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.

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IIT Jodhpur

The tumor suppressor protein programmed cell death 4 (Pdcd4) has been implicated in the translational regulation of specific mRNAs, however, the identities of the natural Pdcd4 target mRNAs and the mechanisms by which Pdcd4 affects their translation are not well understood. Pdcd4 binds to the eukaryotic translation initiation factor eIF4A and inhibits its helicase activity, which has suggested that Pdcd4 suppresses translation initiation of mRNAs containing structured 5′-untranslated regions. Recent work has revealed a second inhibitory mechanism, which is eIF4A-independent and involves direct RNA-binding of Pdcd4 to the target mRNAs. We have now identified the poly(A)-binding protein (PABP) as a novel direct interaction partner of Pdcd4. The ability to interact with PABP is shared between human and Drosophila Pdcd4, indicating that it has been highly conserved during evolution. Mutants of Pdcd4 that have lost the ability to interact with PABP fail to stably associate with ribosomal complexes in sucrose density gradients and to suppress translation, as exemplified by c-myb mRNA. Overall, our work identifies PABP as a novel functionally relevant Pdcd4 interaction partner that contributes to the regulation of translation by Pdcd4. © The Author(s) 2014.

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Nucleic Acids Research

An evolutionarily conserved interaction of tumor suppressor protein Pdcd4 with the poly(A)-binding protein contributes to translation suppression by Pdcd4

Micropatterned surfaces with Tris-NTA and biotin functionalities both in the same micropattern as well as individually in adjacent micropatterns are generated by UV light illumination through photo-masks. These surfaces are extremely useful for the immobilization of oligohistidine and biotin tagged multiple biomolecules/proteins. This journal is © the Partner Organisations 2014.

Soft Matter

Co- and distinct existence of Tris-NTA and biotin functionalities on individual and adjacent micropatterned surfaces generated by photo-destruction

Time resolved confocal microscopy indicates that the cytoplasmic lipid droplets (CLDs) in live cells (normal and cancer lung cells) are less polar, and exhibit slower diffusion (motility) and solvation dynamics than the cytoplasm. The number of CLDs in a human lung cancer cell (A549) is ∼10 times higher than in a non-cancer lung fibroblast cell (WI38). This may result in accumulation of non-polar cell signaling agents in the CLDs of the cancer cell. © 2014 the Partner Organisations.

MedChemComm

Confocal microscopy of cytoplasmic lipid droplets in a live cancer cell: Number, polarity, diffusion and solvation dynamics

Previously, a large volume of papers reports that gold nanorods (Au NRs) are able to effectively kill cancer cells upon high laser doses (usually 808 nm, 1-48 W/cm2) irradiation, leading to hyperthermia-induced destruction of cancer cells, i.e, photothermal therapy (PTT) effects. Combination of Au NRs-mediated PTT and organic photosensitizers-mediated photodynamic therapy (PDT) were also reported to achieve synergistic PTT and PDT effects on killing cancer cells. Herein, we demonstrate for the first time that Au NRs alone can sensitize formation of singlet oxygen (1O2) and exert dramatic PDT effects on complete destrcution of tumors in mice under very low LED/laser doses of single photon NIR (915 nm, &lt;130 mW/cm2) light excitation. By changing the NIR light excitation wavelengths, Au NRs-mediated phototherapeutic effects can be switched from PDT to PTT or combination of both. Both PDT and PTT effects were confirmed by measurements of reactive oxygen species (ROS) and heat shock protein (HSP 70), singlet oxygen sensor green (SOSG) sensing, and sodium azide quenching in cellular experiments. In vivo mice experiments further show that the PDT effect via irradiation of Au NRs by 915 nm can destruct the B16F0 melanoma tumor in mice far more effectively than doxorubicin (a clinically used anti-cancer drug) as well as the PTT effect (via irradiation of Au NRs by 780 nm light). In addition, we show that Au NRs can emit single photon-induced fluorescence to illustrate their in vivo locations/distribution. Gold nanorods (Au NRs)-mediated photodynamic therapy effects on destruction of tumors were demonstrated upon single photon NIR light excitation without additional organic photosensitizers, and simultaneously act as fluorescent markers. © 2013 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim.

Small

First demonstration of gold nanorods-mediated photodynamic therapeutic destruction of tumors via near infra-red light activation

Nanomaterials have been widely used in the biomedical field as gene/drug carriers, magnetic resonance imaging (MRI) contrast reagents, photothermal therapy reagents, fluorescent cellular markers, etc. The origins and working mechanisms of cytotoxicities of nanomaterials, however, are not well understood. It is often stated in the literature that a nanomaterial is non-toxic and biocompatible. In this study, we show that the short term cytotoxicity of a nanomaterial is determined by the surface functionality, rather than the core nanomaterial. A so-called "non-toxic and biocompatible" nanomaterial, such as core/shell iron-filled carbon nanoparticles (Fe@CNPs) and nanodiamonds (NDs), can become cytotoxic when a cationic surface functionality, such as imidazolium (IM) and tertiary methyl ammonium ethyl methacrylate (TMAEA) moieties, was grafted onto the surface. To investigate the contributions of surface functionalities and the core nanomaterials on cytotoxicity, two "non-toxic and biocompatible" Fe@CNPs and NDs were surface-modified with different surface functionalities, including anionic COOH, zwitterionic PVP, neutral OH, cationic IM and TMAEA, and investigated for their cytotoxicities in both in vitro cancer cells (HeLa and U-87MG cells) and in vivo embryo development of zebrafish. Among these surface functionalities, cationic IM and TMAEA functionalities of both Fe@CNPs and NDs cause acute cytotoxicity to a similar extent in the in vitro cancer cell experiments, as well as affect severely the embryonic development and survival rates of zebrafish. Other surface functionalities do not show particularly strong cytotoxicities. To obtain information regarding the origins of cytotoxicities, the effects of surface functionalities were also examined on the lactate dehydrogenase (LDH) levels, cellular ROS generation, apoptosis, and changes in lysosomal membrane integrity, mitochondrial membrane potential, the intracellular pH (pH i), and cell cycles. Our results clearly point out that surface functionality, rather than the core nanomaterials, plays a critical role in dictating the short-term cytotoxicities. © 2014 The Royal Society of Chemistry.

