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

Objective: In a recent analysis, we discovered lower mortality after open abdominal aortic aneurysm repair (OAAA) in the Society for Vascular Surgery Vascular Quality Initiative (VQI) database when compared with previously published reports of other national registries. Understanding differentials in these registries is essential for their utility because such datasets increasingly inform clinical guidelines and health policy. Methods: The VQI, American College of Surgeons National Surgical Quality Improvement Program (NSQIP), and National Inpatient Sample (NIS) databases were queried to identify patients who had undergone elective OAAA between 2013 and 2016. χ2 tests were used for frequencies and analysis of variance for continuous variables. Results: In total, data from 8775 patients were analyzed. Significant differences were seen across the baseline characteristics included. Additionally, the availability of patient and procedural data varied across datasets, with VQI including a number of procedure-specific variables and NIS with the most limited clinical data. Length of stay, primary insurer, and discharge destination differed significantly. Unadjusted in-hospital mortality also varied significantly between datasets: NIS, 5.5%; NSQIP, 5.2%; and VQI, 3.3%; P &lt;.001. Similarly, 30-day mortality was found to be 3.5% in VQI and 5.9% in NSQIP (P &lt;.001). Conclusions: There are fundamental important differences in patient demographic/comorbidity profiles, payer mix, and outcomes after OAAA across widely used national registries. This may represent differences in outcomes between institutions that elect to participate in the VQI and NSQIP compared with patient sampling in the NIS. In addition to avoiding direct comparison of information derived from these databases, it is critical these differences are considered when making policy decisions and guidelines based on these “real-world” data repositories. © 2021 Society for Vascular Surgery

World University root node

Journal of Vascular Surgery

Comparative analysis of open abdominal aortic aneurysm repair outcomes across national registries

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. Here, we design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells. Copyright © 2022 The Authors, some rights reserved.

Science Advances

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Since its first emergence in December 2019, the world has witnessed the eruption of mutations in the SARS-CoV-2 genome that have led to increased viral transmissibility and pathogenicity due to sustained local viral transmission. Zooanthroponotic and zoonotic transmissions have further raised concerns as they could result in the emergence of viral variants with a novel antigenicity and transmissibility that could jeopardize the vaccine efficacy. To understand the viral evolution during such transmissions, 1016 whole-genome sequences (deposited in GISAID as of March 7, 2022) (from 18 countries) corresponding to mink, cat, deer, dog, hyena, tiger, lion, gorilla, Syrian hamster, leopard cat, fishing cat, bear cat, coati, ferret, snow leopard and green monkey have been analysed here. Intriguingly, phyloproteome analysis indicate that Nsp2:R218C, Nsp2:D268-(deletion), Spike:D614G, Nsp12:P323L, Nsp2:A192V, ORF3a protein:Q57H, N protein:R203K and N protein:G204R/L, Spike:A222V, ORF10 protein:V30L and N protein:A220V are moderate or high recurring and clade decisive mutations, leading to 6 primary clades during the early stage of pandemic. Most interestingly, the human evolved delta variant having a combination of 26 (clade decisive) mutations defines the seventh clade and transmits to non-human hosts across the globe without exhibiting any country-specific mutation(s). Nonetheless, Spike:D614G and Nsp12:P323L together with (i)N protein:R203K,N protein:G204R/L,Spike:V70-, Spike:H69-, Nsp12:T739I, and Nsp1:M85-, (ii)Nsp2:A192V, Nsp3:D178Y, (iii)Nsp2:T85I, N protein:P67S and ORF3a protein:Q57H and (iv)Spike:A222V, ORF10 protein:V30L, N protein:A220V and Spike:F486I are specific to Denmark, Netherlands, USA and Latvia respectively and, (v)Nsp2:D268- and Nsp13:R292C that are devoid of Spike:D614G and Nsp12:P323L is specific to Netherlands. SARS-CoV-2 variants consisting of these mutations are also seen in the human SARS-CoV-2 sequences from the same country. Independent country-specific SARS-CoV-2 variant evolution further indicates distinct epidemiological dynamics during zooanthroponotic and zoonotic transmissions. Thus, the results presented here indicate the need for the surveillance of viral evolution in non-human hosts also during the future pandemic. © 2022 Wiley-VCH GmbH.

