Department of Biotechnology

Indian Institute of Technology Hyderabad (IITH) is a premier institute of science and technology established in 2008. IITH has been consistently ranked in the&nbsp;<a href="https://iith.ac.in/reports/" rel="noopener noreferrer">top 10 institutes</a>&nbsp;in India for Engineering&nbsp;<a href="https://www.nirfindia.org/2021/EngineeringRanking.html" rel="noopener noreferrer" target="_blank">according to NIRF</a>&nbsp;making it one of the most coveted schools for science and technology in the country.

IITH offers&nbsp;<a href="https://iith.ac.in/academics/under-graduate/">undergraduate programs</a>&nbsp;in all the classical engineering disciplines, applied sciences, design, as well as several modern interdisciplinary areas. Students are given a flexibility to explore a broad set of areas, and potentially pursue a minor or double major in a discipline that is not their own. Students who wish to seek a deeper understanding of their own discipline are strongly encouraged to get involved in cutting-edge research with the help of a faculty to mentor them, and earn an Honors in their own field.

The very foundation of IIT Hyderabad is based on&nbsp;<a href="https://iith.ac.in/research/">research and innovation</a>. The vibrant research culture is evident from the number of patents and publications that IITH produces consistently every year. IITH offers&nbsp;<a href="https://iith.ac.in/academics/programmes-offered/">graduate programs</a>&nbsp;at both a masters, and a doctoral level, in several diverse areas. There are separate programs for technology, design, science, and liberal arts. The&nbsp;<a href="https://iith.ac.in/academics/post-graduate/">MTech program</a>&nbsp;is offered in various modes and durations to cater to the ever-growing need of postgraduate level professionals in the country.

IITH encourages and supports&nbsp;<a href="https://iic-iith.netlify.app/index.html" rel="noopener noreferrer" target="_blank">innovation and entrepreneurship</a>&nbsp;at every stage. The minor program in entrepreneurship is open to all students of IITH, and many of the courses are offered by industrialists who are entrepreneurs themselves. There are various&nbsp;<a href="https://iith.ac.in/research/centres-incubators/">innovation centers and incubators</a>&nbsp;that promote entrepreneurship and help mentor young innovators. IITH has been very successful in building tie-ups with leading academic institutions around the globe.

IITH enjoys a very special relationship with Japanese universities and industries that goes beyond academic and research collaborations. In fact, some of the iconic buildings in IITH campus will carry the signature of Japanese architecture.

IITH creates a unique holistic ecosystem for education that offers interactive learning, a very flexible academic structure, cutting-edge research, strong industry collaboration, and entrepreneurship. This is an environment which enables students and faculty to translate their dreams into realities.

IIT Hyderabad

Arsenic trioxide loaded biocompatible PHB-PVA. 1PHB-PVA, poly hydroxy butyrate-poly vinyl alcohol copolymer.1 nanoparticles (&lt;100. nm in size) with folate functionalized surface were synthesized using poly-[(R)-3-hydroxybutyric acid] (PHB) produced by Bacillus firmus NII 0830. Folate functionalization was carried using dicyclohexyl carbodiimide (DCC) as a catalyst and 10-bromodecanol as a linker to conjugate glutamic acid terminal of folate with the hydroxylate groups present on the surface of PHBA-PVA. 2PHBA-PVA, arsenic trioxide loaded poly hydroxyl butyrate-poly vinyl alcohol.2 nanotrojans. The effect of fabrication parameters on shape, size distribution and PDI of the PHB nanoparticles were also investigated. It was observed that increase in sonication time and polyvinyl alcohol (PVA) concentration greatly reduced the size of nanoparticles. The drug release studies on arsenic trioxide incorporated PHB-PVA nanoparticles were conducted at physiological pH and temperature. FOL-PHBA-PVA. 3FOL-PHBA-PVA, folate functionalized PHBA-PVA nanoparticles; PDI, polydispersity index.3 nanoparticles showed greater extent of cytotoxicity towards murine fibrosarcoma L929 cells than PHBA-PVA nanoparticles alone without conjugated folate, indicating the significance of folate as ligand for specific targeting of FR+ cancer cells. © 2013 Elsevier Ltd.

World University root node

Bioresource Technology

Microbial synthesis of poly-3-hydroxybutyrate and its application as targeted drug delivery vehicle

Nature Reviews Clinical Oncology

Epidemiology: Biorepositories for cancer research in developing countries

Use of therapeutic peptides in cancer therapy has been receiving considerable attention in the recent years. Present study describes the development of computational models for predicting and discovering novel anticancer peptides. Preliminary analysis revealed that Cys, Gly, Ile, Lys, and Trp are dominated at various positions in anticancer peptides. Support vector machine models were developed using amino acid composition and binary profiles as input features on main dataset that contains experimentally validated anticancer peptides and random peptides derived from SwissProt database. In addition, models were developed on alternate dataset that contains antimicrobial peptides instead of random peptides. Binary profiles-based model achieved maximum accuracy 91.44% with MCC 0.83. We have developed a webserver, which would be helpful in: (i) predicting minimum mutations required for improving anticancer potency; (ii) virtual screening of peptides for discovering novel anticancer peptides, and (iii) scanning natural proteins for identification of anticancer peptides (http://crdd.osdd.net/raghava/anticp/).

