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 photoinduced electron transfer (PET) reaction has been investigated in a room temperature imidazolium ionic liquid (RTIL), 1-ethyl-3-methylimidazolium ethyl sulfate ([Emim][EtSO4]) and also in [Emim][EtSO 4]-co-solvents mixtures from N,N-dimethyl aniline (DMA) to different Coumarin dyes using steady state and time-resolved fluorescence quenching measurements. We have used water and methanol and 2-propanol as the cosolvents of RTILs for the PET study. On going from neat ionic liquid to the RTIL-co-solvents mixtures the electron transfer rate has been largely enhanced. In neat RTIL as well as in [Emim][EtSO4]-co-solvents mixtures, a Marcus type of inversion in the PET rate have been observed. © 2011 American Chemical Society.

World University root node

Journal of Physical Chemistry B

Photoinduced electron transfer in an imidazolium ionic liquid and in its binary mixtures with water, methanol, and 2-propanol: Appearance of Marcus-type of inversion

Mutations in the gene microcephalin/MCPH1 result in the neurodevelopmental disease microcephaly. A recent report provides evidence that MCPH1 controls neuroprogenitor entry into mitosis via the Chk1-Cdc25b centrosome maturation pathway. © 2012 Elsevier Ltd.

Fulltext

Current Biology

Neurogenesis: Premature mitotic entry lets cleavage planes take off!

We present a set of four parameters that in combination can predict DNA-binding residues on protein structures to a high degree of accuracy. These are the number of evolutionary conserved residues (N cons) and their spatial clustering ($\rho$ e), hydrogen bond donor capability (D p) and residue propensity (R p). We first used these parameters to characterize 130 interfaces in a set of 126 DNA-binding proteins (DBPs). The applicability of these parameters both individually and in combination, to distinguish the true binding region from the rest of the protein surface was then analyzed. R pshows the best performance identifying the true interface with the top rank in 83% cases. Importantly, we also used the unbound-bound test cases of the protein-DNA docking benchmark to test the efficacy of our method. When applied to the unbound form of the DBPs, R pcan distinguish 86% cases. Finally, we have applied the SVM approach for recognizing the interface region using the above parameters along with the individual amino acid composition as attributes. The accuracy of prediction is 90.5% for the bound structures and 93.6% for the unbound form of the proteins. {\textcopyright} The Author(s) 2012.

Nucleic Acids Research

Characterization and prediction of the binding site in DNA-binding proteins: Improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters

Recently nano scale zero valent iron particles (nZVI) have been considered as smart adsorbent for environmental and groundwater remediation. Although several synthetic methods are available for the preparation of nZVI, air stable nZVI are not available for remediation works. Further, challenges demand synthesis of nZVI without stabilizers and capping agents. A modified methodology for the synthesis of air stable nZVI has been developed without any capping agents and characterized by powder X-Ray Diffraction (XRD), Scanning Electron Microscopy Energy-dispersive X-Ray (SEM-EDS), Transmission Electron Microscopy (TEM) and X-Ray Photoelectron Spectroscopy (XPS). The results of the present study suggest that the synthetic nZVI are air-stable over a period of one year and consists of particles of 30-40 nm in diameter. Although a layer of less than 3 nm thick oxide/hydroxide is observed by TEM and XPS, it appears to be due to oxidation of outer surface during analysis. Adsorption study has shown that the synthetic nZVI are more effective adsorbent than the commercial nZVI and can remove simultaneously arsenite [AsIII] and arsenate [AsV] from water without prior reduction of AsV to AsIII. The removal process is adsorptive rather than precipitative and the removal of AsIII is greater than that of AsV.

Journal of the Indian Chemical Society

Synthesis of zero valent iron nanoparticles and application to removal of arsenic(III) and arsenic(V) from water

We have isolated a Staphylococcus arlettae strain, strain CVD059, from the blood of a rheumatic mitral stenosis patient. Here, we report the genome sequence and potential virulence factors of this clinical isolate. The draft genome of S. arlettae CVD059 is 2,565,675 bp long with a G+C content of 33.5%. © 2012, American Society for Microbiology.

Journal of Bacteriology

Genome sequence of Staphylococcus arlettae strain CVD059, isolated from the blood of a cardiovascular disease patient

Chemical genomics is a newly emerged and rapidly progressing field in biology, where small chemical molecules bind specifically and reversibly to protein(s) to modulate their function(s), leading to the delineation and subsequent unravelling of biological processes. This approach overcomes problems like lethality and redundancy of classical genetics. Armed with the powerful techniques of combinatorial synthesis, high-throughput screening and target discovery chemical genomics expands its scope to diverse areas in biology. The well-established genetic system of Arabidopsis model allows chemical genomics to enter into the realm of plant biology exploring signaling pathways of growth regulators, endomembrane signaling cascades, plant defense mechanisms and many more events.

