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

Signal transducer and activator of transcription 1 (STAT1) mediates interferon gamma signaling which activates the expression of various genes related to apoptosis, inflammation, cell cycle and angiogenesis. Several experimental and clinical studies have investigated the role of STAT1 in primary tumor growth in breast cancer; however, its role in tumor metastasis remains to be determined. To determine the role of STAT1 in breast cancer metastasis, we analyzed growth and metastasis in WT or STAT1−/− mice orthotopically implanted with metastatic 4T1.2 cells. Primary tumor development was faster in STAT1−/− mice and these mice developed significantly bigger primary tumors and displayed more lung metastasis compared with WT counterparts. STAT1−/− mice showed elevated Ly6G+CD11b+ granulocytic MDSC infiltration in their primary tumors and spleens with concomitant upregulation of Mmp9 and Cxcl1 expression in tumors compared with WT counterparts. Blockade of IL-17A in primary tumor-bearing STAT1−/− mice suppressed accumulation of Ly6G+CD11b+ cells and markedly reduced lung metastasis. These data show that STAT1 is an important suppressor of primary breast tumor growth and metastasis. Importantly, we found anti-IL-17 treatment can rescue STAT1 deficient animals from developing exacerbated metastasis to the lungs which could be important for immunotherapies for immunocompromised breast cancer patients. © 2017 The Author(s). Published with license by Taylor & Francis Group, LLC © 2017, © Sanjay Varikuti, Steve Oghumu, Mohamad Elbaz, Greta Volpedo, Dinesh K. Ahirwar, Pablo C. Alarcon, Rachel H. Sperling, Ellen Moretti, Marissa S. Pioso, Jennifer Kimble, Mohd W. Nasser, Ramesh K. Ganju, Cesar Terrazas, and Abhay R. Satoskar.

World University root node

Oncoimmunology

STAT1 gene deficient mice develop accelerated breast cancer growth and metastasis which is reduced by IL-17 blockade

Activation of proinflammatory macrophages is associated with the inflammatory state of rheumatoid arthritis. Their polarization and activation are controlled by transcription factors such as NF-κB and the AP-1 transcription factor member c-Fos. Surprisingly, little is known about the role of the AP-1 transcription factor c-Jun in macrophage activation. In this study, we show that mRNA and protein levels of c-Jun are increased in macrophages following pro-or anti-inflammatory stimulations. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment cluster analyses of microarray data using wild-Type and c-Jun-deleted macrophages highlight the central function of c-Jun in macrophages, in particular for immune responses, IL production, and hypoxia pathways. Mice deficient for c-Jun in macrophages show an amelioration of inflammation and bone destruction in the serum-induced arthritis model. In vivo and in vitro gene profiling, together with chromatin immunoprecipitation analysis of macrophages, revealed direct activation of the proinflammatory factor cyclooxygenase-2 and indirect inhibition of the antiinflammatory factor arginase-1 by c-Jun. Thus, c-Jun regulates the activation state of macrophages and promotes arthritis via differentially regulating cyclooxygenase-2 and arginase-1 levels. Copyright © 2017 by The American Association of Immunologists, Inc.

Journal of Immunology

The AP-1 transcription factor c-jun promotes arthritis by regulating cyclooxygenase-2 and arginase-1 expression in macrophages

Ovarian cancer is a fatal gynecologic cancer. Altered expression of biomarkers leads to this deadly cancer. Therefore, understanding the underlying biological mechanisms may help in developing a robust diagnostic as well as a prognostic tool. It has been demonstrated in various studies the pathways associated with ovarian cancer have dysregulated miRNA as well as mRNA expression. Identification of miRNA-mRNA regulatory modules may help in understanding the mechanism of altered ovarian cancer pathways. In this regard, an existing robust mutual information based Maximum-Relevance Maximum-Significance algorithm has been used for identification of miRNA-mRNA regulatory modules in ovarian cancer. A set of miRNA-mRNA modules are identified first than their association with ovarian cancer are studied exhaustively. The effectiveness of the proposed approach is compared with existing methods. The proposed approach is found to generate more robust integrated networks of miRNA-mRNA in ovarian cancer. © 2017, Springer International Publishing AG.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Machine Learning Approach for Identification of miRNA-mRNA Regulatory Modules in Ovarian Cancer

