Open Access Repository of Indian Theses

Tatta, Eswara Rao

 xi  Summary  Nosocomial infections are severe in nature and a challenge to treatment due to the emergence and extent of multidrug-resistant nosocomial pathogens, such as Staphylococcus aureus, Escherichia coli, Acinetobacter baumannii, Klebsiella pneumonia, Pseudomonas aeruginosa, and Enterococci spp. The vancomycin-resistant Enterococcus faecalis (E. faecalis) is widely distributed globally in hospital environments as an opportunistic pathogen which can cause a wide range of infections like bacterial meningitis, urinary tract infections, endocarditis, surgical site, and bloodstream infections. The propensity of Enterococcus faecalis to form biofilms by regulating gene expression through quorum-sensing mechanisms is a fundamental element in its pathogenicity. Understanding the role of biofilm formation and quorum sensing in antibiotic resistance is crucial for developing effective strategies to combat infections caused by E. faecalis. In this thesis, we have performed in silico, in vitro, and transcriptome profiling through combinatorial treatment approaches for disrupting biofilm, inhibiting quorum sensing signaling, and developing alternative treatments for biofilm-associated infections for potential drug discovery against E. faecalis infections. The novel phenol (Rubrivivaxin) and indole (Rhodethrin) terpenoid compounds target the preliminary adherence phase of the biofilm development by hindering the cell surface hydrophobicity and extracellular polymeric substance (EPS) production, which is highly resistant to harsh environmental conditions and antibiotic therapy. These terpenoid derivatives (Rhodethrin (Rdn) and Rubrivivaxin (Rbn)) were found to have the antibacterial activity to inhibit bacterial growth as well as the motility of bacterial colony migration and expansion, which are used to control the infections associated with biofilm production. The characteristic feature of the EPSs is to form a protective defense and provide nutrients to the encased biofilm developed microorganisms. These molecules inhibit biofilm formation and disrupt the ultra-structure of biomass. Chloramphenicol has become an attractive antibiotic against E. faecalis due to its antimicrobial and antibiofilm efficacy. However, combining natural indole terpenoid compounds with antibiotics can often lead to synergistic effects, where the combined activity is greater than the sum of their individual effects.  Our results show the in silico and in vitro antimicrobial and antibiofilm activities of Rhodethrin and chloramphenicol against E. faecalis in isolation and combination. Further, we confirmed the efficacy of their mechanism of action on biofilm. After the synergistic combination treatment, they significantly reduced the viable cell count, dry  xii  weight, protein, and eDNA concentrations in matured biofilm. The respective biofilm proteins were found to be 39.7±5.1% (Rhodethrin), 32.6±4.7% (Chloramphenicol), and 69.0±5.3% (Rdn-Chpl) (p ˂ 0.05). Reduction of EPS was found to be 34.6±4.6% (Rhodethrin), 31.0±5.2% (Chloramphenicol), and 76.0± 4.5% (Rdn-Chpl) (p ˂ 0.05). Reduction of EPS was found to be 34.6±4.6% (Rhodethrin), 31.0±5.2% (Chloramphenicol), and 76.0± 4.5% (Rdn-Chpl) (p ˂ 0.05) significantly inhibited the biosynthesis of EPS. Thus, the combination of Rdn and Chpl shows a high activity as compared to individual treatment of E. faecalis. The inhibitory effect on EPS biosynthesis indicates that the combination treatment disrupts the production of key components required for biofilm formation. The synergistic inhibitory effect of Rhodethrin and chloramphenicol on the construction of biofilm and EPS biosynthesis in E. faecalis highlights the potential of using combination therapies to combat biofilm-associated infections. These results show an enhanced activity of the combination compared to the individual treatment. The combination of Rdn and Chpl could be a promising therapeutic strategy to improve treatment efficacy against E. faecalis biofilms. We have performed microscopic analysis to visualize and confirm the effects before and after the treatments. Our observations confirmed that combination treatment led to greater dispersal of bacterial cells, resulting in decreased cell clustering and aggregation within the biofilm matrix. Understanding the mode of action of Rdn in disrupting biofilm formation and inhibition of EPS biosynthesis would provide valuable insights into developing more effective therapies. This dispersal effect indicates that the combination treatment disrupts the bacteria to adhere and form cohesive structures within the biofilm. The total EPS dry weights were estimated to be 97.50 µg/g (Control), 58.37 µg/g (Rhodethrin), 62.04 µg/g (Chloramphenicol), and 23.58 µg/g (Combination). The EPS protein concentrations were 80.88 µg/g (Control), 19.41 µg/g (Chloramphenicol), 15.53 µg/g (Rhodethrin), and 8.84 µg/g (Combination) (p ˂ 0.05). Thermogravimetric and X-ray analysis revealed the pyrolysis of polysaccharide crystals and crystalline domains to be 40-60% and that of amorphous domains to be 60-75% of EPSs distractions. On the other hand, FTIR analysis shows the presence of functional groups (hydroxyl, aliphatic CH2, asymmetrical C=H stretching, aliphatic methyl, and primary amine groups), and LCMS analysis shows the disintegration of biopolymeric EPS components. The SEM analysis of EPSs witnessed a condensed matrix within polymeric carbohydrate and filamentous structures. These results show  xiii  the degradation of high molecular biopolymers into low or intermediate by-products of EPS. This treatment disrupted EPS composition and inhibited biofilm formation in E. faecalis cultures. Further, to evaluate the effects of Rhodethrin in combination with chloramphenicol on E. faecalis cultures, identified the differentially expressed genes (DEGs). In the transcriptome analysis, out of 379 differentially expressed genes, 264 genes were significantly down-regulated, indicating that 69.69% of the E. faecalis genome was altered. These differentially expressed genes included 448 genes in Control Vs. Rdn, 1591 in Control Vs. Chpl, and 379 in Control Vs. Combined (Rhodethrin and chloramphenicol). qRT-PCR was used to analyse the transcriptional sequence data further. The results demonstrated that the treatment significantly suppressed the expression profiles of four genes involved in antibiotic resistance (liaX, typA, EfrA, and lepA), three genes expressed in quorum sensing (camE, fsrC, and sylA), and five genes were essential for biofilm formation (Ace, AtpB, lepA, bopD, and typA). This transcriptome analysis suggested that Rhodethrin and chloramphenicol might have different action mechanisms for inhibiting biofilm formation and quorum sensing in E. faecalis. The chloramphenicol disturbs the biofilm formation and inhibits the synthesis of enterococcal surface protein (ESP), faecal streptococci regulator-C (fsrC), adhesion of collagen of E. faecalis (Ace), biofilm on plastic (Bop) proteins and polysaccharides associated with biofilm formation, promotion of cell aggregation and adherence to surfaces. Whereas, Rhodethrin induces the inhibition of outer membrane protein (liaX), mediating cell membrane remodeling, camE encoding sex pheromone associated with quorum sensing, and large extracellular protease (lepA) associated with virulence expression. The above findings stated that the combination of Rhodethrin and chloramphenicol had shown great promise in inhibiting biofilm encasement, quorum sensing, and antibiotic resistance of E. faecalis. Combining these two compounds is more effective at inhibiting biofilm formation than using either compound. These findings suggest the potential use of this combination as a therapeutic approach to combat E. faecalis infections by targeting multiple aspects of the bacterial phenotype. However, further research is needed to uncover the underlying mechanisms and optimize the treatment strategy for clinical application. 