Journal of Materials Chemistry B

Effects of surface functionality of carbon nanomaterials on short-term cytotoxicity and embryonic development in zebrafish

Nanoparticles, with sizes ranging between 1 and ∼102 nm, show dynamical properties distinctly different than those of bulk materials. Due to their large surface area to volume ratio, their properties often depend on length scales. We investigate the size and the collision velocity (vcoll) dependence of the coefficient of restitution (COR) for nanoparticles made of a face-centered cubic lattice of Lennard-Jones atoms via nonequilibrium molecular dynamics simulations. A sharp crossover between elastic collision and plastic collision occurs when vcoll=vY, where vY is the size-dependent yield velocity. For high-collision velocities the COR ∼vcoll-α, α∼1. This result is in agreement with recent small system simulations and with experiments and is distinct from the elasticity-theory-based result for COR for inelastic collisions which behaves as vcoll-α, with α=14. We find that the size-dependent critical vY approaches the theoretical constant value for macroscopic spheres as our particle sizes grow. Possible insights into the origins of α∼1 and the size dependence of the yield velocity are suggested. The work also suggests that sufficiently fast moving nanoparticles traveling through vacuum could be sticky and hence could be of potential interest in many applications. © 2014 American Physical Society.

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Strong plastic deformation and softening of fast colliding nanoparticles

Polyglutamine diseases are a family of inherited neurodegenerative diseases caused by the expansion of CAG repeats within the coding region of target genes. Still the mechanism(s) by which polyglutamine proteins are ubiquitinated and degraded remains obscure. Here, for the first time, we demonstrate that Mahogunin 21 ring finger 1 E3 ubiquitin protein ligase is depleted in cells that express expanded-polyglutamine proteins. MGRN1 co-immunoprecipitates with expanded-polyglutamine huntingtin and ataxin-3 proteins. Furthermore, we show that MGRN1 is predominantly colocalized and recruits with polyglutamine aggregates in both cellular and transgenic mouse models. Finally, we demonstrate that the partial depletion of MGRN1 increases the rate of aggregate formation and cell death, whereas the overexpression of MGRN1 reduces the frequency of aggregate formation and provides cytoprotection against polyglutamine-induced proteotoxicity. These observations suggest that stimulating the activity of MGRN1 ubiquitin ligase might be a potential therapeutic target to eliminate the cytotoxic threat in polyglutamine diseases. © 2014 Elsevier B.V.

Biochimica et Biophysica Acta - Molecular Basis of Disease

Mahogunin ring finger 1 suppresses misfolded polyglutamine aggregation and cytotoxicity

The microRNAs or miRNAs are short, endogenous RNAs having ability to regulate mRNA expression at the post-transcriptional level. Various studies have revealed that miRNAs tend to cluster on chromosomes. The members of a cluster that are in close proximity on chromosomes are highly likely to be processed as co-transcribed units. Therefore, a large proportion of miRNAs are co-expressed. Expression profiling of miRNAs generates a huge volume of data. Complicated networks of miRNA-mRNA interaction increase the challenges of comprehending and interpreting the resulting mass of data. In this regard, this paper presents a clustering algorithm in order to extract meaningful information from miRNA expression data. It judiciously integrates the merits of rough sets, fuzzy sets, the c-means algorithm, and the normalized range-normalized city block distance to discover co-expressed miRNA clusters. While the membership functions of fuzzy sets enable efficient handling of overlapping partitions in a noisy environment, the concept of lower and upper approximations of rough sets deals with uncertainty, vagueness, and incompleteness in cluster definition. The city block distance is used to compute the membership functions of fuzzy sets and to find initial partition of a data set, and therefore helps to handle minute differences between two miRNA expression profiles. The effectiveness of the proposed approach, along with a comparison with other related methods, is demonstrated for several miRNA expression data sets using different cluster validity indices. Moreover, the gene ontology is used to analyze the functional consistency and biological significance of generated miRNA clusters. © 2014 the Partner Organisations.

Molecular BioSystems

City block distance and rough-fuzzy clustering for identification of co-expressed microRNAs

This book addresses the need for a unified framework describing how soft computing and machine learning techniques can be judiciously formulated and used in building efficient pattern recognition models. The text reviews both established and cutting-edge research, providing a careful balance of theory, algorithms, and applications, with a particular emphasis given to applications in computational biology and bioinformatics. Features: integrates different soft computing and machine learning methodologies with pattern recognition tasks; discusses in detail the integration of different techniques for handling uncertainties in decision-making and efficiently mining large biological datasets; presents a particular emphasis on real-life applications, such as microarray expression datasets and magnetic resonance images; includes numerous examples and experimental results to support the theoretical concepts described; concludes each chapter with directions for future research and a comprehensive bibliography. © Springer International Publishing Switzerland 2014. All rights are reserved.

Scalable Pattern Recognition Algorithms: Applications in Computational Biology and Bioinformatics

Scalable pattern recognition algorithms: Applications in computational biology and bioinformatics

Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation. © The Author(s) 2014.