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

Cancer is one of the most deadly diseases threatening the lives of humans. Although many treatment methods have been developed to tackle cancer, each modality of cancer treatment has its own limitations and drawbacks. The development of minimally invasive treatment modalities for cancers remains a great challenge. Near-infrared (NIR) light-activated nanomaterial-mediated phototherapies, including photothermal and photodynamic therapies, provide an alternative means for spatially and temporally controlled minimally invasive treatments of cancers. Nanomaterials can serve as nanocargoes for the delivery of chemo-drugs, diagnostic contrast reagents, and organic photosensitizers, and can be used to directly generate heat or reactive oxygen species for the treatment of tumors without the need for organic photosensitizers with NIR-light irradiation. Here, current progress in NIR-light-activated nanomaterial-mediated photothermal therapy and photodynamic therapy is summarized. Furthermore, the effects of size, shape, and surface functionalities of nanomaterials on intracellular uptake, macrophage clearance, biodistribution, cytotoxicities, and biomedical efficacies are discussed. The use of various types of nanomaterials, such as gold nanoparticles, carbon nanotubes, graphene, and many other inorganic nanostructures, in combination with diagnostic and therapeutic modalities for solid tumors, is briefly reviewed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

World University root node

Advanced Materials

Near-Infrared-Light-Activatable Nanomaterial-Mediated Phototheranostic Nanomedicines: An Emerging Paradigm for Cancer Treatment

Nucleotide binding domain, leucine-rich repeat containing proteins (NLRs) are a family of pattern recognition receptors involved in major innate immune defense mechanisms. NLRs play a key role in several cancers, autoimmune, and inflammation-associated diseases. Association of NLRP3 has been widely investigated in neurodegenerative diseases, chronic alcoholism, depression, traumatic brain injury, and pathogenic infections. Several research studies have shown possible involvement of various other inflammasome-forming and non-inflammasome-forming NLRs in the brain; however, their mechanisms of action are yet to be defined clearly. Our review provides a comprehensive overview of the expression of NLRs in human brain and their critical association with inflammation and neurodegenerative diseases. The review also summarizes promising NLR-targeted therapeutics and their prospects for brain pathologies. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.

Molecular Neurobiology

NLRs as Helpline in the Brain: Mechanisms and Therapeutic Implications

The chemokine CXCL12 has been shown to regulate breast tumor growth, however, its mechanism in initiating distant metastasis is not well understood. Here, we generated a novel conditional allele of Cxcl12 in mice and used a fibroblast-specific Cre transgene along with various mammary tumor models to evaluate CXCL12 function in the breast cancer metastasis. Ablation of CXCL12 in stromal fibroblasts of mice significantly delayed the time to tumor onset and inhibited distant metastasis in different mouse models. Elucidation of mechanisms using in vitro and in vivo model systems revealed that CXCL12 enhances tumor cell intravasation by increasing vascular permeability and expansion of a leaky tumor vasculature. Furthermore, our studies revealed CXCL12 enhances permeability by recruiting endothelial precursor cells and decreasing endothelial tight junction and adherence junction proteins. High expression of stromal CXCL12 in large cohort of breast cancer patients was directly correlated to blood vessel density and inversely correlated to recurrence and overall patient survival. In addition, our analysis revealed that stromal CXCL12 levels in combination with number of CD31+ blood vessels confers poorer patient survival compared to individual protein level. However, no correlation was observed between epithelial CXCL12 and patient survival or blood vessel density. Our findings describe the novel interactions between fibroblasts-derived CXCL12 and endothelial cells in facilitating tumor cell intrvasation, leading to distant metastasis. Overall, our studies indicate that cross-talk between fibroblast-derived CXCL12 and endothelial cells could be used as novel biomarker and strategy for developing tumor microenvironment based therapies against aggressive and metastatic breast cancer. © 2018, Macmillan Publishers Limited, part of Springer Nature.

Oncogene

Fibroblast-derived CXCL12 promotes breast cancer metastasis by facilitating tumor cell intravasation

Microtubules regulate eukaryotic cell functions, which have tremendous implication in tumor progression. Thus, the design of novel approaches for controlling microtubule function is extremely important. In this manuscript, a novel tetrapeptide Ser-Leu-Arg-Pro (SLRP) has been designed and synthesized from a small peptide library consisting of 14 tetrapeptides, which perturbs microtubule function through interaction in the "anchor region". We have studied the role of peptides on microtubule function on a chemically functionalized 2D platform. Interestingly, we have found that SLRP binds with tubulin and inhibits the kinesin-driven microtubule motility on a kinesin-immobilized chemically functionalized 2D platform. Further, this peptide modulator interacts with intracellular tubulin/microtubule and depolymerizes the microtubule networks. These interesting findings of perturbation of microtubule function both on engineered platforms and inside the cell by this small peptide modulator inspired us to study the effect of this tetrapeptide on cancer cell proliferation. We found that the novel tetrapeptide modulator causes moderate cytotoxicity to the human breast cancer cell (MCF-7 cell), induces the apoptotic death of MCF-7 cell, and activates the tumor suppressor proteins p53 and cyclin-dependent kinase inhibitor 1 (p21). To the best of our knowledge, this is the shortest peptide discovered, which perturbs microtubule function both on an engineered 2D platform and inside the cell. © 2017 American Chemical Society.