English

Synergistic Studies of Rhodethrin and Chloramphenicol on the Biofilm Architecture, Antibiotic Resistance and Quorum Sensing against Enterococcus faecalis

Hajra, Dipasree

xxiii  SYNOPSIS Synopsis of work done by Ms. Dipasree Hajra (SR No. 03-04-00-10-11-18-1-15842) for the award of Ph.D. degree in the Faculty of Science, Indian Institute of Science, Bangalore, India. Thesis Title: Understanding the mechanism of host deacetylases SIRT1 and SIRT3 in the modulation of Salmonella pathogenesis  Chapter 1  Introduction Salmonella continues to be a threat to the human population by taking a toll on the lives of about 20,000 individuals globally per year. Salmonella enterica serovar Typhimurium is a facultative intracellular Gram-negative enteric pathogen, causing a wide array of infections ranging from self-limiting gastroenteritis to diarrhoea in humans. Salmonella enterica serovar Typhi cause systemic infection in humans with typhoidal symptoms. Recent reports reported 21 million typhoid cases and 93 million non-typhoidal cases year-round. The virulence of Salmonella is majorly regulated by two pathogenicity islands, namely, SPI-1 and SPI-2. It uses SPI-1 encoded T3SS and the effector proteins to invade host cells.  Inside the macrophages, they reside within the Salmonella-containing vacuoles (SCV) by virtue of its SPI-2 effectors. Macrophages, dendritic cells, and neutrophils are responsible for successful dissemination throughout the body through the reticulo-endothelial system (RES).  Sirtuins are NAD+-dependent deacetylases that are present in all forms of life. Saccharomyces cerevisiae serve as the founder for the discovery of Sir2. Sirtuins comprise a conserved core catalytic domain that removes acetyl moiety from the lysine residues of proteins in the presence of NAD+ as a cofactor giving rise to 2’O-acetyl-ADP-ribose and free nicotinamide as products. xxiv  Host Sirtuins are one of the important modulators of host immuno-metabolic regulation. However, the role of Sirtuins in the modulation of the immune metabolism pertaining to Salmonellosis is largely unknown. Here, we investigated the role of two important Sirtuins, SIRT1 and SIRT3 in the modulation of Salmonella pathogenesis. We have shown that Salmonella-induced modulation of SIRT1 and SIRT3 is crucial for governing immune-metabolic switch in the host and this switch influences the metabolic profile of intracellular Salmonella (Chapter 2).  Moreover, SIRT1 and SIRT3 regulate the mitochondrial bioenergetics and dynamics in the S. Typhimurium infection scenario. SIRT1 and SIRT3 mediated alteration of mitochondrial bioenergetics help in the maintenance of intracellular pH of both the host and the bacteria, thereby influencing the bacterial intracellular niche (Chapter 3). In in vivo model of mouse infection, SIRT1 and SIRT3 have been shown to regulate Salmonella dissemination in blood and other secondary organs. However, O. splanchnicus gut colonization reversed the Salmonella-associated dissemination in mice. (Chapter 4). Chapter 2 Salmonella-induced SIRT1 and SIRT3 are crucial for maintaining the metabolic switch in bacteria and host for successful pathogenesis                     We have elucidated the role of SIRT1 and SIRT3 in mediating metabolic switch in Salmonella and its implication in establishing pathogenesis. Our study indicated the ability of the live Salmonella Typhimurium to differentially regulate the levels of SIRT1 and SIRT3 for maintaining the high glycolytic metabolism and low fatty acid metabolism in Salmonella. Upon SIRT1 or SIRT3 knockdown or inhibition, the metabolism in intracellular Salmonella switched to high fatty acid oxidation and low glycolysis. This switch led to decreased proliferation of Salmonella in the macrophages. Further, Salmonella-induced higher levels of SIRT1 and SIRT3 led to a skewed polarization state of the macrophages from a pro-inflammatory M1 state xxv  toward an immunosuppressive M2 making it more conducive for the intracellular life of Salmonella. Alongside, immunological functions by modulating p65 NF-κB acetylation, SIRT1, and SIRT3 also skew Salmonella-induced host metabolic switch by regulating the acetylation status of HIF-1α and PDHA1. Interestingly, though knock-down of SIRT1 and SIRT3 attenuated Salmonella proliferation in macrophages, in in vivo mice-model of infection, inhibition of SIRT1 and SIRT3 led to more dissemination and higher organ burden which can be attributed to enhanced ROS and IL-6 production. Our study hence reports for the first time that Salmonella modulates SIRT1 and SIRT3 levels to maintain its own metabolism for successful pathogenesis. Chapter 3 SIRT1 and SIRT3 mediated modulation of mitochondrial bioenergetics and dynamics during Salmonella infection in macrophages skews both host and bacterial intracytosolic pH Mitochondria are considered to play a central role in the regulation of host cellular processes and host responses pertaining to bacterial