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

A short GC rich DNA derived from microbial origin interacts with tubulin/microtubules activates p53 over expression and induces apoptotic death of human breast cancer (MCF-7) cells. © The Royal Society of Chemistry.

World University root node

Chemical Communications

A short GC rich DNA derived from microbial origin targets tubulin/microtubules and induces apoptotic death of cancer cells

The structure and dynamics of an antigen-antibody complex are monitored by circular dichroism (CD) spectroscopy, fluorescence correlation spectroscopy (FCS) and single molecule FRET (smFRET). In this work, the antigen is enhanced GFP (EGFP) and the antibody is anti-EGFP VHH-His6. From FCS measurements, the hydrodynamic radius (rH) of EGFP and its antibody (VHH-His6) is found to be 24 ± 2 Å and 18 ± 2 Å, respectively. For the antigen-antibody complex (EGFP:anti-EGFP VHH-His6), rH is 41 ± 3 Å. CD spectra indicate that the addition of guanidium hydrochloride (GdnHCl) causes unfolding of the antigen, its antibody and their complex, and a consequent increase in size is observed from FCS data. smFRET between EGFP (donor, D) and Alexa 594 (acceptor, A) bound to anti-EGFP VHH-His6 reveals a time dependent fluctuation in donor-acceptor distances. This suggests that the structure of the antigen-antibody complex is dynamic in nature and is not rigid. This journal is © the Owner Societies 2015.

Physical Chemistry Chemical Physics

Fluorescence fluctuation of an antigen-antibody complex: Circular dichroism, FCS and smFRET of enhanced GFP and its antibody

Spectroelectrochemicalinvestigation of racemic alanine on poly crystalline metal surfaces was studied in 1M LiClO4 medium, to achieve cost effective separation of biologically important molecules from the racemic mixture. Analysis of the FTIR spectrum of racemic alanine in 1M LiClO4 indicated degradation of the same. Upon prolonged exposure in LiClO4, byproducts from degradation of alanine increasedin concentration as also observed from UV-Vis spectroscopy. Cyclic Voltammetry studies unraveled different adsorption behaviors on different metal surfaces for the racemic and the enantiomeric solution of alanine. Further FTIR analysis of the alanine solution after Cyclic Voltammetry revealed possible presence of cyanide (-C=N) and terminal alkyne as byproducts. As predicted by Monte Carlo simulations earlier, Circular Dichroism implied the dextro rotation of the racemic alanine solution after Cyclic Voltammetry. These results support the preferential adsorption of L-alanine over D-alanine from racemic mixture that could be attributed to the umbrella inversion of the molecule after adsorption on the metal surface in presence of applied electric field in the LiClO4 environment. A plausible mechanism for the formation of terminal alkyne and - C=N byproducts had also been attempted. © The Electrochemical Society.

Department of Chemistry

ECS Transactions

Separation of enantiomers of alanine from racemic mixture by polycrystalline metal surfaces - A spectroelectrochemical approach

A green one step facile synthesis of graphene nanosheets by Terminalia chebula (T. chebula) extract mediated reduction of graphite oxide (GO) is reported in this work. This method avoids the use of harmful toxic reducing agents. The comparative results of various characterizations of GO and T. chebula reduced graphene oxide (TCG) provide a strong indication of the exclusion of oxygen containing groups from graphene oxide and successive stabilization of the formed reduced graphene oxide (RGO). The functionalization of reduced graphene oxide with the oxidized polyphenols causes their stability by preventing the aggregation. We also have proposed how the oxidized polyphenols are accountable for the stabilization of the formed graphene sheets. © 2015 Elsevier B.V. All rights reserved.

Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy

Bioinspired reduced graphene oxide nanosheets using Terminalia chebula seeds extract

The present study aims to evaluate the comparative effects of methyl parathion and hexaconazole on genotoxicity, oxidative stress, antioxidative defence system and photosynthetic pigments in barley (Hordeum vulgare L. variety karan-16). The seeds were exposed with three different concentrations, i.e. 0.05, 0.1 and 0.5 % for 6 h after three pre-soaking durations 7, 17 and 27 h which represents G1, S and G2 phases of the cell cycle, respectively. Ethyl methane sulphonate, a well-known mutagenic agent and double distilled water, was used as positive and negative controls, respectively. The results indicate significant decrease in mitotic index with increasing concentrations of pesticides, and the extent was higher in methyl parathion. Chromosomal aberrations were found more frequent in methyl parathion than hexaconazole as compared to their respective controls. Treatment with the pesticides induced oxidative stress which was evident with higher contents of H2O2 and lipid peroxidation, and the increase was more prominent in methyl parathion. Contents of total phenolics were increased; however, soluble protein content showed a reverse trend. Among the enzymatic antioxidants, activities of superoxide dismutase and peroxidase were significantly up-regulated, and more increase was noticed in hexaconazole. Increments in total chlorophyll and carotenoid contents were observed up to 0.1 % but decreased at higher concentration (0.5 %), and the reductions were more prominent in methyl parathion than hexaconazole as compared to their respective controls. Methyl parathion treatment caused more damage in the plant cells of barley as compared to hexaconazole, which may be closely related to higher genotoxicity and oxidative stress. © 2015, Springer-Verlag Berlin Heidelberg.

Environmental Science and Pollution Research

Comparative analyses of genotoxicity, oxidative stress and antioxidative defence system under exposure of methyl parathion and hexaconazole in barley (Hordeum vulgare L.)

A device for absorbing and storing short duration impulses in an initially uncompressed one-dimensional granular chain is presented. Simply stated, short regions of sufficiently soft grains are embedded in a hard granular chain. These grains exhibit long-lived standing waves of predictable frequencies regardless of the timing of the arrival of solitary waves from the larger matrix. We explore the origins, symmetry, and energy content of the soft region and its vibrational modes. © 2015 AIP Publishing LLC.

Fulltext

Applied Physics Letters

Localizing energy in granular materials

Cilia are essential for cell signaling and sensory perception. In many cell types, a cytoskeletal structure called the ciliary rootlet links the cilium to the cell body. Previous studies indicated that rootlets support the long-term stability of some cilia. Here we report that Drosophila melanogaster Rootletin (Root), the sole orthologue of the mammalian paralogs Rootletin and C-Nap1, assembles into rootlets of diverse lengths among sensory neuron subtypes. Root mutant neurons lack rootlets and have dramatically impaired sensory function, resulting in behavior defects associated with mechanosensation and chemosensation. Root is required for cohesion of basal bodies, but the cilium structure appears normal in Root mutant neurons. We show, however, that normal rootlet assembly requires centrioles. The N terminus of Root contains a conserved domain and is essential for Root function in vivo. Ectopically expressed Root resides at the base of mother centrioles in spermatocytes and localizes asymmetrically to mother centrosomes in neuroblasts, both requiring Bld10, a basal body protein with varied functions. © 2015 Chen et al.

Journal of Cell Biology

Rootletin organizes the ciliary rootlet to achieve neuron sensory function in Drosophila

