Showing papers by "Chaitanya G. Joshi published in 2020"
TL;DR: The first ever successful effort in India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of wastewater-based epidemiology (WBE) surveillance in India makes a strong case for the environmental surveillance of the COVID-19 pandemic.
371 citations
TL;DR: This study, being the first from India and probably among the first ten reports in the world of gene detection of SARS-CoV-2 in the environmental samples, aims to assist concerned authorities and policymakers to formulate and/or upgrade the COVID-19 surveillance to have an explicit picture of the phase of the pandemic.
Abstract: we made the first ever successful effort from India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of WBE surveillance in India. Sampling was carried out on 8 and 27 May, 2020 from Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat with 106 million liters per day (MLD) capacity receiving effluent of Civil Hospital treating COVID-19 patient. All three i.e. ORF1ab, N and S genes of SARS-CoV-2 were discerned in the influents with no gene spotted in the effluent collected on 8 and 27 May 2020. Temporal difference between 8 and 27 May 2020 samples was of 10x in gene copy loading with corresponding change of 2x in the number active COVID-19 patient in the city. Number of gene copies was found comparable to that reported in the untreated wastewaters of Australia, China and Turkey and lower than that of the USA, France and Spain. This study, being the first from India and probably among the first ten reports in the world of gene detection of SARS-CoV-2 in the environmental samples, aims to assist concerned authorities and policymakers to formulate and/or upgrade the COVID-19 surveillance to have explicit picture of phase of the pandemic. While infectious SARS-CoV-2 has yet to be identified in the aquatic environment, the virus potentially enters the wastewater stream from patient excretions and thus can be a great tool for pandemic monitoring. HIGHLIGHTS □First ever report of the presence of gene of SARS-CoV-2 in the wastewater in India. □CT value is explicitly indicative of the increase of COVID-19 patient in the vicinity. □All three i.e. ORF1ab, N and S genes of SARS-CoV-2 were discerned in the influents. □None of three genes were spotted in the effluent collected on 8 and 27 May 2020. □Wastewater surveillance conclusively specified temporal difference in COVID-19 load. □Temporal difference was 10x and 2x in gene copies and COVID-19 patient, respectively.
79 citations
TL;DR: A systematic review of the literature published between 2003 and 2020 is presented to validate the hypothesis that the pharmacokinetics, collateral acute/chronic side effects of nano drugs and spike proteins arrangement of coronaviruses can revolutionize the therapeutic approach to cure COVID-19.
32 citations
TL;DR: De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita and the role of SNP in Assembly Formation is studied.
Abstract: Citation: Das P, Sahoo L, Das SP, Bit A, Joshi CG, Kushwaha B, Kumar D, Shah TM, Hinsu AT, Patel N, Patnaik S, Agarwal S, Pandey M, Srivastava S, Meher PK, Jayasankar P, Koringa PG, Nagpure NS, Kumar R, Singh M, Iquebal MA, Jaiswal S, Kumar N, Raza M, Das Mahapatra K and Jena J (2020) De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita. Front. Genet. 11:386. doi: 10.3389/fgene.2020.00386 De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita
19 citations
TL;DR: The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal, and Pearson’s correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other.
Abstract: In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.
12 citations
TL;DR: 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences and variants were analyzed from diseased and recovered patients from Gujarat and the World to understanding its role in pathogenesis.
Abstract: Humanity has seen numerous pandemics during its course of evolution. The list includes many such as measles, Ebola, SARS, MERS, etc. Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. As of 4th July 2020, COVID-19 has affected over 10 million people from 170+ countries, and 5,28,364 deaths. Genomic technologies have enabled us to understand the genomic constitution of the pathogens, their virulence, evolution, rate of mutations, etc. To date, more than 60,000 virus genomes have been deposited in the public depositories like GISAID and NCBI. While we are writing this, India is the 3rd most-affected country with COVID-19 with 0.6 million cases, and >18000 deaths. Gujarat is the fourth highest affected state with 5.44 percent death rate compared to national average of 2.8 percent. Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. The other significant deleterious variant found in diseased patients from Gujarat and the world is G25563T, which is located in Orf3a and has a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID.
10 citations
TL;DR: The results obtained from molecular docking and molecular dynamics simulation indicated weaker interaction of C241T mutant stem loops with host transcription factor MADP1 indicating reduced replication efficiency and these results are correlated with increased recovery rates and decreased death rates of global SARS-CoV-2 cases.