One of the important problems in functional genomics is how to select the disease genes. In this regard, the paper presents a new gene selection algorithm, termed as RelSim, to identify disease genes. It integrates judiciously the information of gene expression profiles and protein-protein interaction networks. A new similarity measure is introduced to compute the functional similarity between two genes. It is based on the information of protein-protein interaction networks. The new similarity measure offers an efficient way to calculate the functional similarity between two genes. The proposed algorithm selects a set of genes as disease genes, considering both microarray and protein-protein interaction data, by maximizing the relevance and functional similarity of the selected genes. While gene expression profiles are used to identify differentially expressed genes, the protein-protein interaction networks help to compute the functional similarity among genes. The performance of the proposed algorithm, along with a comparison with other related methods, is demonstrated on several colon cancer data sets. © 2016 Elsevier Inc.

Information Sciences

RelSim: An integrated method to identify disease genes using gene expression profiles and PPIN based similarity measure

The current study delineates the development of novel gelatin–tamarind gum/carboxymethyl tamarind gum-based phase-separated films for probable skin tissue engineering applications. Polyethylene glycol was used as plasticizer. The films were characterized thoroughly using mechanical tester and impedance analyzer. Cell proliferation ability and drug release properties of the films were investigated. Mechanical studies indicated composition-dependent stress relaxation properties. Polysaccharide containing films supported better proliferation of human keratinocytes as compared to control. Drug-loaded films showed good antimicrobial properties against Escherichia coli. Analysis of the results indicated that the prepared films may be tried as matrices for skin tissue engineering. © 2017 Taylor & Francis.

Polymer - Plastics Technology and Engineering

Preparation, Characterization and Assessment of the Novel Gelatin–tamarind Gum/Carboxymethyl Tamarind Gum-Based Phase-Separated Films for Skin Tissue Engineering Applications

The current study discusses the synthesis of novel gelatin–chitosan lactate cohydrogels. Mechanical studies indicated the viscoelastic nature of the cohydrogels. The cohydrogels were predominantly elastic in nature. Inherent mechanical stability of the cohydrogels was better than the pristine gelatin hydrogel. Incorporation of chitosan lactate improved the in vitro swelling and the drug release properties of the cohydrogels. The cohydrogels showed good antimicrobial drug delivery capacity. The properties of the developed cohydrogels demonstrated that they could be used as delivery vehicles for antimicrobial drugs. Cell proliferation study suggested that the cohydrogels supported the proliferation of the human keratinocytes. © 2017 Taylor & Francis.

Synthesis and Assessment of Novel Gelatin–Chitosan Lactate Cohydrogels for Controlled Delivery and Tissue Engineering Applications

Cells regularly synthesize new proteins to replace old or damaged proteins. Deposition of various aberrant proteins in specific brain regions leads to neurodegeneration and aging. The cellular protein quality control system develop various defense mechanisms against the accumulation of misfolded and aggregated proteins. The mechanisms underlying the selective recognition of specific crucial protein or misfolded proteins are majorly governed by quality control E3 ubiquitin ligases mediated through ubiquitin-proteasome system. Few known E3 ubiquitin ligases have shown prominent neurodevelopmental functions, but their interactions with different developmental proteins play critical roles in neurodevelopmental disorders. Several questions are yet to be understood properly. How E3 ubiquitin ligases determine the specificity and regulate degradation of a particular substrate involved in neuronal proliferation and differentiation is certainly the one, which needs detailed investigations. Another important question is how neurodevelopmental E3 ubiquitin ligases specifically differentiate between their versatile range of substrates and timing of their functional modulations during different phases of development. The premise of this article is to understand how few E3 ubiquitin ligases sense major molecular events, which are crucial for human brain development from its early embryonic stages to throughout adolescence period. A better understanding of these few E3 ubiquitin ligases and their interactions with other potential proteins will provide invaluable insight into disease mechanisms to approach toward therapeutic interventions. © 2017 Upadhyay, Joshi, Amanullah, Mishra, Arora, Prasad and Mishra.

