Faculty Publications

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Publications by NITK Faculty

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    Efficient shape descriptors for feature extraction in 3D protein structures
    (2007) Ranganath, A.; Shet, K.C.; Vidyavathi, N.
    Structural Genomics initiatives are generating an increasing number of protein structures with very limited biochemical characterization. Characterization of a protein's function and understanding the specific nature of a protein's binding is a critical part of both protein engineering and structure-based drug discovery. The accurate detection of binding site in these protein structures can be valuable in determining its function. As shape plays a crucial role in bimolecular recognition and function, the development of shape analysis techniques is important for understanding protein structure-function relationships. This paper describes the use of the continuous wavelet transforms (CWT) for characterizing shape features of 3D protein structures. The goal is to explore the CWT as a multiscale tool to generate rotation- and translation-invariant shape features. © 2007 IOS Press. All rights reserved.
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    Development and Evaluation of PEG-Lithium Citrate Salt Based Aqueous Two Phase System and Its Application in Partitioning of Proteins from Fish Industry Effluent
    (2012) Iyyaswami, I.; Belur, P.D.; Girish, B.; Nagaraj, V.H.
    A aqueous two phase system (ATPS) comprising of PEG (Average mol. Wt: 4000, 6000, 8000) - lithium citrate salt-water systems were studied. The basic studies like binodal curve data generation and equilibrium studies were carried out. Furthermore, the binodal model and Othmer-Tobias and Bancroft models for phase equilibria were used for reproducing the experimental binodal data and phase equilibrium composition data, respectively. Good agreement was obtained with the experimental binodal data and tie line data with the models. The effective excluded volume values were obtained from the binodal model for the present ATPS. The tie line length was determined through the phase equilibrium composition data. This system was used to partition crude proteins of the fish industry effluent. The effects of PEG and salt weight fraction in terms of tie line length and effective excluded volume on partitioning coefficient of crude protein were studied in detail. From the results it was observed that, the crude proteins present in the fish effluent were partitioned in the PEG rich phase and the maximum partition coefficient of 7.82 was obtained. The results are discussed in the context of practical potential of this citrate based ATPS in separating crude proteins from fish industry effluent. © 2012 Copyright Taylor and Francis Group, LLC.
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    1-Hexyl-3-Methylimidazolium Chloride-Potassium Carbonate Aqueous Two Phase System: Equilibrium Characteristics and BSA Partitioning Behavior
    (Taylor and Francis Inc. 325 Chestnut St, Suite 800 Philadelphia PA 19106, 2014) Iyyaswami, I.; Monteiro, S.L.
    The partitioning behavior of the model protein (bovine serum albumin) was investigated in ionic liquid (1-hexyl-3-methylimidazolium chloride) -salt (potassium carbonate) based aqueous two phase system (ATPS). The phase diagram with binodal curve and tie lines for the selected ATPS was developed at different temperatures and analyzed through effective excluded volume (EEV) and Othmer-Tobias and Bancroft equations, respectively. The influence of various process parameters like the ionic liquid and salt concentration, system temperature, tie line length, phase volume ratio, and neutral salt addition on partition coefficient/extraction efficiency of BSA protein was evaluated. © 2014 Copyright Taylor & Francis Group, LLC.
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    Aqueous two phase partitioning of fish proteins: partitioning studies and ATPS evaluation
    (Springer India sanjiv.goswami@springer.co.in, 2015) Nagaraja, V.H.; Iyyaswami, R.
    A suitable Aqueous Two Phase System (ATPS) has been identified for the partitioning of crude fish proteins from fish processing industrial effluent. A detailed study has been performed to analyze the influence of various parameters on protein partitioning such as molecular weight of PEG, effect of different salts (MgSO4, K2HPO4, Na3C6H5O7, Na2SO4, (NH4) 2PO4, K3C6H5O7) and their concentrations, pH, temperature, Tie Line Length (TLL), effluent loading and volume ratio. PEG 2000 - sodium sulphate ATPS was found to be a most favourable system among the selected ATPS for higher partition coefficient of proteins. The binodal curve and equilibrium characteristics of PEG 2000 - sodium sulphate were established and fitted to empirical equations. The equilibrium compositions (tie line) were correlated using Othmer–Tobias and Bancroft equations. © 2014, Association of Food Scientists & Technologists (India).