Abstract: Novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has claimed more than 1.5 million lives worldwide and counting. As per the GISAID database, the genomics of SARS-CoV2 is extensively studied with more than 500 genome submissions per day. Out of several hotspot mutations within the SARS-CoV-2 genome, researchers have focused a lot on missense variants but the least work is done on the UTRs. One of the most frequent UTR variants in the SARS-CoV-2 genome is the C241T with a global frequency of more than 0.9. In the present study, the effect of the C241T mutation has been studied with respect to change in RNA structure and its interaction with the host replication factors MADP1 Zinc finger CCHC-type and RNA-binding motif 1 (hnRNP1). The results obtained from molecular docking and molecular dynamics simulation indicated weaker interaction of C241T mutant stem loops with host transcription factor MADP1 indicating reduced replication efficiency. The results are also correlated with increased recovery rates and decreased death rates of global SARS-CoV-2 cases.
8 citations
TL;DR: The role of lncRNAs in manipulating cell cycle regulation during horn squamous cell carcinomas is shown through differential expression analysis on cancer-related coding genes in Indian zebu cattle.
Abstract: Long non-coding RNA (lncRNA) was previously considered as a non-functional transcript, which now established as part of regulatory elements of biological events such as chromosome structure, remodeling, and regulation of gene expression. The study presented here showed the role of lncRNA through differential expression analysis on cancer-related coding genes in horn squamous cell carcinoma of Indian zebu cattle. A total of 10,360 candidate lncRNAs were identified and further analyzed for its coding potential ability using three tools (CPC, CPAT, and PLEK) that provide 8862 common lncRNAs. Pfam analysis of these common lncRNAs gave 8612 potential candidates for lncRNA differential expression analysis. Differential expression analysis showed a total of 59 significantly differentially expressed genes and 19 lncRNAs. Pearson's correlation analysis was used to identify co-expressed mRNA-lncRNAs to established relation of the regulatory role of lncRNAs in horn cancer. We established a positive relation of seven upregulated (XLOC_000016, XLOC_002198, XLOC_002851, XLOC_ 007383, XLOC_010701, XLOC_010272, and XLOC_011517) and one downregulated (XLOC_011302) lncRNAs with eleven genes that are related to keratin family protein, keratin-associated protein family, cornifelin, corneodesmosin, serpin family protein, and metallothionein that have well-established role in squamous cell carcinoma through cellular communication, cell growth, cell invasion, and cell migration. These biological events were found to be related to the MAPK pathway of cell cycle regulation indicating the role of lncRNAs in manipulating cell cycle regulation during horn squamous cell carcinomas that will be useful in identifying molecular portraits related to the development of horn cancer.
8 citations
TL;DR: This study sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology, finding a remarkable similarity between relatively common mutations of 36-nucleotide deletion in ORF8 of Sars-Cov-2.
Abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first reported in Wuhan, China in November 2019 has developed into a pandemic since March 2020, causing substantial human casualties and economic losses. Studies on SARS-CoV-2 are being carried out at an unprecedented rate to tackle this threat. Genomics studies, in particular, are indispensable to elucidate the dynamic nature of the RNA genome of SARS-CoV-2. RNA viruses are marked by their unique ability to undergo high rates of mutation in their genome, much more frequently than their hosts, which diversifies their strengths qualifying them to elude host immune response and amplify drug resistance. In this study, we sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology. In addition to multiple point mutations, we found a remarkable similarity between relatively common mutations of 36-nucleotide deletion in ORF8 of SARS-CoV-2. Our results corroborate with the earlier reported 29-nucleotide deletion in SARS, which was frequent during the early stage of human-to-human transmission. The results will be useful to understand the biology of SARS-CoV-2 and itsattenuation for vaccine development.
7 citations
TL;DR: It is evident by the gene expression analysis that the inhibitory neurotransmitter GABA, altered ratio of T: 11-KT, increased testicular bile acids, and oxytocin-like neuropeptide in the male brain, appear to be involved in arresting the pulsatile motion of testicular smooth muscles.
5 citations
TL;DR: The study explored the vast diversity of buffalo rumen bacteria and archaea, and the diverse wealth of rumen enzymes (CAZymes), which revealed that a major part of CAZymes comes from the less known rumen microbes indicating alternative paths of fiber degradation along with the very well known ones.
Abstract: The aim of this study was to investigate the rumen microbial diversity and functionality in buffaloes fed with a blend of essential oils (BEO) using LSD switch over design. The BEO consisting of blend of Trachyspermum copticum (Ajwain) oil, Cymbopogon citratus (lemon grass) oil and Syzygium aromaticum (clove bud) oleoresin mixed in equal proportion, was fed at the rate of 0, 0.75 and 1.5 ml/100 kg of body weight in 0 (control), 0.75 and 1.5 groups, respectively. The metatranscriptomic libraries of the rumen microbiome were represented by 7 domains, 84 phyla, 64 archeal genera and 663 bacterial genera with Bacteroidetes and Firmicutes constituting 80% of phyla abundance irrespective of feeding regime. Methanogenic archaea was represented by 22 phyla with Methanobrevibacter as the major genus. BEO feeding reduced the abundance of Methanococcus and Thermoplasma (P < 0.05) at all levels. The results revealed that the feeding of BEO shifted the archeal and bacterial population at very low magnitude. The study explored the vast diversity of buffalo rumen bacteria and archaea, and the diverse wealth of rumen enzymes (CAZymes), which revealed that a major part of CAZymes comes from the less known rumen microbes indicating alternative paths of fiber degradation along with the very well known ones.
