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

Highly fluorescent iridium nanoclusters were synthesized and investigated its application as a potential intracellular marker. The iridium nanoclusters were prepared with an average size of ∼2 nm. Further, these nanoclusters were refluxed with aromatic ligands, such as 2,2′-binaphthol (BINOL) in order to obtain fluorescence properties. The photophysical properties of these bluish-green emitting iridium nanoclusters were well characterized by using UV-Visible, fluorescence and lifetime decay measurements. The emission spectrum for these nanoclusters exhibit three characteristic peaks at 449, 480 and 515 nm. The fluorescence quantum yield of BINOL-Ir NCs were estimated to be 0.36 and the molar extinction co-efficients were in the order of 106 M -1cm-1. In vitro cytotoxicity studies in HeLa cells reveal that iridium nanoclusters exhibited good biocompatibility with an IC 50 value of ∼100 μg/ml and also showed excellent co-localization and distribution throughout the cytoplasm region without entering into the nucleus. This research has opened a new window in developing the iridium nanoparticle based intracellular fluorescent markers and has wide scope to act as biomedical nanocarrier to carry many biological molecules and anticancer drugs. © 2013 Springer Science+Business Media New York.

World University root node

Journal of Materials Science: Materials in Medicine

Highly fluorescent and biocompatible iridium nanoclusters for cellular imaging

A new antagonistic bacterial strain PGPR2 was isolated from the mungbean rhizosphere and documented for the production of hydrolytic enzymes with antifungal activity. Based on the phylogenetic analysis of the 16S rRNA gene sequence and phenotyping, this strain was identified as Pseudomonas aeruginosa. Maximum protease activity (235 U/mL) was obtained at 24 h of fermentation. The protease was purified to homogeneity in three steps: ammonium sulphate precipitation, anion exchange chromatography on DEAE- cellulose resin and gel filtration chromatography using P6 column. The purified enzyme had a molecular weight of ~33 kDa. The purified protease exhibited maximum activity at pH 6.0 and retained 80% of activity in a pH range of 5.0 - 9.0. Proteolytic activity was maximum in a temperature range of 40-70 °C. However, the enzyme was stable at 40 °C for 60 min. Among the metals tested, Mg2+ enhanced the protease activity. Internal amino acid sequence of the protease obtained by MALDI -ToF and subsequent Mascot database search showed maximum similarity to the HtpX protease of P. aeruginosa strain PA7. Thus, by virtue of its early production time, thermostability and effective antifungal ability, the protease purified and characterized from P. aeruginosa PGPR2 has several potential applications as fungicidal agents in agriculture.

Indian Journal of Experimental Biology

Proteolytic enzyme mediated antagonistic potential of Pseudomonas aeruginosa against Macrophomina phaseolina

Pseudomonas aeruginosa PGPR2 was found to protect mungbean plants from charcoal rot disease caused by Macrophomina phaseolina. Secondary metabolites from the culture supernatant of P. aeruginosa PGPR2 were extracted with ethyl acetate and the antifungal compound was purified by preparative HPLC using reverse phase chromatography. The purified compound showed antifungal activity against M. phaseolina and other phytopathogenic fungi (Fusarium sp., Rhizoctonia sp. Alternaria sp., and Aspergillus sp.). The structure of the purified compound was determined using 1H, 13C, 2D NMR spectra and liquid chromatography-mass spectrometry (LC-MS). Spectral data suggest that the antifungal compound is 3,4-dihydroxy-N-methyl-4-(4-oxochroman-2-yl)butanamide, with the chemical formula C14H17NO5 and a molecular mass of 279. Though chemically synthesized chromanone derivatives have been shown to have antifungal activity, we report for the first time, the microbial production of a chromanone derivative with antifungal activity. This ability of P. aeruginosa PGPR2 makes it a suitable strain for biocontrol. © Springer Science+Business Media New York 2013.

