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

Background: An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability to reside and thrive in its current environment. Similar to external signaling molecules, cytoplasmic signals are also sensed by methyl-accepting chemotaxis proteins (MCPs) via diverse ligand binding domains. Myxobacteria are complex soil-dwelling social microbes that can perform a variety of physiologic and metabolic activities ranging from gliding motility, sporulation, biofilm formation, carotenoid and secondary metabolite biosynthesis, predation, and slime secretion. To live such complex lifestyles, they have evolved efficient signal transduction systems with numerous one- and two-component regulatory system along with a large array of chemosensory systems to perceive and integrate both external and internal cues. Results: Here we report the in silico characterization of a putative energy taxis cluster, Cc-5, which is present in only one amongst 34 known and sequenced myxobacterial genomes, Corallococcus coralloides. In addition, we propose that this energy taxis cluster is involved in oxygen sensing, suggesting that C. coralloides can sense (either directly or indirectly) and then respond to changing concentrations of molecular oxygen. Conclusions: This hypothesis is based on the presence of a unique MCP encoded in this gene cluster that contains two different oxygen-binding sensor domains, PAS and globin. In addition, the two monooxygenases encoded in this cluster may contribute to aerobic respiration via ubiquinone biosynthesis, which is part of the cytochrome bc1 complex. Finally, we suggest that this cluster was acquired from Actinobacteria, Gammaproteobacteria or Cyanobacteria. Overall, this in silico study has identified a potentially innovative and evolved mechanism of energy taxis in only one of the myxobacteria, C. coralloides. © 2018 The Author(s).

World University root node

Fulltext

BMC Genomics

In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides 06 Biological Sciences 0601 Biochemistry and Cell Biology

A project to construct a compact pre-bunched Free Electron Laser by using a normal conducting photocathode electron gun has been undertaken at Inter University Accelerator Centre (IUAC), New Delhi, India. In this facility, the short laser pulses from a high power laser system will be split into many pulses (2–16) commonly known as ‘Comb beam’ and will strike the photocathode material (metal and semiconductor) to produce electron beam bunches. The electrons will be accelerated up to an energy of ∼8 MeV by a copper cavity operated at a frequency of 2860 MHz and the beam will be injected into a compact, planar permanent undulator magnet to produce THz radiation. The radiation frequency designed to be tuned in the range of 0.15–3 THz by varying the magnetic field of the undulator and/or changing the energy of the electron. The separation of the laser micro-pulses will be varied by adjusting the path length difference to alter the separation of the electron micro-bunches and to maximise the radiation intensity. © 2017 Elsevier B.V.

Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms

Status of the development of Delhi Light Source (DLS) at IUAC

Tumor tissues are known to harbor hypoxic areas. The hypoxic microenvironment promotes angiogenesis. Hypoxic tumor cells also manifest genome instability. DNA damage repair pathways, such as double-strand break repair, mismatch repair and base excision repair are known to be altered during hypoxia. This review is focused on the non-heme Fe(II) and 2-oxoglutarate-dependent dioxygenases which are involved in repair of DNA alkylation adducts. Activities of these DNA repair enzymes are completely oxygen-dependent and little information is available about inhibition of these enzymes during hypoxia. While impairment of function of non-heme dioxygenase during tumor hypoxia has been implicated in different studies, the possible outcomes with respect to mutagenesis and genomic instability are explored here. © 2016 Elsevier B.V.

DNA Repair

Non-heme dioxygenases in tumor hypoxia: They're all bound with the same fate

Stability and quench behavior against transient perturbation expected during operation of a fast cycling energy storage magnet is an important issue for its design and safe operation. Understanding of thermal stability in terms of minimum quench energy (MQE) of a superconducting cable under specific operating scenario is of primary importance for its magnet application. Process of current redistribution from quench strand to adjacent strands depends on inductive coupling and has influence on quench development in the cable. The electrodynamic and thermal behavior of a ten-strand Rutherford-type cable for SMES program in the centre is studied numerically in the framework of discrete network modeling. Influence of several parameters such as uncertainties of inter-strand transverse and adjacent resistance, cooling conditions with liquid helium, etc. on MQE and quench behavior of Rutherford cable is discussed in this paper. © Published under licence by IOP Publishing Ltd.

