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

Oxidative stress is a therapeutic target in TDP-43 proteinopathies like amyotrophic lateral sclerosis (ALS) and FTLD-TDP. TDP-43 over-expression causes oxidative stress in yeast model of ALS. Previously, we developed a red/white color conversion reporter assay using ade1 or ade2 mutant yeast to examine oxidative stress induced by expression of amyloidogenic proteins. Also, a previous study showed that overexpression of yeast Hsp40 chaperone Sis1 could mitigate the toxicity and proteosomal blockage induced by TDP-43 over-expression. Here, using the red/white reporter yeast assay and also by CellROX-staining, we found that an elevated expression of Sis1 mitigates the TDP-43-induced oxidative stress. Furthermore, as redox signalling and the ER stress response pathways cross-talk, we checked if the Sis1-mediated mitigation of the TDP-43-induced oxidative stress can also be observed in yeast deleted for ER stress response gene, IRE1. We find that in the yeast deleted for the IRE1 gene, the elevated expression of Sis1 fails to neutralize the TDP-43-induced oxidative stress. Taken together, Hsp40 chaperone modulation can be further examined towards therapeutic research on the TDP-43 proteinopathies. © 2022 Elsevier Inc.

World University root node

Biochemical and Biophysical Research Communications

Elevated constitutive expression of Hsp40 chaperone Sis1 reduces TDP-43 aggregation-induced oxidative stress in Ire1 pathway dependent-manner in yeast TDP-43 proteinopathy model of amyotrophic lateral sclerosis

Secretion of high-molecular-weight polysaccharides across the bacterial envelope is ubiquitous, as it enhances prokaryotic survival in (a)biotic settings. Such polymers are often assembled by Wzx/Wzy- or ABC transporter-dependent schemes implicating outer membrane (OM) polysaccharide export (OPX) proteins in cell-surface polymer translocation. In the social predatory bacterium Myxococcus xanthus, the exopolysaccharide (EPS) pathway WzaX, major spore coat (MASC) pathway WzaS, and biosurfactant polysaccharide (BPS) pathway WzaB were herein found to be truncated OPX homologues of Escherichia coli Wza lacking OM-spanning a-helices. Comparative genomics across all bacteria (.91,000 OPX proteins identified and analyzed), complemented with cryo-electron tomography cell-envelope analyses, revealed such “truncated” WzaX/S/B architecture to be the most common among three defined OPX-protein structural classes independent of periplasm thickness. Fold recognition and deep learning revealed the conserved M. xanthus proteins MXAN_7418/3226/1916 (encoded beside wzaX/S/B, respectively) to be integral OM b-barrels, with structural homology to the poly-N-acetyl-Dglucosamine synthase-dependent pathway porin PgaA. Such bacterial porins were identified near numerous genes for all three OPX protein classes. Interior MXAN_7418/3226/ 1916 b-barrel electrostatics were found to match properties of their associated polymers. With MXAN_3226 essential for MASC export, and MXAN_7418 herein shown to mediate EPS translocation, we have designated this new secretion machinery component “Wzp” (i.e., Wz porin), with the final step of M. xanthus EPS/MASC/BPS secretion across the OM now proposed to be mediated by WzpX/S/B (i.e., MXAN_7418/3226/1916). Importantly, these data support a novel and widespread secretion paradigm for polysaccharide biosynthesis pathways in which those containing OPX components that cannot span the OM instead utilize b-barrel porins to mediate polysaccharide transport across the OM. IMPORTANCE Diverse bacteria assemble and secrete polysaccharides that alter their physiologies through modulation of motility, biofilm formation, and host immune system evasion. Most such pathways require outer membrane (OM) polysaccharide export (OPX) proteins for sugar-polymer transport to the cell surface. In the prototypic Escherichia coli Group-1-capsule biosynthesis system, eight copies of this canonical OPX protein cross the OM with an a-helix, forming a polysaccharide-export pore. Herein, we instead reveal that most OPX proteins across all bacteria lack this a-helix, raising questions as to the manner by which most secreted polysaccharides actually exit cells. In the model developmental bacterium Myxococcus xanthus, we show this process to depend on OPX-coupled OM-spanning b-barrel porins, with similar porins encoded near numerous OPX genes in diverse bacteria. Knowledge of the terminal polysaccharide secretion step will enable development of antimicrobial compounds targeted to blocking polymer export from outside the cell, thus bypassing any requirements for antimicrobial compound uptake by the cell. Copyright © 2022 Saïdi et al.