Fulltext

Frontiers in Molecular Neuroscience

E3 ubiquitin ligases neurobiological mechanisms: Development to degeneration

Product graphs have been gainfully used in literature to generate mathematical models of complex networks which inherit properties of real networks. Realizing the duplication phenomena imbibed in the definition of corona product of two graphs, we define corona graphs. Given a small simple connected graph which we call seed graph, corona graphs are defined by taking corona product of the seed graph iteratively. We show that the cumulative degree distribution of corona graphs decay exponentially when the seed graph is regular and the cumulative betweenness distribution follows power law when the seed graph is a clique. We determine spectra and signless Laplacian spectra of corona graphs in terms of the corresponding spectra of the seed graph when the seed graph is regular or a complete bipartite graph. Laplacian spectra of corona graphs corresponding to any seed graph is obtained in terms of the Laplacian spectra of the seed graph. (C) 2017 Elsevier B.V. All rights reserved.

DISCRETE APPLIED MATHEMATICS

Structural and spectral properties of corona graphs

Oleaginous yeast closely related to Cystobasidium oligophagum was isolated from soil rich in cellulosic waste. The yeast was isolated based on its ability to accumulate intracellular lipid, grow on carboxymethylcellulose (CMC) and produce lipase. It could accumulate up to 39.44% lipid in a glucose medium (12.45 ± 0.97 g/l biomass production). It was able to grow and accumulate lipids (36.46%) in the medium containing CMC as the sole carbon source. The specific enzyme activities obtained for endoglucanase, exoglucanase, and β-glucosidase were 2.27, 1.26, and 0.98 IU/mg respectively. The specific enzyme activities obtained for intracellular and extracellular lipase were 2.16 and 2.88 IU/mg respectively. It could grow and accumulate lipids in substrates including glycerol (42.04%), starch (41.54%), xylose (36.24%), maltose (26.31%), fructose (24.29%), lactose (21.91%) and sucrose (21.72%). The lipid profile of the organism was suitable for obtaining biodiesel with desirable fuel properties. © 2016 Elsevier Ltd

Bioresource Technology

Isolation, identification and characterization of Cystobasidium oligophagum JRC1: A cellulase and lipase producing oleaginous yeast

Abstract : Intrinsically disordered proteins (IDPs) belong to an important class of proteins that do not fold up spontaneously. The conformational flexibility of IDPs allows them to adopt a wide range of conformations depending upon their biochemical environment. Many IDPs undergo profound conformational conversion that is often coupled to amyloid aggregation in the presence of negatively charged lipid membranes. Here, we show the effect of a well-known anionic lipid mimetic, sodium dodecyl sulfate (SDS), on the aggregation mechanism of a model amyloidogenic IDP, namely, bovine κ -casein. In the absence of SDS, the aggregation kinetics of reduced and carboxymethylated (RCM) κ -casein followed a nucleation dependent polymerization model that comprises both lag- and assembly phases. On the contrary, in the presence of sub-micellar concentration of SDS, the aggregation kinetics did not exhibit a lag phase and appears to follow a non-nucleation pathway. Additionally, the morphologies of the aggregates formed in the absence and presence of SDS were found to be different. In the absence of SDS, κ -casein aggregation proceeded to typical amyloid fibrils, whereas, in the presence of SDS, the aggregation yielded large oligomers. Our results provide important molecular insights into the aggregation mechanism that can be utilized for the designing of novel protein/amyloid based nanomaterials with desired properties. Graphical Abstract : Synopsis: An amyloidogenic intrinsically disordered protein, κ -casein aggregates into amyloid fibrils via a typical nucleation-dependent kinetics that exhibits a lag-phase. However, in the presence of an anionic surfactant, such as sodium dodecyl sulfate, κ -casein aggregation is devoid of a lag-phase and yields large oligomers that do not convert into amyloid fibrils. © 2017, Indian Academy of Sciences.