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

This study deals with the quantitative assessment of nutritionally important fatty acids (FAs) in 94 indige-nous rice (Oryza sativa ssp. indica) landraces of India which are critically endangered, being cultivat-ed only by a handful of marginal farmers. Three mod-ern high-yielding varieties and one local high-yielding farmers’ variety were analysed for comparative as-sessment. Qualitative and quantitative analyses of FAs based on gas chromatography-mass spectrometric analysis of these varieties revealed their significant contribution to daily diet. Two ‘case studies’ were considered on the basis of individual FAs and nutri-tionally correlated FA parameters of the rice cultivars to isolate the most promising landraces, by clustering through linear discriminant function. These folk rice landraces may add important precursors to essential FAs in the staple diet and can provide for FA requirement in normal brain development in infants. We suggest incorporation of these landraces into India’s food and agriculture policy, both for conserving the vanishing landraces and for ensuring nutritional security of the economically marginalized people. © 2021, Current Science. All rights reserved.

World University root node

Current Science

Rare and neglected rice landraces as a source of fatty acids for undernourished infants

With the exponential spread of the coronavirus disease 2019 (COVID-19) pandemic across the world within the 12 months, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains are continuously trying to adapt themselves to the host environment by random mutations. When doing so, some variants with evolutionary advantages such as better human to human transmissibility potential might get naturally selected. This short communication demonstrates how the mutation frequency patterns are evolving in 2457 SAR-CoV-2 strains isolated from COVID-19 patients across diverse Indian states. We have identified 19 such variants showing contrasting mutational probabilities in the span of 7 months. Out of these, 14 variants are showing increasing mutational probabilities suggesting their propagation with time due to their unexplored evolutionary advantages. However, the mutational probabilities of five variants have significantly decreased in June onward as compared to March/April, suggesting their termination with time. Further in-depth investigation of these identified variants will provide valuable knowledge about the evolution, infection strategies, transmission rates, and epidemiology of SARS-CoV-2. © 2020 Wiley Periodicals LLC

Journal of Medical Virology

Dynamic tracking of variant frequencies depicts the evolution of mutation sites amongst SARS-CoV-2 genomes from India

Objective: Informed consent is an essential principle of high-quality health care. A core component of surgical informed consent is patient comprehension of basic information such as the diagnosis, risks, benefits, and alternatives of the proposed surgery. We sought to assess informed consent among vascular surgery patients and the association between frailty, education, decisional conflict, and patient comprehension. Methods: We tested patient comprehension of basic information required for informed consent with a procedure-specific questionnaire in 102 consecutive patients undergoing selected vascular surgery procedures. Two patients who underwent open aortic aneurysm repair were excluded because of small sample size. All patients underwent assessment using the decisional conflict scale and the Frail/Nondisabled questionnaire. Analyses were performed to determine relationships between being informed and frailty, education level, and decisional conflict score. Patients included in this cohort had a median age of 71 years, and 25%, 14%, 28%, and 33% underwent carotid endarterectomy, endovascular aortic aneurysm repair, dialysis access creation, and percutaneous lower extremity procedures. Results: Overall, 14% of patients were classified as “informed” and correctly answered all questions. Procedure type (P =.001), consent obtained by the attending surgeon vs a trainee (P =.04), and frailty score (P =.005) were all associated with whether a patient was informed or not. However, after multivariable adjustment, only frailty score was independently associated with being informed (odds ratio, 0.54; 95% confidence interval, 0.30-0.95; P =.03). The median decisional conflict scale score was 7.8, suggesting that patients feel well informed and supported in spite of poor understanding of procedural indications, risks, benefits, and alternatives. Conclusions: As a group, patients have a poor comprehension of basic information related to surgical informed consent. These findings have potential ethical and clinical implications, and additional work is required to best determine causes of poor comprehension and strategies to mitigate the same. © 2020 Society for Vascular Surgery

Journal of Vascular Surgery

Patient comprehension necessary for informed consent for vascular procedures is poor and related to frailty