The tumor suppressor gene Pdcd4 (programmed cell death gene 4) has drawn considerable attention because its downregulation is involved in the development of several types of cancer. Because Pdcd4 interacts with the translation initiation factor eIF4A and inhibits its helicase activity, Pdcd4 has been implicated in the translational suppression of cellular mRNAs containing structured 5′-untranslated regions. However, Pdcd4's role in translation regulation is still poorly understood, because only very few physiological Pdcd4 target mRNAs are known. By using a Pdcd4-deficient clone of the chicken B-cell line DT40, we have discovered that the mRNA of the A-myb proto-oncogene is a novel Pdcd4 target RNA whose translation is suppressed by Pdcd4. Interestingly, the inhibitory effect of Pdcd4 is independent of the Pdcd4-eIF4A interaction, but is dependent on an RNA-binding domain at the N terminus of Pdcd4 and on sequences located within the coding region of A-myb mRNA, indicating that Pdcd4 suppresses A-myb translation by a novel mechanism. Our data show that the Pdcd4 RNA-binding domain preferentially recognizes an RNA secondary structure element formed by the part of the A-myb coding region that mediates Pdcd4-dependent suppression. Previously, we have shown that Pdcd4 also suppresses the translation of the c-myb mRNA by a similar mechanism involving binding of Pdcd4 to RNA secondary structure formed by the c-myb coding region. Surprisingly, our data show that Pdcd4 exerts its inhibitory activity only when the target region of Pdcd4 in A-myb and c-myb mRNA is itself translated, consistent with a mechanism in which Pdcd4 suppresses translation by interfering with translation elongation. Taken together, our work reveals a novel mechanism by which Pdcd4 affects the translational of cellular RNAs. Furthermore, as c-myb and A-myb are members of the Myb proto-oncogene family whose deregulation has been implicated in tumorigenesis, inhibiting their translation might contribute to the tumor-suppressive activity of Pdcd4. © 2015 Macmillan Publishers Limited All rights reserved.

Oncogene

A novel mechanism for the control of translation of specific mRNAs by tumor suppressor protein Pdcd4: Inhibition of translation elongation

Oncoscience

Translation, Pdcd4 and eIF4A

Background: Extreme constitution "Prakriti" types of Ayurveda exhibit systemic physiological attributes. Our earlier genetic study has revealed differences in EGLN1, key modulator of hypoxia axis between Prakriti types. This was associated with differences in high altitude adaptation and susceptibility to high altitude pulmonary edema (HAPE). In this study we investigate other molecular differences that contribute to systemic attributes of Prakriti that would be relevant in predictive marker discovery. Methods: Genotyping of 96 individuals of the earlier cohort was carried out in a panel of 2,800 common genic SNPs represented in Indian Genomic Variation Consortium (IGVC) panel from 24 diverse populations. Frequency distribution patterns of Prakriti differentiating variations (FDR correction P < 0.05) was studied in IGVC and 55 global populations (HGDP-CEPH) panels. Genotypic interactions between VWF, identified from the present analysis, and EGLN1 was analyzed using multinomial logistic regression in Prakriti and Indian populations from contrasting altitudes. Spearman's Rank correlation was used to study this genotypic interaction with respect to altitude in HGDP-CEPH panel. Validation of functional link between EGLN1 and VWF was carried out in a mouse model using chemical inhibition and siRNA studies. Result: Significant differences in allele frequencies were observed in seven genes (SPTA1, VWF, OLR1, UCP2, OR6K3, LEPR, and OR10Z1) after FDR correction (P < 0.05). A non synonymous variation (C/T, rs1063856) associated with thrombosis/bleeding susceptibility respectively, differed significantly between Kapha (C-allele) and Pitta (T-allele) constitution types. A combination of derived EGLN1 allele (HAPE associated) and ancestral VWF allele (thrombosis associated) was significantly high in Kapha group compared to Pitta (p < 10-5). The combination of risk-associated Kapha alleles was nearly absent in natives of high altitude. Inhibition of EGLN1 using (DHB) and an EGLN1 specific siRNA in a mouse model lead to a marked increase in vWF levels as well as pro-thrombotic phenotype viz. reduced bleeding time and enhanced platelet count and activation. Conclusion: We demonstrate for the first time a genetic link between EGLN1 and VWF in a constitution specific manner which could modulate thrombosis/bleeding susceptibility and outcomes of hypoxia. Integration of Prakriti in population stratification may help assemble common variations in key physiological axes that confers differences in disease occurrence and patho-phenotypic outcomes. © 2015 Aggarwal et al.