Department of Bioscience & Bioengineering

&ldquo;IIT Jodhpur is committed to impart quality education to facilitate the creation of qualified, competent and responsible human resources to meet the emerging technological challenges of the world. It is working towards creating an equitable learning platform that is positive, accessible and effective in the face of the modern societal and scientific advancements.

Flexibility in curriculum, in all its academic programs, encompassing elements of teaching, research, creativity, innovation and entrepreneurship is the most unique feature of IIT Jodhpur. The Department of Science and Technology (DST), under the National Mission on Cyber Physical Systems, has identified IIT Jodhpur as a Technology &amp; Innovation Hub in the area of Augmented Reality and Virtual Reality. The institute has also been nominated as the coordinator for the Jodhpur City and Knowledge Cluster by the Office of Principal Scientific Adviser, Government of India.

The sprawling 852-acre IIT Jodhpur campus is a majestic tribute to the deep-rooted diverse cultural heritage of the region. The campus is an architectural masterpiece, which is slated to become an international exemplar of sustainability with net-zero energy, and advanced water and waste management strategies.&rdquo;

IIT Jodhpur

A biotin functionalised SiO2 electron microscope grid has been developed for studying various biotin/avidin tagged biomolecules onto the grid surface under electron microscope. As an application, we have shown successful immobilisation of streptavidin gold nanoparticles and biotinylated microtubules through biotin-streptavidin-biotin interaction. This grid will be useful for studying the structures of various biotin-tagged proteins and their complexes under electron microscope.

World University root node

Indian Journal of Chemistry - Section A Inorganic, Physical, Theoretical and Analytical Chemistry

Fabrication of biotin functionalised SiO2 EM grid for studying biotin tagged biomolecules

Microtubule organization in living cells is determined by spatial control of microtubule nucleation, their dynamic properties, and transport by molecular motors. Here, we establish a new micropattern-guided method for controlling local microtubule nucleation by spatially confined immobilization of a microtubule polymerase and show that these nucleated microtubules can be transported and organized in space by motor proteins. This assay provides a new platform for deciphering the principles underlying mesoscale microtubule organization. © 2013 American Chemical Society.

ACS Chemical Biology

Micropattern-controlled local microtubule nucleation, transport, and mesoscale organization

ChemBioChem

A Biotin Micropatterned Surface Generated by Photodestruction Serves as a Novel Platform for Microtubule Organisation and DNA Hybridisation

Impairment in the elimination of misfolded proteins generates cellular toxicity and leads to various late-onset neurodegenerative diseases. However, the mechanisms by which cells recognize abnormal cellular proteins for selective clearance remain unknown. Lack of the mahogunin ring finger-1 (MGRN1) E3 ubiquitin ligase in mice causes the development of age-dependent spongiform neurodegeneration. Here, we report for the first time that the MGRN1 E3 ubiquitin ligase interacts and nicely co-localizes with the cytosolic molecular chaperone Hsp70. The expression of MGRN1 increased following exposure to a variety of stressors. The inhibition of autophagy not only elevated endogenous MGRN1 levels but also caused MGRN1 to be recruited to cytosolic ubiquitin-positive inclusion bodies. Finally, we showed that the overexpression of MGRN1 protects against cell death mediated by oxidative and endoplasmic reticulum stress. These data suggest that MGRN1 selectively targets misfolded proteins for degradation and may exhibit viable therapeutic potential for the treatment of spongiform neurodegeneration. © 2013 Macmillan Publishers Limited. All rights reserved.

Fulltext

Scientific Reports

Mahogunin ring finger-1 (MGRN1) suppresses chaperone-associated misfolded protein aggregation and toxicity

Membrane-induced disorder-to-helix transition of α-synuclein, a presynaptic protein, has been implicated in a number of important neuronal functions as well as in the etiology of Parkinson's disease. In order to obtain structural insights of membrane-bound α-synuclein at the residue-specific resolution, we took advantage of the fact that the protein is devoid of tryptophan and incorporated single tryptophan at various residue positions along the sequence. These tryptophans were used as site-specific markers to characterize the structural and dynamical aspects of α-synuclein on the negatively charged small unilamellar lipid vesicles. An array of site-specific fluorescence readouts, such as the spectral-shift, quenching efficiency and anisotropy, allowed us to discern various features of the conformational rearrangements occurring at different locations of α-synuclein on the lipid membrane. In order to define the spatial localization of various regions of the protein near the membrane surface, we utilized a unique and sensitive indicator, namely, red-edge excitation shift (REES), which originates when a fluorophore is located in a highly ordered micro-environment. The extent of REES observed at different residue positions allowed us to directly identify the residues that are localized at the membrane-water interface comprising a thin (~ 15 Å) layer of motionally restrained water molecules and enabled us to construct a dynamic hydration map of the protein. The combination of site-specific fluorescence readouts allowed us to unravel the intriguing molecular details of α-synuclein on the lipid membrane in a direct model-free fashion. Additionally, the combination of methodologies described here are capable of distinguishing subtle but important structural alterations of α-synuclein bound to different negatively charged lipids with varied head-group chemistry. We believe that the structural modulations of α-synuclein on the membrane could potentially be related to its physiological functions as well as to the onset of Parkinson's diseases. © 2013 Jain et al.

