| 141 |
IPD2610 |
Divergent Plasmodium Aurora related kinases ARK1 and ARK2 coordinate spindle biogenesis and karyokinesis by regulating key centromere-kinetochore proteins |
Dr. T S Keshava Prasad |
Human malaria parasite Plasmodium falciparum is a unicellular eukaryote that proliferates within human and mosquito hosts via highly specialized cell division processes that are markedly different from those of conventional eukaryotic model organisms. Aurora kinases are central regulators of eukaryotic cell division. Although Plasmodium species encode three divergent Aurora-related kinases...
Human malaria parasite Plasmodium falciparum is a unicellular eukaryote that proliferates within human and mosquito hosts via highly specialized cell division processes that are markedly different from those of conventional eukaryotic model organisms. Aurora kinases are central regulators of eukaryotic cell division. Although Plasmodium species encode three divergent Aurora-related kinases (ARK1–3) that are essential for parasite survival. In this study, we show that conditional knockout of PfARK2 disrupts spindle formation, leading to defects in karyokinesis and subsequent failure of cytokinesis. Recently, we reported similar role for PfARK1; however, the underlying mechanisms remained unclear. Phosphoproteomic analyses reveal that PfARK1 and PfARK2 target distinct sets of substrates, several of which are key kinetochore proteins. Strikingly, PfARK2 regulates the phosphorylation-dependent localization of PfCENH3, a centromere-specific histone H3 variant essential for spindle assembly and nuclear division. NUF2, an outer kinetochore component, is differentially regulated by both kinases at distinct sites. The regulation of these proteins by PfARK1/2 is critical for proper kinetochore assembly and spindle formation. Furthermore, we have identified small-molecule inhibitors targeting these Aurora kinases that effectively block asexual stage proliferation of P. falciparum by disrupting PfARK1/2-dependent processes. These findings provide novel insights into parasite division and highlight a promising avenue for the development of novel antimalarial therapies.
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NITTE, Deemed to be University, Mangaluru, Karnataka, India |
Bottom-up |
2027-06-04 |
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| 142 |
IPD1816 |
Mycobacterium tuberculosis PknB phosphoproteome profiling |
Dr. T S Keshava Prasad |
Mass spectrometry-based proteomic characterization of Mycobacterium tuberculosis protein kinase B (PknB), including PknB-associated protein interactors and phosphorylation-dependent changes associated with PknB juxtamembrane (JM) mutants. The interactome experiment compared wild-type PknB (Rv-pptr-B::pknB), a PknB-JMMim mutant, and a PknB-JMAbl mutant using FLAG-based immunoprecipitation followed by LC-MS/MS. The phosphoproteomic experiment profiled wild-type PknB,...
Mass spectrometry-based proteomic characterization of Mycobacterium tuberculosis protein kinase B (PknB), including PknB-associated protein interactors and phosphorylation-dependent changes associated with PknB juxtamembrane (JM) mutants. The interactome experiment compared wild-type PknB (Rv-pptr-B::pknB), a PknB-JMMim mutant, and a PknB-JMAbl mutant using FLAG-based immunoprecipitation followed by LC-MS/MS. The phosphoproteomic experiment profiled wild-type PknB, PknB-JMMim, and PknB-JMAbl using phosphopeptide enrichment followed by DIA LC-MS/MS on an Orbitrap Astral Zoom. The resulting datasets were used to identify PknB-associated proteins and quantify phosphorylation-site changes.
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NITTE, Deemed to be University, Mangaluru, Karnataka, India |
Bottom-up |
2027-09-28 |
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| 143 |
IPD7489 |
IP for TpSH3a |
Dr Nidhi Adlakha |
Pull down for TpSH3a in Talaromyces pinophilus
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Bottom-up |
2028-01-01 |
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| 144 |
IPD9591 |
Differential Proteome of Talaromyces pinophilus |
Dr Nidhi Adlakha |
Differential Proteome of Talaromyces pinophilus WT strain and Tpsh3a mutant
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Bottom-up |
2028-01-01 |
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| 145 |
IPD2560 |
Interactome Profiling of SENP5 during Colitis-Associated Colorectal Cancer Progression |
Prof. C.V. Srikanth |
This dataset describes an antibody-based pull-down mass spectrometry interactome study investigating the role of SENP5 in colitis-associated colorectal cancer (CAC) progression in the azoxymethane–dextran sodium sulfate (AOM-DSS)-induced murine model. SENP5 showed a dynamic expression profile during disease progression, with elevated expression observed in chronic colitis (CC) and non-polyp (NP) regions,...
