PhD Theses (Biosciences and Bioengineering)


Recent Submissions

Now showing 1 - 20 of 260
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    Enhancing Water Quality through Adsorptive Removal of Contaminants of Emerging Concern using Bio-based Engineered Adsorbents: Modeling and Toxicological Evaluation
    (2024) Priyan, Vishnu V
    Rapid industrialization and urbanization cause tremendous stress on the natural resources which leads to severe ecological impacts, amongst water is the foremost concern that can be easily polluted by contaminants of emerging concern (CECs). The persistence and/or pseudo-persistence nature of these pollutants could cause various environmental and health impacts on water ecosystems and living beings. Thereby, sequestration of these contaminants from the water systems is mandatory. So, adsorption is the prominent approach for the sequestration of these contaminants due to its efficiency at lower pollutant concentration, easy implementation, cost-effective, selectivity, and economic feasibility. The research focuses on the development and characterization of bio-based engineered adsorbents derived from bio-based precursors. These adsorbents are designed to possess high surface area and tailored surface chemistry to efficiently capture CECs from water sources. Furthermore, the thesis integrates mathematical modeling techniques to predict the adsorption behavior of CECs onto bio-based adsorbents under different scenarios. This modeling approach facilitates the optimization of adsorption processes and provides insights into the mechanisms governing pollutant removal. In addition to assessing the adsorption efficiency, the thesis evaluates the potential toxicological implications of using bio-based adsorbents for CEC removal. Toxicological evaluations encompass the analysis of adsorbent leachates and the assessment of any adverse effects on model organisms. Overall, this interdisciplinary study contributes to the advancement of sustainable water treatment technologies by offering insights into the efficacy, mechanisms, and environmental implications of using bio-based engineered adsorbents for the removal of CECs. The findings hold significant implications for water resource management and public health protection in the face of emerging contaminants.
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    Mechanism of Antimicrobial Peptide Binding to Membrane-mimetic Systems: Insight from Molecular Dynamics Simulations
    (2023) Ghosh, Suvankar
    The focus of the Ph.D. thesis was to understand the mechanism of cationic antimicrobial peptide (7 and 14 amino acid residue long) binding to membrane-mimetic systems (micelle and bilayer) using classical molecular dynamics free energy simulations. The peptides were modeled and subjected to conventional classical MD simulations in the presence and absence of micelle/bilayer [micelles: SDS/DPC and bilayers: (DOPE:DOPG and POPE:POPG)/POPC as bacterial/mammalian membrane-mimic]. The structures of the free peptides in water and in complex with the membrane-mimetic systems were predicted from the conventional MD simulations and verified by our experimental collaborators. The MD structures were used as a template for estimating the energetics of peptide: micelle/bilayer binding (ΔGbind; absolute binding affinity and ΔΔG; Binding free energy difference between two peptides to the membrane-mimetic system) by employing various popular methods: Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), Steered Molecular Dynamics (SMD), Umbrella Sampling (US), and Alchemical free energy simulations (FEP, TI, BAR). The simulations of peptide binding to the simplest membrane-mimetic systems provide insight into the kinetics and establish a direct link between the calculated energetics and molecular structures.
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    Spectroscopic, structural and functional characterization of Intrinsically Disordered Protein DHN1 from Zea mays
    (2023) Ahari, Dileep
    Intrinsically Disordered proteins (IDPs) emerged as an essential class of proteins in the past two decades due to their functional relevance without having a proper 3-dimensional structure. Here, we investigated dehydrin (DHN1) protein from Zea mays, an IDP that belongs to the Late Embryogenesis Abundant (LEA) protein family. This thesis work focused on studying DHN1 structural dynamics and functional role using the novel spectroscopic tool Protein Charge Transfer Spectroscopy (ProCharTS) and other spectroscopic techniques like UV-visible and fluorescence spectroscopy. To investigate the structural change and functional role of DHN1, two mutants: DHN1 CW1 (Trp122 −Cys62) and DHN1 W3 (Trp3), were generated using sitedirected mutagenesis. The structural analysis of the DHN1 protein divulges its complete random coil conformation in the native state. ProCharTS absorption was found to be sensitive to the conformational changes in DHN1 induced by the changes in pH and temperature of aqueous medium. Next, we investigated the luminescence characteristic of this novel ProCharTS in the DHN1 protein. This study suggests that ProCharTS in DHN1 protein is luminescent in nature. We found that the observed luminescence is excitation wavelength dependent and possesses a significant presence in the UV-Visible region. ProCharTS luminescence has a low quantum yield and lower luminescence lifetime. The origin behind this luminescence could be charge recombination. Further, ProCharTS luminescence found to modulate the fluorescence of other chromophores like Trp in the same spectral region. Spectroscopic studies reveal that DHN1 and its mutant proteins are highly dynamic in nature and displays the disorder-to-order structural transitions in presence of TFE, SDS and at high temperatures. Further, the overall structural change in DHN1 protein in presence of SDS was measured using the Förster Resonance Energy Transfer (FRET) from excited Trp122 (donor) to dansyl-labelled Cys62 (acceptor). Intramolecular FRET distance between Trp—Dansyl indicated that the distance between Trp122 and Cys62 in DHN1 CW1 was reduced from 34 Å to 25 Å in the presence of SDS. Finally, the functional studies of DHN1 and its mutant protein indicate that DHN1 has significant cryoprotective and heat-protective functions via potential weak electrostatic binding to the target enzyme. Taken together, ProCharTS can serve as a label-free tool to study and detect structural transitions in the IDPs rich in charged amino acid residues and devoid of aromatic chromophores. The structural changes and the cryoprotection and heat-protection function of DHN1 protein could be attributed to its significant role in the stress tolerance mechanism in plants.