Fulltext

Scientific Reports

In silico models for designing and discovering novel anticancer peptides

Background: Cell penetrating peptides have gained much recognition as a versatile transport vehicle for the intracellular delivery of wide range of cargoes (i.e. oligonucelotides, small molecules, proteins, etc.), that otherwise lack bioavailability, thus offering great potential as future therapeutics. Keeping in mind the therapeutic importance of these peptides, we have developed in silico methods for the prediction of cell penetrating peptides, which can be used for rapid screening of such peptides prior to their synthesis.Methods: In the present study, support vector machine (SVM)-based models have been developed for predicting and designing highly effective cell penetrating peptides. Various features like amino acid composition, dipeptide composition, binary profile of patterns, and physicochemical properties have been used as input features. The main dataset used in this study consists of 708 peptides. In addition, we have identified various motifs in cell penetrating peptides, and used these motifs for developing a hybrid prediction model. Performance of our method was evaluated on an independent dataset and also compared with that of the existing methods.Results: In cell penetrating peptides, certain residues (e.g. Arg, Lys, Pro, Trp, Leu, and Ala) are preferred at specific locations. Thus, it was possible to discriminate cell-penetrating peptides from non-cell penetrating peptides based on amino acid composition. All models were evaluated using five-fold cross-validation technique. We have achieved a maximum accuracy of 97.40% using the hybrid model that combines motif information and binary profile of the peptides. On independent dataset, we achieved maximum accuracy of 81.31% with MCC of 0.63.Conclusion: The present study demonstrates that features like amino acid composition, binary profile of patterns and motifs, can be used to train an SVM classifier that can predict cell penetrating peptides with higher accuracy. The hybrid model described in this study achieved more accuracy than the previous methods and thus may complement the existing methods. Based on the above study, a user- friendly web server CellPPD has been developed to help the biologists, where a user can predict and design CPPs with much ease. CellPPD web server is freely accessible at http://crdd.osdd.net/raghava/cellppd/. © 2013 Gautam et al.; licensee BioMed Central Ltd.

Journal of Translational Medicine

In silico approaches for designing highly effective cell penetrating peptides

Cancer therapies are limited by the development of drug resistance, and mutations in drug targets is one of the main reasons for developing acquired resistance. The adequate knowledge of these mutations in drug targets would help to design effective personalized therapies. Keeping this in mind, we have developed a database CancerDR, which provides information of 148 anti-cancer drugs, and their pharmacological profiling across 952 cancer cell lines. CancerDR provides comprehensive information about each drug target that includes; (i) sequence of natural variants, (ii) mutations, (iii) tertiary structure, and (iv) alignment profile of mutants/variants. A number of web-based tools have been integrated in CancerDR. This database will be very useful for identification of genetic alterations in genes encoding drug targets, and in turn the residues responsible for drug resistance. CancerDR allows user to identify promiscuous drug molecules that can kill wide range of cancer cells. CancerDR is freely accessible at http://crdd.osdd.net/raghava/cancerdr/.

CancerDR: Cancer drug resistance database

RATIONALE: Compartmentation of ion channels on the cardiomyocyte surface is important for electric propagation and electromechanical coupling. The specialized T-tubule and costameric structures facilitate spatial coupling of various ion channels and receptors. Existing methods such as immunofluorescence and patch clamp techniques are limited in their ability to localize functional ion channels. As such, a correlation between channel protein location and channel function remains incomplete. OBJECTIVE: To validate a method that permits routine imaging of the topography of a live cardiomyocyte and study clustering of functional ion channels from a specific microdomain. METHODS AND RESULTS: We used scanning ion conductance microscopy and conventional cell-attached patch clamp with a software modification that allows controlled increase of pipette tip diameter. The sharp nanopipette used for topography scan was modified into a larger patch pipette that could be positioned with nanoscale precision to a specific site of interest (crest, groove, or T-tubules of cardiomyocytes) and sealed to the membrane for cell-attached recording of ion channels. Using this method, we significantly increased the probability of detecting activity of L-type calcium channels in the T-tubules of ventricular cardiomyocytes. We also demonstrated that active sodium channels do not distribute homogenously on the sarcolemma instead, they segregate into clusters of various densities, most crowded in the crest region, that are surrounded by areas virtually free of functional sodium channels. CONCLUSIONS: Our new method substantially increases the throughput of recording location-specific functional ion channels on the cardiomyocyte sarcolemma, thereby allowing characterization of ion channels in relation to the microdomain where they reside. Copyright © 2013 American Heart Association, Inc.

