Department of Bioscience & Bioengineering

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IIT Jodhpur

Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic. © 2020 Kumar P et al.

World University root node

Fulltext

Wellcome Open Research

Integrated genomic view of SARS-CoV-2 in India

Mycobacteria survive in macrophages despite triggering pattern recognition receptors and T cell-derived IFN-g production. Mycobacterial cord factor trehalose-6,6-dimycolate (TDM) binds the C-type lectin receptor MINCLE and induces inflammatory gene expression. However, the impact of TDM on IFN-g-induced macrophage activation is not known. In this study, we have investigated the cross-regulation of the mouse macrophage transcriptome by IFN-g and by TDM or its synthetic analogue trehalose-6,6-dibehenate (TDB). As expected, IFN-g induced genes involved in Ag presentation and antimicrobial defense. Transcriptional programs induced by TDM and TDB were highly similar but clearly distinct from the response to IFN-g. The glycolipids enhanced expression of a subset of IFN-g-induced genes associated with inflammation. In contrast, TDM/TDB exerted delayed inhibition of IFN-g-induced genes, including pattern recognition receptors, MHC class II genes, and IFN-g-induced GTPases, with antimicrobial function. TDM downregulated MHC class II cell surface expression and impaired T cell activation by peptide-pulsed macrophages. Inhibition of the IFN-g-induced GTPase GBP1 occurred at the level of transcription by a partially MINCLE-dependent mechanism that may target IRF1 activity. Although activation of STAT1 was unaltered, deletion of Socs1 relieved inhibition of GBP1 expression by TDM. Nonnuclear Socs1 was sufficient for inhibition, suggesting a noncanonical, cytoplasmic mechanism. Taken together, unbiased analysis of transcriptional reprogramming revealed a significant degree of negative regulation of IFN-g-induced Ag presentation and antimicrobial gene expression by the mycobacterial cord factor that may contribute to mycobacterial persistence. Copyright © 2020 by The American Association of Immunologists, Inc.

Journal of Immunology

Mycobacterial cord factor reprograms the macrophage response to IFN-g towards enhanced inflammation yet impaired antigen presentation and expression of GBP1

The novel coronavirus SARS-CoV-2, which was identified after a recent outbreak in Wuhan, China, in December 2019, has kept the whole world in tenterhooks due to its severe life-threatening nature of the infection. The virus is unlike its previous counterparts, SARS-CoV and MERS-CoV, or anything the world has encountered before both in terms of virulence and severity of the infection. If scientific reports relevant to the SARS-CoV-2 virus are noted, it can be seen that the virus owes much of its killer properties to its unique structure that has a stronger binding affinity with the human angiotensin-converting enzyme 2 (hACE2) protein, which the viruses utilize as an entry point to gain accesses to its hosts. Recent reports suggest that it is not just the lung that the virus may be targeting; the human brain may soon emerge as the new abode of the virus. Already instances of patients with COVID-19 have been reported with mild (anosmia and ageusia) to severe (encephalopathy) neurological manifestations, and if that is so, then it gives us more reasons to be frightened of this killer virus. Keeping in mind that the situation does not worsen from here, immediate awareness and more thorough research regarding the neuroinvasive nature of the virus is the immediate need of the hour. Scientists globally also need to up their game to design more specific therapeutic strategies with the available information to counteract the pandemic. In this Viewpoint, we provide a brief outline of the currently known neurological manifestations of COVID-19 and discuss some probable ways to design therapeutic strategies to overcome the present global crisis. Copyright © 2020 American Chemical Society.