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    Isolation, characterization and pharmacological application of bioactive compound from leaves of Alpinia nigra (Gaertn.) B.L. Burtt
    (2022) Gupta, Manish Kumar
    The present study is focused on investigating the potential uses of the herbaceous plant Alpinia nigra (Gaertn.) B.L. Burtt (Zingiberaceae). Traditionally this plant is used in folk remedies for curing gastritis and infectious diseases. The plant leaves are used as a food-flavoring agent by tribal people in Northeast (NE) India. However, the scientific community has not explored the plant leaf for its medicinal properties. Thus in the present study, the leaf extracts hexane (L-Hex), ethyl acetate (L-EtAc), and methanol (L-Met) were subjected to phytochemical analysis. The antibacterial, anti-biofilm, and anti-quorum sensing activities of the L-EtAc extract was determined by in-vitro analysis and was found to be potential. Further, the compound 3, 5-dihydroxy 4′,7-dimethoxy flavone (DHDM) was purified from L-EtAc, crystallized, and structural characterization was performed using multispectroscopic techniques including HRMS, FTIR, Raman, SC-XRD, 1-D NMR, and 2-D NMR. The cell viability assay showed no inhibition of DHDM at ≤200 μM concentration in THP-1 (human macrophage) and ≤80 μM in HaCaT (human keratinocyte) cell lines. Additionally, strong antioxidant properties and reduced ROS
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    Evolutionary landscape of dipteran insects
    (2022) Kabiraj, Debojit
    Insects are the most successful animals on the planet, in terms of both ecological and evolutionary success. Diptera are typical insect order having two wings and accounts for one-tenth of all living creatures on the earth. Their ability to feed on a variety of foods has allowed them to thrive in a wide range of food chains and climatic niches. Our knowledge of the evolution of flies is muddled by limited and contradictory morphological and genomic data, as well as the difficulty of capturing the huge species diversity in a single complete phylogenetic analysis.
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    Targeting Notch Signalling in the EMT Dynamics of Triple-Negative Breast Cancer cells
    (2023) Sen, Plaboni
    The thesis work describes the identification and targeting the pivotal molecules of the Notch signalling pathway to combat the aggressive characteristics of TNBC cells (such as EMT, drug resistance and stemness). Initially, the identification of the nodes was carried out, which provided us with the major proteases. They were further targeted using a Polypharmacology approach by a repurposed drug, selected from extensive in silico screening. Furthermore, an effective combination therapy was established, which aimed in targeting the Notch signalling pathway along with the VEGF pathway. Finally, a combination therapeutic module was established, which aimed in increasing the effectiveness and outcome of an HDAC inhibitor (SAHA), thereby inhibiting EMT, stemness and survival of the TNBC cells. The effectiveness of combination treatment on monolayer cultures, and complex tumour spheroids illustrates the therapeutic significance of combination treatment as an attractive alternative in cancer therapeutics.
