Department of Bioscience & Bioengineering

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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

The present study reports the analysis of properties of tamarind gum-based hydroethanolic physical hydrogels. The extent of hydrogen bonding in hydrogels decreased with an increase in tamarind gum content. The hydrogel with the highest tamarind gum content was found to be highly stable in terms of mechanical properties. There was a decrease in the resistive component of the hydrogels with an increase in tamarind gum content. The drug release from the hydrogels increased with an increase in the tamarind gum content. The antimicrobial activity of the drug-loaded hydrogels against Escherichia coli was excellent. © 2017 Taylor & Francis.

World University root node

Polymer - Plastics Technology and Engineering

Understanding the Effect of Tamarind Gum Proportion on the Properties of Tamarind Gum-Based Hydroethanolic Physical Hydrogels

Generating intense upconversion photoluminescence from a single-phase nanocrystal is a fundamental problem. Herein, we report engineered NaYF4 nanocrystals capable of converting NIR (980 nm) excitation into sharp and diverse emissions in the UV-Vis-NIR regions, which is desirable for triggering multiple photoactive agents for enhanced photo-theranostics. This unique emission profile is used for NIR-induced photo-theranostic applications by developing a nanoplatform with a white-emitting NaYF4 (WEN) core, with comparable blue, green and red emissions, and a mesoporous silica shell decorated with two different photosensitizers (PSs), Rose Bengal (hydrophilic) and zinc(II)phthalocyanine (hydrophobic) to utilize green and red emissions, respectively. A chemical assay demonstrates efficient generation of 1O2 under NIR excitation by the dual PS nanoplatform compared to the conventional systems. Furthermore, NIR-induced ROS generation leads to the enhanced photodynamic destruction of cancer cells (HeLa) in vitro. The white light from the nanoplatform is also utilized in cellular bioimaging. Unlike the previously reported upconversion probes, which required sophisticated imaging setups, the high intensity white light emission from this nanoplatform allows the probing of animal cells by a digital camera attached externally to an optical microscope. This is the first report on the theranostic application of a white-light-emitting photoluminescent nanomaterial. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

ChemNanoMat

White-light-emitting NaYF4 Nanoplatform for NIR Upconversion-mediated Photodynamic Therapy and Bioimaging

This paper presents a framework to explore the effect of music (motivational song) on cardiac physiology using recurrence analysis. For the characterization of the ECG signals, recurrence has been reported to be an effective tool. This non-linear dynamic method has been considered economical than other computational methods. The ECG data were acquired from eighteen male volunteers. The signals were further processed to extract the R-R intervals (RRI). Recurrence analysis of the ECG and the RRI signals suggested a reduction in the isometric recurrence in the post-stimulus condition, and hence, a corresponding increase in the heart rate variability. The variation was also evidenced from the ANN classification of the ECG and the RRI signals with efficiency of ≥ 85%. © 2017 IEEE.

2017 14th IEEE India Council International Conference, INDICON 2017

Understanding the Effect of a Motivational Music on Indian Male Volunteers Using Recurrence Analysis and ANN Classification

Protein structures are key to understanding biomolecular mechanisms and diseases, yet their interpretation is hampered by limited knowledge of their biologically relevant quaternary structure (QS). A critical challenge in inferring QS information from crystallographic data is distinguishing biological interfaces from fortuitous crystal-packing contacts. Here, we tackled this problem by developing strategies for aligning and comparing QS states across both homologs and data repositories. QS conservation across homologs proved remarkably strong at predicting biological relevance and is implemented in two methods, QSalign and anti-QSalign, for annotating homo-oligomers and monomers, respectively. QS conservation across repositories is implemented in QSbio (http://www.QSbio.org), which approaches the accuracy of manual curation and allowed us to predict >100,000 QS states across the Protein Data Bank. Based on this high-quality data set, we analyzed pairs of structurally conserved interfaces and this analysis revealed a striking plasticity whereby evolutionary distant interfaces maintain similar interaction geometries through widely divergent chemical properties.