TL;DR: The study presents successful cloning, expression and purification of active serratiopeptidase, using Escherichia coli BL21 [DE3] and pET SUMO vector followed by optimization of synthetic media and culture conditions for enhanced Serratia marcescens production.
TL;DR: High proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data, indicating differences in organisms present and organisms active in the rumen.
Abstract: The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet
TL;DR: First report on characterization of 17β-HSD2 and SPATA2 full-length cDNA in catfish showed both proteins are hydrophilic in nature, and SPata2 showed significantly higher expression in preparatory phase compared to spawning phase in both ovary and testis.
Abstract: The 17-beta-hydroxysteroid dehydrogenase 2 (17β-HSD2) enzyme regulates steroid levels by the inactivation of estrogen and androgens. Spermatogenesis associated protein 2 (SPATA2) plays a vital role...
TL;DR: The study provides the first draft genome of the entire fungalDirinaria genus and provides insights into the Dirinaria lichen metagenome from Gujarat region.
TL;DR: The data obtained during the annotation of the genome enriched from metagenomic data from the lichen samples are presented.
05 Feb 2020
TL;DR: Functional analysis showed that the upregulated keratins support metastasis of tumor via cell proliferation, migration, and affecting cell stability, while downregulated interleukins deprive the immune response to tumor posing clear path for metastases of horn cancer.
Abstract: Horn cancer is most prevalent in Bos indicus and poorly defined genetic landscape makes disease diagnosis and treatment difficult. In this study, RNA-Seq and data analysis using CLC Genomics Workbench was employed to identify biomarkers associated with horn cancer. As a result, a total of 149 genes were found significant differentially expressed in horn cancer samples compared to horn normal samples. The study revealed ‘keratins’ and ‘interleukins’ as apex groups of significant differentially expressed genes (DEGs). Functional analysis showed that the upregulated keratins support metastasis of tumor via cell proliferation, migration, and affecting cell stability, while downregulated interleukins along with other associated chemokine receptors deprive the immune response to tumor posing clear path for metastasis of horn cancer. Combi-action of both the group facilitates the tumor microenvironment to reproduce tumorigenesis. Analysis of pathways enriched in DEGs and exemplified protein–protein interaction network indicated actual role of DEGs in horn cancer at a fine level. Important effect of deregulated expression of keratin and interleukin genes in horn cancer enrolling their candidacy as potential biomarkers for horn cancer prognosis. This study appraises the possibility to mitigate horn cancer at fine resolution to extract attainable identification of prognostic molecular portraits.
TL;DR: Using molecular approaches a total of 10 SSR primers of rice microsatellite were used to screen 24 genotypes of rice (Oryza sativa L.), and eight of these primers were successful in producing polymorphic as well as monomorphic alleles in 24 rice genotypes.
Abstract: Rice (Oryza sativa L.) is the primary food source for over a third of the world’s population. The rice production is limited by various biotic and abiotic stress factors. Of the abiotic stresses, high soil salinity, largely contributed by NaCl, is one of the major factors limiting the distribution and productivity of large crops, including rice. Looking to this problem, using molecular approaches total of 10 SSR primers of rice microsatellite were used to screen 24 genotypes of rice (Oryza sativa L.). Eight of these primers were successful in producing polymorphic as well as monomorphic alleles in 24 rice genotypes. The selected molecular markers (RM 145, RM160, RM7075 and RM 253) showed polymorphism in 24 rice cultivars.
01 Jan 2020
TL;DR: In this paper, the authors delved deep into biogas commercialization over decades considering different models developed, key commercial players who have robust at scale operations, and the market movements that have shaped biogAS industries.
Abstract: Circular bio-economy with focus on sustainable and renewable energy source has become the need of the hour as mandated by the United Nations. Countries across the globe have united in the quest for deriving value in terms of energy from organic sources earlier considered as waste. A valuable contribution toward sustainability, bio-economy, and maintenance of environmental standards comes from biogas production wherein organic contents are converted under controlled conditions of microbial digestion into biogas that is rich in methane. This chapter delves deep into biogas commercialization over decades considering different models developed, key commercial players who have robust at scale operations, and the market movements that have shaped biogas industries. Current policies across the world and the investment scenarios that are redefining the landscape of the biogas plants have been explained in depth. Government and nongovernment incentives, legislations, policies, and regulatory framework have renewed the focus on biogas considering the overawing advantages of management of waste and environmental credits along with co-product value gain. Details of planning with permissions for setup and operations along with supply chain logistics of pre- and post-biogas processes is covered. Last but not the least is a case study of a large commercial biogas plant that has had huge commercial, social, and environmental impact.
