Papers by Jacinta D'Souza
Molecular Chaperones in Human Disorders, 2018
Gaucher's disease (GD) is the most commonly known lysosomal disorder that occurs due to mutat... more Gaucher's disease (GD) is the most commonly known lysosomal disorder that occurs due to mutations in the β-glucocerebrosidase (GBA) protein. Our previous findings (Thirumal Kumar, Eldous, Mahgoub, George Priya Doss, Zayed, 2018) and other reports concluded that the mutations N370S and L444P are the most significant mutations that could cause disruptions in protein stability and structure. These disruptions lead to protein misfolding and result in a diseased condition. Enzyme Replacement Therapy (ERT) and Pharmacological chaperone therapy (PCT) are currently used to treat GD caused by mutations in the GBA protein. The extreme disparity in cost between ERT and chaperone therapy, shifted the attention toward chaperone therapy. The most common chaperones in the market and trial phases to treat GD are Isofagomine, Miglustat, Eliglustat, NN-DNJ, and Ambroxol. In the era of personalized medicine, it is often necessary to understand the drug likeliness of each chaperone. In this context, the present study utilized molecular docking analysis to understand the interaction behavior of the chaperone toward the native and the two mutants N370S and L444P. The molecular dynamics simulation analyses performed on chaperones (NN-DNJ and Ambroxol) interaction showed that the chaperone NN-DNJ possesses better affinity toward the protein with N370S mutation whereas chaperone Ambroxol showed better activity against both the significant mutations (N370S and L444P). This study is expected to serve as a platform for drug repurposing.
Journal of Biological Physics, Sep 30, 2012
Chlamydomonas reinhardtii has long been used as a model organism in studies of cell motility and ... more Chlamydomonas reinhardtii has long been used as a model organism in studies of cell motility and flagellar dynamics. The motility of the well-conserved '9+2' axoneme in its flagella remains a subject of immense curiosity. Using high-speed videography and morphological analyses, we have characterized long-flagella mutants (lf1, lf2-1, lf2-5, lf3-2, and lf4) of C. reinhardtii for biophysical parameters such as swimming velocities, waveforms, beat frequencies, and swimming trajectories. These mutants are aberrant in proteins involved in the regulation of flagellar length and bring about a phenotypic increase in this length. Our results reveal that the flagellar beat frequency and swimming velocity are negatively correlated with the length of the flagella. When compared to the wild-type, any increase in the flagellar length reduces both the swimming velocities (by 26-57%) and beat frequencies (by 8-16%). We demonstrate that with no apparent aberrations/ultrastructural Electronic supplementary material The online version of this article
Biochemical and Biophysical Research Communications, Jun 1, 2009
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Applied Physics Letters, Sep 10, 2018
Femtosecond laser-induced damage to plasmid DNA in aqueous medium manifests itself as strand brea... more Femtosecond laser-induced damage to plasmid DNA in aqueous medium manifests itself as strand breaks arising from interactions with slow OH-radicals (and electrons) in the laser-induced plasma generated in water. Such strand breakages are found to be significantly inhibited upon addition of salts (in physiologically significant concentrations) to the aqueous medium. A simple model rationalizes our observations and suggests the feasibility of electrostatically "engineering" DNA's ion atmosphere so as to prevent damage-inducing free radicals accessing DNA strands. These findings may aid development of new strategies for cancer treatment.
Biochemical and Biophysical Research Communications, Mar 1, 2009
Optically trapped single cells of the biflagellated, green alga, Chlamydomonas reinhardtii, rotat... more Optically trapped single cells of the biflagellated, green alga, Chlamydomonas reinhardtii, rotate. The rotational dynamics of trapped wild-type and mutant cells show that functional flagella play a decisive role: the entire flagellar apparatus (central microtubules, radial spokes, and dynein arms) is involved. Any aberration in this apparatus leads to non-functionality, indicating a gear-type mechanism. The translational and rotational motions of the wild-type and mutant cells do not differ significantly. Optical forces alone do not play a vital role in the rotational dynamics of this cellular motor, making them useful as probes of the internal dynamics without external influence.