IOP Conference Series: Materials Science and Engineering

Transient stability of NbTi Rutherford cables for energy storage magnet applications

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by selective loss of motor neurons with inclusions frequently containing the RNA/DNA binding protein TDP-43. Using a yeast model of ALS exhibiting TDP-43 dependent toxicity, we now show that TDP-43 overexpression dramatically alters cell shape and reduces ubiquitin dependent proteolysis of a reporter construct. Furthermore, we show that an excess of the Hsp40 chaperone, Sis1, reduced TDP-43’s effect on toxicity, cell shape and proteolysis. The strength of these effects was influenced by the presence of the endogenous yeast prion, [PIN+]. Although overexpression of Sis1 altered the TDP-43 aggregation pattern, we did not detect physical association of Sis1 with TDP-43, suggesting the possibility of indirect effects on TDP-43 aggregation. Furthermore, overexpression of the mammalian Sis1 homologue, DNAJB1, relieves TDP-43 mediated toxicity in primary rodent cortical neurons, suggesting that Sis1 and its homologues may have neuroprotective effects in ALS. © 2017 Park et al.

PLoS Genetics

Overexpression of the essential Sis1 chaperone reduces TDP-43 effects on toxicity and proteolysis

Breast fibroepithelial lesions (fibroadenomas and phyllodes tumors) are underpinned by recurrent MED12 exon 2 mutations, which are more common in fibroadenomas and benign phyllodes tumors. TERT promoter hotspot mutations have been documented in phyllodes tumors, and found to be more frequent in borderline and malignant lesions. Several lines of evidence suggest that a subset of phyllodes tumors might arise from fibroadenomas. Here we sought to investigate the genetic differences between phyllodes tumors with fibroadenoma-like areas vs. those without. We retrieved data for 16 borderline/ malignant phyllodes tumors, including seven phyllodes tumors with fibroadenoma-like areas and nine phyllodes tumors without fibroadenoma-like areas, which had been previously subjected to targeted capture massively parallel sequencing. Whilst MED12 exon 2 mutations were significantly more frequent in tumors with fibroadenoma-like areas (71 vs. 11%), an enrichment in genetic alterations targeting bona fide cancer genes was found in those without fibroadenoma-like areas, in particular in EGFR mutations and amplifications (78 vs. 14%). No significant difference in the frequency of TERT genetic alterations was observed (71% in cases with fibroadenoma-like areas vs 56% in those without fibroadenoma-like areas). Our data suggest that the development of phyllodes tumors might follow two different evolutionary pathways: a MED12-mutant pathway that involves the progression from a fibroadenoma to a malignant phyllodes tumor; and a MED12-wild-type pathway, where malignant phyllodes tumors arise de novo through the acquisition of genetic alterations targeting cancer genes. Additional studies are warranted to confirm our observations and define whether the outcome differs between both pathways. © The Author(s) 2017.

npj Breast Cancer

Phyllodes tumors with and without fibroadenoma-like areas display distinct genomic features and may evolve through distinct pathways

Objective Wound complications (WCs) after lower extremity arterial surgery (LEAS) are common, resulting in readmissions and reinterventions. Whereas diabetes and obesity are known risk factors for WCs, gender-specific variability in body fat distribution (android vs gynoid) may drive differential risks of WCs after LEAS. We analyzed the independent and synergistic effects of gender and body mass index (BMI) on WCs. Methods We performed a retrospective review of prospectively collected data from a published, randomized, multicenter trial assessing the incidence of WCs (dehiscence, surgical site infections, seroma, and hematoma) after LEAS. Postoperative outcomes were compared between genders. A multivariable regression model assessed the impact of gender and BMI on WCs. Subanalysis focused on the synergy of gender and body habitus, groin-only incisions, and clinical outcomes. Results There were 502 patients who underwent LEAS between October 2010 and September 2013. The cohort was elderly (67.6 ± 10.5 years), mostly male (72%), and overweight (BMI, 27.6 ± 5.7); 225 (45%) patients had a groin-only incision. In 171 patients (37.9%), a WC developed within 30 days, 85% of which were infectious in etiology. On multivariable regression, obesity (odds ratio [OR], 2.10; 95% confidence interval [CI], 1.17-3.77), morbid obesity (OR, 2.87; 95% CI, 1.32-6.23), and female gender (OR, 1.17; 95% CI, 1.06-2.75) were independent predictors of infectious WCs at 30 days. When stratified by groin-only incision, BMI was no longer significant, but female gender (OR, 2.70; 95% CI, 1.24-5.87) was predictive of infectious WCs at 30 days. There was no synergistic effect of BMI and gender on WCs. Conclusions WCs are common after LEAS. BMI is an independent risk factor for the development of any WC. Female gender, a potential surrogate for high hip to waist ratio body habitus, is also an independent predictor of groin WCs, suggesting the clinical importance of gynoid vs android fat distribution. © 2017 Society for Vascular Surgery