ACS Chemical Neuroscience

Neurological Insights of COVID-19 Pandemic

We study how the dynamics of solitary wave (SW) interactions in integrable systems is different from that in nonintegrable systems in the context of crossing of two identical SWs in the (integrable) Toda and the (non-integrable) Hertz systems. We show that the collision process in the Toda system is perfectly symmetric about the collision point, whereas in the Hertz system, the collision process involves more complex dynamics. The symmetry in the Toda system forbids the formation of secondary SWs (SSWs), while the absence of symmetry in the Hertz system allows the generation of SSWs. We next show why the experimentally observed by-products of SW-SW interactions, the SSWs, must form in the Hertz system. We present quantitative estimations of the amount of energy that transfers from the SW after collision to the SSWs using (i) dynamical simulations, (ii) a phenomenological approach using energy and momentum conservation, and (iii) using an analytical solution introduced earlier to describe the SW in the Hertz system. We show that all three approaches lead to reliable estimations of the energy in the SSWs. © 2020 Author(s).

Chaos

Interactions of solitary waves in integrable and nonintegrable lattices

We numerically study uncompressed granular crystals excited by sinusoidal signals at 1–100 kHz. A simple system such as two beads in a line reveals that for a fixed driven frequency, incident signals can be transmitted or filtered depending on the driving amplitude. We show that using square tapered crystals with decoration it becomes possible to enhance the low frequency filtration properties of granular systems. In addition to filtration, we find that 80 % or more of the input force is attenuated using a crystal thickness of 4 grains. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

Granular Matter

Decorated granular crystal as filter of low-frequency ultrasonic signals

Amyloids are a class of protein with unique self-aggregation properties, and their aberrant accumulation can lead to cellular dysfunctions associated with neurodegenerative diseases. While genetic and environmental factors can influence amyloid formation, molecular triggers and/or facilitators are not well defined. Growing evidence suggests that non-identical amyloid proteins may accelerate reciprocal amyloid aggregation in a prion-like fashion. While humans encode ~30 amyloidogenic proteins, the gut microbiome also produces functional amyloids. For example, curli are cell surface amyloid proteins abundantly expressed by certain gut bacteria. In mice overexpressing the human amyloid α-synuclein (α Syn), we reveal that colonization with curli-producing Escherichia coli promotes α Syn pathology in the gut and the brain. Curli expression is required for E. coli to exacerbate α Syn-induced behavioral deficits, including intestinal and motor impairments. Purified curli subunits accelerate α Syn aggregation in biochemical assays, while oral treatment of mice with a gut-restricted amyloid inhibitor prevents curli-mediated acceleration of pathology and behavioral abnormalities. We propose that exposure to microbial amyloids in the gastrointestinal tract can accelerate aSyn aggregation and disease in the gut and the brain. © Sampson et al.

eLife

A gut bacterial amyloid promotes a-synuclein aggregation and motor impairment in mice

Fragile X-associated tremor ataxia syndrome is an untreatable neurological and neuromuscular disorder caused by unstable expansion of 55–200 CGG nucleotide repeats in 5′ UTR of Fragile X intellectual disability 1 (FMR1) gene. The expansion of CGG repeats in the FMR1 mRNA elicits neuronal cell toxicity through two main pathogenic mechanisms. First, mRNA with CGG expanded repeats sequester specific RNA regulatory proteins resulting in splicing alterations and formation of ribonuclear inclusions. Second, repeat-associated non-canonical translation (RANT) of the CGG expansion produces a toxic homopolymeric protein, FMRpolyG. Very few small molecules are known to modulate these pathogenic events, limiting the therapeutic possibilities for FXTAS. Here, we found that a naturally available biologically active small molecule, Curcumin, selectively binds to CGG RNA repeats. Interestingly, Curcumin improves FXTAS associated alternative splicing defects and decreases the production and accumulation of FMRpolyG protein inclusion. Furthermore, Curcumin decreases cell cytotoxicity promptly by expression of CGG RNA in FXTAS cell models. In conclusion, our data suggest that small molecules like Curcumin and its derivatives may be explored as a potential therapeutic strategy against the debilitating repeats associated neurodegenerative disorders. © Copyright © 2020 Verma, Khan, Mishra, Mishra, Charlet-Berguerand and Kumar.