Fulltext

Nature Methods

PDB-wide identification of biological assemblies from conserved quaternary structure geometry

Aβ peptide and hyper-phosphorylated microtubule associated protein (Tau) aggregation causes severe damage to both the neuron membrane and key signal processing microfilament (microtubule) in Alzheimer's disease (AD) brains. To date, the key challenge is to develop nontoxic, proteolytically stable amyloid inhibitors, which can simultaneously target multiple pathways involved in AD. Various attempts have been made in this direction; however, clinical outcomes of those attempts have been reported to be poor. Thus, we choose development of peptoid (N-substituted glycine oligomers)-based leads as potential AD therapeutics, which are easy to synthesize, found to be proteolytically stable, and exhibit excellent bioavailability. In this paper, we have designed and synthesized a new short peptoid for amyloid inhibition from 30-34 hydrophobic pocket of amyloid beta (Aβ) peptide. The peptoid selectively binds with 17-21 hydrophobic region of Aβ and inhibits Aβ fibril formation. Various in vitro assays suggested that our AI peptoid binds with tubulin/microtubule and promotes its polymerization and stability. This peptoid also inhibits AChE-induced Aβ fibril formation and provides significant neuroprotection against toxicity generated by nerve growth factor (NGF) deprived neurons derived from rat adrenal pheochromocytoma (PC12) cell line. Moreover, this peptoid shows serum stability and is noncytotoxic to primary rat cortical neurons. © 2018 American Chemical Society.

ACS Chemical Neuroscience

Genesis of Neuroprotective Peptoid from Aβ30-34 Inhibits Aβ Aggregation and AChE Activity

Identification of key amino acids is required for development of efficient cell-penetrating peptides (CPPs) and has tremendous implications in medicine. Extensive research work has enlightened us about the importance of two amino acids, arginine and tryptophan, in cell penetration. Here, we present a top-down approach to show how spatial positions of two tryptophans regulate the cellular entry and nuclear localization. This enables us to develop short, non-toxic tetrapeptides with excellent potential for cell penetration and nuclear localization. Among them, Glu-Thr-Trp-Trp (ETWW) emerges as the most promising. Results suggest that it enters into cancer cells following an endocytic pathway and binds at the major groove of nuclear DNA, where successive tryptophan plays major role. We subsequently show that it is not a P-glycoprotein substrate and is non-toxic to PC12-derived neurons, suggesting its excellent potential as a CPP. Furthermore, its potential as a CPP is validated in multi-cellular 3D cell culture (spheroid) and in in vivo mice model. This study provides major fundamental insights about the positional importance of tryptophan and opens new avenues toward the development of next-generation CPPs and major-groove-specific anticancer drugs. © 2017 American Chemical Society.

Journal of the American Chemical Society

Spatial position regulates power of tryptophan: Discovery of a major-groove-specific nuclear-localizing, cell-penetrating tetrapeptide

Reconstitution of a complex biological structure or system following a simple and facile strategy using minimum physiochemical cues is challenging for an in-depth understanding of the system. In particular, the brain is a highly sophisticated and complex network of trillions of neurons and glial cells that controls function of our body. Understanding this complex machinery requires an innovative and simple bottom-up approach. In this venture, we report an easy and efficient strategy to culture cortical and hippocampal primary neurons from the E14-E16 embryo of Sprague-Dawley rat. This generates spontaneous neurospheres within 6-7 days of primary neuron culture of E14-E16 embryo. It further proliferates and forms radial glia-like structures, which are known to be the primary neural progenitor cells that differentiate into neurons, astrocytes, and oligodendrocytes. Interestingly, neurospheres lead to the formation of large projection neurons and radial glia, which mimic the early stage of cortical development in an in vivo system. Overall, this new, facile, strategic mixed primary neuron culture method offers a potential platform for understanding the effect of neurochemical modulators, which has tremendous future implications in the screening of neurotherapeutics. Copyright © 2018 American Chemical Society.

