Browsing by Author "Sarkar, Abhijit"
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Publication Antifungal Activity of Siderophore Isolated From Escherichia coli Against Aspergillus nidulans via Iron-Mediated Oxidative Stress(Frontiers Media S.A., 2021) Khan, Azmi; Singh, Pratika; Kumar, Ravinsh; Das, Sujit; Singh, Rakesh Kumar; Mina, Usha; Agrawal, Ganesh Kumar; Rakwal, Randeep; Sarkar, Abhijit; Srivastava, AmritaMicroorganisms produce various secondary metabolites for growth and survival. During iron stress, they produce secondary metabolites termed siderophores. In the current investigation, antifungal activity of catecholate siderophore produced by Escherichia coli has been assessed against Aspergillus nidulans. Exogenous application of the bacterial siderophore to fungal cultures resulted in decreased colony size, increased filament length, and changes in hyphal branching pattern. Growth inhibition was accompanied with increased intracellular iron content. Scanning electron microscopy revealed dose-dependent alteration in fungal morphology. Fluorescent staining by propidium iodide revealed cell death in concert with growth inhibition with increasing siderophore concentration. Antioxidative enzyme activity was also compromised with significant increase in catalase activity and decrease in ascorbate peroxidase activity. Siderophore-treated cultures showed increased accumulation of reactive oxygen species as observed by fluorescence microscopy and enhanced membrane damage in terms of malondialdehyde content. Antifungal property might thus be attributed to xenosiderophore-mediated iron uptake leading to cell death. STRING analysis showed interaction of MirB (involved in transport of hydroxamate siderophore) and MirA (involved in transport of catecholate siderophore), confirming the possibility of uptake of iron�xenosiderophore complex through fungal transporters. MirA structure was modeled and validated with 95% residues occurring in the allowed region. In silico analysis revealed MirA�Enterobactin�Fe3+ complex formation. Thus, the present study reveals a promising antifungal agent in the form of catecholate siderophore and supports involvement of MirA fungal receptors in xenosiderophore uptake. � Copyright � 2021 Khan, Singh, Kumar, Das, Singh, Mina, Agrawal, Rakwal, Sarkar and Srivastava.Publication Assessing the skill of NCMRWF global ensemble prediction system in predicting Indian summer monsoon during 2018(Elsevier Ltd, 2021) Chakraborty, Paromita; Sarkar, Abhijit; Bhatla, R.; Singh, R.The quality of probabilistic precipitation and zonal wind forecasts from National Centre for Medium Range Weather Forecasting (NCMRWF) Global Ensemble Prediction System (NEPS-G) is investigated for Indian summer monsoon period between June�September 2018. Integrated Multi-satellite Retrievals for Global Precipitation Measurement (IMERG GPM) are used for verification of precipitation forecasts. The predictive skill of different categories of rainfall is examined with respect to daily climatology based on Tropical Rainfall Measuring Mission (TRMM) observations and reanalysis data from the Indian Monsoon Data Assimilation and Analysis (IMDAA). ERA Interim and IMDAA reanalysis daily climatologies are used to compute skill for the zonal wind forecasts at 850 hPa (u850). The model has a systematic tendency to over-predict the low level westerlies associated with the monsoon circulation. RMSE over Gangetic plains near Himalayan foothills is more in day-3 as compared to subsequent forecast lead times due to its overestimation of the easterly zonal wind flow. Spread in u850 is comparable to RMSE in day-1 forecast. The ensemble forecasting system is slightly under-dispersive for longer forecast lead times, since the rate of growth of forecast uncertainty is larger than that could be predicted by the ensemble system. Forecasts are sharper for lower thresholds of rainfall and exhibit more reliability and better discrimination of events over shorter lead times. Similar to reliability, the rank distribution depends on forecast lead time as well as ensemble spread. The positive Brier skill score and Continuous Ranked Probability Skill Score values above 0.4 for probabilistic wind as well as precipitation forecasts of light to moderate category, consistently show high predictive skill till day-7, with reference to the long-term climatology. NEPS-G could predict an extreme rainfall event with high probabilities of precipitation exceeding thresholds classified by India Meteorological department, which are in good correspondence with that of rainfall observed by GPM IMERG. A monsoon index based on large-scale features of monsoon circulation could be predicted by the EPS with high probabilistic skill during the peak monsoon. � 2020 Elsevier B.V.Publication Assessment of Lead-Lag and Spatial Changes in simulating different epochs of the Indian summer monsoon using RegCM4(Elsevier Ltd, 2022) Ghosh, Soumik; Sinha, P.; Bhatla, R.; Mall, R.K.; Sarkar, AbhijitThe present study examines the efficacy of the regional climate model RegCM4 in depicting the onset, active, and break phases of the Indian summer monsoon (ISM). The model is driven by National Centers for Environmental Prediction (NCEP)/NCAR Reanalysis 1 project (NNRP1) data of 28 years (1981�2008) for each monsoon separately. High-resolution gridded rainfall analysis dataset of India Meteorological Department (IMD) and the