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

An efficient synthetic framework was assembled (G8-FKE-FA-Dox), consisting of a lysosome-targeting octaguanidine molecular transporter with a cathepsinB (cathB)-specific peptide substrate, folic acid, and the potent chemotherapeutic drug doxorubicin (Dox). Because the folate receptor (FR) and cathB are overexpressed in malignant cells, this transporter conjugate successfully executed lysosome-mediated transport of Dox to FR-positive tumor cells, illustrating this framework as an excellent targeted drug delivery system (TDDS). G8-FKE-FA-Dox was shown to exhibit selective toxicity toward FR-overexpressing cancer cells, with an IC50 value superior to that of the USFDA-approved LipodoxTM and proportional to that of free Dox via selective induction of apoptosis by the activation of caspases8, 9, and 3. This TDDS was observed to be nontoxic to red blood cells and lymphocytes at neutral pH. Furthermore the tumor-targeting dissemination pattern of this system was revealed by monitoring the invivo biodistribution of the carrier (G8-FKE-FA-FL) in normal and FR-overexpressing tumor-bearing mice. A new G8 summit: An efficient dualtargeting octaguanidine transporter-doxorubicin (Dox) conjugate (G8-FKE-FA-Dox) shows significantly higher cytotoxicity toward folate receptor (FR)- and cathepsinB-overexpressing malignant cells than the USFDA-approved Lipodox. Interestingly, G8-FKE-FA-Dox exhibits negligible hemolysis effects toward red blood cells and induces extensive apoptosis. The selective biodistribution of the transporter (G8-FKE-FA-FL) is reflected in FR-positive tumor-bearing mice. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

World University root node

ChemMedChem

A Dual-Targeting Octaguanidine-Doxorubicin Conjugate Transporter for Inducing Caspase-Mediated Apoptosis on Folate-Expressing Cancer Cells

Polypeptide aggregation into amyloid is linked with several debilitating human diseases. Despite the inherent risk of aggregation-induced cytotoxicity, bacteria control the export of amyloid-prone subunits and assemble adhesive amyloid fibres during biofilm formation. An Escherichia protein, CsgC potently inhibits amyloid formation of curli amyloid proteins. Here we unlock its mechanism of action, and show that CsgC strongly inhibits primary nucleation via electrostatically-guided molecular encounters, which expands the conformational distribution of disordered curli subunits. This delays the formation of higher order intermediates and maintains amyloidogenic subunits in a secretion-competent form. New structural insight also reveal that CsgC is part of diverse family of bacterial amyloid inhibitors. Curli assembly is therefore not only arrested in the periplasm, but the preservation of conformational flexibility also enables efficient secretion to the cell surface. Understanding how bacteria safely handle amyloidogenic polypeptides contribute towards efforts to control aggregation in disease-causing amyloids and amyloid-based biotechnological applications.

Fulltext

Scientific Reports

Electrostatically-guided inhibition of Curli amyloid nucleation by the CsgC-like family of chaperones

We present dynamical simulations and simple mechanics arguments to propose a system of stacked blocks of square lattices of elastic spheres that can be used to decimate an incident impulse. Mass mismatch between adjacent blocks is accomplished by making the sphere radius in the upper block twice that of the lower block. The system decimates impact energies by converting the initial impulse into two solitary waves and then progressively into many smaller amplitude solitary waves. We also show that near perfect impact decimation capability can be realized with increased mass mismatch between adjacent blocks by creating sandwiched structures in which a block with smaller density spheres is surrounded on both sides with blocks of denser spheres. The proposed systems are expected to be scalable down to spheres of ∼ 100 nm and work for solid and hollow spheres. © 2016, Springer-Verlag Berlin Heidelberg.

Granular Matter

Decorated granular layers for impact decimation

Piperine, a naturally occurring alkaloid, is well known as anti-oxidant, anti-mutagenic, anti-tumor and anti-proliferative agent. Piperine exerts such pharmacological activities by binding or interacting with various cellular targets. Recently, the first report for Piperine interaction with duplex DNA has been published last year but its interaction with G-quadruplex structures has not been studied yet. Herein, we report for the first time the interaction of Piperine with various DNA G-quadruplex structures. Comprehensive biophysical techniques were employed to determine the basis of interaction for the complex formed between Piperine and G-quadruplex DNA sequences. Piperine showed specificity for G-quadruplex DNA over double stranded DNA, with highest affinity for G-quadruplex structure formed at c-myc promoter region. Further, in-vitro studies show that Piperine causes apoptosis-mediated cell death that further emphasizes the potential of this natural product, Piperine, as a promising candidate for targeting G-quadruplex structure and thus, acts as a potent anti-cancer agent.

