Department of Bioscience & Bioengineering

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IIT Jodhpur

Heterogeneity amidst healthy individuals at genomic level is being widely acknowledged. This, in turn, is modulated by differential response to environmental cues and treatment regimens, necessitating the need for stratified/personalized therapy. We intend to understand the molecular determinants of Ayurvedic way (ancient Indian system of medicine) of endo-phenotyping individuals into distinct constitution types termed "Prakriti," which forms the basis of personalized treatment. In this study, we explored and analyzed the healthy human gut microbiome structure within three predominant Prakriti groups from a genetically homogenous cohort to discover differentially abundant taxa, using 16S rRNA gene based microbial community profiling. We found Bacteroidetes and Firmicutes as major gut microbial components in varying composition, albeit with similar trend across Prakriti. Multiple species of the core microbiome showed differential abundance within Prakriti types, with gender specific signature taxons. Our study reveals that despite overall uniform composition of gut microbial community, healthy individuals belonging to different Prakriti groups have enrichment of specific bacteria. It highlights the importance of Prakriti based endo-phenotypes to explain the variability amongst healthy individuals in gut microbial flora that have important consequences for an individual's health, disease and treatment. © 2018 Chauhan, Pandey, Mondal, Gupta, Verma, Jain, Ahmed, Patil, Agarwal, Girase, Shrivastava, Mobeen, Sharma, Srivastava, Juvekar, Prasher, Mukerji and Dash.

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Fulltext

Frontiers in Microbiology

Western Indian rural gut microbial diversity in extreme Prakriti endo-phenotypes reveals signature microbes

Background: Genetic susceptibility to atypical hemolytic uremic syndrome (aHUS) may lie within genes regulating or activating the alternate complement and related pathways converging on endothelial cell activation. Methods: We tested 32 Indian patients of aHUS negative for antibodies to complement factor H for genetic variations in a panel of 15 genes, i.e., CFH, CFHR1-5, CFI, CFB, C3, CD46, MASP2, DGKE, ADAMTS13, THBD and PLG using next-generation DNA sequencing and for copy number variation in CFHR1-3. Results: Despite absence of a public database of exome variations in the Indian population and limited functional studies, we could establish a genetic diagnosis in 6 (18.8%) patients using a stringent scheme of prioritization. One patient carried a likely pathogenic variation. The number of patients carrying possibly pathogenic variation was as follows: 1 variation: 5 patients, 2 variations: 9 patients, 3 variations: 5 patients, 4 variations: 9 patients, 5 variations: 2 patients and 6 variations: 2 patients. Homozygous deletion of CFHR1-3 was present in five patients; none of these carried a diagnostic genetic variation. Patients with or without diagnostic variation did not differ significantly in terms of enrichment of genetic variations that were rare/novel or predicted deleterious, or for possible environmental triggers. Conclusion: We conclude that genetic testing for multiple genes in patients with aHUS negative for anti-FH antibodies reveals multiple candidate variations that require prioritization. Population data on variation frequency of the Indian population and supportive functional studies are likely to improve diagnostic yield. © 2017, Japanese Society of Nephrology.

Clinical and Experimental Nephrology

Targeted exome sequencing in anti-factor H antibody negative HUS reveals multiple variations

Chronic deafferentations in adult mammals result in reorganization of the brain. Lesions of the dorsal columns of the spinal cord at cervical levels in monkeys result in expansion of the intact chin inputs into the deafferented hand representation in area 3b, second somatosensory (S2) and parietal ventral (PV) areas of the somatosensory cortex, ventroposterior lateral nucleus (VPL) of the thalamus, and cuneate nucleus of the brainstem. Here, we describe the extent and nature of reorganization of the cuneate and gracile nuclei of adult macaque monkeys with chronic unilateral lesions of the dorsal columns, and compare it with the reorganization of area 3b in the same monkeys. In both, area 3b and the cuneate nucleus chin inputs expand to reactivate the deafferented neurons. However, unlike area 3b, neurons in the cuneate nucleus also acquire receptive fields on the shoulder, neck, and occiput. A comparison with the previously published results shows that reorganization in the cuneate nucleus is similar to that in VPL. Thus, the emergent topography following deafferentations by spinal cord injuries undergoes transformation as the reorganized inputs ascend from subcortical nuclei to area 3b. The results help us understand mechanisms of the brain plasticity following spinal cord injuries. © The Author 2017. Published by Oxford University Press. All rights reserved.

