Faculty Publications
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Publications by NITK Faculty
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Item Controlled release of nutrients to mammalian cells cultured in shake flasks(2012) Hegde, S.; Pant, T.; Pradhan, K.; Badiger, M.; Gadgil, M.Though cell culture-based protein production processes are rarely carried out under batch mode of operation, cell line and initial process development operations are usually carried out in batch mode due to simplicity of operation in widely used scale down platforms like shake flasks. Nutrient feeding, if performed, is achieved by bolus addition of concentrated feed solution at different intervals, which leads to large transient increases in nutrient concentrations. One negative consequence is increased waste metabolite production. We have developed a hydrogel-based nutrient delivery system for continuous feeding of nutrients in scale down models like shake flasks without the need for manual feed additions or any additional infrastructure. Continuous delivery also enables maintaining nutrient concentrations at low levels, if desired. The authors demonstrate the use of these systems for continuous feeding of glucose and protein hydrolysate to a suspension Chinese Hamster Ovary (CHO) culture in a shake flask. Glucose feeding achieved using the glucose-loaded hydrogel resulted in a 23% higher integral viable cell density and an 89% lower lactate concentration at the end of the culture when compared with a bolus-feed of glucose. © 2011 American Institute of Chemical Engineers (AIChE).Item Isolation, screening and production studies of uricase producing bacteria from poultry sources(Taylor and Francis Inc. 325 Chestnut St, Suite 800 Philadelphia PA 19106, 2014) Nanda, P.; JagadeeshBabu, P.E.Uricase (urate oxidase EC 1.7.3.3) is a therapeutic enzyme that is widely used to catalyze the enzymatic oxidation of uric acid in the treatment of hyperuricemia and gout diseases. In this study, three bacterial species capable of producing extracellular uricase were isolated from a poultry source and screened based on the size of the clear zone using a uric acid agar plate. The bacterial species capable of producing uricase with the highest uricolytic activity was identified as Bacillus cereus strain DL3 using a 16SrRNA gene sequencing approach. The time-course study of uricase production was performed and the medium was optimized. Carboxymethylcellulose and asparagine were found to be the best carbon and nitrogen sources. Maximum uricolytic activity was observed at pH 7.0 with an inducer concentration of 2.0 g/L. Inoculum size of 5% gave maximum uricolytic activity. The maximum uricolytic activity of 15.43 U/mL was achieved at optimized conditions, which is 1.61 times more than the initial activity. Further, enzymatic stability was determined at different pH and temperature. © 2014 Taylor and Francis Group, LLC.Item Synthesis and biological evaluation of new imidazo[2,1-b][1,3,4]thiadiazole-benzimidazole derivatives(Elsevier Masson SAS infos@masson.fr 62 rue Camille Desmoulins Issy les Moulineaux Cedex 92442, 2015) Ramprasad, J.; Nayak, N.; Udayakumar, U.; Yogeeswari, P.; Sriram, D.; Peethambar, S.K.; Achur, R.; Santosh Kumar, H.S.S.In this report, we describe the synthesis and biological evaluation of a new series of 2-(imidazo[2,1-b][1,3,4]thiadiazol-5-yl)-1H-benzimidazole derivatives (5a-ac). The molecules were analyzed by 1H NMR, 13C NMR, mass spectral and elemental data. The structure of one of the pre-final compounds, 6-(4-methoxyphenyl)-2-(4-methylphenyl)imidazo[2,1-b][1,3,4]thiadiazole-5-carbaldehyde (4d) and that of a target compound, 2-[2-methyl-6-(4-methyl phenyl) imidazo[2,1-b][1,3,4]thiadiazol-5-yl]-1H-benzimidazole (5aa) were confirmed by single crystal XRD studies. All the target compounds were screened for in vitro anti-tuberculosis activity against Mycobacterium tuberculosis H37Rv strain. Seven (5c, 5d, 5l, 5p, 5r, 5z and 5aa) out of twenty nine compounds showed potent anti-tubercular activity with a MIC of 3.125 ?g/mL. A p-substituted phenyl group (p-tolyl or p-chlorophenyl) in the