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

In situ generated fluorescent gold nanoclusters (Au-NCs) are used for bio-imaging of three human cancer cells, namely, lung (A549), breast (MCF7), and colon (HCT116), by confocal microscopy. The amount of Au-NCs in non-cancer cells (WI38 and MCF10A) is 20-40 times less than those in the corresponding cancer cells. The presence of a larger amount of glutathione (GSH) capped Au-NCs in the cancer cell is ascribed to a higher glutathione level in cancer cells. The Au-NCs exhibit fluorescence maxima at 490-530 nm inside the cancer cells. The fluorescence maxima and matrix-assisted laser desorption ionization (MALDI) mass spectrometry suggest that the fluorescent Au-NCs consist of GSH capped clusters with a core structure (Au8-13). Time-resolved confocal microscopy indicates a nanosecond (1-3 ns) lifetime of the Au-NCs inside the cells. This rules out the formation of aggregated Au-thiolate complexes, which typically exhibit microsecond (≈1000 ns) lifetimes. Fluorescence correlation spectroscopy (FCS) in live cells indicates that the size of the Au-NCs is ≈1-2 nm. For in situ generation, we used a conjugate consisting of a room-temperature ionic liquid (RTIL, [pmim][Br]) and HAuCl4. Cytotoxicity studies indicate that the conjugate, [pmim][AuCl4], is non-toxic for both cancer and non-cancer cells. Bio-imaging: The authors demonstrate the specific generation of fluorescent Au nanoclusters in cancer cells, which can be used as an excellent probe for imaging different cell organelles. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

World University root node

ChemPhysChem

Cancer Cell Imaging Using in Situ Generated Gold Nanoclusters

Synthetic tripeptide based noncytotoxic hydrogelators have been discovered for releasing an anticancer drug at physiological pH and temparature. Interestingly, gel stiffness, drug release capacity and proteolytic stability of these hydrogels have been successfully modulated by incorporating d-amino acid residues, indicating their potential use for drug delivery in the future. © The Royal Society of Chemistry 2016.

Chemical Communications

Peptide based hydrogels for cancer drug release: Modulation of stiffness, drug release and proteolytic stability of hydrogels by incorporating d-amino acid residue(s)

Fluctuation in the local microenvironment of a dynamic microtubule, undergoing continuous growth and shrinkage, is monitored by time resolved confocal microscopy. For this, we have attached a fluorescent probe (CPM, 7-diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin), covalently to tubulin dimers. In this experiment, the laser is focused on a small microtubule seed immobilized on a glass slide by neutravidin and biotin interaction. Tubulin monomers and other agents present in the solution cause growth and shrinkage. We have monitored emission maximum and solvation dynamics of the probe, CPM. Emission maximum ƛemmax of CPM labeled tubulin dimer indicates a highly exposed medium similar to that in human serum albumin, HSA denatured by 6 M Guanidinium Hydrochloride (GdnHCl). However, solvation dynamics of CPM in tubulin dimer is more than 10 times slower than that in denatured HSA. ƛemmax and solvation dynamics of CPM in tubulin dimer is similar to those in fluctuating microtubules and taxol (paclitaxel) stabilized microtubules. The fluorescence intensity of CPM exhibits intermittent oscillation in 1–2 seconds time scale in dynamic microtubules. No such fluctuation is observed in the case of unpolymerized tubulin dimer or when microtubules are stabilized by taxol. This strategy offers a new physicochemical approach of monitoring polymerization (growth) and depolymerization (shrinkage) of tubulin. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

ChemistrySelect

Fluorescence Probing of Fluctuating Microtubule using a Covalent Fluorescent Probe: Effect of Taxol

