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

World University root node

Nature genetics

Genomic landscapes of breast fibroepithelial tumors

Single molecule Förster resonance energy transfer (FRET) has been applied, for the first time, to monitor the growth (polymerization) and the shrinkage (depolymerization) of the dynamic microtubules, employing EGFP (attached to Mal3) as a donor and alexa-568 bound to tubulin as an acceptor. This journal © the Owner Societies 2015

Physical Chemistry Chemical Physics

Direct observation of the growth and shrinkage of microtubules by single molecule Förster resonance energy transfer

A molecular dynamics study on the collisional dynamics of soft and sticky single face-centered cubic crystal nanoparticles is presented. The softness and stickiness of the nanoparticles are controlled by varying parameters in the Lennard-Jones potential that is used to describe the interatomic interactions. Softening of nanoparticles due to extensive plastic deformations is observed as was previously found in hard nanoparticles. Further, two primary plastic deformation modes, slip and twinning, of the nanoparticles are found to play important roles in the temperature dependence of the coefficient of restitution. Additionally, we observe the effects of surface roughness, facets, and edges in the collisional behaviors of the sticky nanoparticles in low-velocity collisions. Nevertheless, the Johnson-Kendall-Roberts theory for macroscopic adhesive bodies still remains valid in nearly spherical nanoparticles. © 2015 American Physical Society.

Fulltext

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

Rich collision dynamics of soft and sticky crystalline nanoparticles: Numerical experiments

Designing various inorganic nanomaterials that are cost effective, water soluble, optically photostable, highly fluorescent and biocompatible for bioimaging applications is a challenging task. Similar to semiconducting quantum dots (QDs), silicon QDs are another alternative and are highly fluorescent, but non-water soluble. Several surface modification strategies were adopted to make them water soluble. However, the photoluminescence of Si QDs was seriously quenched in the aqueous environment. In this report, highly luminescent, water-dispersible, blue- and green-emitting Si QDs were prepared with good photostability. In vitro studies in monocytes reveal that Si QDs exhibit good biocompatibility and excellent distribution throughout the cytoplasm region, along with the significant fraction translocated into the nucleus. The in vivo zebrafish studies also reveal that Si QDs can be evenly distributed in the yolk-sac region. Overall, our results demonstrate the applicability of water-soluble and highly fluorescent Si QDs as excellent in vitro and in vivo bioimaging probes. © 2015 IOP Publishing Ltd.

Nanotechnology

Preparation, cytotoxicity and in vivo bioimaging of highly luminescent water-soluble silicon quantum dots

Surface-level ozone (O3) has been regarded as one of the most significant phytotoxic pollutants worldwide. Investigations addressing adverse impacts of elevated O3 on mung bean (Vigna radiata L.), an important leguminous crop of the Indian subcontinent, are still limited. The present study analyzed the differences on the foliar injury, reactive oxygen species (ROS) generation, antioxidative defense system, physiology, and foliar protein profile of two tropical mung bean cultivars (HUM-2 and HUM-6) exposed to elevated O3 under near-natural conditions. Both cultivars were negatively affected by the pollutant, but the response was cultivar-specific. Results revealed that elevated O3 induced higher levels of ROS (O2 ·− and H2O2) and lipid peroxidation leading to greater foliar injury in HUM-2 compared to HUM-6. Photosynthetic pigments, photosynthetic rate, stomatal conductance, and photochemical efficiency reduced under elevated O3 exposure and the extent of reduction was higher in HUM-2. Principal component analysis revealed that photosynthetic performance and quantum yield were drastically affected in HUM-2 as compared to HUM-6. Activities of antioxidative enzymes were also stimulated, suggesting generation of oxidative stress under elevated O3. HUM-6 showed higher induction of antioxidative enzymes than HUM-2. One-dimensional gel electrophoresis analysis showed drastic reductions in the abundantly present ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large and small subunits and the decrease was higher in HUM-2. Altogether, results suggested that higher accumulation of ROS and limited induction of antioxidant defense system led to more leaf injury and impairment of photosynthesis in HUM-2 than HUM-6 depicting its higher sensitivity towards elevated O3. © 2014, Springer-Verlag Wien.

Protoplasma

Biochemical and physiological characteristics of tropical mung bean (Vigna radiata L.) cultivars against chronic ozone stress: an insight to cultivar-specific response

The present investigation was performed to evaluate the effects of an insecticide and fungicide, namely, chlorpyrifos (CP) and propiconazole (PZ) on barley (Hordeum vulgare L. variety Karan-16). The seeds were treated with three concentrations of CP and PZ, i.e., 0.05%, 0.1% and 0.5% for 6 hours after different pre-soaking durations of 7, 17 and 27 hours. Different pre-soaking durations (7, 17 and 27 h) represent three phases of the cell cycle i.e., G1, S and G2, respectively. Double distilled water and ethyl methane sulfonate were used as negative and positive controls, respectively. As compared to their respective controls, treated root tip meristematic cells of barley showed significant reductions in the germination percentage, seedling height, mitotic index and comparative increase in chromosomal aberrations against both the pesticides, and the magnitude was higher in CP. After treatment with the pesticides, chlorophyll and carotenoid contents increased up to 0.1% but reduced at 0.5% and the decrease was more prominent in CP as compared to PZ. In treated cells, fragmentation, stickiness, bridges, multipolar anaphase and diagonal anaphase were observed as aberrations. As compared to control, chromosomal aberrations were higher in CP as compared to PZ. The results of the present study concluded that CP induced chromosomal aberrations were more frequent than PZ; hence it has higher probability to cause genotoxicity in barley. © 2015 Elsevier Inc.