imidazo[2,1-b][1,3,4]thiadiazole ring and/or a chloro group in the benzimidazole ring enhance anti-tuberculosis activity whereas a nitro group in the benzimidazole ring reduces the activity. In the antibacterial screening, compounds 5i, 5w and 5ac showed promising activity against the tested bacterial strains. Further, antifungal and antioxidant activities of these molecules were also investigated. In the cytotoxicity study, the active antitubercular compounds exhibited very low toxicity against a normal cell line. © 2015 Elsevier Masson SAS.Item Design of new phenothiazine-thiadiazole hybrids via molecular hybridization approach for the development of potent antitubercular agents(Elsevier Masson SAS 62 rue Camille Desmoulins Issy les Moulineaux Cedex 92442, 2015) Ramprasad, J.; Nayak, N.; Udayakumar, U.A new library of phenothiazine and 1,3,4-thiadiazole hybrid derivatives (5a-u) was designed based on the molecular hybridization approach and the molecules were synthesized in excellent yields using a facile single-step chloro-amine coupling reaction between 2-chloro-1-(10H-phenothiazin-10-yl)ethanones and 2-amino-5-subsituted-1,3,4-thiadiazoles. The compounds were evaluated for their in vitro inhibition activity against Mycobacterium tuberculosis H37Rv (MTB). Compounds 5g and 5n were emerged as the most active compounds of the series with MIC of 0.8 ?g/mL (?1.9 ?M). Also, compounds 5a, 5b, 5c, 5e, 5l and 5m (MIC = 1.6 ?g/mL), and compounds 5j, 5k and 5o (MIC = 3.125 ?g/mL) showed significant inhibition activity. The structure-activity relationship demonstrated that an alkyl (methyl/npropyl) or substituted (4-methyl/4-Cl/4-F) phenyl groups on the 1,3,4-thiadiazole ring enhance the inhibition activity of the compounds. The cytotoxicity study revealed that none of the active molecules are toxic to a normal Vero cell line thus proving the lack of general cellular toxicity. Further, the active molecules were subjected to molecular docking studies with target enzymes InhA and CYP121. © 2015 Elsevier Masson SAS. All rights reserved.Item A non-invasive approach to investigation of ventricular blood pressure using cardiac sound features(IOP Publishing Ltd, 2017) Tang, H.; Zhang, J.; Chen, H.; Mondal, A.; Park, Y.Heart sounds (HSs) are produced by the interaction of the heart valves, great vessels, and heart wall with blood flow. Previous researchers have demonstrated that blood pressure can be predicted by exploring the features of cardiac sounds. These features include the amplitude of the HSs, the ratio of the amplitude, the systolic time interval, and the spectrum of the HSs. A single feature or combinations of several features have been used for prediction of blood pressure with moderate accuracy. Experiments were conducted with three beagles under various levels of blood pressure induced by different doses of epinephrine. The HSs, blood pressure in the left ventricle and electrocardiograph signals were simultaneously recorded. A total of 31 records (18 262 cardiac beats) were collected. In this paper, 91 features in various domains are extracted and their linear correlations with the measured blood pressures are examined. These features are divided into four groups and applied individually at the input of a neural network to predict the left ventricular blood pressure (LVBP). The analysis shows that non-spectral features can track changes of the LVBP with lower standard deviation. Consequently, the non-spectral feature set gives the best prediction accuracy. The average correlation coefficient between the measured and the predicted blood pressure is 0.92 and the mean absolute error is 6.86 mmHg, even when the systolic blood pressure varies in the large range from 90 mmHg to 282 mmHg. Hence, systolic blood pressure can be accurately predicted even when using fewer HS features. This technique can be used as an alternative to real-time blood pressure monitoring and it has promising applications in home health care environments. © 2017 Institute of Physics and Engineering in Medicine.Item Therapeutic potential of benfotiamine and its molecular targets(Verduci Editore s.r.l g.lombardi@verduci.it, 