monsoon epochal report from National Climate Center (NCC) are used for verification. Besides assessment of model performance using qualitative methods, several standard statistical techniques are used to understand the capability of the model in representing monsoonal epochs. A relationship between the SST changes over the Ni�o-3.4 region and the ISM over all India and the monsoon core region (MCR) is established where a strong dependency in the rainfall variation over the MCR with the SST variation is found than all India rainfall. The performance of the model is satisfactory in portraying the spatial and temporal intraseasonal variability (ISV) of monsoon over MCR and all India regions. It is found that the model performance is higher in simulating the onset and break phases (dry days) than the active phases. The limited skill of the RegCM4 model in representing the active phase is due to the model simulated low temperature and weak pressure gradient over the MCR which prevents the convection and given rise to small and weak active phases over the region. The mechanism from the pre-onset to onset of monsoon, and the monsoon advance between the onset and the monsoon ISV is also well captured by the RegCM4. Weak tropospheric temperature gradient over the Indian subcontinent during the pre-onset period causes delay onset over the Indian subcontinent and the subsequent high tropospheric temperature gradient during the mid of June causes a faster progression of the active/break phases of monsoon. At the same time, simulation of the monsoon phase by the model is heavily regulated by the changes of SST over the Ni�o-3.4 region. The signal of ENSO variability, forces to the model through the ICBC, modulates the capability of the regional model in identifying the interannual and ISV of monsoon over the MCR region. � 2021 Elsevier B.V.Publication Changes in the mechanism of the South-Asian summer monsoon onset propagation induced by the pre-monsoon aerosol dust storm(Elsevier Ltd, 2023) Ghosh, Soumik; Sarkar, Abhijit; Bhatla, R.; Mall, R.K.; Payra, Swagata; Gupta, PriyanshuA modeling effort is considered to understand the effect of dust aerosol storms in the Indian summer monsoon (ISM) onset propagation over the Indian subcontinent. The study found how the dust aerosol loading during the pre-monsoon period over the Indian subcontinent positively impacts the advancing ISM onset. The heavy loading of dust aerosol from middle east Asia to the northwest (NW) Indian region boosts the temperature gradient over the mid-troposphere. This sudden rise in the mid-tropospheric atmospheric temperature triggers the low-pressure belt over the monsoon trough. It amplifies the Elevated Heat Pump mechanism and loads enough dust for the dust storm over north India. The formation of the monsoon trough over the Indo-Gangetic Plain (IGP) pulls the moisture-loaded wind towards the Indian subcontinent and the IGP, followed by the onset of monsoon over Kerala within a week. Due to this storm, the intense heat gradient in the troposphere also induces the monsoon propagation and the monsoon advancement from Kerala to BoB within a short time. However, it makes up for the naturally delayed monsoon on time. Plain language summary: Study shows how the pre-monsoon dust storm modulates the Indian summer monsoon (ISM) propagation over the Indian region. The onset of the monsoon was delayed in a particular year, and the pre-monsoon dust storm over northwest India changed the regular monsoon mechanism and generated an entirely different mechanism. The elevated heat pump theory applies that pushes the monsoon advancement faster than usual. A dust storm over north India causes a sudden rise in the mid-tropospheric temperature gradient and more rapid monsoon advancement than usual. � 2023Publication Changes in tropospheric ozone concentration over Indo-Gangetic Plains: the role of meteorological parameters(Springer, 2022) Payra, Swagata; Gupta, Priyanshu; Sarkar, Abhijit; Bhatla, R.; Verma, SunitaThis study seeks to understand and quantify the changes in tropospheric ozone (O3) in lower troposphere (LT), middle troposphere (MT) and upper middle troposphere (UMT) over the Indo-Gangetic Plains (IGPs), India during the COVID-19 lockdown 2020 with that of pre-lockdown 2019. The gridded datasets of ozone from the European Centre for Medium-range Weather Forecasts (ECMWF) reanalysis product, ERA5 in combination with statistical interpolated (IDWs) surface NO2 observations, present a consistent picture and indicate a significant tropospheric ozone enhancement over IGP during COVID-19 lockdown restrictions in May 2020. The�Paper also examines the influencing role of meteorological parameters on increasing ozone concentration. Over LT, an increase in O3 concentration (23%) is observed and in MT to UMT an enhancement of about 9�18% in O3 concentration have been seen during May 2020 with respect to May 2019. An investigation on causes�of�increasing ozone concentration (35�85�ppbv) from MT to UMT during May 2020 reveals that there was significant rise (by 1�6%) in low cloud cover (LCC). Notably, higher LCC increases the backscattering of upward solar radiation from the top of the�atmosphere. A positive difference of 5�25�W/m2 in upward solar radiation (USR) is observed across the entire study region. The�result suggests that higher LCC significantly contributed to the enhanced USR. Thereby, resulting in