Manuscripts Under Submission
48. A mutation in the NF-kappaB dimeric interface influences phosphorylation, destabilizes Dorsal, and disrupts embryonic Dorso-Ventral patterning. Das S, Mukundan S, Roy S, Madhusudhan MS, Ratnaparkhi GS. Manuscript in preparation.
Revisiting Dorsal phosphorylation, stability and nuclear import in DV patterning via an interface mutaion in the DL-dimer..
47. Age-dependant deterioration of Circadian function in a Drosophila Model of ALS8 (2024). Kelkar V, Thulasidharan A, Kulkarni N, Ratnaparkhi GS. Manuscript in preparation.
The VAPB disease model shows circadian and sleep perturbations. VAPB may modulate circadian function.
Preprints/Publications
46. Reproducibility of Scientific Claims in Drosophila Immunity: A Retrospective Analysis of 400 Publications. 2025. Westlake H, ......., Lemaitre B. biorXiv. https://doi.org/10.1101/2025.07.07.663442.
Akshata Kotwal, an IISER Undergraduate student who completed her MS project in the Lemaitre lab, tested the Caspar(lof) alleles, which are well-validated and routinely used in the Ratnaparkhi lab for experiments related to PGC formation. She compared the host-defence abilities of these mutants against the previously published results. Her data is part of Prof. Lemaitre's reproducibility project.
45. Caspar modulates primordial germ fate both in an Oskar-dependent and Oskar-independent manner. Das S, Roy AE, Kanika, Deshpande G, Ratnaparkhi GS. Biology Open. 2025. doi: 10.1242/bio.062119.
A follow-up of Subhradip/Sushmitha's eLife paper. This study clarifies Caspar's multifunctional role in specifying primordial germ cells.
This paper is associated with a First-Person interview with Subradip Das (https://doi.org/10.1242/bio.062174).
44. Bioinformatics Analysis Identifies Sequence Determinants of Enzymatic Activity for the PHARC-Associated Lipase ABHD12. Chakraborty A, Devarajan A, Kumar K, C S R, Madhusudhan MS, Ratnaparkhi GS, Kamat SS. Biochemistry. 2025 Mar 26. doi: 10.1021/acs.biochem.4c00865.
Further insights on ABHD12 from the Kamat lab.
43. A face-off between Smaug and Caspar modulates primordial germ cell count and identity in Drosophila embryos. Deshpande G, Das S, Roy AE, Ratnaparkhi GS. Fly. 2024 Dec;19(1):2438473. doi: 10.1080/19336934.2024.2438473. Epub 2024 Dec 24.
An ‘Extra View’ mini-review with commentary on Das et. al., 2024 and Siddiqi et al., 2024.
42. CG17192 is a phospholipase that regulates signaling lipids in the Drosophila gut upon infection. Biochemistry (2024). Kumar K, Pazare M, Ratnaparkhi GS & Kamat S. 10.1021/acs.biochem.4c00579.
Part of the Ratnaparkhi/Kamat labs exploration of orphan Serine Hydrolases; we are assigning biochemical and biological functions to fly SH enzymes.
41. Caspar specifies primordial germ cell count and identity in Drosophila melanogaster (2024). Das S, Hegde S, Wagh N, S Jyothish, Roy A, Deshpande G, Ratnaparkhi GS. eLife. https://doi.org/10.7554/eLife.98584.2
Caspar plays a role in determining pole cells. The pole cell determinants Smaug/Oscar appear to be modulated by Caspar/TER94 degradative activity during the late MZT.
40. Age-dependent dynamics of neuronal VAPBALS inclusions in the adult brain. (2024). Thulasidharan A, Garg L, Tendulkar S, Ratnaparkhi GS. Neurobiol Disease. Jun 15;196:106517. doi: 10.1016/j.nbd.2024.106517. Epub 2024 Apr 26.PMID: 38679111
VAPB(P58S) aggregates appear to stay stable with age. Maintainance of these aggregates appears to be regulated by autophagy with TER94/VCP playing a significant role.
39. dAsap regulates cellular protrusions via an Arf6-dependent actin regulatory pathway in S2R+ cells. Kushwaha S, Mallik B, Bisht A, Mushtaq Z, Pippadpally S, Chandra N, Das S, Ratnaparkhi GS, Kumar V. FEBS Lett. 2024 Jun 11. doi: 10.1002/1873-3468.14954.
Vimlesh Kumar's laboratory @IISER Bhopal shows that Asap (ArfGAP with SH3 domain, ankyrin repeat and PH domain) maintains the balance between active and inactive states of Arf6 to regulate cell shape.