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    Targeting Triple Negative Breast Cancer Using Membrane-Derived Nanocarriers for Potential Therapeutic Applications
    (2023) Saha, Muktashree
    The current thesis focusses on targeting metastatic triple negative breast cancer via modulation of the tumor micro environment by targeted delivery of inhibitors using a biologically derived nanosystem. Significant signaling pathways and the drug resistant potentiality of the TNBC cells were primarily targeted via the biologically derived nano-carriers which resulted in efficient suppression of metastatic breast cancer and development of an effective treatment module for targeting TNBC. Firstly, nano-vesicles were synthesised from the cell membranes of cancer cells and were evaluated for its homologous targeting efficiency with further loading of the nano-vesicles with an inhibitor. The use of cell membranes as biological nano-carrier, demonstrated impressive self-homing capabilities, thereby leading to the development of a potential nano-delivery system for cancer therapy in vivo, as they can be derived from the patient’s own cells. In the subsequent endeavor, exosomes were employed for the modulation of tumor microenvironment and MDR dynamics of metastatic triple negative breast cancer cells. The exosomes from non-invasive breast cancer cells lead to the decrement in the expression of the ABC transporters, thereby making the metastatic TNBC cells more susceptible to chemotherapeutic drugs for effective anti-cancer activities. Taking into consideration, the advantages of the nano-vesicles and exosomes, a hybrid nanosystem was synthesised by fusing the nano-vesicles and exosomes. Significant signaling networks were targeted by loading an HDAC inhibitor into the fused nanosystem in combination with a tyrosine kinase inhibitor. The study showed that the targeted co-therapy resulted in an efficient subduing of metastatic TNBC that not only resulted in apoptosis of the MDA MB-231 cells, but also affected the regulatory pathways at the genetic and proteomic levels in a synergistic manner. Thus, the study showed that targeted co-therapy via the developed biomimetic hybrid nanocarriers played a very substantial role in the site specific delivery of the drugs for a more efficacious outcome. Thus the corroborations of this research might open up new horizons for the curtailment of metastatic TNBC with further validations in in vivo system.
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    Analyzing Charge Transfer Spectra arising from non-aromatic amino acids in proteins, aggregating peptides and viral capsid assemblies
    (2023) Alom, Shah Ekramul
    Novel intrinsic chromophores in apo-proteins lacking aromatic amino acids have gained importance and have been a recent topic of interest. Here in this thesis, Protein Charge Transfer Spectra (ProCharTS), which is proposed to be the origin of such intrinsic absorbance and luminescence features, is being studied. Although the major contribution of Lysine towards ProCharTS phenomenon has been ascertained in highly charge rich proteins. Here we report for the first time, ProCharTS in proteins and peptides rich in Arginine, Aspartate residues, but lacking Lysine residues. Similar absorbance and luminescence properties as that in Lysine-rich protein were observed. ProCharTS can be expected to be evident as long as charge transfer takes place, irrespective of the type of charged species. Since ProCharTS and conventional chromophores like Tryptophan share a similar spectral domain, the influence of ProCharTS on the indole fluorescence in Tryptophan was studied and was found to contaminate the indole fluorescence. Moreover, the decay kinetics from the excited state population in the indole ring was found to be affected by the presence of charged residues, which may explain the multi-exponentiality of Tryptophan fluorescence intensity decay often observed in proteins. Finally, the applicability of ProCharTS on peptide aggregation and viral capsid assembly was studied. ProCharTS was able to monitor the early stages of aggregation in Aβ-derived switch peptides, where the random coil peptides interconvert into β-sheets. Similarly, ProCharTS could detect the formation of the large clusters of HBV core protein dimers into capsids with T=4 and T=3 icosahedral geometry in real-time. The increased interactions among the charged residues at close proximity in the peptide oligomers or HBV capsids are proposed to enhance ProCharTS signal. ProCharTS, being a simple, label-free technique can thus be used for rapid initial screening of drugs for amyloid-linked diseases and viral core protein allosteric modulators (CpAMs), without interfering with the aggregation or capsid assembly kinetics.
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    To gain insights into the function of yeast Dnm1 in mitochondrial dynamics
    (2024) Banerjee, Riddhi
    Mitochondria, vital hubs of cellular metabolism, continuously modulate their shape and number through fission and fusion. The central mediator of mitochondrial fission is the GTPase Dnm1 in yeast, and its homolog DRP1 in humans. Dnm1 comprises four domains - an N-terminal GTP-binding domain, a middle domain, a variable B-insert domain, and a C-terminal GTPase effector domain. Dnm1 undergoes assembly/disassembly cycles driven by GTP binding and hydrolysis to facilitate fission. While substantial progress has been made in understanding the domain architecture, function, and interacting partners of Dnm1, critical aspects, including the regulation of oligomeric forms, their spatio-temporal distribution, and the impact of post-translational modifications (PTMs), remain unclear. Moreover, disruptions in the delicate balance between mitochondrial function and dynamics are associated with various human diseases, with specific mutations in DRP1 linked to pathological conditions. Despite previous studies on the effects of these mutations on mitochondrial morphology, their impact on protein localization, distribution, function, and structure remains unexplored. This study aimed to investigate specific residues in Dnm1 that may undergo modifications or are mutated in disease conditions, examining their impact on the protein's structure, localization, and function. To achieve this, functional FL-Dnm1-GFP and Dnm1-HisHA fusion proteins were constructed, for in vivo and in vitro assessment, respectively. Five putative Dnm1 phosphorylation sites were selected for mutagenesis based on stringent conservation criteria. Interestingly, mutating S624, analogous to the reported regulatory DRP1 S616 site, did not affect mitochondrial morphology in yeast. However, mutating T62 and S277 in G2 and G5 motifs of the GTPase domain yielded non-functional proteins despite differences in their localization and dynamics. Structurally, T62A/D formed atypical large puncta, while S277A/D resembled WT Dnm1. Further computational analyses and molecular dynamics simulations provided insights into conformational changes and altered atomistic motion, particularly highlighting the dominant-negative impact of S277 mutation without altering protein localization. Furthermore, the study extended the investigation to mimic four disease-causing DRP1 mutations in Dnm1, uncovering diverse functional outcomes. For instance, the A430D mutation led to a complete loss of Dnm1 function, disrupting typical punctate phenotypes and presence of diffused cytosolic fluorescence, indicating defective oligomerization. Simulations revealed the mutation induced major conformational and dynamics changes in a helix region. In contrast, the G397D mutation resulted in fewer, larger, and less dynamic puncta, likely due to change in orientation of a loop surrounding the mutated residue. Thus, investigating each mutation in detail is crucial for gaining insights into their respective roles in disease-associated alterations of mitochondrial dynamics. In conclusion, this research provides novel insights into the molecular basis of Dnm1 function and regulation, contributing to a deeper understanding of conserved mitochondrial fission processes. Additionally, it paves the way for the development of targeted therapies for several neurological diseases where mitochondrial fission-fusion regulation is impaired.