Microbiology Spectrum

Bacterial Outer Membrane Polysaccharide Export (OPX) Proteins Occupy Three Structural Classes with Selective b-Barrel Porin Requirements for Polymer Secretion

Objective: High-flow hemodialysis accesses are a well-recognized source of patient morbidity. Among available management strategies inflow constriction based on real-time physiologic flow monitoring offers a technically straightforward data-driven approach with potentially low morbidity. Despite the benefits offered by this approach, large contemporary series are lacking. Methods: A retrospective review of a prospectively maintained clinical database was undertaken to capture patients undergoing precision banding within a signal tertiary care institution between 2010 and 2019. Multivariable logistic regression modeling of thrombosis within 30 days and re-banding within 1 year were performed. Results: In total, 297 patients underwent banding during the study period for a total number of 398 encounters. Median [IQR] follow-up was 157 [52–373] days. Most accesses were upper arm with brachial artery inflow (84%) and half of the banding procedures were performed for flow imbalance based on exam, duplex, or fistulogram. Median flow rate reduction was 58%. The 30-day thrombosis rate after banding was 15 of 397 (3.8%) with a median time to event of 5.5 days (2–102). The re-banding rate within a year was 54 of 398 (14%) with a median time to re-banding of 134 days [56–224]. Multivariate logistic regression analysis using a univariate screen did not identify any predictors of 30-day thrombosis. Having a forearm radial-cephalic AVF compared to all other access types was protective against need for rebanding at 1 year (OR 0.12 95% CI 0.02–0.92, p = 0.04), as was flow imbalance as the indication for banding (OR 0.43 95% 0.23-0.79, p = 0.006). Conclusions: Precision banding offers an effective, low-morbidity approach for high-flow hemodialysis accesses. Early thrombosis is a rare event after precision banding, although in the long term, one in four patients will require re-banding to maintain control of flow volumes. © The Author(s) 2022.

Journal of Vascular Access

Contemporary outcomes of precision banding for high flow hemodialysis access

The human DNA repair enzyme AlkB homologue-2 (ALKBH2) repairs methyl adducts from genomic DNA. Overexpression of ALKBH2 has been implicated in both tumorigenesis and chemotherapy resistance in some cancers, including glioblastoma and renal cancer rendering it a potential therapeutic target and a diagnostic marker. However, no inhibitor is available against these important DNA repair proteins. Intending to repurpose a drug as an inhibitor of ALKBH2, we performed in silico evaluation of HIV protease inhibitors and identified Ritonavir as an ALKBH2-interacting molecule. Using molecular dynamics simulation, we elucidated the molecular details of Ritonavir-ALKBH2 interaction. The present work highlights that Ritonavir might be used to target the ALKBH2-mediated DNA alkylation repair. Graphical abstract: [Figure not available: see fulltext.] © 2022, The Author(s), under exclusive licence to Springer Nature Switzerland AG.

Molecular Diversity

Interactions between HIV protease inhibitor ritonavir and human DNA repair enzyme ALKBH2: a molecular dynamics simulation study

Ideal dressing materials for complex and large asymmetric burns should have the dual properties of anti-bacterial and regenerative with advanced applicability of direct deposit on the wound at the patient bedside. In this study, core-shell nanofibers (polycaprolactone; PCL and polyethylene oxide; PEO) with different percent of silver sulfadiazine (SSD) loading (2–10%) were prepared by the airbrushing method using a custom build device. Results indicate a sustained release profile of silver sulfadiazine (SSD) up to 28 days and concentration-dependent anti-bacterial activity. The morphology and proliferation of human dermal fibroblast (HDF) cells and human dental follicle stem cells (HDFSC) on the silver sulfadiazine loaded nanofibers confirm the biocompatibility of airbrushed nanofibers. Moreover, upregulation of extracellular matrix (ECM) proteins (Col I, Col III, and elastin) support the differentiation and regenerative properties of silver sulfadiazine nanofiber mats. This was further confirmed by the complete recovery of rabbit burn wound models within 7 days of silver sulfadiazine loaded nanofiber dressing. Histopathology data show silver sulfadiazine loaded core-shell nanofibers' anti-inflammatory and proliferative activity without any adverse response on the tissue. Overall data display that the airbrushed silver sulfadiazine-loaded core-shell nanofibers are effective dressing material with the possibility of direct fiber deposition on the wound to cover, heal, and regenerate large asymmetric burn wounds. © 2021

Department of Biomedical Engineering

International Journal of Pharmaceutics

Silver sulfadiazine loaded core-shell airbrushed nanofibers for burn wound healing application

Minichromosome maintenance (Mcm) proteins are well-known for their functions in DNA replication. However, their roles in chromosome segregation are yet to be reviewed in detail. Following the discovery in 1984, a group of Mcm proteins, known as the ARS-nonspecific group consisting of Mcm13, Mcm16-19, and Mcm21-22, were characterized as bonafide kinetochore proteins and were shown to play significant roles in the kinetochore assembly and high-fidelity chromosome segregation. This review focuses on the structure, function, and evolution of this group of Mcm proteins. Our in silico analysis of the physical interactors of these proteins reveals that they share non-overlapping functions despite being copurified in biochemically stable complexes. We have discussed the contrasting results reported in the literature and experimental strategies to address them. Taken together, this review focuses on the structure-function of the ARS-nonspecific Mcm proteins and their evolutionary flexibility to maintain genome stability in various organisms. © 2021 Wiley Periodicals LLC