38. A Simple Immunofluorescence Method to Characterize Neurodegeneration and Tyrosine Hydroxylase Reduction in Whole Brain of a Drosophila Model of Parkinson's Disease. Chaurasia R, Ayajuddin M, Ratnaparkhi GS, Lingadahalli SS, Yenisetti SC. Bio Protoc. 2024 Feb 20;14(4):e4937. doi: 10.21769/BioProtoc.4937. eCollection 2024 Feb 20.
A fluorescence based method to identify tyrosine hydroxylase levels from Sarat Yenisetti's laboratory. Utility in fly neurodegenerative models.
37. Bidirectional regulation between AP-1 and SUMO genes modulates inflammatory signaling during Salmonella Typhimurium infection (2022). Kumar P, Soory A, Mustfa SA, Sarmah DT, Chatterjee S, Bossis G, Ratnaparkhi GS and Srikanth CV. J Cell Sci., Aug 15;135(16):jcs260096. doi: 10.1242/jcs.260096.
The Srikanth lab discovers that the transcription factor AP1 regulates the SUMO cycle during gut infection.
36. A multi-omics analysis reveals that the lysine deacetylase ABHD14B regulates glucose metabolism in mammals. Rajendran A, Soory A, Khandelwal N, Ratnaparkhi GS, Kamat S (2022). J. Biol. Chem. 298(7):102128. doi: 10.1016/j.jbc.2022.102128.
The Kamat lab shows that the novel lysine deacetylase ABHD14B (Rajendran et. al., 2022, Biochemistry) regulates (liver) glucose metabolism.
35. SUMOylation of Dorsal attenuates Toll/NF-κB signaling. Hegde S, Sreejan A, Gadgil CJ, Ratnaparkhi GS (2022). Genetics. May 14:iyac081. doi: 10.1093/genetics/iyac081.
Dorsal, the fly NFkB is SUMO conjugated. We find that SUMO conjugation acts to attenuate transcriptional activation in dorso-ventral patterning, in the humoral response to pathogens as well as in the melanization of crystal cells.
34. Caspar, an adapter for VAP and TER94 delays the progression of the disease by regulating glial inflammation in a Drosophila model of ALS8. Tendulkar S, Hegde S, Thulasidharan A, Garg L, Kaduskar B, Ratnaparkhi A, Ratnaparkhi GS (2022). Hum Mol Genet. Apr 4:ddac076. doi: 10.1093/hmg/ddac076.
Caspar is an adapter connecting VAPB (ALS8) and TER94 (ALS11). A dissection of roles for fly orthologs of ALS loci in neurons, muscle, and glia with reference to the ALS8 disease model.
33. SUMOylation of Jra fine-tunes the Drosophila gut immune response (2022). Soory A, Ratnaparkhi GS (2022). PLoS Pathog. Mar 7;18(3):e1010356. doi: 10.1371/journal.ppat.1010356.
Jra, the Drosophila ortholog of c-Jun regulates a large immune gene regulatory network in the fly gut. SUMO conjugation of Jra attenuates the negative regulation of the Jra-mediated gut immune response.
32. SUMO conjugation of Arginyl tRNA synthetase attenuates the Drosophila immune response. Nayak P., Kejriwal A, Ratnaparkhi GS (2021). Frontiers in Cell & Developmental Biology. Special issue on ‘SUMO proteins in host Defense’. doi: 10.3389/fcell.2021.695630.
Roles for SUMO conjugation of ArgRS in regulating the systemic immune response. ArgRS is a member of the 1.2 megaDa Multiacyl tRNA synthetase complex, a hub for immune signaling.
31. A Superfamily-wide activity atlas of Serine hydrolases in Drosophila melanogaster. Kumar K, Mhetre A, Ratnaparkhi GS, Kamat, SS (2021). Biochemistry. doi: 10.1021/acs.biochem.1c00171.
Activity-based protein profiling of serine hydrolases (SHs) in Drosophila. The atlas highlights differential SH activity in development; Tissue specific activity and also dimorphic expression.
30. Gene knockouts in Drosophila using CRISPR-Cas9 based genome editing. Hegde S, Nayak P, Trivedi D, Ratnaparkhi GS (2021). In ‘Experiments with Drosophila for Biology Courses’. Editors, SC Lakhotia and HA Ranganath. ebook.Indian Academy of Sciences. p219-224.
A stepwise protocol for knocking out a gene using CRISPR Cas9 genome editing. Targeted towards UG and PG students.
