Comparative Analysis of Sugar Metabolites and Their Transporters in Sugarcane Following Sugarcane mosaic virus (SCMV) Infection

Sugarcane mosaic virus (SCMV) is one of the major pathogens of sugarcane. SCMV infection causes dynamic changes in plant cells, including decreased photosynthetic rate, respiration, and sugar metabolism. To understand the basics of pathogenicity mechanism, we performed transcriptome and proteomics analysis in two sugarcane genotypes (Badila: susceptible to SCMV and B-48: SCMV resistant). Using Saccharum spontaneum L. genome as a reference, we identified the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) that participate in sugar metabolism, transport of their metabolites, and Carbohydrate Activating enZYmes (CAZymes). Sequencing data revealed 287 DEGs directly or indirectly involved in sugar metabolism, transport, and storage, while 323 DEGs are associated with CAZymes. Significant upregulation of glucose, sucrose, fructose, starch, and SWEET-related transcripts was observed in the Badila after infection of SCMV. B-48 showed resistance against SCMV with a limited number of sugar transcripts up-regulation at the post-infection stage. For CAZymes, only glycosyltransferase (GT)1 and glycosyl hydrolase (GH)17 were upregulated in B-48. Regulation of DEGs was analyzed at the proteomics level as well. Starch, fructose, glucose, GT1, and GH17 transcripts were expressed at the post-translational level. We verified our transcriptomic results with proteomics and qPCR data. Comprehensively, this study proved that Badila upregulated sugar metabolizing and transporting transcripts and proteins, which enhance virus multiplication and infectionl.

Lipid Interactions Between Flaviviruses and Mosquito Vectors

Mosquito-borne flaviviruses, such as dengue (DENV), Zika (ZIKV), yellow fever (YFV), West Nile (WNV), and Japanese encephalitis (JEV) viruses, threaten a large part of the human populations. In absence of therapeutics and effective vaccines against each flaviviruses, targeting viral metabolic requirements in mosquitoes may hold the key to new intervention strategies. Development of metabolomics in the last decade opened a new field of research: mosquito metabolomics. It is now clear that flaviviruses rely on mosquito lipids, especially phospholipids, for their cellular cycle and propagation. Here, we review the biosyntheses of, biochemical properties of and flaviviral interactions with mosquito phospholipids. Phospholipids are structural lipids with a polar headgroup and apolar acyl chains, enabling the formation of lipid bilayer that form plasma- and endomembranes. Phospholipids are mostly synthesized through the de novo pathway and remodeling cycle. Variations in headgroup and acyl chains influence phospholipid physicochemical properties and consequently the membrane behavior. Flaviviruses interact with cellular membranes at every step of their cellular cycle. Recent evidence demonstrates that flaviviruses reconfigure the phospholipidome in mosquitoes by regulating phospholipid syntheses to increase virus multiplication. Identifying the phospholipids involved and understanding how flaviviruses regulate these in mosquitoes is required to design new interventions.

Surface Temperature Distribution Aluminum Block with Cone Tube Profile Calculated Using ANSYS Fluent

Thermal Cycler is the main part of the Polymerase Chain Reaction (PCR), which becoming a gold standard for Covid-19 diagnosis. The virus multiplication in an order to a detectable concentration is done by placing the virus solution at a deterministic temperature cycle. The solution is placed in a small tube inserted in a temperature block. Temperature distribution of the thermal block is important to make all the tube with sample treated at the same at desired target temperature. Study on the thermal block made of aluminium 7075 was simulated using fluid dynamic finite element method. Heating and colling to the target temperature was done by providing heat source and heat absorber. The temperature distribution on the surface was mapped. The temperature gradient perpendicular to the heat source was calculated. Assuming the environment of the thermal block was still air, the heating and cooling speed at given heat source and heat removal were calculated using the model. The temperature gradient from the top surface to the bottom surface is less than 2.5°C. The temperature difference among point at the surface is less than 0.1°C.

Oxygen Deficient (OD) Combustion and Metabolism: Allometric Laws of Organs and Kleiber’s Law from OD Metabolism?