Indian Journal of Biochemistry and Biophysics

Chemical genomics in plant biology

Purpose: The role of innate immune regulators is investigated in injury sustained from irradiation as in the clinic for cancer treatment or from a nuclear incident. The protective benefits of flagellin signaling through Toll-like receptors (TLR) in an irradiation setting warrant study of a key intracellular adaptor of TLR signaling, namely Myeloid differentiation primary response factor 88 (MyD88). The role of MyD88 in regulating innate immunity and Nuclear factor kappa-B (NF-κB)-activated responses targets this critical factor for influencing injury and recovery as well as maintaining immune homeostasis. Materials and methods: To examine the role of MyD88, we examined immune cells and factors during acute pneumonitic and fibrotic phases in Myd88-deficient animals receiving thoracic gamma (γ)-irradiation. Results: We found that MyD88 supports survival from radiation-induced injury through the regulation of inflammatory factors that aid in recovery from irradiation. The absence of MyD88 resulted in unresolved pulmonary infiltrate and enhanced collagen deposition plus elevated type 2 helper T cell (Th2) cytokines in long-term survivors of irradiation. Conclusions: These results based only on a gene deletion model suggest that alterations of MyD88-dependent inflammatory processes impact chronic lung injury. Therefore, MyD88 may contribute to attenuating long-term radiation-induced lung injury and protecting against fibrosis. © 2012 Informa UK, Ltd.

International Journal of Radiation Biology

MyD88 provides a protective role in long-term radiation-induced lung injury

The DNA double strand break repair gene XRCC4, an important caretaker of genome stability and XRCC3 are suggested to play an imperative role in the development of carcinogenesis. However, no evidence has been provided showing that these genes are associated with risk of urinary bladder cancer (UBC). The study was designed to examine the polymorphisms associated with two genes namely XRCC4 G1394T (rs6869366), intron 3 (rs28360317), intron 7 rs1805377 and rs2836007 and XRCC3 (rs861539 and rs1799796), respectively and investigate their role as susceptible markers for UBC risk in North Indian cohort. In this hospital-based case-control study histologically confirmed 211 UBC patients and 244 age and gender matched controls of similar ethnicity were genotyped by means of PCR-RFLP. Significant different distributions in the frequency of the XRCC4 intron 3 genotype, but not the XRCC4 G1394T or intron 7 genotypes, between the UBC and control groups were observed. XRCC4 intron 7 Del/Del conferred enhanced risk (OR 1.94; P 0.017) in UBC. Interestingly, XRCC -1394 G[T variant genotype GG was associated with reduced risk (OR 0.27; P 0.020). However, none of the four polymorphisms in XRCC4 were associated with tobacco smoking and risk of recurrence in patients treated with BCG immunotherapy. Similarly, none of the XRCC3 polymorphisms were associated with UBC susceptibility. Our results suggested that the XRCC4 intron 3 rs6869366 genotype and intron 7 rs28360317 may be associated with UBC risk and may be a novel useful marker for primary prevention and anticancer intervention. © 2011 Springer Science+Business Media B.V.

Molecular biology reports

Gene variants of XRCC4 and XRCC3 and their association with risk for urothelial bladder cancer

American Journal of Human Genetics

Erratum: Recent admixture in an Indian population of African ancestry (American Journal of Human Genetics (2011) 89 (111-120))

We have conjugated chloroquine, an anti-malarial, antiviral and anti-tumor drug, with thiol-functionalized gold nanoparticles and studied their binding interaction with bovine serum albumin (BSA) protein. Gold nanoparticles have been synthesized using sodium borohydride as reducing agent and 11-mercaptoundecanoic acid as thiol functionalizing ligand in aqueous medium. The formation of gold nanoparticles was confirmed from the characteristic surface plasmon absorption band at 522. nm and transmission electron microscopy revealed the average particle size to be ∼7. nm. Chloroquine was conjugated to thiolated gold nanoparticles by using EDC/NHS chemistry and the binding was analyzed using optical density measurement and Fourier transform infrared spectroscopy. The chloroquine-conjugated gold nanoparticles (GNP-Chl) were found to interact efficiently with BSA. Thermodynamic parameters suggest that the binding is driven by both enthalpy and entropy, accompanied with only a minor alteration in protein's structure. Competitive drug binding assay revealed that the GNP-Chl bind at warfarin binding site I in subdomain IIA of BSA and was further supported by Trp212 fluorescence quenching measurements. Unraveling the nature of interactions of GNP-Chl with BSA would pave the way for the design of nanotherapeutic agents with improved functionality, enriching the field of nanomedicine. {\textcopyright} 2010 Elsevier Inc.