This dataset describes an antibody-based pull-down mass spectrometry interactome study investigating the role of SENP5 in colitis-associated colorectal cancer (CAC) progression in the azoxymethane–dextran sodium sulfate (AOM-DSS)-induced murine model. SENP5 showed a dynamic expression profile during disease progression, with elevated expression observed in chronic colitis (CC) and non-polyp (NP) regions, whereas reduced expression was detected in polyp tissues. To understand the biological significance of this differential expression pattern and to identify associated molecules and signaling pathways linked with SENP5-mediated tumorigenesis, an interactome analysis was performed using SENP5 immunoprecipitation.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Interactome analysis |
2028-08-24 |
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| 146 |
IPD9257 |
Characterization of Coronin1A (Coro1A)-Associated SUMOylated Protein Interactions in the 75–150 kDa Range in J774 Macrophages |
Prof. C.V. Srikanth |
This dataset describes an antibody-based pull-down mass spectrometry interactome study of Coronin1A aimed at identifying SUMOylated proteins associated with Coronin1A (Coro1A). Coro1A was initially identified as a potential SENP5-associated protein during SENP5 interactome analysis in the AOM-DSS-induced murine model of colitis-associated colorectal cancer (CAC). Based on this observation, it...
This dataset describes an antibody-based pull-down mass spectrometry interactome study of Coronin1A aimed at identifying SUMOylated proteins associated with Coronin1A (Coro1A). Coro1A was initially identified as a potential SENP5-associated protein during SENP5 interactome analysis in the AOM-DSS-induced murine model of colitis-associated colorectal cancer (CAC). Based on this observation, it was speculated that Coro1A may undergo SUMOylation.
To examine this possibility, Coro1A immunoprecipitation followed by SUMO immunoblotting was performed. Prominent SUMO2/3-reactive bands were observed in the 75–150 kDa molecular weight range. However, no apparent molecular weight shift corresponding to SUMOylated Coro1A was detected. These findings suggested that Coro1A itself may not undergo direct SUMOylation but instead interacts with SUMOylated proteins.
To identify proteins associated with Coro1A through SUMO-dependent interactions and to understand their relevance to Coro1A-mediated signaling, an interactome experiment was performed using J774 wild-type macrophage cells.
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DBT-Regional Centre for Biotechnology, Haryana, Faridabad, India |
Interactome analysis |
2028-08-24 |
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| 147 |
IPD6181 |
Delineating pathogenesis of obese and lean PCOS phenotype using integrated transcriptomics and proteomics approach |
Dr. Pallavi Shukla |
This study explores the metabolic and hormonal impact of polycystic ovary syndrome
(PCOS) in women aged 18-39, incorporating plasma protein analysis to deepen
understanding of its biological mechanisms. Patients were recruited from the PCOS Clinic at
the National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH) and
non-PCOS participants from general clinics and...
This study explores the metabolic and hormonal impact of polycystic ovary syndrome
(PCOS) in women aged 18-39, incorporating plasma protein analysis to deepen
understanding of its biological mechanisms. Patients were recruited from the PCOS Clinic at
the National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH) and
non-PCOS participants from general clinics and communities. Blood and plasma samples
were collected for comprehensive biochemical and proteomic profiling. Participants were
categorized into four groups: Obese PCOS (N=33), Lean PCOS (N=11), Obese non-PCOS
(N=12), and Lean non-PCOS (N=25), with diagnoses based on the Rotterdam criteria.
Exclusion criteria ensured chronic diseases, medications, or interfering conditions did not
affect reproductive physiology. A total of 117 women were studied, with 57 diagnosed with
PCOS and 60 serving as controls.