The biology literature presents allometric relations for the specific metabolic rate (SMRk) of an organ k of mass mk within the body of mass mB: SMR_k ∝ mBfk (body mass allometry, BMA). Wang et al. used BMA, summed-up energy from all organs and validated Kleiber’s law of the whole body: SMRM ∝ mBb’, b’ = −0.25. The issues raised in biology are: (i) why fk and b’ < 0, (ii) how do the organs adjust fk to yield b’? The current paper presents a “system” approach involving the field of oxygen deficient combustion (ODC) of a cloud of carbon particles and oxygen deficient metabolism (ODM), and provides partial answers by treating each vital organ as a cell cloud. The methodology yields the following: (i) a dimensionless “group” number GOD to indicate extent of ODM, (ii) SMRk of an organ in terms of the effectiveness factor; (iii) curve fitting of the effectiveness factor to yield the allometric exponents for the organ mass-based allometric laws (OMA); (iv) validation of the results with data from 111 biological species (BS) with mB ranging from 0.0075 to 6500 kg. The “hypoxic” condition at organ level, particularly for Covid-19 patients, and the onset of cancer and virus multiplication are interpreted in terms of ODM and glycolysis.

Glycolytic inhibitor 2-Deoxy-D-glucose attenuates SARS-CoV-2 multiplication in host cells and weakens the infective potential of progeny virions

The COVID-19 pandemic is an ongoing public health emergency of international concern. Millions of people lost their lives to this pandemic. While a lot of efforts are being invested in vaccinating the population, there is also an emergent requirement to find potential therapeutics to effectively counter this fast mutating SARS-CoV-2 virus-induced pathogenicity. Virus-infected host cells switch their metabolism to a more glycolytic phenotype. This switch induced by the virus is needed for faster production of ATP and higher levels of glycolytic intermediates, which are required for anabolic processes such as fatty acid synthesis and nucleotide generation for new virion synthesis and packaging. In this study, we used 2-Deoxy-D-glucose (2-DG) to target and inhibit the metabolic reprogramming induced by SARS-CoV-2 infection. Our results showed that virus infection induces glucose influx and glycolysis resulting in selective high accumulation of the fluorescent glucose/2-DG analogue, 2-NBDG in these cells. Subsequently, 2-DG reduces the virus multiplication and alleviates the cells from infection-induced cytopathic effect (CPE) and cell death. Herein, we demonstrate that progeny virions produced from 2-DG treated cells are defective with compromised infectivity potential. Further, it was also observed that mannose inhibits 2-NBDG uptake at a very low concentration, suggesting that 2-DG uptake in virus-infected cells might be exploiting the specific mannose transporter or high-affinity glucose transporter, GLUT3, which was found to be increased on SARS-CoV-2 infection. In conclusion, our findings suggest that 2-DG effectively inhibits the SARS-CoV-2 multiplication and can be used as a treatment regimen. Based on these preliminary in-vitro findings this molecule reached clinical trial in COVID patients.

Cauliflower Mosaic Virus Utilizes Processing Bodies to Escape Translational Repression in Arabidopsis

Viral infections impose extraordinary RNA stress on a cell, triggering cellular RNA surveillance pathways like RNA decapping, nonsense-mediated decay and RNA silencing. Viruses need to maneuver between these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigate the role of Arabidopsis thaliana PBs during Cauliflower Mosaic Virus (CaMV) infection. We find that several PB components are co-opted into viral replication factories and support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we could establish PB components as essential helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, PB dysfunctions expose the virus to this pathway, similar to previous observations on transgenes. Transgenes, however, undergo RNA Quality Control dependent RNA degradation, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence between PBs, RNA silencing and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.

