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1.
Environ Res ; 204(Pt B): 112067, 2021 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-34543636

RESUMO

COVID-19 positive patients can egest live SARS-CoV-2 virus and viral genome fragments through faecal matter and urine, raising concerns about viral transmission through the faecal-oral route and/or contaminated aerosolized water. These concerns are amplified in many low- and middle-income countries, where raw sewage is often discharged into surface waterways and open defecation is common. Nonetheless, there has been no evidence of COVID-19 transmission via ambient urban water, and the virus viability in such aquatic matrices is believed to be minimal and not a matter of concern. In this manuscript, we attempt to discern the presence of SARS-CoV-2 genetic material (ORF-1ab, N and S genes) in the urban water (lakes, rivers, and drains) of the two Indian cities viz., Ahmedabad (AMD), in western India with 9 wastewater treatment plants (WWTPs) and Guwahati (GHY), in the north-east of the country with no such treatment facilities. The present study was carried out to establish the applicability of environmental water surveillance (E-wat-Surveillance) of COVID-19 as a potential tool for public health monitoring at the community level. 25.8% and 20% of the urban water samples had detectable SARS-CoV-2 RNA load in AMD and GHY, respectively. N-gene > S-gene > ORF-1ab-gene were readily detected in the urban surface water of AMD, whereas no such observable trend was noticed in the case of GHY. The high concentrations of SARS-CoV-2 genes (e.g., ORF-1ab; 800 copies/L for Sabarmati River, AMD and S-gene; 565 copies/L for Bharalu urban river, GHY) found in urban waters suggest that WWTPs do not always completely remove the virus genetic material and that E-wat-Surveillance of COVID-19 in cities/rural areas with poor sanitation is possible.

2.
Sci Total Environ ; 792: 148367, 2021 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-34465041

RESUMO

Following the proven concept, capabilities, and limitations of detecting the RNA of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) in wastewater, it is pertinent to understand the utility of wastewater surveillance data on various scale. In the present work, we put forward the first wastewater surveillance-based city zonation for effective COVID-19 pandemic preparedness. A three-month data of Surveillance of Wastewater for Early Epidemic Prediction (SWEEP) was generated for the world heritage city of Ahmedabad, Gujarat, India. In this expedition, 116 wastewater samples were analyzed to detect SARS-CoV-2 RNA, from September 3rd to November 26th, 2020. A total of 111 samples were detected with at least two out of three SARS-CoV-2 genes (N, ORF 1ab, and S). Monthly variation depicted a significant decline in all three gene copies in October compared to September 2020, followed by a sharp increment in November 2020. Correspondingly, the descending order of average effective gene concentration was: November (~10,729 copies/L) > September (~3047 copies/L) > October (~454 copies/L). Monthly variation of SARS-CoV-2 RNA in the wastewater samples may be ascribed to a decline of 20.48% in the total number of active cases in October 2020 and a rise of 1.82% in November 2020. Also, the monthly recovered new cases were found to be 16.61, 20.03, and 15.58% in September, October, and November 2020, respectively. The percentage change in the gene concentration was observed in the lead of 1-2 weeks with respect to the percentage change in the provisional figures of confirmed cases. SWEEP data-based city zonation was matched with the heat map of the overall COVID-19 infected population in Ahmedabad city, and month-wise effective gene concentration variations are shown on the map. The results expound on the potential of WBE surveillance of COVID-19 as a city zonation tool that can be meaningfully interpreted, predicted, and propagated for community preparedness through advanced identification of COVID-19 hotspots within a given city.


Assuntos
COVID-19 , Humanos , Índia/epidemiologia , Pandemias , RNA Viral , SARS-CoV-2 , Águas Residuárias
3.
Inform Med Unlocked ; : 100670, 2021 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-34307830

RESUMO

Novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has claimed more than 3.3 million lives worldwide and still counting. As per the GISAID database, the genomics of SARS-CoV-2 has been extensively studied, with more than 500 genome submissions per day. Out of several hotspot mutations within the SARS-CoV-2 genome, recent research has focused mainly on the missense variants. Moreover, significantly less attention has been accorded to delineate the role of the untranslated regions (UTRs) of the SARS-CoV-2 genome in the disease progression and etiology. One of the most frequent 5' UTR variants in the SARS-CoV-2 genome is the C241T, with a global frequency of more than 95 %. In the present study, the effect of the C241T mutation has been studied with respect to the changes 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 the host transcription factor MADP1, indicating a reduced replication efficiency. The results are also correlated with increased recovery rates and decreased death rates of global SARS-CoV-2 cases.