Applied Biochemistry and Biotechnology

Identification and structure elucidation of a novel antifungal compound produced by Pseudomonas aeruginosa PGPR2 against Macrophomina phaseolina

Protein aggregation leading to various nanoscale assemblies is under scrutiny due to its implications in a broad range of human diseases. In the present study, we have used ovalbumin, a model non-inhibitory serpin, to elucidate the molecular events involved in amyloid assembly using a diverse array of spectroscopic and imaging tools such as fluorescence, laser Raman, circular dichroism spectroscopy, and atomic force microscopy (AFM). The AFM images revealed a progressive morphological transition from spherical oligomers to nanoscopic annular pores that further served as templates for higher-order supramolecular assembly into larger amyloid pores. Raman spectroscopic investigations illuminated in-depth molecular details into the secondary structural changes of the protein during amyloid assembly and pore formation. Additionally, Raman measurements indicated the presence of antiparallel β-sheets in the amyloid core. Overall, our studies revealed that the protein conformational switch in the context of the oligomers triggers the hierarchical assembly into nanoscopic amyloid pores. Our results will have broad implications in the structural characterization of amyloid pores derived from a variety of disease-related proteins. © 2013 American Chemical Society.

Journal of Physical Chemistry Letters

Nanoscopic amyloid pores formed via stepwise protein assembly

Wound pH strongly influences residence time and activity of various growth factors during wound healing. Hence, a pH-responsive sustained release growth factor delivery system could be beneficial for effective treatment of wound. In this context, an effort was made to evaluate the potential of a poly(N-isopropylacrylamide-co-acrylic acid) hydrogel as pH-sensitive sustained release system for wound-pH-dependent therapeutics delivery. The polymer was synthesized via radical copolymerization and influence of pH on lower critical solution temperature (LCST), microarchitechture and swelling of the hydrogel was evaluated. Results showed a pH-dependent variation in the physical properties of the hydrogel within the wound pH range. Fluorescence recovery after photobleaching (FRAP) analysis endorsed a pH dependent restricted diffusion of the BSA in the hydrogel. Later, release of bovine serum albumin (BSA), vascular endothelial growth factor (VEGF) and epidermal growth factor (EGF) (each 5%, w/v) from the hydrogel within the range of wound pH (pH 6.7-7.9) were examined. Analysis showed non-Fickian release of therapeutics from the hydrogel with a significant variation in release rate and cumulative release with the increase in pH. Retention of the bioactivity of the released EGF was confirmed by studying murine dermal fibroblast cell proliferation in vitro. Finally, a growth factor (EGF or VEGF)-loaded hydrogel was applied on a murine excisional wound model and showed augmentation of wound healing in comparison to conventional sustained release growth factor therapy. © 2012 VSP.

Journal of Biomaterials Science, Polymer Edition

Wound pH-responsive sustained release of therapeutics from a poly(NIPAAm-co-AAc) hydrogel

Variants in the UGT1A1 gene and its promoter are known to determine levels of unconjugated bilirubin (UCB), but do not explain all cases of unconjugated hyperbilirubinemia. To discover associations with variants in genes other than UGT1A1, we undertook a genome-wide association study. We recruited 200 participants to cover the entire range of quantitative variation in UCB level. The data set-after data curation, including analyses for population stratification and cryptic relatedness-comprised genotypes at 512,349 SNP loci on 182 individuals. Quantitative trait locus (QTL) association analyses were performed, after adjusting the UCB level for effects of age, gender, and genotype at the dinucleotide (TA) insertion locus in UGT1A1 that is known to significantly modulate UCB level. A significant association of a polymorphic marker (rs2328136) near the NUP153 gene (which produces a 153 kDa nucleoporin) was obtained (p = 0.002, after multiple-testing correction). The frequency of the variant allele (A) at the rs2328136 locus in our study population is 40%, higher than most global populations. NUP153, whose product is a major regulatory factor in bidirectional transport of biomolecules across nucleus to cytosol, is associated with the transport of biliverdin reductase, which is important for bilirubin conjugation. © 2011 The Authors Annals of Human Genetics © 2011 Blackwell Publishing Ltd/University College London.