Journal of Vascular Surgery

Impact of body mass index and gender on wound complications after lower extremity arterial surgery

Background. Current knowledge of the impact of facial vascularized composite allograft (VCA) procurement on the transplantation outcomes of the concomitantly recovered solid organs is limited to isolated case reports and short-term results. Here we report on a nationwide analysis of facial allograft donor surgery experience and long-term outcomes of the concomitantly recovered solid organs and their recipients.Methods. There were 10 facial VCA procurements in organ donors between December 2008 and October 2014.We identified the population of subjects who received solid organs from these 10 donors using the Scientific Registry of Transplant Recipients. We retrospectively reviewed operative characteristics, intraoperative parameters, and postoperative outcomes. Results. Six of 10 donor surgeries were performed at outside institutions, all on brain-dead donors. Mean operative duration for facial VCA recovery was 6.9 hours (range, 4-13.25 hours). A total of 36 solid organs were recovered and transplanted into 35 recipients. Survival rates for kidney and liver recipients were 100% and 90% at a median follow-up of 33 and 27.5 months, respectively (range, 6-72 months). Graft survival rates for kidneys and livers were 15 of 16 (94%) and 9 of 10 (90%), respectively. Recipient and graft survival rates for hearts and lungs were 75% (n = 4) and 100% (n = 3) at mean follow-up time of 14.75 and 16months, respectively. A liver recipient died at 22months fromunknown causes and a heart recipient died of leukemia at 10 months. Conclusions. Facial VCA procurement does not appear to adversely affect the outcomes of transplant recipients of concomitantly recovered solid organ allografts. © 2017 Wolters Kluwer Health, Inc. All rights reserved.

Transplantation

Outcomes of solid organ transplants after simultaneous solid organ &amp; vascularized composite allograft procurements: A nationwide analysis

Toxic cyanobacteria blooms populate water bodies by consuming external nutrients and releasing cyanotoxins that are detrimental for other aquatic species, producing a significant impact on the plankton ecosystem and food web. To exercise population-level control of toxin production, understanding the biochemical mechanisms that explain cyanotoxin regulation within a bacterial cell is of utmost importance. In this study, we explore the mechanistic events to investigate the dependence of toxin microcystin on external nitrogen, a known regulator of the toxin, and for the first time, propose a kinetic model that analyzes the intracellular conditions required to ensure nitrogen dependence on microcystin. We hypothesize that the GS-GOGAT cycle is manipulated by variable influx of different intracellular metabolites that can either disturb or promote the balance between the enzyme microcystin synthetase and substrate glutamate to produce variable microcystin levels. As opposed to the popular notion that nitrogen starvation increases microcystin synthesis, our analyses suggest that under certain intracellular metabolite regimes, this relationship can either be completely lost or reversed. External nitrogen can only complement the conditions fixed by intracellular glutamate, glutamine and 2-oxoglutarate. This mechanistic understanding can provide an experimentally testable hypothesis for exploring the less-known biology of microcystin synthesis and designing specific interventions. © 2017 The Royal Society of Chemistry.

Molecular BioSystems

Exploring the role of GS-GOGAT cycle in microcystin synthesis and regulation-a model based analysis

Rapid urbanization and industrialization have accelerated the energy demand which cannot be met by decreasing fossil fuels thereby substantiate the need for lignocellulosic ethanol. The present study is one such attempt towards bioethanol production in an eco-friendly manner using enzymes in which a mixture of lignocellulosic biomass namely, Ricinus communis, Saccharum officinarum (tops) and Saccharum spontaneum were taken as a substrate. The mixed biomass was processed through partially consolidated bioprocessing (PCBP) approach which involves a non-isothermal simultaneous pretreatment and saccharification step where a concoction of laccase (Pleurotus djamor) and holocellulase (Trichoderma reseei RUT C30) was used followed by co-fermentation within the same reactor. The process parameters influencing PCBP were optimized using feed-forward ANN model which resulted in a maximum ethanol concentration of 7.86% (v/v) (62.01 g/L) at pentose to hexose strain ratio of 0.696 (v/v), substrate loading of 27.54% (w/v) and incubation time of 21.96 h. © 2017 Elsevier Ltd