4.
J Biomol Struct Dyn ; : 1-15, 2021 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-33988079

RESUMO

Herbal formulations mentioned in traditional medicinal texts were investigated for in silico effect against SARS-COV-2 proteins involved in various functions of a virus such as attachment, entry, replication, transcription, etc. To repurpose and validate polyherbal formulations, molecular docking was performed to study the interactions of more than 150 compounds from various formulations against the SARS-CoV-2 proteins. Molecular dynamics (MD) simulation was performed to evaluate the interaction of top scored ligands with the various receptor proteins. The docking results showed that Liquiritic acid, Liquorice acid, Terchebulin, Glabrolide, Casuarinin, Corilagin, Chebulagic acid, Neochebulinic acid, Daturataturin A, and Taraxerol were effective against SARS-COV-2 proteins with higher binding affinities with different proteins. Results of MD simulations validated the stability of ligands from potent formulations with various receptors of SARS-CoV-2. Binding free energy analysis suggested the favourable interactions of phytocompounds with the recpetors. Besides, in silico comparison of the various formulations determined that Pathyadi kwath, Sanjeevani vati, Yashtimadhu, Tribhuvan Keeratiras, and Septillin were more effective than Samshamni vati, AYUSH-64, and Trikatu. Polyherbal formulations having anti-COVID-19 potential can be used for the treatment with adequate monitoring. New formulations may also be developed for systematic trials based on ranking from these studies.Communicated by Ramaswamy H. Sarma.

5.
Sci Total Environ ; 779: 146184, 2021 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-33752005

RESUMO

Globally, environmental pollution by plastic waste has become a severe ecological and social problem worldwide. The present study aimed to analyse the bacterial community structure and functional potential of the landfill site using high throughput shotgun metagenomic approach to understand plastic degrading capabilities present in the municipal solid waste (MSW) dumping site. In this study, soil, leachate and compost samples were collected from various locations (height and depth) of the Pirana landfill site in Ahmedabad city Gujarat, India. In total 30 phyla, 58 class, 125 order, 278 families, 793 genera, and 2468 species were predicted. The most dominant phyla detected were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria in the soil and compost samples. Whereas, in leachate samples, the predominant phyla belonged to Firmicutes (54.24%) followed by Actinobacteria (43.67%) and Proteobacteria (1.02%). The functional profiling revealed the presence of enzymatic groups and pathways involved in biodegradation of xenobiotics. The results also demonstrated the presence of potential genes that is associated with the biodegradation of different types of plastics such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS). Present study extablishes the relationship between microbial community structure and rich sources of gene pool, which are actively involved in biodegradation of plastic waste in landfill sites.


Assuntos
Microbiota , Eliminação de Resíduos , Poluentes Químicos da Água , Índia , Plásticos , Resíduos Sólidos/análise , Instalações de Eliminação de Resíduos , Poluentes Químicos da Água/análise
6.
Environ Res ; 196: 110946, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33662347

RESUMO

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 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. 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 1 ab 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 1 ab (~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.


Assuntos
COVID-19 , Pandemias , Cidades , Humanos , Índia , RNA Viral , SARS-CoV-2 , Águas Residuárias
7.
Phytochem Anal ; 32(5): 804-810, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-33527609