Aggregations of amyloid-beta (Aβ) peptides were studied inside a reconstituted cell like liposomal system using time-resolved confocal microscopy. Fluorescence correlation spectroscopy (FCS) and confocal images indicate that Aβ forms a very large aggregate in bulk and more efficiently, in the bilayer region of the liposome, respectively. The aggregates formed inside the liposome gradually migrate out to bulk water. FRET, from HiLyte Fluor 488 (covalently attached to an Aβ peptide) to TRITC (tetramethylrhodamine isothiocyanate) covalently attached to a DHPE lipid present in the bilayer, reveals intermittent oscillations in the time scale of ∼0.5 s. This is attributed to the structural fluctuations of the membrane of the liposome. The solvation dynamics of Aβ in monomer and in oligomeric state is studied by monitoring the emission of HiLyte Fluor 488. The solvation dynamics of the Aβ monomer is similar to that of oligomeric aggregates in the liposome.

Physical chemistry chemical physics : PCCP

Amyloid beta peptides inside a reconstituted cell-like liposomal system: aggregation, FRET, fluorescence oscillations and solvation dynamics

Tubulin is the key cytoskeleton component, which plays a crucial role in eukaryotic cell division. Many anticancer drugs have been developed targeting the tubulin surface. Recently, it has been shown that few polyhydroxy carbohydrates perturb tubulin polymerization. Cyclodextrin (CD), a polyhydroxy carbohydrate, has been extensively used as the delivery vehicle for delivery of hydrophobic drugs to the cancer cell. However, interaction of CD with intracellular components has not been addressed before. In this Article, we have shown for the first time that α-CD interacts with tubulin close to the vinblastine site using molecular docking and Förster resonance energy transfer (FRET) experiment. In addition, we have shown that α-CD binds with intracellular tubulin/microtubule. It delivers a high amount of curcumin onto the cancer cell, which causes severe disruption of intracellular microtubules. Finally, we have shown that the inclusion complex of α-CD and curcumin (CCC) preferentially enters into the human lung cancer cell (A549) as compared to the normal lung fibroblast cell (WI38), causes apoptotic death, activates tumor suppressor protein (p53) and cyclin-dependent kinase inhibitor 1 (p21), and inhibits 3D spheroid growth of cancer cell. © 2016 American Chemical Society.

ACS Applied Materials and Interfaces

α-Cyclodextrin Interacts Close to Vinblastine Site of Tubulin and Delivers Curcumin Preferentially to the Tubulin Surface of Cancer Cell

Cells regularly synthesize new proteins to replace old and abnormal proteins for normal cellular functions. Two significant protein quality control pathways inside the cellular milieu are ubiquitin proteasome system (UPS) and autophagy. Autophagy is known for bulk clearance of cytoplasmic aggregated proteins, whereas the specificity of protein degradation by UPS comes from E3 ubiquitin ligases. Few E3 ubiquitin ligases, like C-terminus of Hsc70-interacting protein (CHIP) not only take part in protein quality control pathways, but also plays a key regulatory role in other cellular processes like signaling, development, DNA damage repair, immunity and aging. CHIP targets misfolded proteins for their degradation through proteasome, as well as autophagy; simultaneously, with the help of chaperones, it also regulates folding attempts for misfolded proteins. The broad range of CHIP substrates and their associations with multiple pathologies make it a key molecule to work upon and focus for future therapeutic interventions. E3 ubiquitin ligase CHIP interacts and degrades many protein inclusions formed in neurodegenerative diseases. The presence of CHIP at various nodes of cellular protein-protein interaction network presents this molecule as a potential candidate for further research. In this review, we have explored a wide range of functionality of CHIP inside cells by a detailed presentation of its co-chaperone, E3 and E4 enzyme like functions, with central focus on its protein quality control roles in neurodegenerative diseases. We have also raised many unexplored but expected fundamental questions regarding CHIP functions, which generate hopes for its future applications in research, as well as drug discovery. © 2016 Joshi, Amanullah, Upadhyay, Mishra, Kumar and Mishra.