Springer eBooks, 1990
The transition from chloronema to caulonema marks a major developmental pathway during the format... more The transition from chloronema to caulonema marks a major developmental pathway during the formation of protonema in mosses like Funaria hygrometrica, Physcomitrella patens and Physcomitrium pyriforme. Since the first demonstration of the enhancement of caulonema differentiation specifically by exogenously applied auxins [14], strong evidence for the endogenous presence and function of auxins as natural hormones in mosses is gradually accumulating. The current understanding of auxin regulation of caulonema differentiation is reviewed briefly in this paper.
Plant Physiology and Biochemistry, 2002
Mitogen-activated protein kinases (MAPKs) are components of highly conserved signal transduction ... more Mitogen-activated protein kinases (MAPKs) are components of highly conserved signal transduction pathways. We show that in pH 5-grown chloronema cells of the moss Funaria hygrometrica, abscisic acid (ABA) and NaCl caused a rapid increase in the activity of a 38 kDa protein kinase (PK38) that uses myelin-basic protein (MBP) as a substrate. The activity was dose-dependent, and seemed to saturate with
BMC Cell Biology, Jun 10, 2016
Background: Flagella and cilia are fine thread-like organelles protruding from cells that harbour... more Background: Flagella and cilia are fine thread-like organelles protruding from cells that harbour them. The typical '9 + 2' cilia confer motility on these cells. Although the mechanistic details of motility remain elusive, the dynein-driven motility is regulated by various kinases and phosphatases. A-kinase anchoring proteins (AKAPs) are scaffolds that bind to a variety of such proteins. Usually, they are known to possess a dedicated domain that in vitro interacts with the regulatory subunits (RI and RII) present in the cAMP-dependent protein kinase (PKA) holoenzyme. These subunits conventionally harbour contiguous stretches of a.a. residues that reveal the presence of the Dimerization Docking (D/D) domain, Catalytic interface domain and cAMP-Binding domain. The Chlamydomonas reinhardtii flagella harbour two AKAPs; viz., the radial spoke AKAP97 or RSP3 and the central pair AKAP240. Both these were identified on the basis of their RII-binding property. Interestingly, AKAP97 binds in vivo to two RII-like proteins (RSP7 and RSP11) that contain only the D/D domain. Results: We found a Chlamydomonas Flagellar Associated Protein (FAP174) orthologous to MYCBP-1, a protein that binds to organellar AKAPs and Myc onco-protein. An in silico analysis shows that the N-terminus of FAP174 is similar to those RII domain-containing proteins that have binding affinities to AKAPs. Binding of FAP174 was tested with the AKAP97/RSP3 using in vitro pull down assays; however, this binding was rather poor with AKAP97/RSP3. Antibodies were generated against FAP174 and the cellular localization was studied using Western blotting and immunoflourescence in wild type and various flagella mutants. We show that FAP174 localises to the central pair of the axoneme. Using overlay assays we show that FAP174 binds AKAP240 previously identified in the C2 portion of the central pair apparatus. Conclusion: It appears that the flagella of Chlamydomonas reinhardtii contain proteins that bind to AKAPs and except for the D/D domain, lack the conventional a.a. stretches of PKA regulatory subunits (RSP7 and RSP11). We add FAP174 to this growing list.