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    Development of a Spectrophotometric Biphasic Assay for the Estimation of mPEG-maleimide in Thiol PEGylation Reaction Mixtures
    (Taylor and Francis Ltd. michael.wagreich@univie.ac.at, 2016) Nanda, P.; JagadeeshBabu, P.E.; Gupta, P.; Prasad, A.G.
    Methoxy(polyethylene glycol)-maleimide (mPEG-mal) is a PEG derivative used for thiol PEGylation of protein molecules and finds application in drug delivery studies. The maleimide group undergoes degradation in aqueous media, resulting in the difficult quantitative analysis of mPEG-mal. Routinely employed methods for separation and estimation of mPEG-mal include tedious chromatographic methods like ion exchange, high-performance liquid chromatography with refractive index detector and techniques like mass spectrometry and proton nuclear magnetic resonance. We present a direct and reproducible spectrophotometric method to quantify free and protein bound mPEG-mal in thiol PEGylation reaction mixtures. This method is based on the partitioning of a PEG bound chromophore between an aqueous ammonium isoferrothiocyanate phase to a chloroform phase in the presence of mPEG-mal. Several important parameters influencing the partitioning and stability of the chromophore, volume ratios of liquid phases, ethylenediaminetetraacetic acid concentration in the reaction mixture, mixing time, and chlorinated solvents used for partitioning have been studied. © 2016, Copyright © Taylor & Francis Group, LLC.
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    Hemocompatibility of Sulfuric Acid-Treated Metallocene Polyethylene and its Application in Reducing the Quantity of Medical Plastic Waste
    (Taylor and Francis Inc. 325 Chestnut St, Suite 800 Philadelphia PA 19106, 2017) Jaganathan, S.K.; Balaji, A.; Mohanadas, H.; Sivakumar, G.; Kasi, P.; SelvaKumar, M.; Kadiman, S.B.; Anandhan, S.; Faudzi, A.A.B.; Supriyanto, E.; Mandal, M.
    The hazards of dumping medical plastics have created a huge demand to reduce the quantity of plastic usage without compromising its quality. The metallocene synthesized polyethylene is one such advent, however, its clinical usage is limited by the problem of hemocompatibility. This study investigates the effect of sulfuric acid-induced changes in metallocene polyethylene. Fourier transform infrared spectroscopy analysis illustrated the addition of OH and sulfonic acid group, which subsequently increased the wettability. An improvement in micro as well as nanosurface roughness was observed. Ultimately, the treated surfaces depicted delayed clotting time, adsorption of specific plasma proteins, reduced hemolysis, and resistance against platelet adhesion. © 2017 Taylor & Francis.
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    Exploring the fungal protein cadre in the biosynthesis of PbSe quantum dots
    (Elsevier B.V., 2017) Jacob, J.M.; Sharma, S.; Mohan Balakrishnan, R.M.
    While a large number of microbial sources have recently emerged as potent sources for biosynthesis of chalcogenide quantum dots (QDs), studies regarding their biomimetic strategies that initiate QD biosynthesis are scarce. The present study describes several mechanistic aspects of PbSe QD biosynthesis using marine Aspergillus terreus. Scanning electron microscopic (SEM) studies indicated distinctive morphological features such as abrasion and agglomeration on the fungal biomass after the biosynthesis reaction. Further, the biomass subsequent to the heavy metal/metalloid precursor was characterized with spectral signatures typical to primary and secondary stress factors such as thiol compounds and oxalic acid using Fourier Transform Infra-Red Spectroscopic (FTIR) analysis. An increase in the total protein content in the reaction mixture after biosynthesis was another noteworthy observation. Further, metal-phytochelatins were identified as the prominent metal-ion trafficking components in the reaction mixture using Liquid Chromatography Mass Spectroscopic analysis (LCMS). Subsequent assays confirmed the involvement of metal binding peptides namely metallothioneins and other anti-oxidant enzymes that might have played a prominent role in the microbial metal detoxification system for the biosynthesis of PbSe QDs. Based on these findings a possible mechanism for the biosynthesis of PbSe QDs by marine A. terreus has been elucidated. © 2016 Elsevier B.V.