Zoonoses and Public Health

Geographical distribution of SARS-CoV-2 amino acids mutations and the concomitant evolution of seven distinct clades in non-human hosts

Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes’ structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts. © 2022 American Chemical Society

ACS Chemical Biology

Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design

Various malignancies have been successfully recapitulated in mammalian animal models, where mimicking the systemic and local environment of the developing tumor has contributed to our understanding related to the mechanisms of cancer, their diagnosis and possible therapeutic interventions to contain the growth and survival of the cancer. Advances in research have facilitated generation of these animal models of cancer by application of sophisticated technologies with integration of clinical information. Until now, rodent models especially mouse models have been the traditional models of choice for cancer investigation. Over the last decade, Danio rerio, commonly known as zebrafish, has emerged as a popular model to study many human disorders including cancer. Zebrafish offers several advantages over rodent models such as transparent embryos (allowing time-lapse noninvasive imaging using labeled cell tracking), high fecundity, external fertilization, and rapid development. Moreover, significant genomic similarity with humans especially in the disease-associated genes and their ease of maintenance and cost-effectiveness have made them a cancer model of choice today. Zebrafish has been used in several areas of cancer research including establishing cancer models by chemical and genetic manipulation or manipulation by xenotransplantation, investigating angiogenesis and metastasis, identifying new targets for therapeutics, anticancer drug screening, etc. This chapter is focused on the use of zebrafish as a xenotransplantation model to study cancer biology such as proliferation, metastasis, and angiogenesis. The xenotransplantation of human cancer cells into zebrafish also has a huge application in drug discovery and in identification of drug targets. In this chapter, we describe various zebrafish xenotransplantation cancer models that have been established in adult zebrafish, juveniles, and embryos of the zebrafish. Lastly, we discuss the use of zebrafish xenotransplantation models for precision oncotherapy. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2022.

Zebrafish Model for Biomedical Research

Zebrafish as a Xenotransplantation Model for Studying Cancer Biology and Cancer Drug Discovery

The dyed fabrics from textile industries occupy a significant share in the global economy with a world-wide market. Conventional natural dyes were gradually substituted by synthetic dyes in the wake of burgeoning demand for coloured textiles. Textile dyes are of several types depending on the core chemical structure which determines the solubility, colour and dye class. Often, dyes require treatment with mordants to fix the colour to the fabric and develop different hues. The textile treated dye baths contain residual dye moieties, mordants as well as other chemicals from the overall textile dyeing and finishing processes. For such effluents, proper treatment is a mandate to alleviate dyes associated colour, chemical compounds and organics from the wastewaters prior to release into watercourses. The challenge of textile dye effluents to meet the regulatory limits becomes more problematic when the textile industries are dominated by the unorganised small/medium scale industries and unauthorised sectors. The present review details on the genesis of Indian textile industries, dye types, dyeing process and the impact of dye effluents on health and environment along with a case study. Besides, strategies to replace chemical dyes with natural equivalents and state-of-art textile dye effluent treatment techniques are elaborated. © 2020 Indian Institute of Chemical Engineers.

Indian Chemical Engineer

Small/Medium scale textile processing industries: case study, sustainable interventions and remediation

mBio

Reply to Oren et al., “New Phylum Names Harmonize Prokaryotic Nomenclature”

Background: The inability of a newly created arteriovenous fistula to support hemodialysis due to non-maturation results in increased complications secondary to catheter dependence. Methods: In view of the highly variable approaches by providers with heterogenous backgrounds (general surgery, vascular surgery, interventional radiology and interventional nephrology, urology, transplant surgery, etc.) we sought to describe a collection of algorithms that have functioned well in our hands to manage this challenging clinical problem and guide trainees and practicing clinicians alike. Results: Physical examination along with selective duplex ultrasound and fistulogram can identify most pathologies underlying non-maturation. Conclusion: Both endovascular and open techniques can be employed to optimize maturation rates in this complex population. © The Author(s) 2022.