Applied Nanoscience, Feb 24, 2018
Due to its eco-friendliness, recent times have seen an immense interest in the green synthesis of... more Due to its eco-friendliness, recent times have seen an immense interest in the green synthesis of metallic nanoparticles. We present here, a protocol for the rapid and cheap synthesis of Au and Ag nanoparticles (NPs) using 1 mg/ml tryptone (trypsinized casein) as a reducing and capping agent. These nanoparticles are spherical, ~ 10 nm in diameter and relatively monodispersed. The atoms of these NPs are arranged in face-centered cubic fashion. Further, when tested for their cytotoxic property against HeLa and VERO cell lines, gold nanoparticles were more lethal than silver nanoparticles, with a more or less similar trend observed against both Gram-positive and Gram-negative bacteria. On the other hand, the NPs were least cytotoxic against a unicellular alga, Chlamydomonas reinhardtii implying their eco-friendly property.
Journal of Biosciences, Mar 1, 2003
We have demonstrated the presence of a Ca 2+-dependent/calmodulin-stimulated protein kinase (PK) ... more We have demonstrated the presence of a Ca 2+-dependent/calmodulin-stimulated protein kinase (PK) in chloronema cells of the moss Funaria hygrometrica. The kinase, with a molecular mass of 70,000 daltons (PK70), was purified to homogeneity using ammonium sulphate fractionation, DEAE-cellulose chromatography, and calmodulin (CaM)-agarose affinity chromatography. The kinase activity was stimulated at a concentration of 50 µM free Ca 2+ , and was further enhanced 3-5-fold with exogenously added 3-1000 nm moss calmodulin (CaM). Autophosphorylation was also stimulated with Ca 2+ and CaM. Under in vitro conditions, PK70 phosphorylated preferentially lysine-rich substrates such as HIIIS and HVS. This PK shares epitopes with the maize Ca 2+-dependent/calmodulin-stimulated PK (CCaMK) and also exhibits biochemical properties similar to the maize, lily, and tobacco CCaMK. We have characterized it as a moss CCaMK. [D'Souza J S and Johri M M 2003 Purification and characterization of a Ca 2+-dependent/calmodulin-stimulated protein kinase from moss chloronema cells;
Plant Science, Jul 1, 1999
Using the in-gel kinase assay, four polypeptides of Mr 44, 48, 63, and 70 kDa showed calcium-depe... more Using the in-gel kinase assay, four polypeptides of Mr 44, 48, 63, and 70 kDa showed calcium-dependent phosphorylation in the crude extract of the moss Funaria hygrometrica Hedw. Analysis by SDS-PAGE suggests that these phosphopolypeptides represent the calcium-dependent protein kinases (PK), which could undergo autophosphorylation and phosphorylate casein. Temporal changes in the activity of PK in cells grown under different conditions were detectable using the in-gel kinase assay. The 44 kDa Ca 2 + dPK showed an increase in activity in cells grown either in the presence of auxin, at pH 5, or when starved of nitrate. This PK is shown to share epitopes with calmodulin suggesting that it could be a PK with calmodulin-like domain. The in-gel kinase assay, its possible applications and the existence of multiple Ca 2 + dPKs in moss are discussed.
Scientific Reports, Jun 9, 2016
We report on damage to DNA in an aqueous medium induced by ultrashort pulses of intense laser lig... more We report on damage to DNA in an aqueous medium induced by ultrashort pulses of intense laser light of 800 nm wavelength. Focusing of such pulses, using lenses of various focal lengths, induces plasma formation within the aqueous medium. Such plasma can have a spatial extent that is far in excess of the Rayleigh range. In the case of water, the resulting ionization and dissociation gives rise to in situ generation of low-energy electrons and OH-radicals. Interactions of these with plasmid DNA produce nicks in the DNA backbone: single strand breaks (SSBs) are induced as are, at higher laser intensities, double strand breaks (DSBs). Under physiological conditions, the latter are not readily amenable to repair. Systematic quantification of SSBs and DSBs at different values of incident laser energy and under different external focusing conditions reveals that damage occurs in two distinct regimes. Numerical aperture is the experimental handle that delineates the two regimes, permitting simple optical control over the extent of DNA damage.