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    Fabrication of novel PPSU/ZSM-5 ultrafiltration hollow fiber membranes for separation of proteins and hazardous reactive dyes
    (Taiwan Institute of Chemical Engineers, 2018) Nayak, M.C.; Isloor, A.M.; Moslehyani, A.; Ismail, N.; A.F., A.F.
    Polyphenylsulfone (PPSU) based asymmetric hollow fiber membranes were prepared by the addition of different percentages of ZSM-5 particles by diffusion induced phase separation method. Polyvinylpyrrolidone (PVP) was used as a pore forming agent. The fabricated membranes were characterized by Field Emission scanning electron microscopy (FESEM), Energy Dispersive Spectroscopy (EDS), contact angle, water permeability, water uptake and by porosity measurements. Membranes filtration study was performed using different proteins namely bovine serum albumin (BSA), egg albumin (EA) and hazardous dyes like Reactive black 5 (RB-5), Reactive orange 16 (RO-16) in aqueous solutions. It was found that, addition of ZSM-5 in membrane matrix showed better dye removal capacity because of its hydrophilic and adsorptive nature. The membrane (PZ-3) with higher loading of additive exhibited rejection percentages of 100% for BSA, 95.23% for EA proteins and with reactive dyes 90.81% for RB-5 and 82.84% for RO-16 as compared to the pristine HF membrane. © 2017 Taiwan Institute of Chemical Engineers
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    The combined effects of carbon/nitrogen ratio, suspended biomass, hydraulic retention time and dissolved oxygen on nutrient removal in a laboratory-scale anaerobic–anoxic–oxic activated sludge biofilm reactor
    (IWA Publishing, 2018) Manu, D.S.; Thalla, A.K.
    The current trend in sustainable development deals mainly with environmental management. There is a need for economically affordable, advanced treatment methods for the proper treatment and management of domestic wastewater containing excess nutrients (such as nitrogen and phosphorus) which can cause eutrophication. The reduction of the excess nutrient content of wastewater by appropriate technology is of much concern to the environmentalist. In the current study, a novel integrated anaerobic–anoxic–oxic activated sludge biofilm (A2O-AS-biofilm) reactor was designed and operated to improve the biological nutrient removal by varying reactor operating conditions such as carbon to nitrogen (C/N) ratio, suspended biomass, hydraulic retention time (HRT) and dissolved oxygen (DO). Based on various trials, it was seen that the A2O-AS-biofilm reactor achieved good removal efficiencies with regard to chemical oxygen demand (95.5%), total phosphorus (93.1%), ammonia nitrogen concentration (NH4þ-N) (98%) and total nitrogen (80%) when the reactor was maintained at C/N ratio of 4, suspended biomass of 3 to 3.5 g/L, HRT of 10 h, and DO of 1.5 to 2.5 mg/L. Scanning electron microscopy (SEM) of suspended and attached biofilm showed a dense structure of coccus and bacillus bacteria with the diameter ranging from 0.3 to 1.2 ?m. The Fourier transform infrared (FTIR) spectroscopy results indicated phosphorylated macromolecules and carbohydrates mix or bind with extracellular proteins in exopolysaccharides. © IWA Publishing 2018.
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    Biosynthesis of cobalt oxide nanoparticles using endophytic fungus Aspergillus nidulans
    (Academic Press, 2018) Vijayanandan, A.S.; Mohan Balakrishnan, R.M.
    Metallic oxide nanoparticles have profound applications in electrochemical devices, supercapacitors, biosensors and batteries. Though four fungi were isolated from Nothapodytes foetida, Aspergillus nidulans was found to be suitable for synthesis of cobalt oxide nanoparticles, as it has proficient tolerance towards metal under study. The broth containing precursor solution and organism Aspergillus nidulans had changed from pink to orange indicating the formation of nanoparticles. Characterization by x-ray diffraction analysis (XRD), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR) and energy dispersive x-ray analysis (EDX) confirmed the formation of spinel cobalt oxide nanoparticles at an average size of 20.29 nm in spherical shape with sulfur-bearing proteins acting as a capping agent for the synthesized nanoparticles. The nanoparticles could be applied in energy storage, as a specific capacitance of 389 F/g showed competence. The study was a greener attempt to synthesize cobalt oxide nanoparticles using endophytic fungus. © 2018 Elsevier Ltd