infections. Numerous microbial pathogens modulate mitochondrial functions and dynamics to evade host immune responses. On the other hand, the elicited host immune responses are dependent on the overall mitochondrial bioenergetics and their function. Thus, mitochondrial health is a crucial determinant for the outcome of several bacterial infections. We have explored the role of host deacetylases SIRT1 and SIRT3 in the modulation of mitochondrial bioenergetics and dynamics pertaining to Salmonella infection. Here, we show that inhibition of SIRT1 or SIRT3 function either by shRNA-mediated knockdown or by the application of specific catalytic inhibitors leads to increased mitochondrial dysfunction in the Salmonella-infected macrophages. We have shown that inhibition of SIRT3 function leads to increased production of mitochondrial superoxide xxvi  generation in the infected macrophages. The increased mitochondrial ROS generation in the infected macrophages coincides with mitochondrial membrane hyperpolarization, increased proton leakage and respiration rate, and a decline in ATP production and ETC function. The mitostress profile suggested an overall increase in respiration parameters such as basal respiration, non-mitochondrial respiration, proton leakage and ATP-linked respiration along with an increase in Extracellular Acidification Rate (ECAR) upon both SIRT1 and SIRT3 inhibitor treatment. The mitochondrial bioenergetic alteration triggers increased acidification of the macrophage cytosolic pH which in turn skewed the intra-bacterial pH of the intracellular bacteria within the SIRT1 and SIRT3 knockdown and inhibitor-treated macrophages. Here, we show that loss or inhibition of SIRT1 or SIRT3 trigger increased acidification of the macrophage cytosol which consequently lead to a loss in intra-bacterial acidification together resulting in decreased SPI-2 gene expression. Alongside the decline in mitochondrial bioenergetics, the S. Typhimurium infected macrophages depict alteration in mitochondrial dynamics with increased mitochondrial fission and mitophagy alongside decreased mitochondrial fusion dynamics. Together, our results suggest the role of SIRT1 and SIRT3 in preserving the mitochondrial bioenergetics and dynamics in S. Typhimurium infection scenario and thereby influencing the bacterial intracellular niche. Chapter 4 Odoribacter splanchnicus mitigates Salmonella-induced gut inflammation and its associated pathogenesis in mice  The existence of the gut vascular barrier (GVB) acts as a protective barrier against the entry of microorganisms into systemic blood circulation. Enteric pathogens such as Salmonella enterica can cross the mucus and intestinal epithelial barrier, ultimately leading to GVB damage and systemic dissemination. The gut microbiota plays another major role in the maintenance of the xxvii  intestinal epithelial barrier by the production of several metabolites such as Short-chain fatty acids (SCFAs), indoles, and polyphenol metabolites that contribute to epithelial barrier integrity and turnover by regulating the expression of Tight-junction (TJ) genes. Our previous study reported an incidence of increased Salmonella dissemination in blood, liver, and spleen upon SIRT1 and SIRT3 inhibition owing to the increased inflammatory response. Here, we aimed to understand this exact mechanism of Salmonella dissemination and whether colonization with a gut commensal like Odoribacter splanchnicus could ameliorate the increased Salmonella-induced inflammation and in turn its pathogenic dissemination. Odoribacter splanchnicus, belonging to the order Bacteroidales, is a common, member of the human intestinal microbiota and its decreased abundance has been linked to different microbiota-associated diseases, such as non-alcoholic fatty liver disease, cystic fibrosis and inflammatory bowel disease (IBD). Our study depicts the capability of O. splanchnicus in reversing the Salmonella-associated pathogenesis in mice. O.splanchnicus  gut colonization mitigates the Salmonella-associated epithelial tight junction disruption by restoring epithelial tight junction function and by preventing gut vascular barrier disruption, angiogenesis, and inflammatory response.  Conclusion and Significance Salmonella-induced SIRT1 and SIRT3 together play a pivotal role in the maintenance of the intracellular replication niche of Salmonella Typhimurium by regulating both host and bacterial metabolism and via the modulation of mitochondrial bioenergetics and dynamics within the infected macrophages. In in vivo mice model of infection, inhibition of SIRT1 and SIRT3 led to more dissemination and higher organ burden which can be attributed to enhanced ROS and IL-6 production. O.splanchnicus, a gut commensal,  gut colonization reverses the Salmonella-associated pathogenesis in mice by restoring epithelial tight junction function, inhibiting the inflammatory response, and preventing gut vascular barrier disruption. 