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    Cell functions and molecular mechanisms of zinc transporters in Neurospora crassa
    (2024) Ngiimei, Serena D
    "Thesis Title: Cell functions and molecular mechanisms of zinc transporters in Neurospora crassa In this thesis work, I studied the cellular functions and molecular mechanisms of zinc resistance-conferring 1 (ZRC-1), meiotic sister chromatid 2 (MSC-2), and zinc-regulated gene 17 (ZRG-17) that are members of the cation diffusion facilitator (CDF) family of zinc transporters in Neurospora crassa. The Δzrc-1 mutant was unable to grow under high zinc conditions (≥ 0.5 mM). However, the expression of zrc-1 was elevated ~3-fold under low zinc conditions in comparison to normal and high zinc concentrations. The Δmsc-2 mutant showed colony growth and aerial hyphae similar to wild type and the expression of msc-2 was independent of zinc. Furthermore, the double mutant Δzrc-1; Δmsc-2 and Δzrc-1; Δzrg-17 showed additive phenotypes of both the parental single mutants. However, the phenotypic defects such as slow growth rate, defective in asexual sporulation, and inability to degrade cellulose of the Δzrg-17 single mutant were restored in the Δmsc-2; Δzrg-17 double mutant, which showed phenotypes similar to the wild type. The double mutant Δzrc-1; Δzrg-17 showed severe growth defects, stunted aerial hyphae, short septa, and defects in conidiation. In addition, the Δzrc-1; Δmsc-2 and Δzrc-1; Δzrg-17 double mutants showed sensitivity to DTT-induced ER stress and were unable to grow in the medium containing cellulose. Furthermore, zinc-responsive activator protein 1 (ZAP-1) was also studied to understand the molecular mechanism and the interaction of the CDF zinc transporters with the transcription factor. The zap-1 of N. crassa was found to be crucial for survival under low zinc conditions and ZAP-1 was localized in nucleus under all zinc conditions tested. The double mutants Δzap-1; Δzrc-1, Δzap-1; Δmsc-2, and Δzap-1; Δzrg-17 showed slow growth under low zinc like Δzap-1, indicating that ZAP-1 might be functioning upstream of zrc-1, msc-2, and zrg-17. Furthermore, expression analysis of the CDF family of zinc transporter, zrc-1, msc-2, zrg-17, and zrt-3 in Δzap-1 mutant showed very low-level expressions compared to expression in wild type, indicating that the ZAP-1 transcription factor regulates the CDF zinc transporters under low zinc conditions."
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    New insight into the Adsorptive Removal of Organic and Inorganic Pollutants from Aqueous set up with tailored cellulosic and polymer-based biomaterials: Modeling and Ecotoxicological assessment
    (2022) Shahnaz, Tasrin
    The significance of water as a resource for the survival of humanity is incomparable. With the rapid advancement in various technologies, the demand for water usage has been augmented exponentially. From the industry domain to fulfilling the basic necessity for the people, water conservation with proper qualitative allocation has been at the forefront of all activities. While the swift developments in the technological industries have been a boon for appeasing the hefty consumer demand in the market, it leaves a deterrent impact on the environment. To eradicate the grave danger to the aquatic environment, the treatment of wastewater is crucial and imperative. The first study of the thesis work examines the efficiency of the removal of hexavalent chromium using physicochemically activated lignocellulosic biomass from Acacia auriculiformis (Fabaceae family). The treatment involved sulphuric acid activation followed by pyrolysis resulting in chemically modified activated carbon. Further, it was complexed with a chelating agent i.e. EDTA. Acid treatment and complexation with chelating agents improvised the biosorbent’s sorption capacity towards chromium species. Adsorption parameters like pH, adsorbent dosage, temperature, and initial metal concentration were optimised in the batch study.