Frontiers in Neuroscience

Curcumin Regulates the r(CGG)exp RNA Hairpin Structure and Ameliorate Defects in Fragile X-Associated Tremor Ataxia Syndrome

This study reports for the first time an operation of an outdoor algae assisted Microbial Fuel Cell (MFC). The MFC (10 L) comprised of low-cost materials like rock phosphate blended clayware &amp; low-density polyethylene bags as anodic &amp; cathodic chamber respectively. Algae biomass after lipid extraction at 2 g/l served as electron donor at the anode. Chlorella vulgaris at cathode provided oxygen as electron acceptor and served as lipid source. The MFCs performed well in all aspects namely energy recovery, algae productivity, and cost of operation. The 5% RP-MFCs gave 0.307 kg/m3d algal productivity, 0.09 kg/m3d lipid productivity, and 11.5318 kWh/m3 of net energy recovery (NER). Rock phosphate served as a slow and constant source of phosphorus supporting algae growth. Proteobacteria (45.14%) were the dominant phyla while Alicyliphilus (5.46%) and Dechloromonas (4.74%) were the dominant genera at the anode. The estimated cost of the system was $11.225 only. © 2020 Elsevier Ltd

Department of Electrical Engineering

Bioresource Technology

Performance evaluation of algae assisted microbial fuel cell under outdoor conditions

Development of simple, robust, and noninvasive therapeutic approaches to treat cancers and improve survival rates is a grand challenge in clinical biomedicine. In particular, the sizes and shape of the nanomaterials play a vital role in dictating their biodistribution and clearance pathways. It remains elusive how the size and shape of a nanomaterial affect its therapeutic efficacy in cancer diagnosis and treatments. To tackle the above problem, the effects of size and shape of Cu2(OH)PO4 nanostructures (nanosheets and quantum dots) on the photodynamic therapy (PDT) in destroying malignant drug-resistant lung tumors and on combating the tumor hypoxia problem are investigated and compared. The photocatalytic mechanism of Cu2(OH)PO4 nanostructures mainly involves the generation of reactive oxygen species (ROS), such as hydroxyl radical (·OH) and singlet oxygen (1O2). Under an oxygen deprivation condition, Cu2(OH)PO4 nanosheets still can generate OH radicals to kill cancer cells upon near-infrared (NIR) light irradiation. Overall, in vitro and in vivo experiments show that Cu2(OH)PO4 nanosheets can overcome tumor hypoxia problems and effectively mediate dual modal PDT and photothermal therapeutic (PTT) effects on destruction of NCI-H23 lung tumors in mice using ultralow doses (350 mW cm−2) of NIR (915 nm) light. © 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Particle and Particle Systems Characterization

Size and Shape Effects of Near-Infrared Light-Activatable Cu2(OH)PO4 Nanostructures on Phototherapeutic Destruction of Drug-Resistant Hypoxia Tumors

Microglia are resident innate immune cells of the central nervous system (CNS). Microglia play a critical role during development, in maintaining homeostasis, and during infection or injury. Several independent research groups have highlighted the central role that microglia play in autoimmune diseases, autoinflammatory syndromes and cancers. The activation of microglia in some neurological diseases may directly participate in pathogenic processes. Primary microglia are a powerful tool to understand the immune responses in the brain, cell-cell interactions and dysregulated microglia phenotypes in disease. Primary microglia mimic in vivo microglial properties better than immortalized microglial cell lines. Human adult microglia exhibit distinct properties as compared to human fetal and rodent microglia. This protocol provides an efficient method for isolation of primary microglia from adult human brain. Studying these microglia can provide critical insights into cell-cell interactions between microglia and other resident cellular populations in the CNS including, oligodendrocytes, neurons and astrocytes. Additionally, microglia from different human brains may be cultured for characterization of unique immune responses for personalized medicine and a myriad of therapeutic applications. © 2020 JoVE Journal of Visualized Experiments.