Neurosphere Development from Hippocampal and Cortical Embryonic Mixed Primary Neuron Culture: A Potential Platform for Screening Neurochemical Modulator

Background: To carry out wide range of cellular functionalities, proteins often associate with one or more proteins in a phenomenon known as Protein-Protein Interaction (PPI). Experimental and computational approaches were applied on PPIs in order to determine the interacting partners, and also to understand how an abnormality in such interactions can become the principle cause of a disease. Objective: This review aims to elucidate the case studies where PPIs involved in various human diseases have been proven or validated with computational techniques, and also to elucidate how small molecule inhibitors of PPIs have been designed computationally to act as effective therapeutic measures against certain diseases. Results: Computational techniques to predict PPIs are emerging rapidly in the modern day. They not only help in predicting new PPIs, but also generate outputs that substantiate the experimentally determined results. Moreover, computation has aided in the designing of novel inhibitor molecules disrupting the PPIs. Some of them are already being tested in the clinical trials. Conclusion: This review delineated the classification of computational tools that are essential to investigate PPIs. Furthermore, the review shed light on how indispensable computational tools have become in the field of medicine to analyze the interaction networks and to design novel inhibitors efficiently against dreadful diseases in a shorter time span. © 2018 Bentham Science Publishers.

Current Topics in Medicinal Chemistry

Elucidating protein-protein interactions through computational approaches and designing small molecule inhibitors against them for various diseases

In this study, Microbial Fuel Cell (MFC) capable of treating saline starch water was developed. Sodium chloride (NaCl) concentrations ranging from 500 mM to 3000 mM were tested at the anode. Nitrate was used as an electron acceptor at the biocathode. The halophilic bacteria were isolated from Sambhar Lake, India. Results indicated successful removal of starch (1.83 kg/m3-d) and nitrate (0.13 kg/m3-d NO3−-N) with concomitant power output of 207.05 mW/m2 at 1000 mM NaCl concentration. An increase in power density from 71.06 mW/m2 to 207.05 mW/m2 (2.92 folds) was observed when NaCl concentration was increased from 500 mM to 1000 mM. A decline in power density was observed when the salt concentrations &gt;1000 mM were used. Concentration of 3000 mM supported power output as well as the highest starch degradation (3.2 kg/m3-d) and amylase activity of 2.26 IU/ml. The halophilic exoelectrogens were isolated and identified. The present study demonstrates the utility of MFC for degrading starch in saline water. © 2018 Elsevier Ltd

Bioresource Technology

Halophilic starch degrading bacteria isolated from Sambhar Lake, India, as potential anode catalyst in microbial fuel cell: A promising process for saline water treatment

Nanosize structures activated by near-infrared (NIR) photoexcitation can provide an optical platform for the image-guided removal of small tumor nodules. We have engineered nanoparticles derived from erythrocytes that can be doped with NIR fluorophore indocyanine green (ICG). We refer to these constructs as NIR erythrocyte-derived transducers (NETs). The objective of this study was to determine if ICG-bound albumin (IbA), as the doping material, could enhance the fluorescence emission of NETs, and evaluate the capability of these nanoprobes in imaging cancer cells. Erythrocytes were isolated from bovine whole blood and depleted of hemoglobin to form erythrocyte ghosts (EGs). EGs were then extruded through nanosize porous membranes in the presence of 10-100 μm ICG or Iba (1:1 molar ratio) to form ICG- or IbA-doped NETs. The resulting nanosize constructs were characterized for their diameters, zeta-potentials, absorption, and fluorescence emission spectra. We used fluorescence microscopic imaging to evaluate the capability of the constructs in imaging SKOV3 ovarian cancer cells. Based on dynamic light-scattering measurements, ICG- and IbA-doped NETs had similar diameter distributions (Z-average diameter of 236 and 238 nm, respectively) in phosphate-buffered saline supplemented with 10% fetal bovine serum, which remained nearly constant over the course of 2 h at 37 °C. Despite a much-lower loading efficiency of IbA (∼0.7-8%) as compared to ICG (10-45%), the integrated normalized fluorescence emission of IbA-NETs was 2- to 6-fold higher than ICG-doped NETs. IbA-NETs also demonstrated an enhanced capability in fluorescence imaging of SKOV3 ovarian cancer cells, and can serve as potentially effective nanoprobes for the fluorescence imaging of cancerous cells. © 2018 American Chemical Society.