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    Exploring the Potentials of FIKK Kinase(s) into Development of Antimalarial and Diagnostics
    (2022) Kumar, Anil D
    Kinome of Plasmodium sp. underwent unprecedented evolutionary divergence from other eukaryotic kinases. Some of these kinases do not come under the known kinase family due to their extreme divergence from their ancestors. All these kinases are clustered as orphan kinases, FIKK kinases are one among them. Plasmodium falciparum FIKK’s are the only kinase family among eukaryotic kinases that diverged extraordinarily and expanded from their ancestor. These are trafficked throughout the parasite-infected erythrocytes and pursue important tasks for the survival of plasmodium. The study explored detailed structural characteristics of FIKK9.1 and recommends possible interacting partners in host RBC. FIKK9.1 is essential for parasite survival, but its structural and biochemical characterization will enable us to understand its role in the parasite life cycle. The recombinant FIKK9.1 kinase is monomeric with a native molecular weight of 60 ± 1.6 kDa. Structural characterization of FIKK9.1 kinase reveals that it consists of N-terminal FHA like domain and C-terminal kinase domain. The C-terminal domain has a well-defined pocket, but it displayed an RMSD deviation of 1.38 - 3.2 Å from host kinases. ITC analysis indicates that ATP binds to the protein with a Kd of 45.6±2.4 μM. Co-localization studies revealed FIKK9.1 in the parasite cytosol with a component trafficked to the apicoplast and IRBC. FIKK9.1 has 23 pockets to serve as potential docking sites for substrates. Correlation analysis of peptides from the combinatorial library concluded that peptide P277 (MFDFHYTLGPMWGTL) fitted nicely into the binding pocket. The peptide P277 picked up candidates from parasites and key players from the RBC cytoskeleton. Interestingly, FIKK9.1 is phosphorylating spectrin, CD44, and band-3 from the RBC cytoskeleton. After that, our study explored potential antimalarial from synthetic molecules and natural sources. The rapid emergence of drug-resistant malaria parasites to all frontline antimalarial drugs urges a continuous search for new antimalarial drugs that are beneficial for chemotherapy and prophylaxis. Virtual screening of diverse organic structural scaffolds from the chemical library has identified seven molecules, which could arrest the growth of parasites by inhibiting FIKK9.1 kinase. Evaluation of top hit compounds in antimalarial activity assay indicates that the highly substituted 1,3-selenazolidin-2-imine 1 and thiophene 2 inhibit parasite growth. The functionalized heterocyclic compounds 1 and 2 are killing the malaria parasite with an IC50 of 2.68 ± 0.02 μg/ml and 3.08 ± 0.14 μg/ml, respectively. Isothermal titration calorimetry analysis indicates heterocyclic scaffolds 1 and 2 abolish the binding of ATP into the FIKK9.1 binding pocket. They in-turn reduces the ability of FIKK9.1 kinase to phosphorylate its substrate, and both compounds are potent inhibitor of FIKK9.1 kinase. Inhibition of FIKK9.1 kinase is disturbing the parasite life cycle and resulting in the parasite's death. Further as a natural source, we exploit potentials of Triphala and shukramatrika as antimalarial and efforts to find its mechanism and mode of action as antimalarial. The water extract of Triphala shows promising effects with schizonticidal and parasiticidal in-vitro plasmodium falciparum 3d7 cultures. The antimalarial activity reveals that inhibition of parasites follows parasiticidal nature. The cytotoxicity on HEK293 and hemolysis analysis suggests Triphala and Shukramatrika is safe to use as antimalarial. The underlying mechanism of parasitic death is evaluated through apoptotic biomarkers, including ROS generation, mitochondrial dysfunction, and in situ DNA fragmentation in Triphala, and Shukramatrika treated and untreated parasites. Our results showed that Triphala and Shukramatrika induce oxidative stress by increasing ROS levels, destabilizing the mitochondrial membrane, and increasing the population of fragmented DNA parasites. Certainly, all those major factors, such as the importance of FIKK’s in parasite survival, stable expression in all stages of malaria lifecycle, stable gene transfer, and regions specific to P. falciparum paves a new insight through the field of antimalarial drug discovery and development of a new diagnostic marker for malaria. Each FIKK has its unique N-terminal sequences with non-homologs to eukaryotic kinases and kinases in Plasmodium sp. These exclusive regions are highly potent to be antigenic which helps in producing specific antibodies against the FIKK kinase(s). Therefore we raised antibodies against FIKK9.1 kinase and identified the anti-FIKK9.1 antibody present in serum specifically detects purified FIKK9.1 as well as pfFIKK9.1 present in parasite lysate. These are found to have no cross-reactivity to proteins present in RBC lysate. The antibodies from serum are purified and analyzed for their sensitivity and selectivity. The sensitivity of purified anti-FIKK9.1 polyclonal antibody is validated by estimating the limit of detection using rFIKK9.1 protein. The purified anti-FIKK9.1 detects antigens even at 3 nmole. Further, the cross-reactivity is analyzed using human serum and complete media devoid of parasites. Both the samples show no cross-reactivity with anti-FIKK9.1. The anti-FIKK9.1 antibody detects FIKK9.1 antigens at least to 0.1% parasitemia grown under in-vitro conditions. Surprisingly, purified antibody detects FIKK9.1 in parasite culture media, and further, the detection increases with an increased level of parasitemia. The data suggests FIKK9.1 may export outside the infected parasite. The Semi-quantitative measurements of Parasite load in the infected RBC is studied by performing concentration curve analysis for both rFIKK9.1 and parasite lysate. Further, the anti-FIKK9.1 antibody is validated by mimicking the patient sample and mocking coinfection with other infectious agents. In conclusion, our study highlights the structural and biochemical features of FIKK9.1 to exploit it as a drug target. It provides new insight into the target FIKK9.1 kinase in malaria parasites to develop potent antimalarials. The study finds Triphala and Shukramatrika kill malaria parasites irreversibly through the apoptotic pathway. Further, the research finds that FIKK9.1 is a better biomarker for malaria diagnosis.