Evidences for Piperine inhibiting cancer by targeting human G-quadruplex DNA sequences

Microbial fuel cells (MFCs) are emerging wastewater treatment systems with a proven potential for denitrification. In this study, we have developed a high-rate denitrifying MFC. The anode consisted of cow manure and fruit waste and the cathode consisted of cow manure and soil. The initial chemical oxygen demand (COD)/nitrate nitrogen (NO3 −-N) was varied from 2 to 40 at the cathode while keeping the anode ratio fixed at 100. NO3 −-N removal rate of 7.1 ± 0.9 kg NO3 −-N/m3 net cathodic compartment (NCC)/day was achieved at cathode COD/NO3 −-N ratio 7.31 with the current density of 190 ± 9.1 mA/m2 and power density of 31.92 ± 4 mW/m2 of electrode surface area. We achieved an open-circuit voltage (OCV) of 410 ± 20 mV at initial cathodic NO3 −-N of 0.345 g/l. The cathode COD/NO3 −-N ratio had a significant influence on MFC’s OCV and nitrate removal rate. Lower OCV (&lt;150 mV) and NO3 −-N removal rates were observed at COD/NO3 −-N ratio &gt;12 and &lt;7. Experiments done at different cathode pH values indicated that the optimum pH for denitrification was 7. Under optimized biochemical conditions, nitrate removal rate of 6.5 kg NO3 −-N/m3 net cathodic compartment (NCC)/day and power density of 210 mW/m2 were achieved in a low resistance MFC. The present study thus demonstrates the utility of MFCs for the treatment of high nitrate wastes. © 2016, Springer-Verlag Berlin Heidelberg.

Environmental Science and Pollution Research

Microbial fuel cell assisted nitrate nitrogen removal using cow manure and soil

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 regard, a hybrid unsupervised learning algorithm, termed as rough-fuzzy c-means, is presented in this chapter. It comprises a judicious integration of the principles of rough sets and fuzzy sets. While the concept of lower and upper approximations of rough sets deals with uncertainty, vagueness, and incompleteness in class definition, the membership function of fuzzy sets enables efficient handling of overlapping partitions. The concept of crisp lower approximation and fuzzy boundary of a class, introduced in rough-fuzzy c-means, enables efficient selection of cluster prototypes. The effectiveness of the rough-fuzzy clustering algorithm, along with a comparison with other clustering algorithms, is demonstrated on grouping functionally similar genes from microarray data, identification of co-expressed microRNAs, and segmentation of brain magnetic resonance images using standard validity indices. © 2017 by World Scientific Publishing Co. Pte. Ltd.

Pattern Recognition and Big Data

Fundamentals of rough-fuzzy clustering and its application in bioinformatics

Rats have a complete body representation in the primary motor cortex (M1). Rostrally there are additional representations of the forelimb and whiskers, called the rostral forelimb area (RFA) and the rostral whisker area (RWA). Recently we showed that sources of thalamic inputs to RFA and RWA are similar, but they are different from those for the caudal forelimb area (CFA) and the caudal whisker area (CWA) of M1 (Mohammed and Jain [2014] J Comp Neurol 522:528–545). We proposed that RWA and RFA are part of a second motor area, the rostral motor area (RMA). Here we report ipsilateral cortical connections of whisker representation in RMA, and compare them with connections of CWA. Connections of RFA, CFA, and the caudally located hindlimb area (CHA), which is a part of M1, were determined for comparison. The most distinctive features of cortical inputs to RWA compared with CWA include lack of inputs from the face region of the primary somatosensory cortex (S1), and only about half as much inputs from S1 compared with the lateral somatosensory areas S2 (second somatosensory area) and the parietal ventral area (PV). A similar pattern of inputs is seen for CFA and RFA, with RFA receiving smaller proportion of inputs from the forepaw region of S1 compared with CFA, and receiving fewer inputs from S1 compared with those from S2. These and other features of the cortical input pattern suggest that RMA has a distinct, and more of integrative functional role compared with M1. J. Comp. Neurol. 524:3104–3123, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Journal of Comparative Neurology

