Department of Bioscience & Bioengineering

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IIT Jodhpur

Understanding ion transport dynamics, structure of surfactant aggregates in ionic liquids or ionic liquid/water solutions are quite interesting and potentially important due to widespread applications of surfactant-based systems. In this manuscript we have investigated the effect of 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF4) addition on solvent and rotational relaxation of coumarin-153 (C-153) and coumarin-480 (C-480) in aqueous solution of sodium 1,4-bis(2-ethylhexyl) sulfosuccinate (NaAOT) using steady state and picosecond time resolved fluorescence spectroscopy. The strong adsorption of the bmim+ at the interface and the role of the ionic liquid particularly the cation bmim+ in the modification of the interfacial geometry were probed by the analysis of decay parameters and the rotational relaxation parameters. Since the addition of the NaAOT in water-bmimBF4 mixture above critical micellar concentration (48 mM, obtained from observing pyrene fluorescence) causes strong adsorption of the ionic liquid particularly the cation bmim+, the average solvation time, particularly the slow component increases significantly. More importantly we have found the probe dependent solvation dynamics due to the different location of the probe molecules, C-153 and C-480. C-153 being hydrophobic in nature resides in the stern layer and the adsorption of the bmim+ at the interface modifies stern layer more effectively. So we have observed more pronounced change in solvation dynamics in case of C-153 compared to that in case of C-480. The fluorescence anisotropy decays of the probe molecules were found to be biexponential in nature. The anisotropy decay was interpreted by using a model which consists of the wobbling (rotational) and translational diffusion of the dye coupled with the rotational motion of the micelle as a whole. © 2012 Elsevier B.V. All rights reserved.

World University root node

Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy

Solvent and rotational relaxation of coumarin-153 and coumarin-480 in ionic liquid (1-butyl-3-methylimidazolium tetrafluoroborate) modified sodium 1,4-bis(2-ethylhexyl) sulfosuccinate (NaAOT) micelle

Chemists and material scientists are interested in complex biological systems and morphologies for fabrication of new materials. Bioinspired design of short peptide conjugates produces various self-assembled structures, depending on their structural diversity. Phe-Phe aromatic dipeptide is an interesting candidate for designing variety of molecular scaffolds. This report describes the synthesis of two symmetrical peptide conjugates by a coupling with C2 and C3 symmetric functional linker's, which spontaneously generate different self-assembled ultra-structures. C2 Symmetric, ethylene diamine linker, conjugated two Phe-Phe dipeptides and produced Phe-Phe-EDA-Phe-Phe (5), which undergoes spontaneous self-assembly to form fibrillar morphology, while C3 symmetric tris(2-aminoethylamine) conjugated three Phe-Phe dipeptides, produced (Phe-Phe)3TREN (7) resulted in spherical morphology structures interconnected by fibers. A rational design of two peptide conjugates, by introducing two different linker's, direct different self-assemble pathway, which result in distinct morphologies. © 2013 Elsevier Ltd. All rights reserved.

Tetrahedron

Spacer driven morphological twist in Phe-Phe dipeptide conjugates

A novel Tris-NTA functionalised SiO2 EM grid is generated through covalent chemical functionalisation. Here, we show immobilisation of functional oligohistidine-tagged proteins and nucleation of microtubules from microtubule polymerase immobilised on the SiO2 EM grid surface. © 2013 The Royal Society of Chemistry.

RSC Advances

Microtubule nucleation from a functionalised SiO2 em grid

After a review of the coupled Newton's equations for a small alignment of grains with a fixed reflecting end wall, the equations are put into block diagrams of Simulink. Simulink simulations are given for 6 grain systems for cubic and Hertz intergrain potentials. The expected granular solitary waves are seen in the simulations. The block diagrams hence convert a single impulse into a traveling energy bundle of fixed width. This work forms the necessary first step for the eventual realization of the mathematical system represented by the granular chain as a Very Large Scale Integrated (VLSI) circuit. © 2013 World Scientific Publishing Company.

Modern Physics Letters B

Simulink modeling for circuit representation of granular chains

Impairment in the clearance of misfolded proteins by functional proteins leads to various late-onset neurodegenerative diseases. Cell applies a strict quality control mechanism against malfunctioned proteins which may generate cellular proteoxicity. Under proteotoxic insults, cells immediately adopt two major approaches to either refold the misfolded proteinaceous species or degrade the unmanageable candidates. However, the main cellular proteostasis quality control mechanism is not clear. It is therefore important to understand the events and cellular pathways, which are implicated in the clearance of recalcitrant proteins. Ubiquitin proteasome system manages intracellular protein degradation. In this process, E3 ubiquitin ligase enzyme provides specificity for recognition of client proteins. In this review, we summarize various molecular approaches governed by E3 ubiquitin ligases in the degradation of aberrant proteins. A clear understanding of E3 ubiquitin ligases can offer a well tractable therapeutic approach against neurodegenerative diseases. © 2012 Springer Science+Business Media New York.