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    Structural and Functional Studies of a Phospholipid Transporter Involved in the Maintenance of the Outer Membrane Asymmetry in Gram-negative Bacteria
    (2023) Dutta, Angshu
    Gram-negative bacteria are more resilient than Gram-positive bacteria due to the presence of an outer membrane (OM). Unlike the inner membrane (IM), the OM is asymmetric in nature because of the presence of lipopolysaccharide (LPS) and phospholipid (PL) in the outer and inner leaflets, respectively. This asymmetric organization shields the bacteria from antibiotics, toxins, etc. However, the PLs have the tendency to flip back and accumulate in the OM, leading to the formation of patches and disruption of this barrier function. In order to restore the OM permeability, bacteria utilize the highly conserved inter-membrane ATP-binding cassette (ABC) transporter system, viz. maintenance of lipid asymmetry (Mla). The Mla system consists of three sub-complexes- OM-associated MlaA-Osmoporin F/C complex, periplasmic MlaC and IM-associated MlaFEDB complex. The components of the Mla system are involved in the movement of PLs between the membranes, thereby maintaining OM asymmetry. Owing to this, the system has been suggested to be an excellent drug target although in-depth studies highlighting the mechanism of action are still lacking. Thus, in this study, all the Mla proteins from Escherichia coli were computationally and structurally characterized. Computational studies of the Mla components reveal their unique features which are not observable in typical ABC transporters. These include the identification of conserved motifs, distinct evolutionary relationships, interaction profiles and interfacial residues. Structure elucidation of MlaC and MlaD (EcMlaC and EcMlaD) through X-ray crystallography reveals that both these proteins do not possess the conserved architecture of N-terminal and C-terminal domains present in substrate-binding proteins (SBPs). Instead, EcMlaC comprises two different domains that are arranged in a discontinuous fashion. On the other hand, EcMlaD forms a homo-hexameric ring with a central hydrophobic channel which is continuous but has varying dimensions. Owing to these structural peculiarities, these two proteins have been classified as non-canonical SBPs. Extensive structural analyses of these proteins have led to the proposition of two novel mechanisms of ligand binding that have not been reported in case of any SBP to date. Furthermore, through this study, global and local motions in EcMlaC have been identified that are critical for ligand binding. Altogether, the findings provide significant mechanistic insights into the functioning of the Mla system in E. coli and other Gram-negative bacteria.
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    Investigating the spectroscopic properties of Mammeigin from Mesua ferrea in micro-heterogenous systems
    (2022) Sanjana, S
    Mesua ferrea L. (Calophyllaceae), a medicinal plant abundant in Northeast (NE) India is a vast reservoir of phytochemicals. Mammeigin (MMG) is a neoflavonoid isolated from M. ferrea seed oil with high yield and purity. MMG is non-polar like several bioactive compounds, and its aqueous solubility was enhanced in surfactant micelles and Hen Egg-White lysozyme (HEWL) aggregates. The role of charges on the interaction with MMG was investigated in anionic Sodium dodecyl sulphate (SDS), cationic Cetyltrimethylammonium bromide (CTAB), and neutral Tween 20 (T20) using UV-Visible spectroscopy. The stability of MMG was enhanced at low ionic surfactant concentrations in the presence of sodium chloride at its physiological concentration. The interaction of MMG with HEWL aggregates was found to exist at pH 2 and pH 9, but not pH 5. This study provides insights for developing formulations and better molecular carriers. Furthermore, the application of MMG as acid-base pH indicator was explored in the surfactant systems. At alkaline pH, a stable and bright yellow color was developed by MMG in CTAB micelles. Similarly, the effect of specific ions was investigated in the surfactant systems and the sensitivity of MMG to fluoride ions in CTAB was observed in the range of 2.4-200 mM NaF.