Annals of Human Genetics

A Genome-Wide Search for Non-UGT1A1 Markers Associated with Unconjugated Bilirubin Level Reveals Significant Association with a Polymorphic Marker Near a Gene of the Nucleoporin Family

Background: Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice.Results: Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species.Conclusions: SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice. © 2012 Parida et al.; licensee BioMed Central Ltd.

Fulltext

BMC Genomics

SNPs in stress-responsive rice genes: Validation, genotyping, functional relevance and population structure

The study of the basis of mental phenomena or the mind has always intrigued humans. Our current understanding of the functioning of the brain is the result of insightful research by many scientists, which has led to a detailed knowledge of brain structure and how this structure makes it possible for the mind to emerge from it. © 2012 Indian Academy of Sciences.

Resonance

Landmark discoveries in neurosciences

A multicomponent synthetic strategy involving copper(II) ions, tert-butylphosphonic acid (t-BuPO 3H 2) and 3-substituted pyrazole ligands has been adopted for the synthesis of soluble molecular copper(II) phosphonates. The use of six different 3-substituted pyrazoles, 3-R-PzH [R = H, Me, CF 3, Ph, 2-pyridyl (2-Py), and 2-methoxyphenyl (2-MeO-C 6H 4)] as ancillary ligands afforded nine different decanuclear cages, [Cu 5(μ 3-OH) 2(O 3P-t-Bu) 3(3-R-Pz) 2(X) 2] 2·(Y) where R = H, X = t-BuPO 3H, and Y = (Et 3NH +) 4(solvent) (1); R = Me, X = 3-MePzH, and Y = solvent (2); R = Me, X = t-BuPO 3H, and Y = (Et 3NH +) 4(solvent) (3); R = CF 3, X = t-BuPO 3H, and Y = (Et 3NH +) 4(solvent) (4); R = Ph, X = 3-PhPzH, and Y = solvent (5); R = 2-Py, X = 0.5 MeOH, and Y = solvent (6); R = 2-Py, X = none, and Y = solvent (7); R = 2-Py, X = H 2O, and Y = (Et 3NH +·PF 6 -) 2(solvent) (8); R = 2-MeO-C 6H 4, X = MeOH or 0.5:0.5 MeOH/H 2O, and Y = solvent (9). Compounds 1-6, 8, and 9 were isolated using a direct synthetic method which involves the reaction of copper(II) salts and the ligands, while 7 was obtained from an indirect route involving the reaction of preformed copper-pyridylpyrazolate precursor complexes and t-BuPO 3H 2. The decametallic compounds 1-9 possess a butterfly shaped core. The core of the cages 1, 3, and 4 are tetraanionic and contain more phosphonates than pyrazole ligands, while the other cages are neutral and contain more pyrazoles than phosphonate ligands. Compounds 1-6 have been studied by electrospray ionization-high-resolution mass spectrometry (ESI-HRMS). The decanuclear cage 6 was shown to be a good plasmid modifier. © 2012 American Chemical Society.

Inorganic Chemistry

Multicomponent assembly of anionic and neutral decanuclear copper(II) phosphonate cages

Plants being sessile are susceptible to heavy metals (HMs) toxicity and respond differentially to hostile environments. The toxicity of HM is governed by the type of ion and its concentration, plant physiology and stage of plant growth. Plants counteract the HMs stress by overexpressing numerous stress related proteins, glutathione mediated tolerance pathways and signaling proteins involving networks of various stress regulations. Though the response may vary and be specific in its stress networks regulation for each HM. The intricacy of HM tolerance response involves the set of molecular regulation, which demands to be understood to yield HM tolerant plant. Topical advancements in molecular biology and genomics have facilitated studies in transcriptomics and proteomics to identify regulatory genes implied in HM tolerance in plants. The integration of resources obtained through these studies will be of extreme significance, combining the diverse fields of plant biology to dissect the actual HM stress response network. In this review, we put an endeavor to describe the specific aspects of the molecular mechanisms of a plant response to HMs which may contribute to better understanding of the mode of HMs action and overlaps in metal sensing and signaling/crosstalk to other stresses. © 2012 Springer Science+Business Media, LLC.