PLoS ONE

Structural and dynamical insights into the membrane-bound α-synuclein

The present study deals with the encapsulation of vegetable organogels in alginate microparticles (MPs). Mango butter (MB) and cocoa butter (CB) are natural organogels, which are being used in the preparation of pharmaceutical formulations. In addition to these, mustard oil (MO) was used as the control. The thermal stability of MB and CB can be enhanced by encapsulating them and can be used in oral drug-delivery formulations. Double emulsification method was followed for the preparation of MPs. By this method, spherical MPs were synthesized and the sphericity was confirmed by doing light microscopy and scanning electron microscopy. The size range of MPs was 107 ± 53 μm, 79 ± 43 μm, and 112 ± 78 μm for MPs encapsulating MO, MB, and CB, respectively. The melting endotherms of MPs with MB and CB were in exact match with the melting points of MB and CB. This confirmed the existence of MB and CB within the MPs. The encapsulation of the vegetable organogels altered the release pattern of the drug, metronidazole. The drug release kinetics suggested that the release pattern followed the non-Fickian kinetics. The MPs were found to be hemocompatible in nature and have shown good mucoadhesive and swelling properties. Based on the preliminary results, it was suggested that the vegetable organogels can be encapsulated in alginate MPs and used as drug-delivery vehicles. © 2012 Taylor & Francis.

Designed Monomers and Polymers

Encapsulation of vegetable organogels for controlled delivery applications

Gene expression data clustering is one of the important tasks of functional genomics as it provides a powerful tool for studying functional relationships of genes in a biological process. Identifying coexpressed groups of genes represents the basic challenge in gene clustering problem. In this regard, a gene clustering algorithm, termed as robust rough-fuzzy c-means, is proposed judiciously integrating the merits of rough sets and fuzzy sets. While the concept of lower and upper approximations of rough sets deals with uncertainty, vagueness, and incompleteness in cluster definition, the integration of probabilistic and possibilistic memberships of fuzzy sets enables efficient handling of overlapping partitions in noisy environment. The concept of possibilistic lower bound and probabilistic boundary of a cluster, introduced in robust rough-fuzzy c-means, enables efficient selection of gene clusters. An efficient method is proposed to select initial prototypes of different gene clusters, which enables the proposed c-means algorithm to converge to an optimum or near optimum solutions and helps to discover coexpressed gene clusters. The effectiveness of the algorithm, along with a comparison with other algorithms, is demonstrated both qualitatively and quantitatively on 14 yeast microarray data sets.

IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM

Rough-fuzzy clustering for grouping functionally similar genes from microarray data.

Feature selection is an important data pre-processing step in pattern recognition and data mining. It is effective in reducing dimensionality and redundancy among the selected features, and increasing the performance of learning algorithm and generating information-rich features subset. In this regard, the chapter reports on a rough set-based feature selection algorithm called maximum relevance-maximum significance (MRMS), and its applications on quantitative structure activity relationship (QSAR) and gene expression data. It selects a set of features from a high-dimensional data set by maximizing the relevance and significance of the selected features. A theoretical analysis is reported to justify the use of both relevance and significance criteria for selecting a reduced feature set with high predictive accuracy. The importance of rough set theory for computing both relevance and significance of the features is also established. The performance of the MRMS algorithm, along with a comparison with other related methods, is studied on three QSAR data sets using the R 2 statistic of support vector regression method, and on five cancer and two arthritis microarray data sets by using the predictive accuracy of the K-nearest neighbor rule and support vector machine. © Springer-Verlag Berlin Heidelberg 2013.

Intelligent Systems Reference Library

Rough Set-Based Feature Selection: Criteria of Max-Dependency, Max-Relevance, and Max-Significance

Understanding brain reorganization following long-term spinal cord injuries is important for optimizing recoveries based on residual function as well as developing brain-controlled assistive devices. Although it has been shown that the motor cortex undergoes partial reorganization within a few weeks after peripheral and spinal cord injuries, it is not known if the motor cortex of rats is capable of large-scale reorganization after longer recovery periods. Here we determined the organization of the rat (Rattus norvegicus) motor cortex at 5 or more months after chronic lesions of the spinal cord at cervical levels using intracortical microstimulation. The results show that, in the rats with the lesions, stimulation of neurons in the de-efferented forelimb motor cortex no longer evokes movements of the forelimb. Instead, movements of the body parts in the adjacent representations, namely the whiskers and neck were evoked. In addition, at many sites, movements of the ipsilateral forelimb were observed at threshold currents. The extent of representations of the eye, jaw and tongue movements was unaltered by the lesion. Thus, large-scale reorganization of the motor cortex leads to complete filling-in of the de-efferented cortex by neighboring representations following long-term partial spinal cord injuries at cervical levels in adult rats. © 2013 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

European Journal of Neuroscience

Complete reorganization of the motor cortex of adult rats following long-term spinal cord injuries

In this Letter, our aim is to determine the location of metal Nanoparticles (NPs) inside Room Temperature Ionic Liquid (RTIL)-containing microemulsions by solvation dynamics approach. To locate the NPs we have used three different coumarin probes, C-153, C-480, and C-343, due to their different locations in RTIL-containing microemulsion. The increment in the solvation time is more in case of C-343 compared with other two probe molecules, C-480 and C-153, due to its location at the core of the pool of the RTIL; which confirmed the location of the NPs. © 2013 Elsevier B.V. All rights reserved.

Chemical Physics Letters

Is it possible to apply dynamics of solvent to locate metal nanoparticles inside an ionic liquids-containing microheterogeneous system? A comparative study