29. SUMO conjugation regulates immune signalling. Hegde S, Soory A, Kaduskar B, Ratnaparkhi GS (2020). Fly. Aug 31:1-18. doi: 10.1080/19336934.2020.1808402.
A review that touches upon the regulation of core signalling pathways by SUMO conjugation. Over that last few years, we have generated many SUMO conjugation-resistant proteins (Caspar, Dorsal, EPRS, RRS, Fos, Jun) using CRISPR/Cas9 genome editing. This review is a prequel to the upcoming laboratory papers that will be published in 2021-2022.
28. Caspar SUMOylation regulates Drosophila lifespan. Kaduskar B, Trivedi D, Ratnaparkhi GS (2020) microPublication Biology. 10.17912/micropub.biology.000288.
The first genome edited; Caspar(K551R) mutant generated by our laboratory using CRISPR/Cas9 technology. The paper discusses generation of the line and preliminary characterization of the SUMO conjugation-resistant mutant, in terms of lifespan and infection.
27. Mon1 and Rab7 interact to regulate post-synaptic Glutamate receptor levels in the Drosophila neuromuscular junction. Basargekar A, Shweta Y, Deivasagamani S, Zeeshan M, Kumar V, Ratnaparkhi GS, Ratnaparkhi A (2020). Int. J. Dev. Biol. 64(4-5-6):289-297. doi: 10.1387/ijdb.190153ar.
The ability of Mon1 to regulate post-synaptic GluRIIA levels, as shown earlier (Deivasigamani et. al., 2015) depends on neuronal Rab7.
26. Monensin sensitive 1 modulates dendritic arborization in Drosophila by regulating endocytic flux. Rohit Kumar H, Tendulkar S, Senthilkumar D, Ratnaparkhi A, Ratnaparkhi GS (2019). Frontiers in Cell & Developmental Biology. Special issue on ‘Membrane Trafficking’. doi: 10.3389/fcell.2019.00145.
Mon1 activity regulates the development of larval Type IV da arbors. An increase in activity decreases arborization, while decrease in in activity does the opposite. We hypothesize that Mon1 function affects flux of trafficking to Rab11 marked recycling endosomes, which is the underlying cause of arborization.
25. Rab converter DMon1 constitutes a novel node in the brain-gonad axis essential for female germline maturation. Dhiman N, Kumari S, Tendulkar S, Deshpande G, Ratnaparkhi GS, Ratnaparkhi A (2019) Development. Jul 10;146(13). pii: dev166504. doi: 10.1242/dev.166504.
Female sterile Mon1 mutants can be rescued by neuronal expression of Mon1. Our investigations of this phenomenon led us to an new node in the brain-gonad axis that included communication from Octopaminergic (OPN) neurons which synapsed with Insulin Producing cells, which in turn modulated the Ovarian Vitellogenic checkpoint by regulating levels of Insulin-like peptides (ILP2 and ILP5). Mon1 function in OPN neurons was thus specifically required for regulation of the ovarian vitellogenic checkpoint.
24. Understanding motor disorders using flies (Book Chapter). Chaplot K, Ratnaparkhi A, Ratnaparkhi GS (2019), in ‘Insights into human neurodegeneration: Lessons learnt from Drosophila’. Springer-Nature (2019) In press. ISBN: 978-981-13-2218-1.
A review on fly models of ALS.
23. SOD1 activity threshold and TOR signalling modulate VAP(P58S) aggregation via reactive oxygen species-induced proteasomal degradation in a Drosophila model of amyotrophic lateral sclerosis. Chaplot K, Pimpale L, Ramalingam B, Deivasigamani S, Kamat SS, Ratnaparkhi GS. Dis. Mod. Mech. 2019 Feb 7;12(2). pii: dmm033803. doi: 10.1242/dmm.033803.
A counterintuitive clearance of VAP(P58S) aggregates from the fly brain in response to cellular ROS levels. We demonstrate that aggregate dynamics are sensitive to both SOD1 activity and TOR signaling. The TOR/SOD/ROS/VAPB sub-network may play important roles in the initiation and progression of ALS in human patients.
Interview, First person – Kriti Chaplot (http://dmm.biologists.org/content/12/2/dmm038984)
Cover-Page (http://dmm.biologists.org/content/12/2.cover-expansion).
22. Drosophila DNA/RNA methyltransferase contributes to robust host defense in aging animals by regulating sphingolipid metabolism. Abhyankar V, Kaduskar B, Kamat SS, Deobagkar D, Ratnaparkhi GS. J. Exp. Biol. 2018 Nov 16;221(Pt 22). pii: jeb187989. doi: 10.1242/jeb.187989.