Cerebral Cortex

Altered Expression of Reorganized Inputs as They Ascend from the Cuneate Nucleus to Cortical Area 3b in Monkeys with Long-Term Spinal Cord Injuries

In cells, protein synthesis and degradation are normal processes, which are tightly regulated by various cellular metabolic pathways. Cellular protein quality control (PQC) mechanisms always present a continuous and rigorous check over all intracellular proteins before they can participate in various cellular physiological processes with the help of PQC pathways like autophagy and ubiquitin proteasome system (UPS). The UPS employs few selective E3 ubiquitin ligases for the intracellular degradation of cyclin-dependent kinase inhibitor 1B (p27Kip1) that tightly controls cell cycle progression. But, the complex mechanistic interactions and the interplay between E3 ubiquitin ligases involved in the functional regulation as well as expression of p27 are not well known. Here, we demonstrate that cell surface glycoprotein Gp78, a putative E3 ubiquitin ligase, is involved in the stabilization of intracellular steady-state levels of p27. Transient overexpression of Gp78 increases the accumulation of p27 in cells in the form of massive inclusions like structures, which could be due to its cumulative increased stability in cells. We have also monitored how under stress condition, E3 ubiquitin ligase Gp78 regulates endogenous levels of p27 in cells. ER stress treatment generates a marginal increase in Gp78 endogenous levels, and this elevation effect was prominent for intracellular accumulation of p27 in cells. Taken together, our current findings suggest a valuable multifactorial regulatory mechanism and linkage of p27 with UPS pathway. © 2018 Wiley Periodicals, Inc.

Journal of Cellular Physiology

Gp78 involvement in cellular proliferation: Can act as a promising modulator for cell cycle regulatory proteins?

Chikungunya infection has been a cause of countless deaths worldwide. Due to lack of permanent treatment and prevention of this disease, the mortality rate remains very high. Therefore, we followed an immunoinformatics approach for the development of multi-epitope subunit vaccine which is able to elucidate humoral, cell-mediated and innate immune responses inside the host body. Both structural and non-structural proteins of chikungunya virus were utilized for prediction of B-cell and T-cell binding epitopes along with interferon-γ (IFN-γ) inducing epitopes. The vaccine construct is composed of β-defensin as an adjuvant at the N-terminal followed by Cytotoxic T-Lymphocytes (CTL) and Helper T-Lymphocyte (HTL) epitopes. The same vaccine construct was also utilized for the prediction of B-cell binding epitopes and IFN-γ inducing epitopes. This was followed by the 3D model generation, refinement and validation of the vaccine construct. Later on, the interaction of modeled vaccine with the innate immune receptor (TLR-3) was explored by performing molecular docking and molecular dynamics simulation studies. Also to check the efficiency of expression of this vaccine construct in an expression vector, in silico cloning was performed at the final stage of vaccine development. Further, designed multi-epitope subunit vaccine necessitates experimental and clinical investigation to develop as an immunogenic vaccine candidate. © 2018 Elsevier B.V.

Infection, Genetics and Evolution

Excavating chikungunya genome to design B and T cell multi-epitope subunit vaccine using comprehensive immunoinformatics approach to control chikungunya infection

Proteins actively participate in a wide range of cellular physiological functions. But aggregation of proteins results in cytotoxicity, and unwanted aggregation of misfolded proteins often causes many diseases. During abnormal protein aggregation events, cells try to cope against such deleterious consequences because of the remarkable functional attempts of two distinct proteolytic mechanisms. These tightly regulative and signaling mechanisms are autophagy pathway and ubiquitin proteasome system. Proteasome complex system holds the elimination capacity of intracellular aberrant protein aggregation. Despite the considerable progress that has been achieved, which elucidates wide function and diverse roles of proteasome system, still several crucial problems remain unanswered. For example, how the complex proteasomes assembly and their interactive pathways determine the precise sense of several proteotoxic insults, which can severely affect the cell survival and homeostasis? The specific degradation of various aberrant proteins that can disturb cellular homeostasis is achieved by proper proteasome functionality, which is yet another unclear and critical challenge. Therefore, a better understanding of the various cellular signaling mechanisms composing the proteasome machinery carries broad therapeutic implications linked with proteopathies. This article signifies the urgent need, which is now crucial for us to improve our understanding of the proteasome architecture, structure, and functions that span multiple level strategies from the molecular level to the cellular level. This systematic in-depth information of proteasome may be helpful in the near future to design a new molecular framework based on intrinsic and extrinsic cellular mechanisms that drive the assembly of proteasome to induce cellular survival against proteostasis imbalance and disease conditions. © 2018 Wiley Periodicals, Inc.