Circulation Research

Super-resolution scanning patch clamp reveals clustering of functional ion channels in adult ventricular myocyte

Tumor homing peptides are small peptides that home specifically to tumor and tumor associated microenvironment i.e. tumor vasculature, after systemic delivery. Keeping in mind the huge therapeutic importance of these peptides, we have made an attempt to analyze and predict tumor homing peptides. It was observed that certain types of residues are preferred in tumor homing peptides. Therefore, we developed support vector machine based models for predicting tumor homing peptides using amino acid composition and binary profiles of peptides. Amino acid composition, dipeptide composition and binary profile-based models achieved a maximum accuracy of 86.56%, 82.03%, and 84.19% respectively. These methods have been implemented in a user-friendly web server, TumorHPD. We anticipate that this method will be helpful to design novel tumor homing peptides. TumorHPD web server is freely accessible at http://crdd.osdd.net/raghava/tumorhpd/.

Computational approach for designing tumor homing peptides

The quest for nonoptical imaging methods that can surmount light diffraction limits resulted in the development of scanning probe microscopes. However, most of the existing methods are not quite suitable for studying biological samples. The scanning ion conductance microscope (SICM) bridges the gap between the resolution capabilities of atomic force microscope and scanning electron microscope and functional capabilities of conventional light microscope. A nanopipette mounted on a three-axis piezo-actuator, scans a sample of interest and ion current is measured between the pipette tip and the sample. The feedback control system always keeps a certain distance between the sample and the pipette so the pipette never touches the sample. At the same time pipette movement is recorded and this generates a three-dimensional topographical image of the sample surface. SICM represents an alternative to conventional high-resolution microscopy, especially in imaging topography of live biological samples. In addition, the nanopipette probe provides a host of added modalities, for example using the same pipette and feedback control for efficient approach and seal with the cell membrane for ion channel recording. SICM can be combined in one instrument with optical and fluorescent methods and allows drawing structure-function correlations. It can also be used for precise mechanical force measurements as well as vehicle to apply pressure with precision. This can be done on living cells and tissues for prolonged periods of time without them loosing viability. The SICM is a multifunctional instrument, and it is maturing rapidly and will open even more possibilities in the near future. © 2013 the American Physiological Society.

American Journal of Physiology - Heart and Circulatory Physiology

The scanning ion conductance microscope for cellular physiology

Microdomains that form on the plasma membrane of cells are essential for signalling compartmentation within cells. The localization of ion channels in these surface microdomains is important in defining what signalling cascades will be generated. For example, in cardiomyocytes, similar to other excitable cells, action potential propagation depends essentially on the properties of ion channels that are functionally and spatially coupled. In this chapter we describe a novel advanced patch-clamp technique, "Smart patch-clamp," which enables the study of functional ion channels in the cell surface microdomains in a wide variety of biological cells and tissues. Smart patch-clamp combines conventional patch-clamp and Scanning Ion Conductance Microscopy (SICM). SICM uses a glass micropipette as scanning probe and generates a high-resolution topography image of the cell surface. Next, same micropipette is used as a patch-clamp pipette to record ion channel signals from specific spots on the cell surface as determined by SICM. In this chapter we focus on recording single channel L-type calcium channel currents from T-tubules of adult rat cardiomyocytes. © 2013 Springer Science+Business Media, LLC.

Methods in Molecular Biology

Recording single-channel currents using "smart patch-clamp" technique

The transverse (t)-tubule system plays an essential role in healthy and diseased heart muscle, particularly in Ca2+-induced Ca2+ release (CICR), and its structural disruption is an early event in heart failure. Both mechanical overload and unloading alter t-tubule structure, but the mechanisms mediating the normally tight regulation of the t-tubules in response to load variation are poorly understood. Telethonin (Tcap) is a stretch-sensitive Z-disc protein that binds to proteins in the t-tubule membrane. To assess its role in regulating t-tubule structure and function, we used Tcap knockout (KO) mice and investigated cardiomyocyte t-tubule and cell structure and CICR over time and following mechanical overload. In cardiomyocytes from 3-month-old KO (3mKO), there were isolated t-tubule defects and Ca2+ transient dysynchrony without whole heart and cellular dysfunction. Ca2+ spark frequency more than doubled in 3mKO. At 8 months of age (8mKO), cardiomyocytes showed progressive loss of t-tubules and remodelling of the cell surface, with prolonged and dysynchronous Ca2+ transients. Ca2+ spark frequency was elevated and the L-type Ca2+ channel was depressed at 8 months only. After mechanical overload obtained by aortic banding constriction, the Ca2+ transient was prolonged in both wild type and KO. Mechanical overload increased the Ca2+ spark frequency in KO alone, where there was also significantly more t-tubule loss, with a greater deterioration in t-tubule regularity. In conjunction, Tcap KO showed severe loss of cell surface ultrastructure. These data suggest that Tcap is a critical, loadsensitive regulator of t-tubule structure and function. © The Author 2012. Published by Oxford University Press. All rights reserved.