Understanding the mechanism of host deacetylase SIRT1 and SIRT3 in the modulation of Salmonella Pathogenesis

Rose, Biju Ben

iii  ABSTRACT  A laboratory-scale scramjet thruster was the subject of an experimental investigation to determine the effects of a strut extending across the width of a single expansion ramp. The strut was positioned on the expansion ramp's surface twice: once in the middle of the ramp's span and once at the ramp's trailing end. The trials were carried out at each of the six strut heights using six different thruster pressure ratios (TPR), or ratios of inlet total pressure to ambient pressure, ranging from 5 to 10. The thruster's internal wall pressure distributions and the Schlieren images of the flow were experimentally obtained. It was investigated if it would be possible to control a hypersonic vehicle that typically uses aerodynamic control by adding a strut as a secondary device in the thruster. The combustor's inlet Mach number was 1.8. An isolator, a diverging area combustion chamber, and a single expansion ramp made up the thruster model. A supersonic nozzle with a rectangular exit that matched the proportions of the rectangular isolator provided the flow for the thruster's inlet. The bottom wall of the rectangular diverging combustor was flat, and the upper wall inclined the bottom wall by 2.44 degrees.  The wall pressure was measured at various points between the ramp trailing edge and the combustor inlet. The Schlieren pictures were utilized to study the shock pattern, and it was found that an increase in strut height resulted in a downward deflection of the exhaust. Two-dimensional side force and pitching moment coefficients were computed from the wall pressure distribution, and the influence of strut height variation on the aforementioned coefficients was shown. The presence of the strut produced observable changes in side force and pitching moment, according to experiment results. The increase in strut height produced changes in the direction of the exhaust stream, which may be helpful when steering vehicles powered by scramjets. iv  At all expansion levels of the ramp nozzle, or for all the TPRs used in the current investigation, higher strut heights led to an increase in the side force coefficient (5 to 10). Similar to how the side force coefficient varied with strut height, the pitching moment coefficient did as well. The nature of these variations remained the same when the strut was moved from the expansion ramp's tail end to the ramp's middle location. Although the majority of these variations were nonlinear in nature, the degree of nonlinearity varied depending on the TPR value. At TPRs 5, 9, and 10, there was a greater nonlinearity in the variation of the side force coefficient. When compared to the ramp tail end location, the moment coefficients for the strut's mid-ramp position were larger at lower TPR. Ramp surface flow was noticeably deflected downhill by tall struts. Schlieren’s pictures revealed a downward deflection in the exhaust flow over the expansion ramp, with the position and height of the struts having an impact on the deflection's size. The aforementioned studies were conducted again for ramp inclination angle ranges of 0 to 8 degrees.   In terms of side force and moment coefficients over the scramjet thruster, the results were compared for various TPRs, strut position, strut height, and ramp inclinations. Larger jet deflections were seen at practically all TPRs when comparing the near trailing edge position of the strut on the expansion ramp to the mid-length position. The expansion ramp had larger pressure peaks as a result of the taller struts, which altered the side force coefficient. Large strut heights also resulted in bigger pressure zones on the expansion ramp when the strut was positioned in the middle of the ramp. An increase in ramp inclination angle resulted in a decrease in flow deflection angle when struts were present (downward). This was noticed at every TPR.  