PCOS patients demonstrated higher insulin resistance, as reflected in fasting insulin
levels and HOMA-IR scores. Testosterone levels were elevated across PCOS cases, with lean
PCOS participants exhibiting even higher androgen concentrations. Variations in LH and
FSH ratios further emphasized reproductive hormonal imbalances, while obese PCOS women
had lower sex hormone-binding globulin (SHBG) levels. Lipid profiles revealed elevated
very-low-density lipoprotein (VLDL) cholesterol in PCOS patients, reinforcing concerns
regarding cardiovascular risks. Though total cholesterol and triglyceride levels showed no
clear trend, HDL cholesterol was notably lower in obese PCOS participants.
To understand molecular variations in PCOS, plasma protein quantification and
depletion were performed. A total of 15 samples were pooled into four subgroups for
depletion, following strict protocols using the High Select Top 14 Abundant Protein
Depletion Resin. Plasma samples underwent two rounds of depletion to remove dominant
proteins, such as albumin and immunoglobulins, ensuring accuracy before being sent to IIT-
SAIF for liquid chromatography-mass spectrometry (LC-MS). After depletion, samples were
enzymatically digested and labeled using iTRAQ reagents for multiplex quantification. The
fractions were analyzed using an Orbitrap high-resolution mass spectrometer, generating
MS/MS spectra that mapped peptide identifications back to corresponding proteins. Using
stringent statistical criteria (False Discovery Rate <1%), a distinct list of differentially
expressed proteins (DEPs) was developed. Plasma proteome profiling revealed unique DEPs across four comparative groups:
Obese PCOS vs Obese Control (OP vs OC), Lean PCOS vs Lean Control (LP vs LC), Obese
Control vs Lean Control (OC vs LC), and Obese PCOS vs Lean Control (OP vs LC).
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National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India |
Non targated proteomcis |
2028-12-23 |
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| 148 |
IPD3377 |
Dynamic metabolic remodelling and mitochondrial import machinery facilitate cellular stress survival and artemisinin resistance/tolerance in human malaria parasite Plasmodium falciparum. |
Dr. Asif Mohmmed |
The organellar stress response has emerged as an important factor influencing the survival of Plasmodium falciparum under cellular stress and artemisinin exposure, thus playing critical role in drug resistance/tolerance. However, the mechanisms by which mitochondria respond to cellular stress and their intersection with artemisinin resistance remain to be understood. Here,...
The organellar stress response has emerged as an important factor influencing the survival of Plasmodium falciparum under cellular stress and artemisinin exposure, thus playing critical role in drug resistance/tolerance. However, the mechanisms by which mitochondria respond to cellular stress and their intersection with artemisinin resistance remain to be understood. Here, we analysed mitochondrial stress-induced organelle dynamics and quantitative proteomic changes in the parasite, revealing a dynamic stress response. In the initial phase, parasites activate a reversible, pro-survival response characterised by glycolytic compensation, suppressed TCA cycle activity, and proteostasis remodelling. A subsequent ‘critical survival phase’ activates organelle repair pathways, marked by selective upregulation of the mitochondrial protein import machinery, including PfMPPβ, a key regulator of mitochondrial protein maturation. Ablation of PfMPPβ causes severe growth inhibition, disrupts mitochondrial development and function, and alters metabolic flux. Ultra-Expansion Microscopy (UExM) revealed a loss of coordinated alignment among mitochondria, tubulin, and daughter nuclear segregation, which results in defective merozoite segregation. Substratetrap proteomics showed that PfMPPβ processes important mitochondrial proteins, including the ATPsynthase complex, TCAmetabolite transporters, and the BCKDH complex, thereby suggesting a functional link to pro-survival responses. Importantly, loss of PfMPPβ function rendered both wild-type and artemisinin-resistant parasites hypersensitive to organellar stress and to dihydroartemisinin, suggesting that PfMPPβ-mediated organelle homeostasis is critical for the organelle stress response that underlies artemisinin resistance. Overall, our findings elucidate the association between mitochondrial stress response and drug tolerance, thus identifying PfMPPβ as a potential target for combating artemisinin resistance/tolerance in malaria.
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International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India |
Bottom-up |
2030-09-30 |
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