01 Jan 2020
TL;DR: This chapter is mainly dealing with the application part of the synthetic biotechnology in development of biosensors, for new drug discovery, tools for application in agriculture, for secondary metabolism, for chemical production, and for biofuel production.
Abstract: Synthetic biology is a new and evolving branch of science, which has extensive application in the surrounding as well as human life. This field deals with the knowledge gain from the living system by the means of bioinformatics or other relevant field and try to regulate or restructure the pathways and the system of the higher organism in much simpler microorganism. It actually translates the knowledge gain from an organism or system in simpler system for the benefit of the nature. Evolution in the field of biotechnology, easy fast and high-throughput and accurate technologies available for DNA sequencing, and synthesis, has made it very easy to design and structure a specific pathway, which is useful in a particular organism in a model organism, which in field of synthetic biology is termed as chassis. Synthetic biology brings together different areas such as engineering, molecular biology, cell biology, biotechnology, bioinformatics, and system biology in such a way that they all together forms this new area with vast application in various fields. Synthetic biotechnology has its application in almost all fields such as from cellular programming to drug designing to biofuels production. In this chapter, we will be mainly dealing with the application part of the synthetic biotechnology in development of biosensors, for new drug discovery, tools for application in agriculture, for secondary metabolism, for chemical production, and for biofuel production.
01 Jan 2020
TL;DR: This book chapter is dealing with the various criteria that are utilized for the selection of the strains, various approaches that are routinely utilizing for the higher expression of genes, as well as various metabolic engineering strategies.
Abstract: Metabolic engineering is a field of science, which takes advantage of previously gathered information about a particular pathway in a living organism and utilizes this for the improvement of product that could be either metabolite, enzyme, or any protein. Advances in various field of science specifically r-DNA technology, bioinformatics, synthetic biology, molecular genetics as well as other protein engineering technologies had given wings to metabolic engineering. Metabolic engineering has the capacity to mold the flux of a completely enzymatic pathway to a very newly designed pathway. It allows the modulation and production of either previously working metabolite or the production of a new novel enzyme in a different microbial strain. In the present era, there is huge demand of microbial enzymes and proteins for various purposes such as medication, oil and gas industry, dairy industry, baking industry, etc. Microbial strains are utilized as micro factories for the production of microbial enzymes and proteins via metabolic engineering. Therefore, in this book chapter we are dealing with the various criteria that are utilized for the selection of the strains, various approaches that are routinely utilized for the higher expression of genes, as well as various metabolic engineering strategies.
TL;DR: In this article, the authors analyzed SARS-CoV-2 RNA in the influent wastewater samples (n = 43) from four wastewater treatment plants (WWTPs) in Gandhinagar, India, during August 7th to September 30th, 2020.
Abstract: Wastewater-based Epidemiological (WBE) surveillance offers a promising approach to assess the pandemic situation covering pre-symptomatic and asymptomatic cases in highly populated area under limited clinical tests. In the present study, we analysed SARS-CoV-2 RNA in the influent wastewater samples (n = 43) from four wastewater treatment plants (WWTPs) in Gandhinagar, India, during August 7th to September 30th, 2020. A total of 40 samples out of 43 were found positive i.e. having at least two genes of SARS-CoV-2. The average Ct values for S, N, and ORF 1ab genes were 32.66, 33.03, and 33.95, respectively. Monthly variation depicted a substantial rise in the average copies of N (∼120%) and ORF 1ab (∼38%) genes in the month of September as compared to August, while S-gene copies declined by 58% in September 2020. The SARS-CoV-2 genome concentration was higher in the month of September (∼924.5 copies/ L) than August (∼897.5 copies/ L), corresponding to a ∼ 2.2-fold rise in the number of confirmed cases during the study period. Further, the percentage change in genome concentration level on a particular date was found in the lead of 1-2 weeks of time with respect to the official confirmed cases registered based on clinical tests on a temporal scale. The results profoundly unravel the potential of WBE surveillance to predict the fluctuation of COVID-19 cases to provide an early warning. Our study explicitly suggests that it is the need of hour that the wastewater surveillance must be included as an integral part of COVID-19 pandemic monitoring which can not only help the water authorities to identify the hotspots within a city but can provide up to 2 weeks of time lead for better tuning the management interventions. HIGHLIGHTS □Study unravels the early warning potential of wastewater based surveillance of COVID-19. □Adequate SARS-CoV-2 RNA were detected despite of limited reported case in the vicinity. □Up to 2 weeks of lead is possible from a regular wastewater based COVID-19 surveillance. □SARS-CoV-2 RNA was higher in September than August in response to a ∼ 2.2-fold rise in COVID-19 active cases. Graphical Abstract