EXPERIMENTAL STUDIES ON INTERACTION OF A SUPERSONIC FLOW WITH A STRUT PLACED ON AN EXPANSION RAMP

Mane, Harshali Dnyaneshwar

ABST'ITACTClobal Positioning Systenr (GPS) is one of the rnost widely used r,virelesssystems for navigation. A CiPS receiver has to lock on the satellite signals to calculateits positiott.'l'hc proccss o1'locking and tlacking satellites recluires lreavycorrputation" which consLlrnes both tirne ancl power. The dissertation fbcuses tlredesign and developrnent clf fast and LrninterrLrpted low porner consurning softwarebased CPS rece iver under the cornpressive sensing fiarnework. Ciornpressive serrsingis recently developcd technique that exploits the sparsity,ness ol'the sigrral andaccluircs a sigrral w ith lcss nr.rrtrber of sarnple s and reconstrurct tlre signal r,r,ithoptirnization techniqLres. 'l'lris thesis addresses the developrnent of-various algorithrnsthat inclLrdes (a).srrb ,surnJtlcd Fu.st Fourier 7-runsfbrnt (.s.yFFT) bu,sed GP,\ uc't1ui.;itionalgorithm und lntprrt,cd.s,;l'-l;T bu.sed (iPS uc'qui.sition (b),\ub runtplerl huscd (i[',\trucking ulgorithnt (c) ^r,iI-FI bu,yetl cornpleta SGR tlesign (d) Sub-,yuntplad KulmrtnFillcr bu,yctl GP.\ truc'king ulgorithm and (e) vulitlulion of ltrolto.serl .s1,.y1c171.AcqLrisition is Inost inrportarrt process arrd a challenging tasl< tbr identifyirrgvisible satellites in desigrring sofnvarc CPS receiver.'['his research presents fhsterCPS accluisition via ssFF'l-.'l'his algorithrn cxploits the properties ol Fourier'translbnn. decimator and sparsc FF-f. that redLrces the number of'conrputatiorrs.'l'hecomputational complcxitl* of ;lroposecl algorithnr is 'cl log cl' tirnes lhster tharr theconventic'rt.tztl [-'Fl- basccl acrprisition algorithrn. ulrere 'cl' is an integcr clou,n sant;llinuf-actor. Tlre sitnulation results shows that tlre con"rpLrtation tirne fbr accluisition is8.5571 tirres fastu'tlian tliat olconverttional [rFT'based algorithrn 1or down sarnplingrate d 12.l-lrc tnain goal ol'tracking is to slnchrrrrrize a localll' generatcd PRN code(C/A codc) or replica r:rf the transrlitted PRN code with the incoming signal which issarne iis the accluisition.'l-his thesis desigr-ls an effective and ef'llcient trackirrgalgoritlrnr based ou .sub-sunrplcd tcc'hniqtrc it"t tirne domain and litcuses ondemodLrlation o1' (lPS signal rvith less trackins collpLttation tirne. 'l'he proposedalgorithnr cxploits the propertv o1'recentll, dcveloped Randorn Dernodulator whichellicientll' extract the f'catures o1- received sigrral arrd lras an irnproved in cortrputatic'rntirre by, 31.022% against the convention tracking based algoritlrrr.'l'he rcsealch fbcLrses on design and cievelopment ol courplete SLtb-sarnpled betsed SofiwaleI)eflned GPS Ileceivcr (ssS(ilt) thiit conrbincs the sub-sampled based accluisitiott. sLrb-sanrplecl based ptrll-in-treclLrencv and sub-sarnplecl basecl tracking algorithrns. [:or sallplinglreqrrency. /, I Mtiz Qrc:t1ui.;itiori) and 5 Mtlz (pull in li'equcnt:.1t). resultingconrputation titre is 7' ,i.4684sec. resr-rlting tirne irnprovelrent by l9.l4o%. fler thesigrral is tracked vvith loss o1'llrst 100 sanrples but it is recovered after 100 samples.FLrrther this rescarch clesign a CPS carrier tracking usirtg sttb .scttnpled Kulntun/ittar bu,;ctl l'-l-1. u.;.;i.vletl I'L.L tbr processing a rveak carrier signals durirrsscintillation. Cornpared with tlre traditional PLL.. sLrb sarrpled KF PL.L varies thebandw,idth depending upou thc noise. RcsLrlts slrow tlral the considered s)'stcttt ctlttoperate corrtinuor-rslr, rvilhoLrt losins phase lock cven over pcriods ol-signal otttage. lnsirnulation. visible satellites with a I'}RN 6. 10. 17.23.26.28 channels are acqttiredand are completely tracked. F-or PRN r.rurnber 28. due tolS0"plrase nreasurementerrors. loop started to slip half cycles. and eventually'it complctely lost carrier lock.'l'he sub sarnpled Kaln'rnn based P[.L. starts trl have signilicant problelns when the 1wo[1:p]clouds approach close enough to tlrc origin to callse thc phase lreastlretleltterror standard deviation to be a signillcarrt fl'action of 90". Thtrs. sLrb sanrpled Kallnanbasecl t,t-1. r,r,ill track rnore robustll dLrring scirrtillation indLrced powt:r facies than aPL.L. l6r a sigrral that carries data hits.'I'he navigation positiorr is calcLtlated b1'processing data obtairrecl liorn proposed acquisition and lracking algttrithrrs.'l'he pe rttrnrancc ol- the ssF F'l- based CPS accluisition is cotrpared arrdevaluated using ditfbrcnt sigrral to noise ratios.'l-he Validation ol'proposed algoritlrrnsis done Lrsing rrultipath eltects and b1'adding different signal to noise ratios. Theperfbnnances ol'the ssl-'FT based GPS Acrlrrisitiorr arc cr)nrpared and evaluated usillgdilferent Signal to noise ratios (SNR) in harsh environrnental conditions. Tlresimulation results slrou,that thc corrsidered systetn can operate continuously witlrotrtlail cven with very'wcak Cil'}S sigrrals. Sarre accprisition results have been obtainedwith SNR valLres of -10 dt]. -ti dtl. -5 dB. -4 dB. -ldB. -ldB and ldEl tbr strbsarnplirrulacror of-0. 2. zl. (r. tl. l0 arrd l2 respectively. The proposed algorithrr contibtttestorvards tlre exact positionirrg rcquired irr varioLrs applicatiorrs sttch as llsherrrart. cellphones. rtr issi le gLr idance. veh icle trackirrg. ancl disaster' llletl.)agelncllt.