RESUMO

INTRODUCTION: Ayurveda takes advantage of the beneficial properties of medicinal plants. High demands in combination with inadequate availability of botanicals and a lack of knowledge with respect to their precise identification lead to adulterations in herbal products. Identification becomes more difficult in complex herbal formulations. Four different polyherbal formulations have been analyzed for the present paper. The targeted plants have different pharmacological properties for various ailments. OBJECTIVE: We aimed to examine the rbcL gene based plant DNA mini-barcode to identify target and non-target plants in polyherbal formulations by using high-throughput next generation sequencing. METHODS: Degenerate primers of the selected mini-barcode region have been identified from the literature. A blend of 30 authentic medicinal plant species was used to examine the species resolution capacity of the mini-barcode. DNA was isolated from herbal formulations, an amplicon library was prepared, and sequencing was performed on an IonS5 system. Data were analyzed using various bioinformatics tools. RESULTS: Analysis of control pooled samples revealed the optimum resolving power of the DNA mini-barcode. Data analysis of the commercial samples revealed that only one herbal formulation contained all plants and matched with listed contents. In two formulations, only 10 out of 21 and 11 out of 20 plants were detected, respectively. Additionally, several non-listed plants were also detected in these formulations. Two formulations contained >20% reads assigned to non-target plants. Overall, 21.98% of the reads were assigned to non-target plants. CONCLUSION: The present study clearly demonstrated the successful application and potential of meta-barcoding in the quality control of complex herbal matrices. The results strongly suggest that this approach can be used in pharmacovigilance of processed herbal products.


Assuntos
Código de Barras de DNA Taxonômico , Plantas Medicinais , DNA de Plantas/genética , Medicina Ayurvédica , Plantas Medicinais/genética , Controle de Qualidade
8.
Transbound Emerg Dis ; 2021 Jan 27.
Artigo em Inglês | MEDLINE | ID: mdl-33506644

RESUMO

The geographic location and heterogeneous multi-ethnic population of Dubai (United Arab Emirates; UAE) provide a unique setting to explore the global molecular epidemiology of SARS-CoV-2 and relationship between different viral strains and disease severity. We systematically selected (i.e. every 100th individual in the central Dubai COVID-19 database) 256 patients by age, sex, disease severity and month to provide a representative sample of laboratory-confirmed COVID-19 patients (nasopharyngeal swab PCR positive) during the first wave of the UAE outbreak (January to June 2020). Sociodemographic and clinical data were extracted from medical records and full SARS-CoV-2 genome sequences extracted from nasopharyngeal swabs were analysed. Older age was significantly associated with COVID-19-associated hospital admission and mortality. Overweight/obese or diabetic patients were 3-4 times more likely to be admitted to hospital and intensive care unit (ICU). Sequencing data showed multiple independent viral introductions into the UAE from Europe, Iran and Asia (29 January-18 March), and these early strains seeded significant clustering consistent with almost exclusive community-based transmission between April and June 2020. Majority of sequenced strains (N = 60, 52%) were from the European cluster consistent with the higher infectivity rates associated with the D614G mutation carried by most strains in this cluster. A total of 986 mutations were identified in 115 genomes, 272 were unique (majority were missense, n = 134) and 20/272 mutations were novel. A missense (Q271R) and synonymous (R41R) mutation in the S and N proteins, respectively, were identified in 2/27 patients with severe COVID-19 but not in patients with mild or moderate disease (0/86; p = .05, Fisher's Exact Test). Both patients were women (51-64 years) with no significant underlying health conditions. The same two mutations were identified in a healthy 37-year-old Indian man who was hospitalized in India due to COVID-19. Our findings provide evidence for continued community-based transmission of the European strains in the Dubai population and highlight new mutations that might be associated with severe disease in otherwise healthy adults.

9.
Sci Total Environ ; 754: 142329, 2021 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-33254951

RESUMO

For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and ultrafiltration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. The objectives were achieved through tracking of SARS-CoV-2 genetic loadings i.e. ORF1ab, N and S protein genes on 8th and 27th May 2020 along the wastewater treatment plant (106000 m3 million liters per day) equipped with UASB system in Ahmedabad, India. PEG method performed better in removing materials inhibiting RT-qPCR for SARS-CoV-2 gene detection from the samples, as evident from constant and lower CT values of control (MS2). Using the PEG method, we found a reduction >1.3 log10 reduction in SARS-CoV-2 RNA abundance during UASB treatment, and the RNA was not detected at all in the final effluent. The study implies that i) conventional wastewater treatment systems is effective in SARS-CoV-2 RNA removal, and ii) UASB system significantly reduces SARS-CoV-2 genetic loadings. Finally, PEG method is recommended for better sensitivity and inhibition removal during SARS-CoV-2 RNA quantification in wastewater.


