Department of Bioscience & Bioengineering

&ldquo;IIT Jodhpur is committed to impart quality education to facilitate the creation of qualified, competent and responsible human resources to meet the emerging technological challenges of the world. It is working towards creating an equitable learning platform that is positive, accessible and effective in the face of the modern societal and scientific advancements.

Flexibility in curriculum, in all its academic programs, encompassing elements of teaching, research, creativity, innovation and entrepreneurship is the most unique feature of IIT Jodhpur. The Department of Science and Technology (DST), under the National Mission on Cyber Physical Systems, has identified IIT Jodhpur as a Technology &amp; Innovation Hub in the area of Augmented Reality and Virtual Reality. The institute has also been nominated as the coordinator for the Jodhpur City and Knowledge Cluster by the Office of Principal Scientific Adviser, Government of India.

The sprawling 852-acre IIT Jodhpur campus is a majestic tribute to the deep-rooted diverse cultural heritage of the region. The campus is an architectural masterpiece, which is slated to become an international exemplar of sustainability with net-zero energy, and advanced water and waste management strategies.&rdquo;

IIT Jodhpur

Evaluation of the biological properties of silanized graphene oxide is important in the context of biomedical applications of the material. In this study, we have evaluated the toxicity, immunogenicity and other biological properties like osteogenicity of silanized graphene oxide (SiGO). Graphene oxide (GO) was silanized using a common silanizing agent namely (3-aminopropyl) triethoxysilane (APTES). Silanization was confirmed through infrared spectroscopy and elemental mapping. Post-silanization, we did not observe any significant changes in the morphology of GO. Silanization leads to an increase in the interlayer distance and disorder in the lattice. Study of in vitro toxicity of SiGO on three different cell lines namely primary human dermal fibroblast, murine embryonic fibroblast and human osteosarcoma cell lines revealed that toxicity of SiGO was significantly less than GO. We further showed that in vitro immune activation of macrophage was less in the case of SiGO in comparison to GO. Profiling of osteogenic differentiation of human mesenchymal stem cell revealed that SiGO is less osteogenic than GO. Study of acute toxicity in the murine model indicated that GO was hepatotoxic at experimental concentration whereas SiGO did not show any significant toxicity. This study implied that SiGO is a better biocompatible material than GO. © 2020 Elsevier B.V.

World University root node

Materials Science and Engineering C

Silanization improves biocompatibility of graphene oxide

Objective: In the last few decades, the consumption of cannabis-based products for recreational purposes has dramatically increased. Unfortunately, cannabis consumption has been associated with the incidences of cardiovascular diseases. Hence, there is a necessity for understanding the plausible mechanics of cardiophysiological changes due to cannabis consumption. Accordingly, the current study was designed to understand the suitability of the recurrence quantification analysis (RQA) method in detecting the changes in the heart rate variability (HRV) time-series signals due to the consumption of cannabis (bhang). Further, a machine learning model has been proposed for the automated detection of the cannabis takers. Materials and Methods: The RQA of the HRV time-series signals from 200 healthy Indian male paddy-field workers were carried out. The obtained parameters were statistically analyzed using the Mann-Whitney U test. Further, the decision trees, weight-based feature ranking, and dimensionality reduction methods were employed for identifying the relevant features for the development of a suitable machine learning model. Results: Observable changes in the patterns of the recurrence plots among the bhang consuming and non-consuming groups were noticed. However, there were no significant differences in the RQA parameters. Among the developed machine learning models, the SVM model obtained from the “Information gain ratio” feature selection method exhibited the highest accuracy (%) of 69.09 ± 9.33. Conclusion: Our study suggests that the RQA method is not as effective as the time and frequency domain methods for detecting the alterations in the HRV time-series signals due to cannabis consumption. The SVM model was found to be the best model for the automated detection of cannabis takers. The selection of the features by the information gain ratio method played an important role in the development of the optimized SVM model. © 2020 AGBM