Design and Development of software based GPS receiver using compressive sensing

M, Karuppusamy

  Abstract   423   ABSTRACT  -------------------------------------------------------------------------------------------------------------------------- Name of the Student: M. Karuppusamy Registration No.: 10CC16A11003 Faculty of Study: Chemical Sciences Year of Submission: 2023 AcSIR Academic Centre/CSIR Lab:  CSIR - Central Leather Research Institute Name of the Supervisor: Dr. S. Easwaramoorthi Name of the Co-Supervisor: Dr. V. Subramanian Title of the Thesis: Rational Design and Development of Organic Electronic Materials using Density Functional Theory Methods ---------------------------------------------------------------------------------------------------------------- One crucial aspect of designing organic energy materials is understanding the role of molecular structures and their impact on their properties. In this thesis, an attempt has been made to develop the structure-property relationship by considering examples of different organic electronic materials with application potential in harvesting solar energy and organic light-emitting diodes through computational chemistry methods. Fundamental challenges in the design and development of organic electronic materials and the scope of the investigation are presented in Chapter 1.   The possible development of a structure-aromaticity-conjugation spectroscopy relationship (SACSR) is presented in Chapter-2.  Chapter 3 presents the design of a series of organic dye molecules using ullazine and perylene employing D-π-A topology, with ullazine analogs as donors and perylene dicarboxylic anhydride as an acceptor along with acetylene linker as π-bridge for DSSC applications. The findings will be beneficial in designing efficient and cost-effective organic dyes for solar energy conversion.   A comprehensive investigation into the optoelectronic properties of electron donor-based molecules, having Isoindigo (IIG) moiety for their potential application in efficient OSCs is described in Chapter 4. Findings highlight the potential of central group modifications and spacer effects in enhancing the efficiency of organic solar cells for the D2-A-π-D1-π-A-D2 framework. These findings contribute to the ongoing development of sustainable and efficient solar energy technologies based on organic materials.  Chapter 5 focuses on the design and characterization of a series of triazine-based systems for OLED applications utilizing the TADF mechanism. The molecules investigated include diphenylamine (DPA), triphenylamine (TPA), carbazole (Cbz), indolocarbazole (ICbz), dimethyl acridine (DMAC), phenoxazine (PXZ), phenothiazine (PTZ), diphenyl acridine (DPAC), diphenyl azasiline (DPAS), spiro acridine fluorene (SAF), and spiro silole azasiline (SSiAS). The findings point out the potential of these molecules as blue emitters and underscore the importance of further investigations to optimize their performance and efficiency. The insights gained from this research contribute to the advancement of organic electronics, specifically in the development of high-performance OLED devices.  Chapter 6 summarizes the primary results and conclusions that were derived from the present investigation.  