Assuntos
COVID-19 , Esgotos , Águas Residuárias , Anaerobiose , Reatores Biológicos , Humanos , Índia , Pandemias , RNA , Eliminação de Resíduos Líquidos
10.
Sci Total Environ ; 746: 141326, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32768790

RESUMO

We made 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. Sampling was carried out on 8 and 27 May 2020 at the Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat that receives effluent from Civil Hospital treating COVID-19 patients. All three, i.e. ORF1ab, N and S genes of SARS-CoV-2, were found in the influent with no genes detected in effluent collected on 8 and 27 May 2020. Increase in SARS-CoV-2 genetic loading in the wastewater between 8 and 27 May 2020 samples concurred with corresponding increase in the number of active COVID-19 patients in the city. The number of gene copies was comparable to that reported in untreated wastewaters of Australia, China and Turkey and lower than that of the USA, France and Spain. However, temporal changes in SARS-CoV-2 RNA concentrations need to be substantiated further from the perspectives of daily and short-term changes of SARS-CoV-2 in wastewater through long-term monitoring. The study results SARS-CoV-2 will assist concerned authorities and policymakers to formulate and/or upgrade COVID-19 surveillance to have a more explicit picture of the pandemic curve. While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic.


Assuntos
Infecções por Coronavirus , Pandemias , Pneumonia Viral , Síndrome Respiratória Aguda Grave , Águas Residuárias , Austrália , Betacoronavirus , COVID-19 , China , França , Humanos , Índia/epidemiologia , SARS-CoV-2 , Espanha , Turquia
11.
Environ Res ; 191: 110119, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32846177

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a neoteric virus belonging to the beta coronavirus class has created a global health concern, responsible for an outbreak of severe acute respiratory illness, the COVID-19 pandemic. Infected hosts exhibit diverse clinical features, ranging from asymptomatic to severe symptoms in their genital organs, respiratory, digestive, and circulatory systems. Considering the high transmissibility (R0: ≤6.0) compared to Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV, the quest for the clinical development of suitable antiviral nanotherapeutics (NTPs) is incessant. We are presenting a systematic review of the literature published between 2003 and 2020 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. Our aim is also to critically assess the slow release kinetics and specific target site chemical synthesis influenced competence of NTPs and nanotoxicity based antiviral actions, which are commonly exploited in the synthesis of modulated nanomedicines. The pathogenesis of novel virulent pathogens at the cellular and molecular levels are also considered, which is of utmost importance to characterize the emerging nano-drug agents as diagnostics or therapeutics or viral entry inhibitors. Such types of approaches trigger the scientists and policymakers in the development of a conceptual framework of nano-biotechnology by linking nanoscience and virology to present a smart molecular diagnosis/treatment for pandemic viral infections.


Assuntos
Antivirais , Infecções por Coronavirus , Sistemas de Liberação de Medicamentos , Nanotecnologia , Pandemias , Pneumonia Viral , Betacoronavirus , COVID-19 , Humanos , Redes e Vias Metabólicas , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus/efeitos dos fármacos
12.
Int J Biol Macromol ; 160: 1050-1060, 2020 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-32497664

RESUMO

Serratiopeptidase is an extracellular zinc-containing metalloprotease that is produced by Serratia marcescens having molecular weight of about 53kD. It has shown therapeutic (anti-inflammatory, anti-fibrinolytic and analgesic) as well as industrial applications (detergents, food processing, leather, paper and brewing etc.). The evolution of Serratia marcescens as an opportunistic pathogen associated with various infections has led researchers to think and develop an alternate strategy for its industrial production. 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 serratiopeptidase production. Initial optimization of physical parameters was done followed by a screening of different carbon and nitrogen sources. The significant media components for serratiopeptidase production as shown by factorial screening experiment were subjected to Response Surface Methodology (RSM) based optimization. The optimized media yielded 86 mg L-1 of biologically active refolded serratiopeptidase from 20 g L-1 wet weight of induced pellet as predicted by the equation. The success of the application of a statistical model for designing an optimized media for enhanced serratiopeptidase production also suggests a new insight for the scale-up of serratiopeptidase towards industrial applications.