Vascular and Endovascular Surgery

Contemporary Strategies to Promote Dialysis Access Fistula Maturation

Mononuclear cobalt(II) complexes [CoII(L1)Cl2]; 1, [CoII(L1)(bpy)Cl]PF6; 2, [CoII(L1)(phen)Cl]PF6; 3 and [CoII(L2)Cl2]; 4 (where L1 = N,N-bis(pyridin-2-ylmethyl)aniline, L2 = (2,4,6-trimethyl-N,N-bis(pyridin-2-ylmethyl)aniline, bpy = 2,2/−bipyridine, phen = 1,10-phenanthroline) were synthesized and characterized by different analytical and spectroscopic methods. All the complexes were structurally identified by single-crystal X-ray crystallography. Penta-coordinated complex 1 adopted distorted trigonal bipyramidal and hexacoordinated complexes 2 and 3 having distorted octahedral geometry whereas tetra-coordinated complex 4 has distorted tetrahedral geometry. The interactions of salmon sperm DNA (ss-DNA) with complexes (1-4) were investigated by absorbance, fluorescence spectroscopy and molecular docking studies. All the complexes are very susceptible to DNA binding and the binding affinity (Kb) follows the order 3 (2.05 × 104 M −1) &gt; 4 (1.40 × 104 M −1) &gt; 2 (1.36 × 104 M −1) &gt; 1 (1.34 × 104 M −1) indicating they have superior DNA binding ability. The Stern-Volmer constant (Ksv) ranges from 1.10 × 104 M −1 to 1.95 × 104 M −1 suggesting weak or moderate binding with DNA. DNA cleavage study in plasmid DNA reveals very efficient DNA cleavage factors even in the absence of any external agents. Using multiple biochemical assays, we have demonstrated that 1–4 induces apoptosis of human cancer cells with IC50 values of 26.48 ± 1.45 μM, 10.89 ± 0.55 μM, 7.63 ± 0.4 μM and 37.67 ± 2.06 μM, respectively in A549 lung adenocarcinoma cells and 14.45 ± 0.73 μM, 1.97 ± 0.1 μM, 0.98 ± 0.05 μM and 24.43 ± 1.22 μM, respectively in MDA-MB-231 breast adenocarcinoma cells. © 2022

Department of Chemistry

Journal of Inorganic Biochemistry

Mononuclear cobalt(II) complexes with polypyridyl ligands: Synthesis, characterization, DNA interactions and in vitro cytotoxicity towards human cancer cells

The transition from right-handed to left-handed DNA is not only acts as the controlling factor for switching gene expression but also has equal importance in designing nanomechanical devices. The (CG)n and (GC)n repeat sequences are well known model molecules to study B-Z transition in the presence of higher concentration of monovalent cations. In this communication, we report a cyclic transition in (CG)6 DNA using millimolar concentration of trivalent lanthanide salt LaCl3. The controlled and reversible transition was seen in (CG)12, and (GC)12 DNA employing CD spectroscopy. While LaCl3 failed to induce B-Z transition in shorter oligonucleotides such as (CG)3 and (GC)3, a smooth B-Z transition was recorded for (CG)6, (CG)12 and (GC)12 sequences. Interestingly, the phenomenon was reversible (Z-B transition) with addition of EDTA. Particularly, two rounds of cyclic transition (B-Z-B-Z-B) have been noticed in (CG)6 DNA in presence of LaCl3 and EDTA which strongly suggest that B-Z transition is reversible in short repeat sequences. Thermal melting and annealing behaviour of B-DNA are reversible while the thermal melting of LaCl3-induced Z-DNA is irreversible which suggest a stronger binding of LaCl3 to the phosphate backbone of Z-DNA. This was further supported by isothermal titration calorimetric study. Molecular dynamics (MD) simulation indicates that the mode of binding of La3+ (of LaCl3) with d(CG)8.d(CG)8 is through the minor groove, wherein, 3 out of 11 La3+ bridge the anionic oxygens of the complementary strands. Such a tight coordination of La3+ with the anionic oxygens at the minor groove surface may be the reason for the experimentally observed irreversibility of LaCl3-induced Z-DNA seen in longer DNA fragments. Thus, these results indicate LaCl3 can easily be adopted as an inducer of left-handed DNA in other short oligonucleotides sequences to facilitate the understanding of the molecular mechanism of B-Z transition. © 2022 Elsevier B.V.