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    De novo Design of Bioinspired Peptide based Molecular Constructs
    (2022) Prakash, Vivek
    Molecular self-assembly is a powerful tool for the generation of functional nanostructures in a bottom-up fabrication. Peptides have drawn significant attention to be used as basic building blocks for such hierarchical assemblies. Diversification of chain stereochemistry offers tremendous increase in the peptide and protein design space. The use of D-amino acids in the peptide sequence can possibly help in accessing the otherwise “forbidden” region of the Ramachandran map for the generation of novel functional peptide sequences composed of L and D amino acids. In this thesis, we have de novo designed different sets of peptide molecules for four different application fronts. In the first project, we have designed a 30 amino acid long artificial blue fluorescent protein by impregnating an unnatural amino acid in the hydrophobic core of an altogether novel fold, which gives blue fluorescence. In the second project, we have designed syndiotactic hexamer peptide (Ff)3-OH, which folds into a gramicidin helical architecture, facilitating an extended phenylalanine network forming quantum confinement. In the third project, we have synthesized Fmoc conjugated ultra-short peptide hydrogels, with interesting self-healing property, which make them potential candidates for tissue engineering and drug delivery. The antimicrobial property of the synthesized peptide hydrogel has been verified against Gram-positive and Gram-negative bacteria.
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    Exploring Potential of Silk 3D Matrices for Bioartificial Liver and Regenerative Applications
    (2022) Janani, G
    Advanced liver cirrhotic patients are limited with liver transplants as the only therapeutic option; indeed, the practical applications of liver transplantation possess several drawbacks. The criteria for engineering 3D hepatic constructs for liver regenerative medicine are (i) cell-cell and cell-matrix interactions assisting long-term cell viability, (ii) heterotypic culture of liver cells maintaining cell functionality, (iii) long-term liver-specific synthetic, metabolic, and detoxification functions, and (iv) facilitating the regeneration of damaged tissue. A suitable 3D matrix with appropriate biocompatibility, hemocompatibility, topography, and physicochemical attributes facilitates hepatocyte aggregation, polarity, differentiation, and proliferation. Herein, mulberry Bombyx mori (BM) silk fibroin, non-mulberry Antheraea assamensis (AA) silk fibroin, and decellularized liver extracellular matrix (ECM) are explored in the domain of liver tissue engineering owing to their biochemical composition, mechanical stiffness, biocompatibility, and biodegradability. The presence of intrinsic RGD (arginine-glycine-aspartic acid) motifs and the high mechanical strength of AA silk fibroin has made it a potential biomaterial as it enhances cellular attachment and cell-matrix interactions. The prominent role of LECM hydrogel in liver tissue engineering has been emerging, owing to the presence of growth factors, cytokines, and cell-secreted exosomes.
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    Evaluation of Synthetic Ligands as Staphylococcal Nuclease Inhibitors for Potential Anti-MRSA Therapy
    (2023) Konwar, Barlina
    Mitigation of infections caused by methicillin-resistant Staphylococcus aureus (MRSA) is challenging as the pathogen is resistant to a large number of therapeutic antibiotics. Hence, there is an impending need to develop alternate and effective therapeutic approaches in order to counter life-threatening MRSA infections. The current study is an endeavor to address this important and contemporary issue and highlights the prospect of deploying rationally designed small synthetic ligands and target the staphylococcal nuclease enzyme or MNase, which is a key virulence factor present in the pathogen. The present study demonstrates that an anthraquinone-based ligand (C1) could render a non-competitive inhibition, decrease the turnover number as well as catalytic efficiency of MNase, with an IC50 value of 323 nM. A potentially therapeutic C1-loaded HSA nanocarrier (C1-HNC) was developed, which rendered a sustained and protease-triggered release of the payload in presence of the cell-free extract of a clinical MRSA strain. Interestingly, the eluates from the payload nanocarrier could significantly inhibit MNase-catalyzed DNA cleavage. In another study, it was demonstrated that a benzimidazole-based ligand C2 could significantly inhibit MNase, preserve the integrity of the DNA scaffold and promote higher sequestration of MRSA by DNA, which in turn, enhanced the uptake of the DNA-entrapped-pathogen by activated macrophage-like cells. In continuation of the efforts to identify synthetic MNase inhibitors, model in vitro experiments revealed that a napthalimide-based ligand C1 could inhibit MNase, enhance MRSA entrapment in DNA and mediate enhanced pathogen uptake by activated macrophage-like cells. A pluronic F-127 nano-micellar carrier loaded with C1 was developed, wherein the anti-adhesion activity of both the carrier as well as the payload was leveraged in tandem, resulting in significant inhibition of MRSA adhesion onto collagen. Interestingly, the biocompatible C1-loaded nano-micellar arsenal could also hinder MRSA biofilm formation on orthopaedic titanium wire. The present study contributes to the continuous endeavor of discovering anti-MRSA therapeutics and demonstrates the potential of synthetic MNase inhibitors that can not only curb the virulence of MRSA but also empower the host innate immune cells for effective mitigation of infections caused by the pathogen.