2018) Raj, V.; Ojha, S.; Howarth, F.C.; Belur, P.D.; Subramanya, S.B.OBJECTIVE: The water-soluble vitamin, thiamine forms an important part of the diet because of its role in the energy metabolism. The protective effects of thiamine against diabetic vascular complications have been well documented. However, slower absorption and reduced bioavailability is a major limiting factor for its clinical use. To overcome this issue, lipid-soluble derivatives of thiamine (allithiamines) was developed. Among the many synthetic lipophilic derivatives of thiamine, benfotiamine (BFT) is regarded as the first choice based on its safety and clinical efficacy data. BFT facilitates the action of thiamine diphosphate, a cofactor for the enzyme transketolase. The activation of transketolase enzyme accelerates the precursors of advanced glycation end products (AGEs) towards the pentose phosphate pathway thereby reducing the production of AGEs. The reduction in AGEs subsequently decreases metabolic stress which benefits vascular complications seen in diabetes. The effects of BFT on the AGE-dependent pathway is well established. However, several studies have shown that BFT also modulates pathways other than AGE such as arachidonic acid (AA), nuclear transcription Factor ?B (NF-?ß), protein kinase B, mitogen-activated protein kinases (MAPK) and vascular endothelial growth factor receptor 2 (VEGFR2) signaling pathways. In the present review, we have comprehensively reviewed all the molecular targets modulated by BFT to provide mechanistic perspective to highlight its pleiotropic effects. © 2018 Verduci Editore s.r.l. All rights reserved.Item Transcriptional processes: Models and inference(World Scientific Publishing Co. Pte Ltd wspc@wspc.com.sg, 2018) Shetty, K.S.; Annappa, B.Many biochemical events involve multistep reactions. One of the most important biological processes that involve multistep reaction is the transcriptional process. Models for multistep reaction necessarily need multiple states and it is a challenge to compute model parameters that best agree with experimental data. Therefore, the aim of this work is to design a multistep promoter model which accurately characterizes transcriptional bursting and is consistent with observed data. To address this issue, we develop a model for promoters with several OFF states and a single ON state using Erlang distribution. To explore the combined effects of model and data, we combine Monte Carlo extension of Expectation Maximization (MCEM) and delay Stochastic Simulation Algorithm (DSSA) and call the resultant algorithm as delay Bursty MCEM. We apply this algorithm to time-series data of endogenous mouse glutaminase promoter to validate the model assumptions and infer the kinetic parameters. Our results show that with multiple OFF states, we are able to infer and produce a model which is more consistent with experimental data. Our results also show that delay Bursty MCEM inference is more efficient. © 2018 World Scientific Publishing Europe Ltd.Item Molecular hybridization approach for phenothiazine incorporated 1,2,3-triazole hybrids as promising antimicrobial agents: Design, synthesis, molecular docking and in silico ADME studies(Elsevier Masson SAS 62 rue Camille Desmoulins Issy les Moulineaux Cedex 92442, 2019) Reddyrajula, R.; Udayakumar, U.; Madan Kumar, S.The objective of the current study is to synthesize a library consisting of four sets of phenothiazine incorporated 1,2,3-triazole compounds using molecular hybridization approach. In total, 36 new hybrid molecules were synthesized and screened for in vitro growth inhibition activity against Mycobacterium tuberculosis H37Rv strain (ATCC-27294). Among the tested compounds, nineteen compounds exhibited significant activity with MIC value 1.6 ?g/mL, which is twofold higher than the MIC value of standard first-line TB drug Pyrazinamide. In addition, all these compounds are proved to be non-toxic (with selective index > 40) against VERO cell lines. However, these compounds did not inhibit significantly the growth of Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa strains: the activity profile is similar to that observed for