Rational Design and Development of Organic Electronic Materials Using Density Functional Theory Methods

Srivastava, Shikha

Investigating the Role of Signal Transducer and Activator of Transcription 3 (STAT3) in Dengue Virus Propagation    Dengue fever is an arthropod-borne viral infection affecting millions of people annually during the breeding season of its vector mosquito. To date, no specific antiviral drug or vaccination is invented to fight against dengue virus. Since viruses depend on host factors for their propagation, recent approaches to developing antivirals include targeting host factors for inhibiting viral propagation. DENV has developed several co-existing strategies to avoid eradication by the host antiviral mechanism. DENV modulates host interferon response by attenuating its components, inhibiting their activation or promoting their degradation. This dissertation summarizes the studies we carried out to identify the role of a host transcription factor; STAT3 in dengue virus propagation to identify its potential as a suitable antiviral target. We first wanted to understand how DENV manipulates STAT3 induced interferon response to its benefit. By utilizing various cell culture techniques, we found that STAT3 is increased and activated in DV-2 infected A549 cells and knocking it out resulted in a substantial decrease in viral protein production and viral replication. Our results also demonstrated that DV-2 purposefully manipulates STAT3, which negatively regulates type I IFN signaling, to avoid host interferon response. These results thus established the role of STAT3 as a proviral factor. Moving ahead, we explored the potential of STAT3 inhibitor stattic as an antiviral agent. For this we performed a whole proteome analysis of infected cells by high throughput liquid chromatography mass spectrometry (LC-MS), wherein we observed that treatment with stattic induces multiple host defense mechanisms to counteract dengue infection. We also observed that treatment with stattic downregulates several pathways involved in viral transcription. Taken together these results suggest that inhibiting STAT3 by stattic or its derivatives may prove to be an effective strategy for the development of antiviral interventions.  Furthermore, to identify residues of STAT3 for the development of novel therapeutics we explored its interaction with some of the viral proteins translocating into the nucleus e.g., capsid and NS5 we identified some critical residues which mediate the interaction of STAT3 with viral NS5 protein. Since both STAT3 and NS5 are important antagonists of human innate immune response we propose that targeting the residues which mediate their interaction may aid in the screening of alternative antivirals against dengue. Overall, this study strongly indicates the regulatory role of a host transcription factor STAT3 in modulating viral propagation that may be targeted for the development of effective antiviral therapeutics.   

Investigating The Role of Signal Transducer and Activator of Transcription 3 (STAT3) in Dengue Virus Propagation

Singla, Sushil

BIRKHOFF-JAMES ORTHOGONALITY AND DISTANCE FORMULAS IN C∗-ALGEBRAS ANDFOR TUPLES OF OPERATORSThis thesis is devoted to the study of Birkhoff-James orthogonality in C∗-algebrasand its applications in finding some distance formulas. We start with a thorough survey on the literature of Birkhoff-James orthogonality in the first chapter. Motivatedfrom the characterizations of Birkhoff-James orthogonality in the space of continuousfunctions on a compact Haudorff space and the space of matrices, we prove a characterization of Birkhoff-James orthogonality in general C∗-algebras and Hilbert C∗-modules. We provide three different proofs of our characterization with different themes in thesecond chapter. It is shown that most of the results in the first chapter follow as applications of our characterization. Some new theorems are also proved. In the third chapter, applications of our characterization in the geometry of Banach spaces are mentioned and connection of orthogonality characterizations and distance problems is discussed. In the fourth chapter, we show the applications of our results for finding characterizations of orthogonality for tuples of operators. We also provide a distance formula in terms of variance of tuples of operators. Various possible directions for future work are mentioned throughout the thesis and are collected at the end for easy reference.

Birkhoff-James Orthogonality and Distance Formulas in C∗-Algebras and for Tuples of Operators

Roychowdhury, Prasun

Study of Poincaré-Hardy type inequalities and eigenvalue problems for second-order elliptic PDEs  The major text of this thesis is studying Poincaré-Hardy and Hardy-Rellich type inequalities on one of the most discussed Cartan-Hadamard manifold namely hyperbolic space and studying eigenvalue problems for second-order elliptic PDEs. The thesis is divided into two parts. In the first part we have centralized our attention on the following three problems:  • On some strong Poincaré inequalities on Riemannian models and their improvements. • On higher order Poincaré inequalities with radial derivatives and Hardy improvements on the hyperbolic space. • Hardy-Rellich and second order Poincaré identities on the hyperbolic space via Bessel pairs. In the second part we have focused our essence on the following two problems: • Generalized principal eigenvalues of convex nonlinear elliptic operators in RN. • On ergodic control problem for viscous Hamilton-Jacobi equations for weakly coupled elliptic systems. 

