was to identify the set of serum proteins with discriminatory capabilities towards the four major subtypes of breast cancer. We employed multipronged quantitative proteomic approaches...
Being molecularly heterogeneous, breast cancer tends to be a complicated oncological disease with high incidence rates throughout the world. The primary aim of this study was to identify the set of serum proteins with discriminatory capabilities towards the four major subtypes of breast cancer. We employed multipronged quantitative proteomic approaches like 2D-DIGE, iTRAQ and SWATH-MS and identified 307 differentially regulated proteins. Luminal A subtype consisted of 24, Luminal B subtype 38, HER2 Enriched subtype 17 and Triple negative breast cancer subtype 10 differentially regulated subtype specific proteins. These specific proteins were further subjected to bioinformatic analysis viz. PANTHER, DAVID and LENS which revealed the involvement in platelet degranulation, fibrinolysis, lipid metabolism, immune response, complement activation, blood coagulation, immune cell activation, glycolysis, amino acid biosynthesis and cancer signaling pathways in the subtypes of the breast cancer. The significant discrimination efficiency of the models generated through multivariate statistical analysis was decent to distinguish each of the four subtypes from controls. Further, some of the statistically significant differentially regulated proteins were verified and validated by immunoblotting and mass spectrometry based selected reaction monitoring (SRM) approach. Our Multipronged proteomics approaches revealed panel of serum proteins specifically altered for individual subtypes of breast cancer.
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National Centre for Biological Sciences, Bangalore, Karnataka, India |
SWATH MS, Shotgun proteomics |
2024-09-25 |
28495502
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| 17 |
IPD1849 |
Viral fallout: Semen proteome reveals COVID-19 dysregulates several biological processes linked to male reproductive function |
Dr Sanjeeva Srivastava |
The current global outbreak of COVID-19 has significantly impacted several organ systems. Male reproductive organs are among the potential targets of SARS-CoV-2 infection owing to the presence of abundant viral receptors; ACE2 and TMPRSS2 in the testis. However, the questions pertaining to the long term effects of SARS-CoV-2 infection...
The current global outbreak of COVID-19 has significantly impacted several organ systems. Male reproductive organs are among the potential targets of SARS-CoV-2 infection owing to the presence of abundant viral receptors; ACE2 and TMPRSS2 in the testis. However, the questions pertaining to the long term effects of SARS-CoV-2 infection on male fertility are still unanswered. For this study, we procured the semen samples of COVID-19 recovered patients and performed mass spectrometry based proteomic studies to understand the impact of the disease on the biological processes involved in reproductive health.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-16 |
35309488
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| 18 |
IPD2311 |
medulloblastoma label free proteome analysis from an Indian subpopulation |
Dr Sanjeeva Srivastava |
The label free tissue proteomic analysis of medulloblastoma proteome was perfomed for the identification of protein markers for the developinment of IHC markers for the diagnostic purpose. The pathway al;tyerations and protein signatures of G3 tumor is the major focus.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-16 |
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| 19 |
IPD5040 |
A longitudinal study of COVID-19 patients using proteomics approach |
Dr Sanjeeva Srivastava |
SARS-CoV-2, a highly contagious and infectious virus is responsible for causing this COVID-19 pandemic, which has a substantial impact on global health and economy. The spectrum of clinical manifestations of COVID-19 ranges from mild or non-severe state to severe life-threatening condition in some group of people. Many patients are likely...
SARS-CoV-2, a highly contagious and infectious virus is responsible for causing this COVID-19 pandemic, which has a substantial impact on global health and economy. The spectrum of clinical manifestations of COVID-19 ranges from mild or non-severe state to severe life-threatening condition in some group of people. Many patients are likely to undergo non-severe to severe transition during their infection period. For this study, we have collected blood samples of different time points from patients showing both non-severe to severe and severe to recovered transition. The clinical information of the patient’s condition is obtained from their medical records. We have investigated the proteome of different time points of the patient’s sample to analyse their trend in prognosis of the disease
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-17 |
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| 20 |
IPD5373 |
TOMATO SEEDLING LIGHT INDUCED PROTEOMICS ALTERATON |
Dr Sanjeeva Srivastava |
We use quantitative discovery proteomics along with metabolomics to unravel the role of Phytochrome A in regulating central metabolism.
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Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay |
Shotgun proteomics |
2024-10-17 |
33824368
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