Journal of Biomolecular Structure & Dynamics, Jul 11, 2014
There is a need for continued development of acetylcholinesterase (AChE) inhibitors that could pr... more There is a need for continued development of acetylcholinesterase (AChE) inhibitors that could prolong the life of acetylcholine in the synaptic cleft and also prevent the aggregation of amyloid peptides associated with Alzheimer's disease. The lack of a 3D-QSAR model which specifically deconvulates the type of interactions and quantifies them in terms of energies has motivated us to report a CoRIA model vis-à-vis the standard 3D-QSAR methods, CoMFA and CoMSIA. The CoRIA model was found to be statistically superior to the CoMFA and CoMSIA models and it could efficiently extract key residues involved in ligand recognition and binding to AChE. These interactions were quantified to gauge the magnitude of their contribution to the biological activity. In order to validate the CoRIA model, a pharmacophore map was first constructed and then used to virtually screen public databases, from which novel scaffolds were cherry picked that were not present in the training set. The biological activities of these novel molecules were then predicted by the CoRIA, CoMFA, and CoMSIA models. The hits identified were purchased and their biological activities were measured by the Ellman's method for AChE inhibition. The predicted activities are in unison with the experimentally measured biological activities.
Sensors and Actuators B-chemical, May 1, 2006
An optical trap is used to monitor bio-deleterious effects induced by ultra-violet (UV) radiation... more An optical trap is used to monitor bio-deleterious effects induced by ultra-violet (UV) radiation in a single, live cell. When placed in a laser optical trap, Chlamydomonas reinhardtii cells undergo rotation because of the interplay of flagellar-based forces and ...
Plant Signaling & Behavior, 2014
We report here, the transcriptional regulation of 2 calcium Dependent Protein Kinases in response... more We report here, the transcriptional regulation of 2 calcium Dependent Protein Kinases in response to nutrient starvation of Chlamydomonas reinhardtii vegetative cells. The cDPK proteins, cDPK1 and cDPK3; share 53% identity among themselves, a maximum of 57% and 52% to higher plants respectively and 42% to apicomplexan protozoans. We expressed a cDPK1-GFP fusion protein in the C. reinhardtii vegetative cells and showed its distribution both in the cell body and the membrane-matrix fraction of the flagella. The fusion protein exhibits mobility shift in the presence of ca 2+ , confirming its ca 2+-binding properties. To the best of our knowledge, this is the first report of transcriptional regulation of cDPKs from a unicellular chlorophyte in response to nutrient starvation namely acetate (a), phosphorus (P), and nitrogen (N).
Algal Research-Biomass Biofuels and Bioproducts, Jun 1, 2016
Chlamydomonas reinhardtii is a model, free-living, soil and freshwater alga with unicellular vege... more Chlamydomonas reinhardtii is a model, free-living, soil and freshwater alga with unicellular vegetative cells under favourable growth conditions. When exposed to certain stress agents, however, C. reinhardtii forms multicellular aggregates known as "palmelloids." This study characterizes palmelloid formation in response to sodium chloride (NaCl) salt stress and probes the role of proteins from the spent medium in this process. Detailed morphological and biochemical analysis of NaCl-induced palmelloids of C. reinhardtii were carried out along with quantitative mass spectrometry-based protein analysis of stress and post-stress spent media. Exposure to NaCl concentrations of 100 and 150 mM (equivalent in saline soils) induces palmelloid formation and withdrawal of this stress causes rapid dissociation of these clusters. Heterogeneity in cell size and cells with excised flagella remnants within palmelloid clusters suggests heterogeneous cell cycle arrest during palmelloid formation. Additional hallmarks of palmelloidy include: intracellular starch and lipid accumulation and the presence of an extracellular polysaccharide envelope. Analysis of proteins from the spent media of stressed and post-stress conditions implicated involvement of cell wall proteins in palmelloid formation and maintenance and peptidase and flagellar proteins in palmelloid dissociation. With this report, the relevance of NaCl, as a probable environmental cue for driving unicellular, free-living C. reinhardtii cells into a multicellular, palmelloid stage is discussed.