Langmuir

Designed Tetrapeptide Interacts with Tubulin and Microtubule

A precise knowledge of the quaternary structure of proteins is essential to illuminate both their function and their evolution. The major part of our knowledge on quaternary structure is inferred from X-ray crystallography data, but this inference process is hard and error-prone. The difficulty lies in discriminating fortuitous protein contacts, which make up the lattice of protein crystals, from biological protein contacts that exist in the native cellular environment. Here, we review methods devised to discriminate between both types of contacts and describe resources for downloading protein quaternary structure information and identifying high-confidence quaternary structures. The use of high-confidence datasets of quaternary structures will be critical for the analysis of structural, functional and evolutionary properties of proteins.

Methods in Molecular Biology

Inferring and using protein quaternary structure information from crystallographic data

High-throughput screening and better understanding of small molecule's structure-activity relationship (SAR) using computational biology techniques have greatly expanded the face of drug discovery process in better discovery of therapeutics for various disease. Small Molecule Modulators Database (SMMDB) includes &gt;1100 small molecules that have been either approved by US Food and Drug Administration, are under investigation or were rejected in clinical trial for any kind of neurological diseases. The comprehensive information about small molecules includes the details about their molecular targets (such as protein or enzyme, DNA, RNA, antisense RNA etc.), pharmacokinetic and pharmacodynamic properties such as binding affinity to their targets (K d , K i , IC 50 and EC 50 if available), mode of action, log P-value, number of hydrogen bond donor and acceptors, their clinical trial status, their 2D and three-dimensional structures etc. To enrich the basic annotation of every small molecule entry present in SMMDB, it is hyperlinked to their description present in PubChem, DrugBank, PubMed and KEGG database. The annotation about their molecular targets was enriched by linking it with UniProt and GenBank and STRING database that can be utilized to study the interaction and relation between various targets involved in single neurological disease. All molecules present in the SMMDB are made available to download in single file and can be further used in establishing the SAR, structure-based drug designing as well as shape-based virtual screening for developing the novel therapeutics against neurological diseases. The scope of this database majorly covers the interest of scientific community and researchers who are engaged in putting their endeavor toward therapeutic development and investigating the pathogenic mechanism of various neurological diseases. The graphical user interface of the SMMDB is accessible on http://bsbe.iiti.ac.in/bsbe/smmdb. © The Author(s) 2018. Published by Oxford University Press.

Fulltext

Database

SMMDB: A web-accessible database for small molecule modulators and their targets involved in neurological diseases

Nanoparticles activated by near-infrared (NIR) excitation provide a capability for optical imaging and photodestruction of tumors. We have engineered optical nanoconstructs derived from erythrocytes, which are doped with the FDA-approved NIR dye, indocyanine green (ICG). We refer to these constructs as NIR erythrocyte-mimicking transducers (NETs). Herein, we investigate the phototheranostic capabilities of NETs for fluorescence imaging and photodestruction of SKBR3 breast cancer cells and subcutaneous xenograft tumors in mice. Our cellular studies demonstrate that NETs are internalized by these cancer cells and localized to their lysosomes. As evidenced by NIR fluorescence imaging and in vivo laser irradiation studies, NETs remain available within tumors at 24 h postintravenous injection. In response to continuous wave 808 nm laser irradiation at intensity of 680 mW/cm2 for 10-15 min, NETs mediate the destruction of cancer cells and tumors in mice through synergistic photochemical and photothermal effects. We demonstrate that NETs are effective in mediating photoactivation of Caspase-3 to induce tumor apoptosis. Our results provide support for the effectiveness of NETs as theranostic agents for fluorescence imaging and photodestruction of tumors and their role in photoinduced apoptosis initiated by their localization to lysosomes. © 2018 American Chemical Society.