BioEssays

Minichromosome maintenance proteins in eukaryotic chromosome segregation

Grain boundary processes such as shear coupling and sliding are a consequence of plastic distortion accompanying grain boundary motion. Atomic scale studies using molecular dynamics (MD) and phase field crystal simulations demonstrate non-unique and stress-dependent shear coupling, a key feature that recently motivated the introduction of disconnections as the primary carriers of grain boundary plasticity. In this work, we develop a diffuse-interface finite deformation theory for grain boundary plasticity based on the notion of geometrically necessary disconnections (GND), with a discrete collection of intrinsic coupling factors, defined by the bicrystallography, as inputs to the model. It is emphasized that disconnection density is not a primary variable of the theory, instead it is the plastic slip rate associated with shear coupling that is a fundamental variable, and the resulting incompatibility is measured by the GND density. As an interesting consequence of this framework, we discover that in the presence of grain rotation, plastic shear that is commonly associated with the glide of disconnections, is insufficient to describe grain boundary plasticity, and it must be augmented with an additional plastic rotation. The disconnections-based continuum model can describe phenomena such as state-dependent shear coupling, mode switching, grain boundary sliding and grain rotation. Using finite elements, we simulate grain boundaries driven by shear and synthetic driving forces in bicrystals under various boundary conditions. © 2022

Journal of the Mechanics and Physics of Solids

A finite deformation theory for grain boundary plasticity based on geometrically necessary disconnections

Biogenic municipal solid waste (BMSW) and food waste (FW) with high energy density are ready to tap renewable resources for industrial scale ethanol refinery foreseen for establishing bio-based society. Circular economy has occupied limelight in the domain of renewable energy and sustainable chemicals production. The present review highlights the importance of BMSW/FW as newer feed reserves that can cater as parent molecules for an array of high-visibility industrial products along with bioethanol upon implementing a judicious closed-cascade mass-flow mechanism enabling ultimate feed and waste stream valorisation. Though these organics are attractive resources their true potential for energy production has not been quantified yet owing to their heterogeneous composition and associated technical challenges thus pushing waste refinery and industrial symbiosis concepts to backseat. To accelerate this industrial vision, the novel bioprocessing strategies for enhanced and low-cost production of bioethanol from BMSW/FW along with other commercially imperative product portfolio have been discussed. © 2022 Elsevier Ltd

Bioresource Technology

Emerging innovations for sustainable production of bioethanol and other mercantile products from circular economy perspective

The presence of DNA in the cytoplasm of tumor cells induces the dendritic cell to produce type-I IFNs. Classically, the presence of foreign DNA in host cells' cytoplasm during viral infection elicits cGAS-STING mediated type-I IFN signaling and cytokine production. It is likely that cytosolic DNA leads to senescence and immune surveillance in transformed cells during the early stages of carcinogenesis. However, multiple factors, such as loss of cell-cycle checkpoint, mitochondrial damage and chromosomal instability, can lead to persistent accumulation of DNA in the cytoplasm of metastatic tumor cells. That is why aberrant activation of the type I IFN pathway is frequently associated with highly aggressive tumors. Intriguingly, two powerful intracellular deoxyribonucleases, DNase2 and TREX1, can target the cytoplasmic DNA for degradation. Yet the tumor cells consistently accumulate cytoplasmic DNA. This review highlights recent work connecting the lack of DNase2 and TREX1 function to innate immune signaling. It also summarizes the possible mechanisms that limit the activity of DNase2 and TREX1 in tumor cells and contributes to chronic inflammation. © 2022

Biochimica et Biophysica Acta - Molecular Cell Research

Cytoplasmic DNA in cancer cells: Several pathways that potentially limit DNase2 and TREX1 activities

Biomolecular structural knowledge is important to understand the biological processes and the mechanisms underlying human diseases. In silico modeling plays a vital role in de novo design and docking of biomacromolecules as well as in exploring their conformational dynamics. Additionally, it has a major role in acquiring the structural insights using the parameters derived from experimental techniques such as cryo-electron microscopy. Steric hindrance is one of the important measures to validate the accuracy of the modeled biomolecular structures. A web user interface (WUI), namely, STRIDER (steric hindrance and metal coordination identifier) (www.iith.ac.in/strider/) estimates and reports pairwise inter- and intra- molecular steric hindrances using the van der Waals radius of 117 elements. STRIDER identifies and reports the coordination pattern of 64 metals in an interactive mode. It can provide conformer wise interaction pattern(s) of an ensemble of conformers which is needed in circumventing sampling issue in flexible docking, protein folding and structure based virtual screening. Further, it generates a pymol session file which highlights the aforementioned interaction for an offline analysis. Since STRIDER simply requires the Cartesian coordinates of a molecule in PDB format, any chemical structure can be given as an input. Functionality of STRIDER is illustrated here by considering several examples. © 2022 Elsevier Ltd