IRBM

Comparing the HRV Time-Series Signals Acquired from Cannabis Consuming and Non-Consuming Indian Paddy-Field Workers by Recurrence Quantification Analysis

Epigenetic deregulation remarkably triggers mechanisms associated with tumor aggressiveness like epithelial–mesenchymal transition (EMT). Since EMT is a highly complex, but also reversible event, epigenetic processes such as DNA methylation or chromatin alterations must be involved in its regulation. It was recently described that loss of the cell cycle regulator p21 was associated with a gain in EMT characteristics and an upregulation of the master EMT transcription factor ZEB1. In this study, in silico analysis was performed in combination with different in vitro and in vivo techniques to identify and verify novel epigenetic targets of ZEB1, and to proof the direct transcriptional regulation of SETD1B by ZEB1. The chorioallantoic-membrane assay served as an in vivo model to analyze the ZEB1/SETD1B interaction. Bioinformatical analysis of CRC patient data was used to examine the ZEB1/SETD1B network under clinical conditions and the ZEB1/SETD1B network was modeled under physiological and pathological conditions. Thus, we identified a self-reinforcing loop for ZEB1 expression and found that the SETD1B associated active chromatin mark H3K4me3 was enriched at the ZEB1 promoter in EMT cells. Moreover, clinical evaluation of CRC patient data showed that the simultaneous high expression of ZEB1 and SETD1B was correlated with the worst prognosis. Here we report that the expression of chromatin modifiers is remarkably dysregulated in EMT cells. SETD1B was identified as a new ZEB1 target in vitro and in vivo. Our study demonstrates a novel example of an activator role of ZEB1 for the epigenetic landscape in colorectal tumor cells. © 2020, The Author(s).

Fulltext

Cell Death and Disease

EMT transcription factor ZEB1 alters the epigenetic landscape of colorectal cancer cells

Identification of cancer subtypes is critically important for understanding the heterogeneity present in tumors. Integrating information from multiple sources, homogeneous groups for cancer can be identified. However, there is a lack of computational approaches to identify histological subtypes among the patients suffering from different types of cancers. Assigning weight to the biomarkers prior to the integration of multiple information sources for the same set of samples can play an important role in cancer subtypes identification, which has not been explored previously. Sub-typing of cancers can help in analyzing shared molecular profiles between different histological subtypes of solid tumors. A novel method for feature weighting based on robust regression fit is developed in this study. The weight is utilized to find similarity between patients individually from each of the information sources. Here, miRNA and mRNA expression profiles across the same set of samples have been used. Patient-similarity networks, that are generated from each of the expression profiles are then integrated using the approach of Similarity Network Fusion. Finally, Spectral clustering is applied on the fused network to identify similar groups of patients that represent a cancer subtype. The effectiveness of the proposed method has been demonstrated on different data sets. IEEE

IEEE/ACM Transactions on Computational Biology and Bioinformatics

A Feature Weighting-Assisted Approach for Cancer Subtypes Identification from Paired Expression profiles

Unraveling the large number of various signals in the brain under the influence of physical and chemical cues that govern the formation of individual neurons, axons, dendrites, and their functional synapses during the development of neural network is a challenging task. To understand this task, microfluidic devices equipped with microchannels for reconstitution of cell/tissue-culture environments have been studied. Microfluidic devices are emerging as powerful tools in neurobiology, since they are capable of controlling and manipulating the microenvironment of the brain in a precise manner. They can enhance the physiological relevance of three-dimensional (3D) cell culture by allowing spatial control over fluids in micrometer-sized channels. Recent technological advancement in designing microfluidic platforms for studying neural communication, disease progression, and detection of neurotransmitters enhance our fundamental knowledge and understanding. However, more such advanced and innovative interventions are required. This Viewpoint focuses on highlighting a few of them with future scope of further advancement in this field. © 2019 American Chemical Society.