Assuntos
Proteínas de Bactérias/genética , Engenharia Genética/métodos , Microbiologia Industrial/métodos , Peptídeo Hidrolases/genética , Proteínas de Bactérias/metabolismo , Biomassa , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Peptídeo Hidrolases/metabolismo , Serratia marcescens/enzimologia , Serratia marcescens/genética , Transgenes
13.
Environ Res ; 188: 109765, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32554273

RESUMO

We evaluate the imprints of urbanization, landuse and lifestyle on the prevalence and provenance of antibiotic resistance in the tropical rivers of Sri Lanka (Kelani and Gin) and India (Sabarmati, and Brahmaputra River). The prevalence of E. coli in the Kelani, Sabarmati, and Brahmaputra Rivers was in the range of 10-27, 267-76,600, and <50 CFU ml-1 respectively. Isolated E. coli colonies were subjected to six antibiotics to assess their resistance. We found higher resistance to old generation antibiotics like tetracycline (TC), and sulfamethoxazole (ST) transcends the resistance for fluoroquinolones like norfloxacin (NFX), ciprofloxacin (CIP), and levofloxacin (LVX). Interestingly, both Indian rivers had exhibited relatively higher resistance to TC and ST than the Kelani river or Gin River, implying that the Sri Lankan situation is relatively less critical. At genetic level the resistance for ß-lactams, fluoroquinolones and sulphonamides, were detected in many samples, as reported globally. While the resistance genes for aac-(6')-1b-cr, qnrS and sul1 were detected in both Sri Lankan and Indian Rivers, blaTEM and ampC were specific to the Indian Rivers only. Decoupling of the prevalence of metal contamination and antibiotic resistance has been noticed in India and Sri Lanka. Study implies that urbanization, landuse, and lifestyle (ULL) are the three most critical factors governing multidrug resistance (MDR) and fecal contamination.


Assuntos
Escherichia coli , Rios , Antibacterianos/farmacologia , Resistência Microbiana a Medicamentos , Escherichia coli/genética , Índia/epidemiologia , Prevalência , Sri Lanka/epidemiologia
14.
Data Brief ; 30: 105504, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32346565

RESUMO

This paper describes the additional data to our research article "Bacterial line of defense in Dirinaria lichen from two different ecosystems: First genomic insights of its mycobiont Diriniria sp. GBRC AP01" by Puvar et al. [1]. In this manuscript we are presenting the data obtained during the annotation of the genome enriched from metagenomic data from the lichen samples.

15.
Int J Hyg Environ Health ; 226: 113471, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32078924

RESUMO

There is an increasing trend of developing various low-cost biogenic sorbents for the efficient and economical removal of noxious metals . Curry leaf powder (CLP), a promising non-toxic biosorbent containing several bioactive compounds was prepared by the pulverization of the dried leaves for the effective removal of Lead (Pb) and Cadmium (Cd). Various batch sorption experiments were carried out under constant temperature (25 °C), different pH (4.5-10.5), initial concentrations (50-200 mg L-1), adsorbent dosages (0.10-0.40 g) and contact times (0-60 min) to understand the optimum experimental conditions and simultaneously evaluate the adsorption isotherms and removal kinetics of CLP. Adsorption equilibrium was established in less than an hour interval (50 min). The pseudo-equilibrium process was best described by the pseudo-second-order kinetic (R2 ≥ 0.99), Freundlich and Langmuir isotherm model (R2 ≥ 0.94). The removal rate of Pb and Cd gradually increased (15.7 and 12.7 mg g-1 for Pb and Cd) at 100 mg L-1 of initial concentration till 60 min of contact period in a single contaminant system, the effect was non-significant for multiple adsorbent dosage systems (p > 0.05; t-test) though. The regeneration potential of the exhausted biosorbent was excellent upto 5 cycles with the better efficiency observed for Pb. The obtained results explicitly validated the probable utilization of CLP as a promising green adsorbent for metal removal . Future study may highlight the decontamination aspects of emerging contaminants with such green bio sorbents in large scale as well as mimicing the stomach conditions.