Fulltext

Frontiers in Molecular Neuroscience

A decade of boon or burden: What has the chip ever done for cellular protein quality control mechanism implicated in neurodegeneration and aging?

Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ΔTm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author's name and techniques that were used to detect their interactions. G4IPDB also provides an efficient web-based "G-quadruplex predictor tool" that searches putative G-quadruplex forming sequences simultaneously in both sense and anti-sense strands of the query nucleotide sequence and provides the predicted G score. Studying the interaction between proteins and nucleic acids forming G-quadruplex structures could be of therapeutic significance for various diseases including cancer and neurological disease, therefore, having detail information about their interactions on a single platform would be helpful for the discovery and development of novel therapeutics. G4IPDB can be routinely updated (twice in year) and freely available on http://bsbe.iiti.ac.in/bsbe/ipdb/index.php. © The Author(s) 2016.

Scientific Reports

G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins

Designing a single multifunctional nanoparticle that can simultaneously impart both diagnostic and therapeutic functions is considered to be a long-lasting hurdle for biomedical researchers. Conventionally, a multifunctional nanoparticle can be constructed by integrating organic dyes/magnetic nanoparticles to impart diagnostic functions and anticancer drugs/photosensitizers to achieve therapeutic outcomes. These multicomponents systems usually suffer from severe photobleaching problems and cannot be activated by near-infrared (NIR) light. Here, it is demonstrated that all-in-one lanthanide-doped mesoporous silica frameworks (EuGdOx@MSF) loaded with an anticancer drug, doxorubicin (DOX) can facilitate simultaneous bimodal magnetic resonance (MR) imaging with approximately twofold higher T1-MR contrast as compared to the commercial Gd(III)-DTPA complex and fluorescence imaging with excellent photostability. Upon a very low dose (130 mW cm−2) of NIR light (980 nm) irradiation, the EuGdOx@MSF not only can sensitize formation of singlet oxygen (1O2) by itself but also can phototrigger the release of the DOX payload effectively to exert combined chemo-photodynamic therapeutic (PDT) effects and destroy solid tumors in mice completely. It is also discovered for the first time that the EuGdOx@MSF-mediated PDT effect can suppress the level of the key drug resistant protein, i.e., p-glycoprotein (p-gp) and help alleviate the drug resistant problem commonly associated with many cancers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Advanced Functional Materials

Unprecedented “All-in-One” Lanthanide-Doped Mesoporous Silica Frameworks for Fluorescence/MR Imaging and Combination of NIR Light Triggered Chemo-Photodynamic Therapy of Tumors

We have engineered hybrid nanostructures derived from erythrocytes, which can be doped with various near infrared (NIR) organic chromophores, including the FDA-approved indocyanine green (ICG). We refer to these vesicles as NIR erythrocyte-mimicking transducers (NETs), as they are capable of generating heat, reactive oxygen species (ROS) or emit fluorescence light. We present preliminary results that demonstrate the effectiveness of NETs for fluorescence imaging and photodynamic therapeutic destruction of breast cancer cells, upon photo-excitation using NIR light. These hybrid nanostructures present a promising platform with theranostic capability for future biomedical clinical applications. © 2016 SPIE.

Proceedings of SPIE - The International Society for Optical Engineering

Light-based theranostics using hybrid structures derived from biological and organic materials

NLRs (nucleotide-binding domain, leucine-rich repeat containing receptors) are pattern recognition receptors associated with immunity and inflammation in response to endogenous and exogenous pathogen and damage associated molecular patterns (PAMPs and DAMPs respectively). Dysregulated NLR function is associated with several diseases including cancers, metabolic diseases, autoimmune disorders and autoinflammatory syndromes. In the last decade, distinct cell and organ specific roles for NLRs have been identified however; their roles in cancer initiation, development and progression remain controversial. This review summarizes the emerging role of NLRs in cancer and their possible future as targets for cancer therapeutics. © 2015 Springer International Publishing.