ACS Chemical Neuroscience

Three-Dimensional Microfluidic Platform with Neural Organoids: Model System for Unraveling Synapses

Traumatic brain injury (TBI) and spinal cord injury (SCI) cause millions of deaths and permanent or prolonged physical disabilities around the globe every year. It generally happens due to various incidents, such as accidents during sports, war, physical assault, and strokes which result in severe damage to brain and spinal cord. If this remains untreated, traumatic CNS injuries may lead to early development of several neurodegenerative diseases like Alzheimer's, Parkinson, multiple sclerosis, and other mental illnesses. The initial physical reaction, which is also termed as the primary phase, includes swelling, followed by inflammation as a result of internal haemorrhage causing damage to indigenous tissue, i.e., axonal shear injury, rupture of blood vessels, and partial impaired supply of oxygen and essential nutrients in the neurons, thereby initiating a cascade of events causing secondary injuries such as hypoxia, hypotension, cognitive impairment, seizures, imbalanced calcium homeostasis and glutamate-induced excitotoxicity resulting in concomitant neuronal cell death and cumulative permanent tissue damage. In the modern era of advanced biomedical technology, we are still living with scarcity of the clinically applicable comparative non-invasive therapeutic strategies for regeneration or functional recovery of neurons or neural networks after a massive CNS injury. One of the key reasons for this scarcity is the limited regenerative ability of neurons in CNS. Growth-impermissive glial scar and the lack of a synthetic biocompatible platform for proper neural tissue engineering and controlled supply of drugs further retard the healing process. Injectable or implantable hydrogel materials, consisting majorly of water in its porous three-dimensional (3D) structure, can serve as an excellent drug delivery platform as well as a transplanted cell-supporting scaffold medium. Among the various neuro-compatible bioinspired materials, we are limiting our discussion to the recent advancement of engineered biomaterials comprising mainly of peptides and proteins due to their growing demand, low immunogenicity and versatility in the fabrication of neuro regenerative medicine. In this article, we try to explore all the recent scientific avenues that are developing gradually to make peptide and peptide-conjugated biomaterial hydrogels as a therapeutic and supporting scaffold for treating CNS injuries. © 2020 The Royal Society of Chemistry.

Soft Matter

Recent trends in the development of peptide and protein-based hydrogel therapeutics for the healing of CNS injury

Background: Neurocysticercosis (NCC) is infection by cestode Taenia solium/pork tapeworm. Sero-diagnosis of NCC is still a challenge. Radiological imaging (CT/MRI) are cost intensive, requires technical expertise and resource intensive. Hence, its availability is restricted in endemic zone. Existing Enzyme electro immune transfer blot (EITB) antigens are difficult to make and is not standardized for endemic population. Therefore, there is a definite need for easy and reliable EITB tool. Methods: T. solium metacestode were harvested from naturally infected swine post slaughter. The cyst fluid/vesicular fluid was aspirated and processed with ultracentrifugation and immune blot was performed with this antigen. Results: A total of 406 cases [rural 256 (NCC 78, seizures other than NCC 108 and healthy controls 70); urban 150 (NCC 41, seizures other than NCC 59 and healthy controls 50)] were enrolled. Positive EITB (detection of band <50 kDa) was significantly associated with NCC patients of urban population only (p < 0.001) but not in rural populations (p = 0.292). However, identification of 15 kDa band had significant association with NCC both in urban and rural populations with overall sensitivity of 91.5% and specificity of 91.6%. Presence of 35 kDa band was associated with multiple NCC (p < 0.001). The study shows that 15 kDa reactive band on EITB is highly sensitive and specific for diagnosis of NCC in endemic population. Conclusions: Presence of 35 kDa band on EITB was associated with infection by multiple cysticerci. The observations demand purification of cyst fluid antigens to develop simple and easy to execute test in field studies. © 2020