Fems Microbiology Letters, Dec 20, 2012
Escherichia coli BolA protein is a stress-inducible morphogene, regulates transcription, forms bi... more Escherichia coli BolA protein is a stress-inducible morphogene, regulates transcription, forms biofilms and interacts with monothiol glutaredoxins. Its presence has been documented in plants but its role remains enigmatic. This study attempts to functionally dissect the role of a BolA-domain-containing protein in the alga Chlamydomonas reinhardtii. Of the five C. reinhardtii bolA-like genes annotated for the presence of BolA-domain, the open reading frame with the highest similarity to algal systems was cloned and the protein overexpressed in E. coli. This over-expression did not affect E. coli growth but induced biofilm formation and changed its morphology, indicating functional conservancy. This is the first compelling evidence depicting the role of a plant BolA-like protein in morphogenetic pathway and biofilm formation. The implications of the phenotypic consequences of this heterologous expression are discussed.
Advanced Bioprocessing for Alternative Fuels, Biobased Chemicals, and Bioproducts, 2019
Abstract Plants obtain their much needed structural support from lignin present in their cell wal... more Abstract Plants obtain their much needed structural support from lignin present in their cell walls. After celluloses, lignins are the most complex and abundant terrestrial phenolic polymers present in higher plant tissues. When compared to cellulose and hemicellulose, lignin is often considered as a hindrance in the production of cellulosic bioethanol. This is largely attributed to the complexity that is involved in separating it from other polymers. Lignin is considered as a good source of upgradable building blocks and valuable aromatic chemical compounds. However, due to the random nature of the polymerization process, lignin’s application in production of useful bioproducts is limited. The lack of a detailed methodology for the degradation of lignin polymer offers a promising research opportunity. This chapter covers recent research in lignin biosynthesis, genetic engineering of lignin, various chemical and biological means of lignin depolymerization, and exploitation of its properties for conversion of lignin into biofuels and bioproducts.
Plant Science, 1999
Using the in-gel kinase assay, four polypeptides of Mr 44, 48, 63, and 70 kDa showed calcium-depe... more Using the in-gel kinase assay, four polypeptides of Mr 44, 48, 63, and 70 kDa showed calcium-dependent phosphorylation in the crude extract of the moss Funaria hygrometrica Hedw. Analysis by SDS-PAGE suggests that these phosphopolypeptides represent the calcium-dependent protein kinases (PK), which could undergo autophosphorylation and phosphorylate casein. Temporal changes in the activity of PK in cells grown under different conditions were detectable using the in-gel kinase assay. The 44 kDa Ca 2 + dPK showed an increase in activity in cells grown either in the presence of auxin, at pH 5, or when starved of nitrate. This PK is shown to share epitopes with calmodulin suggesting that it could be a PK with calmodulin-like domain. The in-gel kinase assay, its possible applications and the existence of multiple Ca 2 + dPKs in moss are discussed.
Encyclopedia of Signaling Molecules, 2012
G phosphatase-2A (PP2A) holoenzyme, non-receptor tyrosine kinases (Tec, Bmx, Bruton's tyrosine ki... more G phosphatase-2A (PP2A) holoenzyme, non-receptor tyrosine kinases (Tec, Bmx, Bruton's tyrosine kinase), potential regulators of ▶ cadherin stabilization (p120 catenin and aSNAP) the tight junctional protein zonula occludens-1, proteins harboring a regulator of G protein signaling domain (axin and RGS1), the polycystic kidney disease-related protein polycystin-1, and the Rho-stimulatory A-kinase-anchoring protein AKAP-Lbc (Kelly et al. 2007; Yu et al. 2011). Efforts are ongoing to connect specific Ga12-target interactions to known Ga12-mediated signaling responses. The pathways in which RhoGEF cadherins BTK,
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Papers by Jacinta D'Souza