standard anti-TB drugs (isoniazid and pyrazinamide), indicating the specificity of these compounds towards the Mycobacterium tuberculosis strain. Also, we report the molecular docking studies against two target enzymes (Inh A and CYP121) to further validate the antitubercular potency of these molecules. Furthermore, prediction of in silico-ADME and pharmacokinetic parameters indicated that these compounds have good oral bioavailability. The results suggest that these phenothiazine incorporated 1,2,3-triazole compounds are a promising class of molecular entities for the development of new antitubercular leads. © 2019 Elsevier Masson SASItem Clumped-MCEM: Inference for multistep transcriptional processes(Elsevier Ltd, 2019) Shetty, K.S.; B, A.Many biochemical events involve multistep reactions. Among them, an important biological process that involves multistep reaction is the transcriptional process. A widely used approach for simplifying multistep reactions is the delayed reaction method. In this work, we devise a model reduction strategy that represents several OFF states by a single state, accompanied by specifying a time delay for burst frequency. Using this model reduction, we develop Clumped-MCEM which enables simulation and parameter inference. We apply this method to time-series data of endogenous mouse glutaminase promoter, to validate the model assumptions and infer the kinetic parameters. Further, we compare efficiency of Clumped-MCEM with state-of-the-art methods – Bursty MCEM2 and delay Bursty MCEM. Simulation results show that Clumped-MCEM inference is more efficient for time-series data and is able to produce similar numerical accuracy as state-of-the-art methods – Bursty MCEM2 and delay Bursty MCEM in less time. Clumped-MCEM reduces computational cost by 57.58% when compared with Bursty MCEM2 and 32.19% when compared with delay Bursty MCEM. © 2019 Elsevier LtdItem Poly(N,N-diethyl acrylamide)/functionalized graphene quantum dots hydrogels loaded with doxorubicin as a nano-drug carrier for metastatic lung cancer in mice(Elsevier Ltd, 2019) Havanur, S.; Batish, I.; Cheruku, S.P.; Gourishetti, K.; JagadeeshBabu, J.; Kumar, N.Cancer has emanated as a daunting menace to human-kind even though medicine, science, and technology has reached its zenith. Subsequent scarcity in the revelation of new drugs, the exigency of salvaging formerly discovered toxic drugs such as doxorubicin has emerged. The invention of drug carrier has made drug delivery imminent which is ascribable to its characteristic traits of specific targeting, effective response to stimuli and biocompatibility. In this paper, the nanoscale polymeric drug carrier poly(N,N-diethyl acrylamide) nanohydrogel has been synthesized by inverse emulsion polymerization. Lower critical solution temperature of the polymeric carrier has been modified using graphene quantum. The particle size of pure nanohydrogel was in the range of 47 to 59.5 nm, and graphene quantum dots incorporated nanohydrogels was in the range of 68.1 to 87.5 nm. Doxorubicin (hydroxyl derivative of anthracycline) release behavior as a function of time and temperature was analyzed, and the Lower critical solution temperature of the synthesized nanohydrogels has been found to be in the range of 28–42 °C. Doxorubicin release characteristics have improved significantly as the surrounding temperature of the release media was increased near to physiological temperature. Further, the cumulative release profile was fitted in the different kinetic model and found to follow a Fickian diffusion release mechanism. The hydrogel was assessed for its cytotoxicity in B16F10 cells by MTT assay. In-vivo studies were done to study the lung metastasis by melanoma cancer and the results showed a rational favorable prognosis which was confirmed by evaluating hematological parameters and the non-immunogenic nature of nanohydrogel by cytokine assay. Comprehensively, the results suggested that poly(N,N-diethyl acrylamide) nanohydrogels have potential application as an intelligent drug carrier for melanoma cancer. © 2019 Elsevier B.V.
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