Clinica Chimica Acta

Evaluation of Taenia solium cyst fluid-based enzyme linked immunoelectro transfer blot for Neurocysticercosis diagnosis in urban and highly endemic rural population of North India

Pseudomonas aeruginosa generally forms strong biofilm during chronic condition of wound. The whole mechanism of biofilm formation works in tandem with quorum sensing circuit of the organism in order to produce virulence. Here we report the draft genome sequence of two diabetic foot ulcer Pseudomonas aeruginosa isolates (VIT PC 7 and VIT PC 9) displaying homoserine lactone, rhamnolipid producing, biofilm phenotype and antibiotic resistance genes related to carbapenem, aminoglycoside, beta- lactamase and tetracycline resistance. The whole genome sequencing library was prepared according to the Oxford Nanopore's SQK-LSK108 kit protocol on Oxford Nanopore's Minion platform. The 7.1 Mb and 6.3-Mb draft genome sequence with GC content of 65.8% and 66.4% respectively provides insight into their resistance mechanism and virulence factors. © 2020 The Authors

Data in Brief

Comparative data analsysis of two multi-drug resistant homoserine lactone and rhamnolipid producing Pseudomonas aeruginosa from diabetic foot infected patient

Nanosized carriers engineered from red blood cells (RBCs) provide a means for delivering various cargos, including drugs, biologics, and imaging agents. We have engineered nanosized particles from RBCs, doped with the near-infrared (NIR) fluorochrome, indocyanine green (ICG). An important issue related to clinical translation of RBC-derived nanocarriers, including these NIR nanoparticles, is their stability postfabrication. Freezing may provide a method for long-term storage of these and other RBC-derived nanoparticles. Herein, we have investigated the physical and optical stability of these particles in response to a single freeze-thaw cycle. Nanoparticles were frozen to -20 °C, stored frozen for up to 8 weeks, and then thawed at room temperature. Our results show that the hydrodynamic diameter, zeta potential, optical density, and NIR fluorescence emission of these nanoparticles are retained following the freeze-thaw cycle. The ability of these nanoparticles in NIR fluorescence imaging of ovarian cancer cells, as well as their biodistribution in reticuloendothelial organs of healthy Swiss Webster mice after the freeze-thaw cycle is similar to that for freshly prepared nanoparticles. These results indicate that a single cycle of freezing the RBC-derived nanoparticles to -20 °C followed by thawing at room temperature is an effective method to retain the physical and optical characteristics of the nanoparticles, and their interactions with biological systems without the need for use of cryoprotectants. Copyright © 2020 American Chemical Society.

Langmuir

RBC-Derived Optical Nanoparticles Remain Stable after a Freeze-Thaw Cycle

A field study was conducted to understand the physiological responses, yield and grain quality of an old (HUW234) and a modern (HD3118) wheat cultivar exposed to elevated ozone (O3). The cultivars were grown under ambient O3 (NF) and ambient +20 ppb O3 (NF+) conditions using open-top chambers (OTCs). The comparative study of an old and a modern cultivar showed variable physiological responses under elevated O3 exposure. Elevated O3 in old cultivar caused high reductions in Rubisco activity (Vcmax) and electron transport rate (J) compared to modern cultivar with simultaneous reductions in the rate of photosynthesis and chlorophyll fluorescence. In modern cultivar, high stomatal density and conductance caused higher O3 uptake thereby triggering more damage to the adjacent stomatal cells and photosynthetic pigments coupled with reductions in photosynthetic rate and photosynthetic nitrogen use efficiency (PNUE). Modern cultivar also showed relatively high reduction in grain yield compared to old one under NF + treatment. Furthermore, grain quality traits (such as starch, protein and amino acids) of modern cultivar were better than old cultivar under ambient O3, but showed more deterioration under NF + treatment. Results thus indicated that modern cultivar is relatively more susceptible to O3 and showed more negative impacts on plant performance, yield and quality of grains compared to old cultivar. © 2020 Elsevier Ltd