Pesticide Biochemistry and Physiology

Differential sensitivity of barley (Hordeum vulgare L.) to chlorpyrifos and propiconazole: Morphology, cytogenetic assay and photosynthetic pigments

Textile effluent is characterized by high colour, chemical oxygen demand and conductivity due to presence of a large number of recalcitrant compounds. The effluent is often discharged without an effective treatment leading to contamination of water bodies. In the present study, a combination of mediator assisted laccase and chemical treatment was used for decolorization of effluent from a local textile mill in a continuous enzyme membrane reactor (EMR). Treatment of the effluent first with laccase and ABTS (2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid)) lead to about 60% decolorization but was accompanied by membrane fouling. Addition of alum further coagulated 90% of the residual colour but the process was associated with dye sludge formation and ABTS could not be recovered from the treated effluent. Reversal of the treatment sequence was effective in that 85% decolorization was achieved in the EMR and the process could be operated for over a period of 15 days. No sludge formation was noticed and membrane fouling was negligible. Most importantly, about 60% ABTS could be recovered from the treated effluent. Analysis of the treated effluent by mass spectrometery indicated extensive breakdown of the dye molecules by laccase and ABTS and the breakdown products were neither toxic nor mutagenic as assessed by measurement of the oxygen consumption rate and the standard Ames test. © 2014 Elsevier B.V.

Biochemical Engineering Journal

Combination of chemical and enzymatic treatment for efficient decolorization/degradation of textile effluent: High operational stability of the continuous process

The problem of scheduling independent tasks with a common deadline for a multicore processor is investigated. The speed of cores can be varied (from a finite set of core speeds) using software controlled Dynamic Voltage Scaling. The energy consumption is to be minimized. This problem was called the Energy Efficient Task Scheduling Problem (EETSP) in a previous work in which a Monte Carlo algorithm was proposed for solving it. This work investigates the complexity of the EETSP problem. The EETSP problem is proved to be NP-Complete. Under the assumption of P not equal NP, the EETSP problem is also proved to be inapproximable. (C) 2014 Wiley Periodicals, Inc.

COMPLEXITY

Complexity of a Problem of Energy Efficient Real-Time Task Scheduling on a Multicore Processor

The anti-tumor role and mechanisms of Cannabidiol (CBD), a non-psychotropic cannabinoid compound, are not well studied especially in triple-negative breast cancer (TNBC). In the present study, we analyzed CBD's anti-tumorigenic activity against highly aggressive breast cancer cell lines including TNBC subtype. We show here -for the first time-that CBD significantly inhibits epidermal growth factor (EGF)-induced proliferation and chemotaxis of breast cancer cells. Further studies revealed that CBD inhibits EGF-induced activation of EGFR, ERK, AKT and NF-kB signaling pathways as well as MMP2 and MMP9 secretion. In addition, we demonstrated that CBD inhibits tumor growth and metastasis in different mouse model systems. Analysis of molecular mechanisms revealed that CBD significantly inhibits the recruitment of tumor-associated macrophages in primary tumor stroma and secondary lung metastases. Similarly, our invitro studies showed a significant reduction in the number of migrated RAW 264.7 cells towards the conditioned medium of CBD-treated cancer cells. The conditioned medium of CBD-treated cancer cells also showed lower levels of GM-CSF and CCL3 cytokines which are important for macrophage recruitment and activation. In summary, our study shows -for the first time-that CBD inhibits breast cancer growth and metastasis through novel mechanisms by inhibiting EGF/EGFR signaling and modulating the tumor microenvironment. These results also indicate that CBD can be used as a novel therapeutic option to inhibit growth and metastasis of highly aggressive breast cancer subtypes including TNBC, which currently have limited therapeutic options and are associated with poor prognosis and low survival rates. © 2015 Federation of European Biochemical Societies.

Molecular oncology

Modulation of the tumor microenvironment and inhibition of EGF/EGFR pathway: Novel anti-tumor mechanisms of Cannabidiol in breast cancer

The microRNAs are small, endogenous non-coding RNAs found in plants and animals, which suppresses the expression of genes post-transcriptionally. It is suggested by various genome-wide studies that a substantial fraction of miRNA genes is likely to form clusters. The coherent expression of the miRNA clusters can then be used to classify samples according to the clinical outcome. In this background, a new rough hypercuboid based supervised similarity measure is proposed that is integrated with the supervised attribute clustering to find groups of miRNAs whose coherent expression can classify samples. The proposed method directly incorporates the information of sample categories into the miRNA clustering process, generating a supervised clustering algorithm for miRNAs. The effectiveness of the rough hypercuboid based algorithm, along with a comparison with other related algorithms, is demonstrated on three miRNA microarray expression data sets using the B.632+ bootstrap error rate of support vector machine. The association of the miRNA clusters to various biological pathways are also shown by doing pathway enrichment analysis. © Springer International Publishing Switzerland 2015.