Assuntos
Cádmio/química , Chumbo/química , Murraya , Preparações de Plantas/química , Polifenóis/química , Pós/química , Poluentes Químicos da Água/química , Adsorção , Análise Custo-Benefício , Química Verde/economia , Cinética , Folhas de Planta , Reciclagem , Purificação da Água/economia , Purificação da Água/métodos
16.
Microbiol Res ; 233: 126407, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31945518

RESUMO

Lichens have been widely studied for their symbiotic properties and for the secondary metabolites production by its fungal symbiont. Recent molecular studies have confirmed coexistence of bacteria along with the fungal and algal symbionts. Direct nucleic acid study by -omics approaches is providing better insights into their structural and functional dynamics. However, genomic analysis of individual members of lichen is difficult by the conventional approach. Hence, genome assembly from metagenome data needs standardization in the eukaryotic system like lichens. The present study aimed at metagenomic characterization of rock associated lichen Dirinaria collected from Kutch and Dang regions of Gujarat, followed by genome reconstruction and annotation of the mycobiont Dirinaria. The regions considered in the study are eco-geographically highly variant. The results revealed higher alpha diversity in the dry region Kutch as compared to the tropical forest associated lichen from Dang. Ascomycota was the most abundant eukaryote while Proteobacteria dominated the bacterial population. There were 23 genera observed only in the Kutch lichen (KL) and one genus viz., Candidatus Vecturithrix unique to the Dang lichen (DL). The exclusive bacterial genera in the Kutch mostly belonged to groups reported for stress tolerance and earlier isolated from lithobionts of extreme niches. The assembled data of KL & DL were further used for genome reconstruction of Dirinaria sp. using GC and tetra-pentamer parameters and reassembly that resulted into a final draft genome of 31.7 Mb and 9556 predicted genes. Twenty-eight biosynthesis gene clusters were predicted that included genes for polyketide, indole and terpene synthesis. Association analysis of bacteria and mycobiont revealed 8 pathways specific to bacteria with implications in lichen symbiosis and environment interaction. The study provides the first draft genome of the entire fungal Dirinaria genus and provides insights into the Dirinaria lichen metagenome from Gujarat region.


Assuntos
Bactérias/classificação , Ecossistema , Fungos/genética , Líquens/genética , Metagenoma , Ascomicetos/genética , Vias Biossintéticas , Genômica , Família Multigênica , Filogenia , Proteobactérias/genética , Análise de Sequência de DNA , Simbiose/genética
17.
Mol Genet Genomic Med ; 7(7): e00692, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31070016

RESUMO

BACKGROUND: Obesity, especially early onset of obesity is a serious health concern in both developed and developing countries. This is further associated with serious comorbidities like a fatty liver disease, cardiovascular diseases, type-2 diabetes, obstructive sleep apnea, renal complications and respiratory problems. Many times early onset of obesity is linked with heritable monogenic, polygenic and syndromic forms. Globally, studies on roles of genes involved in early onset of obesity are limited. METHODS: Here in this study, a consanguineous family of Western Indian origin having four siblings, one unaffected and three affected with severe early onset of obesity was enrolled. Affected siblings also displayed comorbidities like mild to moderate obstructive sleep apnea, raised Renal Resistance Index, oliguria, and severe anemia. Whole Exome Sequencing (WES) of Trio with one affected and unaffected sibling was done. Data analysis was performed to check pathogenic mutation segregation in unaffected parents with affected and unaffected sibling. RESULTS: WES of trio identified novel frameshift mutation in the LEPR gene resulting in truncated leptin receptor (LEPR). The same mutation was confirmed in other affected siblings and two siblings of distant relatives by Sanger sequencing. The possible effects of truncating mutation in LEPR function by in silico analysis were also studied. CONCLUSION: Understanding genetic basis of obesity might provide a clue for better management and treatment in times to come. This work demonstrates identification of novel mutation in LEPR gene resulting into early onset of obesity. Discovery of novel, population-specific genomics markers will help population screening programs in creating base for possible therapeutic applications and prevention of this disease for next generations.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Obesidade/patologia , Receptores para Leptina/genética , Índice de Massa Corporal , Estudos de Casos e Controles , Pré-Escolar , Exoma/genética , Feminino , Mutação da Fase de Leitura , Homozigoto , Humanos , Índia , Lactente , Masculino , Obesidade/genética , Linhagem , Apneia Obstrutiva do Sono/patologia , Sequenciamento Completo do Exoma/métodos
18.
PLoS One ; 13(5): e0197306, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29771956