We uncover an interesting age-dependent deterioration of Mt2 null animals in the Drosophila immune response.
21. Stonewall and Brickwall: Two Partially Redundant Determinants Required for the Maintenance of Female Germline in Drosophila. Shukla V, Dhiman N, Nayak P, Dahanukar N, Deshpande G, Ratnaparkhi GS. G3 (Bethesda). 2018 May 31;8(6):2027-2041. doi: 10.1534/g3.118.200192.
Brickwall, christened such because of its functional similarity to Stonewall, is involved in female germline specification. Maternal Stonewall expression rescues some aspects of brickwall loss of function phenotypes, suggesting redundant functions.
20. RDGBα localization and function at membrane contact sites is regulated by FFAT-VAP interactions. Yadav S, Thakur R, Georgiev P, Deivasigamani S, Krishnan H, Ratnaparkhi G, Raghu P. J Cell Sci. 2018 Jan 8;131(1). pii: jcs207985. doi: 10.1242/jcs.207985.
Research from the Padinjat lab shows that VAPB interacts with the FFAT motif in RGDBα and modulates its function in the fly eye.
19. SUMO-Enriched Proteome for Drosophila Innate Immune Response. Handu M, Kaduskar B, Ravindranathan R, Soory A, Giri R, Elango VB, Gowda H, Ratnaparkhi GS. G3 (Bethesda). 2015 Aug 18;5(10):2137-54. doi: 10.1534/g3.115.020958.
A quantitative proteomics screen for proteins that change their SUMOylated state on infection. The list of 702 proteins that we have generated includes targets for (future) mechanistic studies.
18. A Presynaptic Regulatory System Acts Transsynaptically via Mon1 to Regulate Glutamate Receptor Levels in Drosophila. Deivasigamani S, Basargekar A, Shweta K, Sonavane P, Ratnaparkhi GS, Ratnaparkhi A. Genetics. 2015 Oct;201(2):651-64. doi: 10.1534/genetics.115.177402. Epub 2015 Aug 19.
Activity of Mon1 in neurons influences Glutamate receptors sitting on the Muscle, in the NMJ. The pathway for this signalling across the synaptic cleft is unknown.
17. A genetic screen identifies Tor as an interactor of VAPB in a Drosophila model of amyotrophic lateral sclerosis. Deivasigamani S, Verma HK, Ueda R, Ratnaparkhi A, Ratnaparkhi GS. Biol Open. 2014 Oct 31;3(11):1127-38. doi: 10.1242/bio.201410066.
The VAPB Gene Regulatory Network appears to include other ALS causing loci, e.g., SOD1, ALSIN and TDP43. Tor signaling appears to be higher in neurons expressing VAPB(P58S) and lower in cells expressing VAPB(wt).
16. Gene duplication, lineage-specific expansion, and subfunctionalization in the MADF-BESS family patterns the Drosophila wing hinge. Shukla V, Habib F, Kulkarni A, Ratnaparkhi GS. Genetics. 2014 Feb;196(2):481-96. doi: 10.1534/genetics.113.160531. Epub 2013 Dec 13.
A dissection of redundancy in the MADF-BESS gene family, using genetics.
15. Signaling Cascades, Gradients and Gene Networks in Dorsal/ Ventral patterning. Ratnaparkhi GS, Courey A in “Principles in Developmental Genetics” (2014) Sally Moody Editor, Elsevier Press.
A review on Dorsal/ventral patterning, from the oocyte to the embryo. Updated, revised version of the 2008 review.
14. The Hydra small ubiquitin-like modifier. Khan U, Mehere P, Deivasigamani S, Ratnaparkhi GS. Genesis. 2013 Sep;51(9):619-29. doi: 10.1002/dvg.22408. Epub 2013 Jul 23.
Identification, characterization and analysis of SUMO cycle genes/proteins in Hydra. We also generated the first Transgenic animal, a SUMO:GFP expressing animal in the laboratory.
Girish’s Ph.D. and Post-Doctoral Publications
1. Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S. Thomson J, Ratnaparkhi GS, Varadarajan R, Sturtevant JM, Richards FM. Biochemistry. 1994 Jul 19;33(28):8587-93.
This paper used a non-standard amino acid, Norleucine in the S-peptide (amino-acid position #13) to characterize changes in RNase S structure and thermodynamic parameters. This study led to the 2000 Biochemistry paper.
