| 51 |
IPD1891 |
Deep proteome analysis of more than 12000 proteins in buffalo mammary epithelial cells identifies protein signatures for active proliferation and lactation |
Dr. Ashok Kumar Mohanty |
Extensive branching morphogenesis takes place during pregnancy in the mammary gland. It is accompanied by the rapid proliferation of the Mammary Epithelial Cells (MECs). To gain insights into the proteomic changes that occur during the proliferation of MECs from buffalo (Bubalus bubalis) origin, we explored the deep proteome profile of...
Extensive branching morphogenesis takes place during pregnancy in the mammary gland. It is accompanied by the rapid proliferation of the Mammary Epithelial Cells (MECs). To gain insights into the proteomic changes that occur during the proliferation of MECs from buffalo (Bubalus bubalis) origin, we explored the deep proteome profile of buffalo mammary epithelial cells (BuMECs) using mass spectrometry (MS). To achieve this, we employed the sub-cellular fractionation approach and secretome analysis. Proteins were isolated separately from four subcellular fractions (SCFs) containing cytosolic (SCF-I), membranous and membranous organelle’s (SCF-II), nuclear (SCF-III) and cytoskeletal (SCF-IV). These sub-cellular specific protein fractions were processed using in-solution digestion and analyzed with nano-LCMS/MS. The MS analysis identified 8330, 5970, 5288 and 4818 non-redundant proteins in the fractions SCF I, II, III and IV respectively. To evaluate the secretory proteins in these cells, gel-based proteome approach was used which revealed a total of 792 non-redundant proteins. Altogether, combined analysis of all the five fractions including four sub-cellular fractions and secretome resulted in the identification of 12,609 non-redundant proteins. A total of 325 molecular pathways were identified after extensive analysis. The most enriched pathways associated with these proteins were metabolic, PI3-AKT, MAPK, mTOR, Insulin, estrogen and Oxytocin signaling. Our study demonstrated for the first time highest number of proteins identified by MS in any cell types including MECs.
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Proteomics and Structural Biology Lab, Animal biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India |
Shotgun proteomics |
2025-08-15 |
32179766
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| 52 |
IPD2682 |
Profiling of cow urinary proteins using various extraction methods reveals more than 1550 proteins |
Dr. Ashok Kumar Mohanty |
Urine can help in diagnosis of different diseases including cancer and other patho-physiological conditions. Urine proteome studies have been mainly human- centric. No information is available on urinary proteome from bovine till date. In the present study, we have used 3 protein extraction methods such as ammonium sulphate precipitation, ProteoSpin...
Urine can help in diagnosis of different diseases including cancer and other patho-physiological conditions. Urine proteome studies have been mainly human- centric. No information is available on urinary proteome from bovine till date. In the present study, we have used 3 protein extraction methods such as ammonium sulphate precipitation, ProteoSpin column and diafiltration method from bovine urine for identification of urinary proteome. The tryptic peptides generated after In-gel and In-solution method were identified using LC/MS/MS (ESI-qTOF) which resulted in identification of 1582 proteins. In-gel trypsin digestion method revealed more protein (1191) in comparison to in-solution digestion method (541). Maximum proteins were identified in ammonium sulphate precipitation method (938) followed by ProteoSpin (606) and diafiltration (444) methods respectively. The profile of the identified proteins were compared with human urinary proteome of which 311 bovine urinary proteins matched with human. An exclusive list of 38 bovine urinary proteins with high protein scores were listed which are absent in human urine. All identified proteins were analyzed according to Gene Ontology which were classified according to cellular component, biological processes and molecular functions. This study reports for the first time an exclusive evidence of more than 1550 proteins in urine of healthy cow donors.
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Proteomics and Structural Biology Lab, Animal biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India |
Shotgun proteomics, Gel-based experiment |
2025-08-15 |
26021477
|
| 53 |
IPD7996 |
Vibrio cholerae (p)ppGpp and DksA mutants SWATH |
Prof.Bhabatosh Das |
This study elucidates the whole proteome changes in the wild type and gnetically modified strains of Vibrio cholerae. Label-free SWATH-MS is used for protein quantitation following genetic modifications in alarmone (p)ppGpp metabolizing genes and transcription factor DksA.
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DBT-Translational Health Science and Technology Institute, Faridabad, Haryana, India |
SWATH MS |
2025-11-27 |
39992161
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| 54 |
IPD8604 |
MDR K. penumoniae, A. baumannii, E. coli, and P. aeruginiosa SWATH |
Prof.Bhabatosh Das |
This study elucidates the whole proteome changes in the MDR isolates of K. penumoniae, A. baumannii, E. coli, and P. aeruginiosa in the presence of Ampicillin, Kanamycin, and Nalidixic acid. Label-free SWATH-MS is used for protein quantitation of antibiotics treated and untreated samples.
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DBT-Translational Health Science and Technology Institute, Faridabad, Haryana, India |
SWATH MS |
2025-11-27 |
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| 55 |
IPD6285 |
Temporal proteome profiling of Botrytis cinerea reveals proteins involved in plant invasion and survival |
Dr. Nidhi Adlakha |
Botrytis cinerea is a necrotrophic fungal pathogen that poses a significant threat to many
crops. Understanding the proteome dynamics of phytopathogens during infection can help
combat plant diseases. However, most proteomics studies in phytopathogens face
interference from abundant host proteins. Here, we optimized a solid media that better
mimics in-planta conditions and used it...