Ipsilateral cortical inputs to the rostral and caudal motor areas in rats

The current study delineates the development of gelatin–amylopectin-based phase-separated hydrogels for drug delivery applications. Gelatin and amylopectin were used as the representative protein and polysaccharide phases, respectively. The hydrogels were prepared by adding different proportions of amylopectin to gelatin solutions and subsequently cross-linking the mixture using glutaraldehyde. Microscopic analysis showed formation of phase-separated hydrogels. Secondary structure of gelatin was conserved within the hydrogels. The presence of amylopectin drastically reduced the rate of water absorption by the hydrogels. Viscoelastic analysis using stress relaxation study suggested an increase in the viscous component of the hydrogels with the increase in the amylopectin content. After incorporating amylopectin within the gelatin hydrogel, even though the bulk resistance remained unaltered, there was a corresponding variation in the capacitive elements of the equivalent electrical models. The release of the drug from the hydrogels was diffusion mediated. Suitable mathematical models were used for the analysis of the swelling (Peleg’s model), viscoelastic (Weichert model), electrical (RQQ model) and drug release (Korsmeyer–Peppas and Peppas–Sahlin models) properties. The drug retained its antimicrobial activity within the hydrogels. An analysis of the results suggested that the developed hydrogels may be explored as matrices for controlled drug delivery applications. © 2016, Iran Polymer and Petrochemical Institute.

Iranian Polymer Journal (English Edition)

Gelatin and amylopectin-based phase-separated hydrogels: An in-depth analysis of the swelling, mechanical, electrical and drug release properties

This work deals with the investigation of the polymorphic changes associated with stearic acid in the presence of Tween 20 during the formation of oleogels. Tween 20 was utilized as a crystal habit modifier and its effect on the physical and thermal properties of the oleogels have been studied. Tween 20 was found to stabilize the polymorph B of stearic acid, marked by an increase in the leaf-like structures. Fluorescent recovery after photobleaching studies suggested Tween 20 concentration-dependent reduction in the mobile fractions. Gelation studies suggested a delay in the induction time of nucleation of stearic acid in the presence of Tween 20 was due to the decrease in the degree of supercooling. Avrami analysis supported the stabilization of the polymorph B of stearic acid in the presence of Tween 20. XRD measurements indicated that Tween 20 promoted the growth of the stearic acid crystals while forming leaf-like structures. The molecular rearrangement of the gelator network was quicker and ordered in the Tween 20-containing oleogels. The increase in ordered arrangement of the stearic acid molecules has lowered the crystal imperfections. In other words, it enhanced the crystal gaps (pores) associated with the gelators. When stress (either thermal or mechanical) was introduced, the strength of the oleogels was decreased due to the syneresis of oil through the pores. An increase in the Tween 20 concentration-dependent relaxation of the oleogels was also observed due to the polymorphic change and arrangement of the gelators. © 2016, AOCS.

JAOCS, Journal of the American Oil Chemists' Society

Effect of Tween 20 on the Properties of Stearate Oleogels: an in-Depth Analysis

Fluorescent gold nanoclusters (AuNCs) capped with lysozymes are used to deliver the anticancer drug doxorubicin to cancer and noncancer cells. Doxorubicin-loaded AuNCs cause the highly selective and efficient killing (90 %) of breast cancer cells (MCF7) (IC50=155 nm). In contrast, the killing of the noncancer breast cells (MCF10A) by doxorubicin-loaded AuNCs is only 40 % (IC50=4500 nm). By using a confocal microscope, the fluorescence spectrum and decay of the AuNCs were recorded inside the cell. The fluorescence maxima (at ≈490-515 nm) and lifetime (≈2 ns), of the AuNCs inside the cells correspond to Au10-13. The intracellular release of doxorubicin from AuNCs is monitored by Förster resonance energy transfer (FRET) imaging. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.