2. Dynamics of ribonuclease A and ribonuclease S: computational and experimental studies. Nadig G, Ratnaparkhi GS, Varadarajan R, Vishveshwara S. Protein Sci. 1996 Oct;5(10):2104-14.
Surprisingly, Molecular Dynamic simulations of RNASE-A and RNASE-S suggest that the molecules are effectively the same. If true, then the observed faster hydrogen exchange rates in RNASE-S are NOT a reflection of a more 'dynamic' and flexible RNASE-S, but rather an artefact of faster hydrogen exchange through the dissociated entities (S-protein, S-peptide). This mystery is finally resolved, by experimentation, in the 1999 PNAS paper.
3. Structural studies of protein denaturation. Ratnaparkhi GS, Varadarajan R. Current Science (1997) 72:826-830.
Structural tools such as NMR and X-ray are increasingly being used to observe protein denaturation.
4. Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. Ratnaparkhi GS, Ramachandran S, Udgaonkar JB, Varadarajan R. Biochemistry. 1998 May 12;37(19):6958-66.
Analysis of packing densities of available protein structures solved both by X-ray crystallography and Nuclear Magnetic Resonance. This study pointed out quality issues related to NMR structures (of that generation).
5. Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments. Chakshusmathi G/ Ratnaparkhi GS, Madhu PK, Varadarajan R. Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):7899-904.
Native state hydrogen exchange using NMR studies could be used to get structural information on uncharacterized S-Protein or S-peptide fragments in solution.
6. X-ray crystallographic studies of the denaturation of ribonuclease S. Ratnaparkhi GS, Varadarajan R. Proteins. 1999 Aug 15;36(3):282-94.
Crystallographic snapshots of initial stages of denaturation of proteins in the crystalline state.
7. Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics. Ratnaparkhi GS, Varadarajan R. Biochemistry. 2000 Oct 10;39(40):12365-74.
Structural analysis of cavities in a series of RNAS-S mutations and their correlation to thermodynamic data suggests that packing of hydrophobic amino acids in the core, rather that the hydrophobic effect is the dominant force involved. Analysis of all available large (hydrophobic) to small mutants in the Protein Data bank supports this hypothesis.
8. Structural and thermodynamic consequences of introducing alpha-aminoisobutyric acid in the S peptide of ribonuclease S. Ratnaparkhi GS, Awasthi SK, Rani P, Balaram P, Varadarajan R. Protein Eng. 2000 Oct;13(10):697-702.
A structural and thermodynamic analysis of the substitution of AIB, which is not one of the standard amino-acids, on the structure and dynamics of RNASE-S.
9. Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states. Ratnaparkhi GS, Varadarajan R. J Biol Chem. 2001 Aug 3;276(31):28789-98. Epub 2001 May 23.
An attempt to visualize the presence of osmolyte molecules in protein crystals and correlate this observation with precise thermodynamic measurements of osmolyte stabilization of proteins using titration calorimetry.
10. Uncoupling dorsal-mediated activation from dorsal-mediated repression in the Drosophila embryo. Ratnaparkhi GS, Jia S, Courey AJ. Development. 2006 Nov;133(22):4409-14. Epub 2006 Oct 11.
The Activation and Repression abilities of NFkappa-B/ Dorsal are separated using protein engineering/design, and the Dorsal variants were used to demonstrate redundancy in gene regulatory networks during Drosophila development.
11. Signaling Cascades, Gradients and Gene Networks in Dorsal/ Ventral patterning. Ratnaparkhi GS, Courey AJ in “Principles of Developmental Genetics” (2007) Sally Moody Editor, Academic Press.
A review on Dorsal/ventral patterning, from the oocyte to the embryo. This chapter was revised 7 years later for a second edition of the book.
12. Dorsal interacting protein 3 potentiates activation by Drosophila Rel homology domain proteins. Ratnaparkhi GS, Duong HA, Courey AJ. Dev Comp Immunol. 2008;32(11):1290-300. doi: 10.1016/j.dci.2008.04.006. Epub 2008 May 16.
Dip3 synergistically enhances Dorsal/Twist activation, acting as a co-activator. Most of the protein is, however, localized in pericentric heterochromatin, indicating novel Dorsal-independent roles.
13. Non-cell-autonomous inhibition of photoreceptor development by Dip3. Duong HA, Nagaraj R, Wang CW, Ratnaparkhi G, Sun YH, Courey AJ. Dev Biol. 2008 Nov 1;323(1):105-13. doi: 10.1016/j.ydbio.2008.08.004. Epub 2008 Aug 9.
Dip3 is also required for photoreceptor development in the Drosophila eye.