RESUMO

This study outlines the biodiversity of mushrooms of India. It reveals the molecular biodiversity and divergence time estimation of basidiomycetes from Gujarat, India. A total of 267 mushrooms were collected from 10 locations across the state. 225 ITS sequences were generated belonging to 105 species, 59 genera and 29 families. Phylogenetic analysis of Agaricaceae reveals monophyletic clade of Podaxis differentiating it from Coprinus. Further, the ancient nature of Podaxis supports the hypothesis that gasteroid forms evolved from secotioid forms. Members of Polyporaceae appeared polyphyletic. Further, our results of a close phylogenetic relationship between Trametes and Lenziteslead us to propose that the genera Trametes may by enlarged to include Lenzites. The tricholomatoid clade shows a clear demarcation for Entolomataceae. However, Lyophyllaceae and Tricholomataceae could not be distinguished clearly. Distribution studies of the mushrooms showed omnipresence of Ganoderma and Schizophyllum. Further, divergence time estimation shows that Dacrymycetes evolved in the Neoproterozoic Era and Hymenochaetales diverged from Agaricomycetes during the Silurian period.


Assuntos
Agaricales/genética , Biodiversidade , Evolução Molecular , Teorema de Bayes , DNA Fúngico , Índia , Modelos Genéticos , Filogenia , Análise de Sequência de DNA , Fatores de Tempo
19.
3 Biotech ; 7(2): 129, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28573399

RESUMO

The exorbitant yield loss incurred by Indian farmers every year (10-90%) in rapeseed-mustard (Brassica juncea) is chiefly attributed to the progressive infestation of mustard fields by Lipaphis erysimi (Kalt.), a major insect pest belonging to the family of Homoptera. Currently there are no successful tolerant cultivars developed by conventional means in Brassica juncea with systemic plant responses in the form of direct or indirect defenses against aphid attack. Lack of specific methods for screening large numbers of genotypes required in breeding for selection of tolerant cultivars in mustard is one of the main causes of slow progress in developing resistant varieties of Brassica juncea. Traditional phenotype-based breeding has to be augmented with recent molecular approaches for potential genotype selection and cultivar development in Brassica juncea. In current study a pathogen-responsive gene panel was developed which could be used for expression-assisted breeding program in mustard for selection of tolerant types against aphid infestation, minimizing the huge crop losses suffered by farmers every year.

20.
Extremophiles ; 19(5): 973-87, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26186976

RESUMO

Here we present the first report on the taxonomic diversity of the microbial communities of the saline desert of the Great Rann of Kutch, Gujarat, India, using a metagenomic approach. Seven samples, differing in salinity levels and covering different seasons, were analysed to investigate the dynamics of microbial communities in relation to salinity and season. Metagenomic data generated using whole metagenome sequencing revealed that despite its very high salinity (4.11-30.79 %), the saline desert's microbiota had a rich microbial diversity that included all major phyla. Notably, 67 archaeal genera, representing more than 60 % of all known archaeal genera, were present in this ecosystem. A strong positive correlation (0.85) was observed between the presence of the extremely halophilic bacterium Salinibacter and salinity level. Taxonomic and functional comparisons of the saline desert metagenome with those of other publicly available metagenomes (i.e. sea, hypersaline lagoon, solar saltern, brine, hot desert) was carried out. The microbial community of the Kutch was found to be unique yet more similar to the sea biomes followed by hypersaline lagoon.


Assuntos
Clima Desértico , Microbiota , Tolerância ao Sal , Microbiologia do Solo , Biomassa , Genoma Arqueal , Genoma Bacteriano , Índia , Filogenia , Estações do Ano
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