Study of Poincaré-Hardy type inequalities and eigenvalue problems for second-order elliptic PDEs

CHAUDHARY, NIDHI

 Deciphering the Mechanism of a Host Cellular Factor High Mobility Group Box1 Protein in Dengue Virus Pathogenesis   Dengue disease is a highly prevalent mosquito-borne infection-causing millions of infections annually. The global rapid emergence and distribution of dengue in tropical and sub-tropical regions are exposing almost half of the world’s population to the threat. Dengue virus (DENV) causes the overexpression and secretion of many proinflammatory cytokines, including high-mobility group box-1 protein (HMGB1). HMGB1 is the most abundant, extremely conserved, ubiquitously expressed nuclear protein that executes the localization-dependent function. HMGB1 translocation and secretion have been implicated in many chronic infections, metabolic disorders, cancer, and viral and inflammatory diseases. In this study, we explored the contribution of HMGB1 in dengue virus replication in A549 cells. Results showed that HMGB1 is translocated and secreted out during dengue infection. Moreover, blockage of HMGB1 release using ethyl pyruvate resulted in enhanced dengue replication and the knockdown of HMGB1 abolished viral replication. In-silico, in-vitro assays, and co-immunoprecipitation revealed the binding of HMGB1 to both untranslated regions of viral RNA. This interaction further induces the expression of proinflammatory cytokines like TNF-α, IL-6, and IL-1β which contributes to the severity of DENV disease. Therefore, our study suggests that the DENV tweaks HMGB1 translocation and its interaction with the DENV genome to stimulate proinflammatory cytokines expression in A549 cells.  DENV exploits various cellular pathways including autophagy to assure enhanced virus propagation. The mechanisms of DENV-mediated control of the autophagy pathway are largely unknown. Our investigations have revealed a novel role for HMGB1 protein in the regulation of the cellular autophagy process in the DENV-2 infected A549 cell line. While induction of autophagy by rapamycin treatment resulted in enhanced DENV-2 propagation, the blockade of autophagy flux with bafilomycin A1 suppressed viral replication. Furthermore, siRNA-mediated silencing of HMGB1 significantly abrogated DENV-induced autophagy, while LPS-induced HMGB1 expression counteracted these effects. Interestingly, silencing of HMGB1 showed a reduction of BECN1 and stabilization of BCL-2 protein. On the contrary, LPS induction of HMGB1 resulted in enhanced BECN1 and a reduction in BCL-2 levels. This study shows that the modulation of autophagy by DENV-2 in A549 cells is HMGB1/ BECN1 dependent. In addition, glycyrrhizic acid (GA), a potent HMGB1 inhibitor suppressed autophagy as well as DENV-2 replication. Altogether, our data suggest that HMGB1 induces BECN1-dependent autophagy to promote DENV-2 replication. Therefore, we postulate HMGB1 as a crucial host element promoting viral propagation and must be considered as an alternative approach for targeting DENV infection. The complex pathogenesis of DENV infection can be better resolved by understanding the complicated correlation between the DENV virus and its host factors.  Growing pieces of evidence demonstrate the importance of metabolic control on proinflammatory response, however, the regulatory mechanism is not known. Here, we suggest a novel mechanism for pyruvate kinase M2 (PKM2) in mediating HMGB1 release during DENV infection. Results showed that the PKM2 expression and nuclear localization were increased in the DENV-2 infection group. Inhibition of PKM2 nuclear translocation by DASA-58 and ML-265 results in decreased HMGB1 release in the supernatant. Furthermore, we observed that DASA-58 and ML-265 resulted in reduced viral protein expression and autophagy. Altogether, our results shed light on an important process for metabolic regulation of proinflammatory response by controlling HMGB1 release and emphasize the role of a metabolic enzyme in understanding the DENV disease pathogenesis.  Collectively, we have deciphered the proviral mechanism of HMGB1 in DENV virus replication by its interaction with the viral genome to induce a proinflammatory response and inducing autophagy. Furthermore, we unraveled that release of HMGB1 during DENV infection is controlled metabolically by a glycolytic enzyme PKM2 expression and its nuclear translocation. Therefore, the molecular mechanisms associated with host factors that regulate inflammation must be further explored to understand the pathogenesis of severe DENV disease.  

DECIPHERING THE MECHANISM OF A HOST CELLULAR FACTOR HIGH MOBILITY GROUP BOX1 PROTEIN IN DENGUE VIRUS PATHOGENESIS

Sharma, Rahul

Isolation, Purification, Structural Characterization and Assessment of Larvicidal Activity of Major N-alkylamides from Acmella ciliata HBKIn the present study, an attempt was made to develop methods for isolation and estimation of major N-alkylamides from A. ciliata that exhibit larvicidal activity (LA) against late III – early IV instar larvae of Aedes aegypti and Culex quinquefasciatus. The isolated compounds were 2E,4E-N-isobutyl undeca-2,4-diene-8,10-diynamide (NUD) and 2E,4E,8Z,10E-N-isobutyl dodeca-2,4,8,10-tetraenamide (NDT). LC50 of NUD and NDT against Ae. aegypti was 44.19 ppm and 18.28 ppm, and for Cx. quinquefasciatus these were 30.89 ppm and 11.75 ppm, respectively. NDT was found more toxic than NUD with both having a higher potency than the commercial larvicide methoprene (MET). HPLC of different parts of the plant showed that NAAs accumulate maximally in flowers as compared to other parts of the plant

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