Medicinal Research Reviews

Proteasome-mediated proteostasis: Novel medicinal and pharmacological strategies for diseases

In this study, a promising microbial fuel cell (MFC) system has been developed, wherein algae is cultivated in the cathode chamber, algae biomass is harvested and lipids are extracted. The lipid extracted algal (LEA) biomass was then used as an electron donor substrate. The performance of MFCs fed with LEA biomass was compared with that of fruit waste fed MFCs (FP-MFCs), wherein LEA-fed MFC was superior in all aspects. Power density of 2.7 W m−3 was obtained by LEA-fed MFCs which is 145% and 260% higher than FP MFC and control MFC respectively. The volumetric algae productivity of 0.028 kg m−3 day−1 in cathode chamber was achieved. The system was able to generate 0.0136 kWh Kg−1 COD day−1 of electric energy and 0.0782 kWh m−3 day−1 of algal oil energy. The proposed system is a net energy producer which does not rely heavily on the external supply of electron donor substrates. © 2017 Elsevier Ltd

Department of Physics

Department of Electrical Engineering

Bioresource Technology

Microbial fuel cell powered by lipid extracted algae: A promising system for algal lipids and power generation

The FASEB Journal 32, 677.21-677.

NON‐CONTACT ELECTRIC FIELDS POTENTLY HINDER EGF PROMOTED BREAST CANCER MOTILITY BY DOWNREGULATING EGFR PHOSPHORYLATION

Spinocerebellar ataxia type-12 (SCA12) is a neurological disorder caused due to triplet (CAG) repeat expansion in 5’ UTR of PPP2R2B. It is one of the most prominent SCA-subtype in Indian population and till date no patient specific models have been described. Human-induced-pluripotent-stem cell (HiPSC) based disease modelling has become the next generation tool for studying various human pathologies. In the present study we established three SCA12 patient specific iPSC lines. All the generated lines have shown pluripotency markers, normal karyotype, in-vitro three germ layers differentiation potential, vector clearance, SCA12 mutation, parental genomic identity and contamination free culture. © 2018

Stem Cell Research

Generation of three spinocerebellar ataxia type-12 patients derived induced pluripotent stem cell lines (IGIBi002-A, IGIBi003-A and IGIBi004-A)

Nanomaterials with antimicrobial properties triggered by external stimuli appear to be a promising and innovative substitute for the destruction of antibiotic-resistant superbugs as they can induce multiple disruptions in the cellular mechanism. This study demonstrates the use of squaraine (SQ) dye as the photosensitive material, activated in the near-infrared tissue-transparent therapeutic window. The dye has been covalently attached to the ZnO nanoparticle surface, forming ZnO-SQ nanohybrids. The formation of the nanohybrids is confirmed using Fourier transform infrared and other optical spectroscopic methods. The photoinduced interfacial electron transfer process (as confirmed using the time-resolved fluorescence technique) from the excited state of SQ to the conduction band of ZnO is responsible for the greater reactive oxygen species (ROS) generation ability of the nanohybrid. The production of photoactivated ROS (especially singlet oxygen species) by ZnO-SQ provides remarkable antimicrobial action against clinically significant Staphylococcus aureus. Detailed investigations suggest synergistic involvement of cell membrane disruption and nanoparticle internalization followed by photoinduced intracellular ROS generation, which result in an unprecedented 95% bacterial killing activity by the nanohybrid. Moreover, the efficacy of the nanohybrid for disruption of bacterial biofilms has been examined. The electron microscopic images suggest significant bacterial cell death following structural alteration and reduced adherence property of the biofilms. Nanodimension-driven greater internalization of ZnO-SQ followed by an improved dissolution of ZnO in an acidic environment of the biofilm as well as red-light-driven interfacial charge separation and ROS generation improves the efficacy of the material for biofilm destruction. An artificial medical implant mimicking titanium sheets coated with ZnO-SQ depicts light-triggered disruption in the adherence property of matured biofilms. The cytotoxicity and hemolysis assays show inherent biocompatibility of the photoactive nanohybrid. This study is notably promising for the treatment of life-threatening drug-resistant infections and eradication of biofilms formed within artificial implants. © 2018 American Chemical Society.