Molecular Neurobiology

Misfolded proteins recognition strategies of e3 ubiquitin ligases and neurodegenerative diseases

Protein aggregation and ordered fibrillar amyloid deposition inside and outside of the central nervous system cells is the common pathologic hallmark of most aging-related neurodegenerative disorders. Dominant mutations in the gene encoding superoxide dismutase 1 (SOD1) protein are linked to familial amyotrophic lateral sclerosis (ALS), a neurodegenerative disease characterized by progressive degeneration of motor neurons, leading to muscle paralysis and death. The major histochemical hallmark in the remaining motor neurons of ALS is the intracellular accumulation of ubiquitinated inclusions consisting of insoluble aberrant protein aggregates. However, the molecular pathomechanisms underlying the process have been elusive. Here for the first time, we report that E6-AP, a homologous to E6-AP C terminus-type E3 ubiquitin ligase depleted in ALS mouse models before neurodegeneration. E6-AP coimmunoprecipitates with the SOD1 protein and is predominantly mislocalized in mutant SOD1-containing inclusion bodies. Overexpression of E6-AP increases the ubiquitination and facilitates degradation of SOD1 proteins. Finally, we show that the overexpression of E6-AP suppresses the aggregation and cell death mediated by mutated SOD1 proteins and cellular protective effect is more prominent when E6-AP is overexpressed along with Hsp70. These data suggest that enhancing the activity of E6-AP ubiquitin ligase might be a viable therapeutic strategy to eliminate mutant SOD1-mediated toxicity in ALS. © 2013 Elsevier Inc.

Neurobiology of Aging

E6-AP association promotes SOD1 aggresomes degradation and suppresses toxicity

International Journal of Cardiology

Contrasting circulating microbiome in cardiovascular disease patients and healthy individuals

Exploring the symbiotic nature of biological systems can result in valuable knowledge for computer networks. Biologically inspired approaches to security in networks are interesting to evaluate because of the analogies between network security and survival of human body under pathogenic attacks. Wireless Sensor Network (WSN) is a network based on multiple low-cost, low-energy sensor nodes connected to physical signals. The network is made up of sensor nodes and gateways, where the server nodes acquire physical world data, while the gateway forwards the data to the end-user. While the spread of viruses in wired systems has been studied in-depth, applying trust in wireless sensor network nodes is an emerging area. This paper uses machine learning techniques to first differentiate between fraudulent and good nodes in the system. Next, it derives inspiration from the human immune system to present an idea of virtual antibodies in the system, to disable the fraudulent nodes in the system. © 2013 IEEE.

2013 World Congress on Nature and Biologically Inspired Computing, NaBIC 2013

Bio-inspired machine learning based wireless sensor network security

Cluster analysis is a technique that divides a given data set into a set of clusters in such a way that two objects from the same cluster are as similar as possible and the objects from different clusters are as dissimilar as possible. In this background, different rough-fuzzy clustering algorithms have been shown to be successful for finding overlapping and vaguely defined clusters. However, the crisp lower approximation of a cluster in existing rough-fuzzy clustering algorithms is usually assumed to be spherical in shape, which restricts to find arbitrary shapes of clusters. In this regard, this paper presents a new rough-fuzzy clustering algorithm, termed as robust rough-fuzzy c-means. Each cluster in the proposed clustering algorithm is represented by a set of three parameters, namely, cluster prototype, a possibilistic fuzzy lower approximation, and a probabilistic fuzzy boundary. The possibilistic lower approximation helps in discovering clusters of various shapes. The cluster prototype depends on the weighting average of the possibilistic lower approximation and probabilistic boundary. The proposed algorithm is robust in the sense that it can find overlapping and vaguely defined clusters with arbitrary shapes in noisy environment. An efficient method is presented, based on Pearson's correlation coefficient, to select initial prototypes of different clusters. A method is also introduced based on cluster validity index to identify optimum values of different parameters of the initialization method and the proposed clustering algorithm. The effectiveness of the proposed algorithm, along with a comparison with other clustering algorithms, is demonstrated on synthetic as well as coding and non-coding RNA expression data sets using some cluster validity indices.