Strategies for the Production of Soluble Interferon-Alpha Consensus and Potential Application in Arboviruses and SARS-CoV-2

Biopharmaceutical production is currently a multibillion-dollar industry with high growth perspectives. The research and development of biologically sourced pharmaceuticals are extremely important and a reality in our current healthcare system. Interferon alpha consensus (cIFN) is a non-natural synthetic antiviral molecule that comprises all the most prevalent amino acids of IFN-α into one consensus protein sequence. For clinical use, cIFN is produced in E. coli in the form of inclusion bodies. Here, we describe the use of two solubility tags (Fh8 and DsbC) to improve soluble cIFN production. Furthermore, we analyzed cIFN production in different culture media and temperatures in order to improve biopharmaceutical production. Our results demonstrate that Fh8-cIFN yield was improved when bacteria were cultivated in autoinduction culture medium at 30 °C. After hydrolysis, the recovery of soluble untagged cIFN was 58% from purified Fh8-cIFN molecule, fourfold higher when compared to cIFN recovered from the DsbC-cIFN, which achieved 14% recovery. The biological activity of cIFN was tested on in vitro model of antiviral effect against Zika, Mayaro, Chikungunya and SARS-CoV-2 virus infection in susceptible VERO cells. We show, for the first time, that cIFN has a potent activity against these viruses, being very low amounts of the molecule sufficient to inhibit virus multiplication. Thus, this molecule could be used in a clinical approach to treat Arboviruses and SARS-CoV-2.

Purification of Murine Gammaherpesvirus 68 With Use of Differential Centrifugation

The method for separation of viral particles in a concentrated form from the environment is called virus purification. Viruses are required to be purified for a range of studies in which it is necessary to distinguish the properties or structure of a virus from the host cells or culture media, including analysis of viral polypeptide structures and membrane glycoprotein function. Our objective was to purify murine gammaherpesvirus 68 (MHV-68, MuHV-4) using the centrifuge, equipment and other materials available in our laboratory. After infection of baby hamster kidney 21 (BHK-21) cells with MHV-68 with the multiplicity of infection (MI) of 0.01 and following virus multiplication, we repeatedly froze and thawed the cell culture to disrupt the cells and release the virus particles into the culture medium. We used low-speed centrifugation (3000 rpm at 4°C) to separate the viral particles from cell debris. Subsequently, we transferred the supernatant containing virus particles to a fresh centrifuge tube and centrifuged at a speed of 8000 rpm (8801 g) and 11,000 rpm (=16,639 g) and at 4°C. We tested different centrifugation durations of 2, 4, 6 and 8 hours. To evaluate the quality of the obtained purified MHV-68 virus by this method and compare it to purified MHV-68 sample acquired by conventional ultracentrifugation on sucrose cushion (30%, w/v), we used the SDS-PAGE separation method using a 4%–20% (w/v) and 6%–14% (w/v) gradient gel. We obtained the best results with 6-hour-long centrifugation at 11,000 rpm. In conclusion, we managed to optimise virus purification method using the equipment available in our laboratory and prepared purified MHV-68 virus in sufficient concentration for determination of MHV-68 virus proteins.

Ayurvedic management for COVID-19 – A review

As the corona pandemic has emerged, researchers around the globe are working on finding specific treatment for it. But till date, no conclusive specific treatment has been found, and we are following the protocols with symptomatic management. Ayurveda is an ancient science of healing, with highly sophisticated literature about diseases, their pathogenesis, clinical features, and management. The evaluation of different modalities for treating COVID-19 pandemic patients is the foremost aim of the study. For review, we used the knowledge of the ancient classics and past literature regarding human treatment guidelines mentioned in Ayurveda classics, for prevention and treatment of communicable diseases, to provide appropriate direction in the prevention of COVID-19. The thorough review has been done, of literature, Samhitas(Ayurveda Classics), and research articles which were published between January and June 2020 by PubMed, Google Scholar, WHO, Ministry of AYUSH. The opinions of experts have also been referred to. As individuals with lower immunity have a higher risk of COVID-19, so the herbal Rasayana(Rejuvenating) drug, which has proven immunomodulatory activity, is also included in the given study. The Review for Ayurveda formulations, which might help in preventing the progression of COVID-19, has also been made. The Indian herbs are widely utilized in the preparation of Ayurvedic medicines or formulations or in the form of drinks to manage various respiratory disorders such as cough, cold, and flu. Hence, these drugs are formulated by using active parts of the plants, which are used for preventing and treating the COVID-19. These formulations are immunity modulators and they prevent the spread of the virus, by intruding at a different stage of virus multiplication in the infected person.