Base pair mismatches can erroneously be incorporated in the DNA. An adenine pairing with another adenine is one of the eight possible mismatches. The atomistic insights about the structure and dynamics of an A…A mismatch in a DNA (unbound form) is not yet accessible to any experimental technique. Earlier molecular dynamics (MD) simulations have shown that A…A mismatch in the midst of 5′CAG/3′GAC, 5′GAC/3′CAG and 5′CAA/3′GAT (underline represents the mismatch) are highly dynamic in nature. By employing MD simulation, the influence of an A…A mismatch in the midst of 5′GAA/3′CAT, 5′GAG/3′CAC, 5′AAC/3′TAG, 5′AAG/3′TAC, 5′TAA/3′AAT, 5′TAT/3′AAA and 5′AAT/3′TAA sequences have been investigated here. The results indicate that irrespective of the flanking sequences, the mismatch samples a variety of transient conformations, including a B-Z junction. Further, circular dichroism studies have been carried out to explore the ability of these sequences to bind with hZαADAR1 which specifically recognizes B-Z junction/Z-DNA. The results indicate that hZαADAR1 could not lead to a complete B to Z transition in the above sequences. Notably, a complete transition to Z-form has been reported earlier for 5′GAC/3′CAG upon titrating with hZαADAR1. Intriguingly, 5′AAC/3′TAG, 5′AAG/3′TAC and 5′GAA/3′CAT exhibit a B-Z junction formation rather than a complete transition to Z-form, similar to the situation of 5′CAA/3′GAT. These indicate that although A…A mismatch could induce a local B-Z junction transiently, hZαADAR1 requires the presence of a G…C/C…G base pair adjacent to the A…A mismatch for the binding. Additionally, the extent of B-Z junction has enhanced upon binding with hZαADAR1 in the presence of the A…A mismatch (specifically when CG, CA, AC, GA and AG steps occur), but not in the presence of the canonical base pairs. These confirm the inclination of A…A mismatch towards the B-Z junction. © 2020 Elsevier Inc.

Journal of Structural Biology

Sequence dependent influence of an A…A mismatch in a DNA duplex: An insight into the recognition by hZαADAR1 protein

Insertion of silent mutations allowing for restriction site modification aids in the screening of successful mutants during site directed mutagenesis. Introducing a new restriction site requires the analysis of degenerate sequences within mutant primer. As the total number of degenerate codons increases, the analysis becomes increasingly laborious, time-consuming and prone to errors. Towards this, a software named as ‘REMP’ (for REstriction site in Mutant Primer) was developed and described here. From the input sequence, REMP instantaneously generates degenerate sequences having restriction sites that are 6–8 base pairs in length. The output sequences are arranged based on the number of bases changed compared to the input sequence. REMP software can be installed and run as a stand-alone program on different operating systems. Any user of REMP can edit the list of restriction sites to be considered by the software, without a need for writing a computer code or knowing a program language. © 2021

Department of Computer Science and Engineering

SoftwareX

REMP software to introduce a screening REstriction site in site-directed Mutagenesis Primer

Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for applications in biophysics, cell biology, and synthetic biology. Understanding DNA-membrane interactions is crucial for rationally designing functional DNA. Here we study the interactions of hydrophobically tagged DNA with synthetic and cell membranes using a combination of experiments and atomistic molecular dynamics (MD) simulations. The DNA duplexes are rendered hydrophobic by conjugation to a terminal cholesterol anchor or by chemical synthesis of a charge-neutralized alkyl-phosphorothioate (PPT) belt. Cholesterol-DNA tethers to lipid vesicles of different lipid compositions and charges, while PPT DNA binding strongly depends on alkyl length, belt position, and headgroup charge. Divalent cations in the buffer can also influence binding. Our MD simulations directly reveal the complex structure and energetics of PPT DNA within a lipid membrane, demonstrating that longer alkyl-PPT chains provide the most stable membrane anchoring but may disrupt DNA base paring in solution. When tested on cells, cholesterol-DNA is homogeneously distributed on the cell surface, while alkyl-PPT DNA accumulates in clustered structures on the plasma membrane. DNA tethered to the outside of the cell membrane is distinguished from DNA spanning the membrane by nuclease and sphingomyelinase digestion assays. The gained fundamental insight on DNA-bilayer interactions will guide the rational design of membrane-targeting nanostructures. ©

Journal of the American Chemical Society

Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes

Reproducing the structure and function of biological membrane channels, synthetic nanopores have been developed for applications in membrane filtration technologies and biomolecular sensing. Stable stand-alone synthetic nanopores have been created from a variety of materials, including peptides, nucleic acids, synthetic polymers, and solid-state membranes. In contrast to biological nanopores, however, furnishing such synthetic nanopores with an atomically defined shape, including deliberate placement of each and every chemical group, remains a major challenge. Here, we introduce a chemosynthetic macromolecule—extended pillararene macrocycle (EPM)—as a chemically defined transmembrane nanopore that exhibits selective transmembrane transport. Our ionic current measurements reveal stable insertion of individual EPM nanopores into a lipid bilayer membrane and remarkable cation type-selective transport, with up to a 21-fold selectivity for potassium over sodium ions. Taken together, direct chemical synthesis offers a path tode novodesign of a new class of synthetic nanopores with custom transport functionality imprinted in their atomically defined chemical structure. © 2021 American Chemical Society

Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport

The outstanding capacity of aquaporins (AQPs) for mediating highly selective superfast water transport1–7 has inspired recent development of supramolecular monovalent ion-excluding artificial water channels (AWCs). AWC-based bioinspired membranes are proposed for desalination, water purification and other separation applications8–18. While some recent progress has been made in synthesizing AWCs that approach the water permeability and ion selectivity of AQPs, a hallmark feature of AQPs—high water transport while excluding protons—has not been reproduced. We report a class of biomimetic, helically folded pore-forming polymeric foldamers that can serve as long-sought-after highly selective ultrafast water-conducting channels with performance exceeding those of AQPs (1.1 × 1010 water molecules per second for AQP1), with high water-over-monovalent-ion transport selectivity (~108 water molecules over Cl– ion) conferred by the modularly tunable hydrophobicity of the interior pore surface. The best-performing AWC reported here delivers water transport at an exceptionally high rate, namely, 2.5 times that of AQP1, while concurrently rejecting salts (NaCl and KCl) and even protons. © 2021, The Author(s), under exclusive licence to Springer Nature Limited.

Nature Nanotechnology

Foldamer-based ultrapermeable and highly selective artificial water channels that exclude protons

The interplay between nucleic acids and lipids underpins several key processes in molecular biology, synthetic biotechnology, vaccine technology, and nanomedicine. These interactions are often electrostatic in nature, and much of their rich phenomenology remains unexplored in view of the chemical diversity of lipids, the heterogeneity of their phases, and the broad range of relevant solvent conditions. Here we unravel the electrostatic interactions between zwitterionic lipid membranes and DNA nanostructures in the presence of physiologically relevant cations, with the purpose of identifying new routes to program DNA-lipid complexation and membrane-active nanodevices. We demonstrate that this interplay is influenced by both the phase of the lipid membranes and the valency of the ions and observe divalent cation bridging between nucleic acids and gel-phase bilayers. Furthermore, even in the presence of hydrophobic modifications on the DNA, we find that cations are still required to enable DNA adhesion to liquid-phase membranes. We show that the latter mechanism can be exploited to control the degree of attachment of cholesterol-modified DNA nanostructures by modifying their overall hydrophobicity and charge. Besides their biological relevance, the interaction mechanisms we explored hold great practical potential in the design of biomimetic nanodevices, as we show by constructing an ion-regulated DNA-based synthetic enzyme. ©

Fulltext

Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kills thousands of people worldwide every day, thus necessitating rapid development of countermeasures. Immunoinformatics analyses carried out here in search of immunodominant regions in recently identified SARS-CoV-2 unannotated open reading frames (uORFs) have identified eight linear B-cell, one conformational B-cell, 10 CD4+ T-cell, and 12 CD8+ T-cell promising epitopes. Among them, ORF9b B-cell and T-cell epitopes are the most promising followed by M.ext and ORF3c epitopes. ORF9b40-48 (CD8+ T-cell epitope) is found to be highly immunogenic and antigenic with the highest allele coverage. Furthermore, it has overlap with four potent CD4+ T-cell epitopes. Structure-based B-cell epitope prediction has identified ORF9b61-68 to be immunodominant, which partially overlaps with one of the linear B-cell epitopes (ORF9b65-69). ORF3c CD4+ T-cell epitopes (ORF3c2-16, ORF3c3-17, and ORF3c4-18) and linear B-cell epitope (ORF3c14-22) have also been identified as the candidate epitopes. Similarly, M.ext and 7a.iORF1 (overlap with M and ORF7a) proteins have promising immunogenic regions. By considering the level of antigen expression, four ORF9b and five M.ext epitopes are finally shortlisted as potent epitopes. Mutation analysis has further revealed that the shortlisted potent uORF epitopes are resistant to recurrent mutations. Additionally, four N-protein (expressed by canonical ORF) epitopes are found to be potent. Thus, SARS-CoV-2 uORF B-cell and T-cell epitopes identified here along with canonical ORF epitopes may aid in the design of a promising epitope-based polyvalent vaccine (when connected through appropriate linkers) against SARS-CoV-2. Such a vaccine can act as a bulwark against SARS-CoV-2, especially in the scenario of emergence of variants with recurring mutations in the spike protein. © Copyright © 2021 Uttamrao, Sathyaseelan, Patro and Rathinavelan.

Frontiers in Immunology

Revelation of Potent Epitopes Present in Unannotated ORF Antigens of SARS-CoV-2 for Epitope-Based Polyvalent Vaccine Design Using Immunoinformatics Approach