Botrytis cinerea is a necrotrophic fungal pathogen that poses a significant threat to many
crops. Understanding the proteome dynamics of phytopathogens during infection can help
combat plant diseases. However, most proteomics studies in phytopathogens face
interference from abundant host proteins. Here, we optimized a solid media that better
mimics in-planta conditions and used it to perform the temporal protein dynamics in Botrytis
cinerea. An agar media with 20% tomato fruit extract and 2% deproteinised leaf extract was
utilized for label-free quantitative proteomics at 12, 36, 72 and 120 hpi. Out of 3244
quantified proteins, 2045 showed differential regulation. Glycosyl hydrolases, pectin
esterases, stress protein DDR48, RhoGEF and essential transcription factors were found to be
upregulated during the early phase, highlighting their role in fungal virulence. Meanwhile,
pathways such as macromolecule synthesis, purine, and carbohydrate metabolism were
upregulated in the late-growth phase. Overall, the study provides a comprehensive
understanding of proteome dynamics during Botrytis infection.
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Department of Biotechnology, Central University Of Haryana |
Bottom-up |
2025-11-28 |
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| 56 |
IPD1819 |
Proteomic analysis of somatic embryo development in Musa spp. cv. Grand Naine (AAA) |
Dr. Uma Subbaraya |
Somatic embryos are very much similar to zygotic counterparts in many morphological aspects and the somatic embryos are derived from somatic cells by undergoing various metabolic regulations. The somatic embryos have been used in artificial seed technology, genetic engineering and germplasm conservation. Though somatic embryo development is an important topic...
Somatic embryos are very much similar to zygotic counterparts in many morphological aspects and the somatic embryos are derived from somatic cells by undergoing various metabolic regulations. The somatic embryos have been used in artificial seed technology, genetic engineering and germplasm conservation. Though somatic embryo development is an important topic in growth and developmental studies, the molecular mechanism underlying the developmental process remains unclear. Therefore, understanding the molecular basis behind somatic embryo development can provide insight on the signaling pathways integrating this process. Proteomic analysis of somatic embryo development in cv. Grand Naine (AAA) was carried out to identify the differentially accumulated protein using two dimensional gel electrophoresis coupled with mass spectrometry. In total, 25 protein spots were differentially accumulated in different developmental stages of somatic embryos. Among them, three proteins were uniquely present in 30 days globular stage somatic embryos and six proteins were uniquely present in 60 days matured somatic embryo. Functional annotation of identified spots showed that major proteins are involved in growth and developmental process (17 %) followed by defense response (12%) and signal transportation events (12 %). In early stage, cell division and growth related proteins were involved in the induction of somatic embryos whereas in late developmental stage, cell wall modification proteins along with stress related proteins like played a defense role against dehydration and osmotic stress and resulted in maturation of somatic embryo. Alongside some identified stage specific proteins are valuable indicators and have been used as genetic markers.
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National Research Centre for Banana, Trichy, Tamil Nadu, India |
Gel-based experiment |
2025-12-26 |
32161309
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| 57 |
IPD5253 |
Molecular analysis of somatic embryogenesis through proteomic approach and optimization of protocol in recalcitrant Musa spp. |
Dr. Uma Subbaraya |
Somatic embryogenesis (SE) is a complex stress related process regulated by numerous biological factors. SE is mainly applicable to mass propagation and genetic improvement of plants through gene transfer technology and mutation breeding. In banana, SE is highly genome dependent as the efficiency varies with cultivars. To understand molecular mechanism...
Somatic embryogenesis (SE) is a complex stress related process regulated by numerous biological factors. SE is mainly applicable to mass propagation and genetic improvement of plants through gene transfer technology and mutation breeding. In banana, SE is highly genome dependent as the efficiency varies with cultivars. To understand molecular mechanism of SE, proteomics approach was carried out to identify genes responsible for embryogenic calli (EC) induction, regeneration and germination of somatic embryos (se) in cv. Rasthali (AAB). In total, 70 spots were differentially expressed in various developmental stages of SE. Of which, 16 were uniquely expressed and 17 were highly abundant in EC than nonembryogenic calli and explant and four spots were also uniquely expressed in germinating se. Functional annotation of identified proteins revealed that calcium signaling along with stress and endogenous hormones related proteins played a vital role in EC induction and germination of se. Thus based on the outcome, callus induction media was modified and tested in five cultivars. In cv. Grand Naine (AAA), increased concentration of 3- IAA and tryptophan recorded highest EC induction of 24.28% while Red Banana with similar genome showed 18.96% in kinetin supplemented media. Similarly, in cultivars Monthan and Karpuravalli with ABB genome showed maximum EC induction in tryptophan supplemented media (8.54%) and CaCl2 enriched media (17.34%) respectively. In cv. Neypoovan (AB), higher concentration of tryptophan induced more EC. These results illustrated that EC formation is genome as well as cultivar dependent. Simultaneously, germination media was modified to induce proteins responsible for germination. In cv. Rasthali, media supplemented with 10 mM CaCl2 showed maximum increase in germination (51.79%) over control. Thus present study revealed that media modification based on proteomic studies can induce SE in recalcitrant cultivars and also enhance germination in cultivars amenable for SE.
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National Research Centre for Banana, Trichy, Tamil Nadu, India |
Gel-based experiment |
2025-12-26 |
30883793
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