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    Understanding the Molecular Mechanisms for Alleviating Boron Deficiency in Indian Mustard
    (2022) Muthuvel, J
    "Boron (B) is an essential micronutrient required for the optimal growth and development of vascular plants. Globally B deficiency is the second most important micronutrient deficiency that causes significant yield reductions in crop plants. Often, seed yield and quality are compromised in plants grown under limited soil B availability without any apparent visual symptoms. B forms borate diester crosslinking with a pectic polysaccharide, rhamnogalacturonan II, during the cell wall formation and therefore, B deficiency primary affects meristem growth, vitality of the pollen grains, flower development and seed set. Brassica juncea is an important oilseed crop in India and other parts of the world and is extremely sensitive to B deficiency. Although the application of foliar B fertilizer improves the yield significantly in B. juncea, excessive application of B can be toxic due to the narrow window between its deficiency and toxicity. Molecular mechanisms of B transport have been initiated by the discovery of B transporters in Arabidopsis thaliana. Several aquaporins (AQP’s) and borate efflux transporter (BORs) family genes have been reported to be involved in the efficient uptake and translocation of B to maintain optimal plant growth under low soil B condition and B exclusion under high soil B conditions. Soil B content in major mustard producing states of India is potentially low and hence it is important to study the B transport mechanisms in B. juncea for the optimal yield.
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    In silico prediction of precursor microRNA in insects
    (2023) Nath, Adhiraj
    Pre-MicroRNAs are the hairpin loops from which microRNAs are produced that have been found to negatively regulate gene expression in several organisms. In insects, microRNAs participate in several biological processes including metamorphosis, reproduction, immune response, etc. Numerous tools have been designed in recent years to predict novel pre-microRNA using binary machine learning classifiers where prediction models are trained with true and pseudo pre-microRNA hairpin loops. Currently, there are no existing tool that is exclusively designed for insect pre-microRNA detection.
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    Functional elucidation of CRISPR-Cas I-B interference machinery of Leptospira interrogans
    (2023) Hussain, Md Saddam
    Leptospira interrogans is the causative agent of leptospirosis, a zoonotic disease accounting for approximately 60,000 human deaths every year globally. The leptospires show incompetence to conventional genetic manipulation tools, and therefore, the molecular mechanism of its pathogenesis remains poorly comprehended using the reverse genetics approach. One possible reason for its incompetence in genetic manipulation is the presence of the CRISPR-Cas system in its genome. A CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) is an RNA-directed inheritable adaptive immunity in prokaryotes against invasive mobile genetic elements (MGEs), including bacteriophages and plasmids. The system encodes an effector complex (Cascade) that utilizes small crRNA (CRISPR RNA) to sense and interfere with the invasive MGEs having the crRNA-complementary sequence next to a protospacer adjacent motif (PAM). The predominant CRISPR-Cas type I-B system, marked in several pathogenic Leptospira genomes, presents a promising alternative to be explored as an endogenous genome editing tool. Moreover, to exploit Leptospira’s CRISPR-Cas type I-B (Lin_I-B) system for targeted genetic manipulation, characterization of its interference machinery and associated PAMs is a prerequisite. To this end, the present study reports the molecular and functional characterization of interference machinery of a Lin_I-B system, recently identified in L. interrogans serovar Copenhageni strain Fiocruz L1-130. The comprehensive biochemical analysis of the LinCas7, a major subunit of the Cascade, revealed it to be a Mg2+ ion-dependent non-specific endoDNase, unlike other Cas7 family proteins. Moreover, LinCas7 exhibits distinct binding to crRNA in the presence of Mg2+ ions, testifying its canonical role in Lin_I-B defense response. The molecular characterization of LinCas8b disclosed it as a genetic fusion of large (LinCas8b) and small subunit (LinCas11b) proteins of the Cascade (LinCascade). In this study, LinCas11b is demonstrated to co-translate from an in-frame internal translation start codon encoded within the lincas8b gene. LinCas11b displays structural and functional analogy with the well-studied Cas11 family proteins. In addition, the interference machinery of the Lin_I-B, when expressed in a surrogate host E. coli, was able to annihilate the target DNA with the predicted PAM. In sum, the current study presents the molecular and functional insight of the Leptospira subtype I-B interference machinery that, soon, may pave the way for scientists to harness the system as a programmable endogenous tool for genetic manipulation.