ACS Applied Materials and Interfaces

Erythrocyte-Derived Theranostic Nanoplatforms for Near Infrared Fluorescence Imaging and Photodestruction of Tumors

Curli amyloid fibers are produced as part of the extracellular biofilm matrix and are composed primarily of the major structural subunit CsgA. The CsgE chaperone facilitates the secretion of CsgA through CsgG by forming a cap at the base of the nonameric CsgG outer membrane pore. We elucidated a series of finely tuned nonpolar and charge-charge interactions that facilitate the oligomerization of CsgE and its ability to transport unfolded CsgA to CsgG for translocation. CsgE oligomerization in vitro is temperature dependent and is disrupted by mutations in the W48 and F79 residues. Using nuclear magnetic resonance (NMR), we identified two regions of CsgE involved in the CsgE-CsgA interaction: a head comprising a positively charged patch centered around R47 and a stem comprising a negatively charged patch containing E31 and E85. Negatively charged residues in the intrinsically disordered N-and C-terminal “tails” were not implicated in this interaction. Head and stem residues were mutated and interrogated using in vivo measurements of curli production and in vitro amyloid polymerization assays. The R47 head residue of CsgE is required for stabilization of CsgA-and CsgE-mediated curli fiber formation. Mutation of the E31 and E85 stem residues to positively charged side chains decreased CsgE-mediated curli fiber formation but increased CsgE-mediated stabilization of CsgA. No single-amino-acid substitutions in the head, stem, or tail regions affected the ability of CsgE to cap the CsgG pore as determined by a bile salt sensitivity assay. These mechanistic insights into the directed assembly of functional amyloids in extracellular biofilms elucidate possible targets for biofilm-associated bacterial infections. IMPORTANCE Curli represent a class of functional amyloid fibers produced by Escherichia coli and other Gram-negative bacteria that serve as protein scaffolds in the extracellular biofilm matrix. Despite the lack of sequence conservation among different amyloidogenic proteins, the structural and biophysical properties of functional amyloids such as curli closely resemble those of amyloids associated with several common neurodegenerative diseases. These parallels are underscored by the observation that certain proteins and chemicals can prevent amyloid formation by the major curli subunit CsgA and by alpha-synuclein, the amyloid-forming protein found in Lewy bodies during Parkinson’s disease. CsgA subunits are targeted to the CsgG outer membrane pore by CsgE prior to secretion and assembly into fibers. Here, we use biophysical, biochemical, and genetic approaches to elucidate a mechanistic understanding of CsgE function in curli biogenesis. © 2018 Klein et al.

mBio

Structure-function analysis of the curli accessory protein CsgE defines surfaces essential for coordinating amyloid fiber formation

The U-Box E3 ubiquitin ligase, AtPUB46, functions in the drought response: T-DNA insertion mutants of this single paralogous gene are hypersensitive to water- and oxidative stress (Adler et al. BMC Plant Biology 17:8, 2017). Here we analyze the phenotype of AtPUB46 overexpressing (OE) plants. AtPUB46-OE show increased tolerance to water stress and have smaller leaf blades and reduced stomatal pore area and stomatal index compared with wild type (WT). Despite this, the rate of water loss from detached rosettes is similar in AtPUB46-OE and WT plants. Germination of AtPUB46-OE seeds was less sensitive to salt than WT whereas seedling greening was more sensitive. We observed a complex response to oxidative stress applied by different agents: AtPUB46-OE plants were hypersensitive to H2O2 but hyposensitive to methyl viologen. AtPUB46-GFP fusion protein is cytoplasmic, however, in response to H2O2 a considerable proportion translocates to the nucleus. We conclude that the differential stress phenotype of the AtPUB46-OE does not result from its smaller leaf size but from a change in the activity of a stress pathway(s) regulated by a degradation substrate of the AtPUB46 E3 and also from a reduction in stomatal pore size and index. © 2018 Elsevier B.V.

Plant Science

Overexpression of Arabidopsis ubiquitin ligase AtPUB46 enhances tolerance to drought and oxidative stress

In this molecular dynamics study, we examine the local surface geometric effects of the normal impact force between two approximately spherical nanoparticles that collide in a vacuum. Three types of surface geometries - (i) crystal facets, (ii) sharp edges, and (iii) amorphous surfaces of small nanoparticles with radii R < 10nm - are considered. The impact forces are compared with their macroscopic counterparts described by nonlinear contact forces based on Hertz contact mechanics. In our simulations, edge and amorphous surface contacts with weak surface energy reveal that the average impact forces are in excellent agreement with the Hertz contact force. On the other hand, facet collisions show a linearly increasing force with increasing compression. Our results suggest that the nearly spherical nanoparticles are likely to enable some nonlinear dynamic phenomena, such as breathers and solitary waves observed in granular materials, both originating from the nonlinear contact force. © 2018 The Author(s) Published by the Royal Society. All rights reserved.