higher photolysis rate�that lead to an increase in mid tropospheric ozone concentration during May 2020. The results highlight the importance of LCC as an�important pathway in ozone formation and aid in scientific understanding of it. � 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.Publication Contribution of lagged members to the performance of a global ensemble prediction system(Elsevier Ltd, 2022) Shanker, Gauri; Sarkar, Abhijit; Mamgain, Ashu; Prasad, S. Kiran; Bhatla, R.; Mitra, A.K.National Centre for Medium Range Weather Forecasting (NCMRWF), India runs operationally a global ensemble prediction system (NEPS-G) which has 23 ensemble members. The control and 11 perturbed ensemble members have the initial conditions of 00 UTC. The start time of the other 11 perturbed members is 12 UTC of the previous day. The objective of the present paper is to study the effect of the lagged ensemble members on the forecast quality of NEPS-G. For this, we have carried out an inter-comparison of the relative skills of (i) 11-member ensemble starting from 00 UTC i.e., E00_11, (ii) 11 lagged ensemble members starting from 12 UTC i.e., E12_11 and the (iii) operational 23-member ensemble i.e. E23 using the verification of temperature, wind and geopotential height forecasts for 7-day forecast lead times for April�May-June 2019 (AMJ) of summer and December 2019�January 2020 (DJ) of winter. The temperature at 850 hPa and geopotential height at 500 hPa are verified over the northern hemisphere. The zonal and meridional winds at 850 hPa and 200 hPa are verified over the region 0oN-40oN, 60�E-110�E. The metrics used for validation are ensemble-spread and root-mean-square error (RMSE) relationship, brier skill score (BSS), reliability diagram, outliers statistics, relative operating characteristics (ROC) score and ranked probability score (RPS). For brevity, only the results for Z500, T850 and U850 have been discussed in detail here. The results show that in both seasons, the RMSE-spread relationship is better for E23 than for E00_11 and E12_11. For T850 and Z500 over NH, both E23 and E00_11 have higher RMSE and higher ensemble spread in DJ season as compared to AMJ season. In case of wind over the Indian region, both RMSE and ensemble spread exhibit lower values during DJ as compared to AMJ for both ensemble configurations. For both seasons, the BSS of E23 is positive and the ROC score is >0.5 beyond 7 days forecast times for all the variables for all three ensembles and the percentage of outliers in E23 is also less. Overall, the contribution of 11 lagged ensemble members improves the skill of NEPS-G in both seasons and skill is better during winter (DJ season). The error in the mean forecast track for tropical cyclone �Fani� for E23 is found to be less than for E00_11. We have also compared the forecast skill of E23 with that of the ensemble formed by 22 members, all running from 00 UTC i.e. E00_22 for the same set of variables as well as precipitation for one month forecast data from each season, namely June 2019 from summer and January 2020 from winter. Results show that the RMSE-spread relationship is very much similar for both configurations and both seasons. For E00_22 and E23, the ensemble spread is closer to the RMSE of ensemble mean for all the variables in January compared to June. BSS was slightly higher for E00_22 but was not significant at all lead time for all the variables except Z500 in January which shows significant improvement in BSS of E00_22 from day 2 to day 5. In precipitation forecast verification, RPS for E00_22 is slightly less (though significant) than E23 at all forecast lead times in June while in January there was no significant difference. So, E23 dataset of NEPS-G which demands less computational resources at the same time offers more skilful forecast than E00_11 over a longer forecast lead time and is nearly as skilful as E00_22. � 2022 Elsevier B.V.Publication How much does a high-resolution global ensemble forecast improve upon deterministic prediction skill for the Indian summer monsoon?(Springer, 2023) Chakraborty, Paromita; Dube, Anumeha; Sarkar, Abhijit; Mitra, A.K.; Bhatla, R.; Singh, R.S.The global Ensemble Prediction System (EPS) at NCMRWF (NEPS-G) comprises of 22 perturbed members in addition to the control (CNTL) member at 12�km horizontal resolution. Running this state-of-the-art ensemble configuration employs large computational resources compared to a deterministic system; hence it is crucial to determine if and to what extent it enhances the prediction skill of forecasts over the Indian region. In this study, we attempt to quantify the improvement in the skill of NEPS-G relative to the deterministic forecast for the 2018 Indian summer monsoon season. The ensemble mean shows substantially reduced forecast errors in the monsoon precipitation when verified against the Integrated Multi-satellite Retrievals for Global Precipitation Measurement (IMERG) data. NEPS-G mean demonstrates an improved skill for forecasts of moderate rainfall categories based on Peirce�s skill score, probability of detection and critical success index. The ensemble mean also shows an enhanced forecast skill at longer lead times, based on the anomaly correlation coefficient for both zonal winds at 850�hPa and precipitation. The model tends to underpredict very light precipitation and overpredict light precipitation. The Symmetric Extremal Dependence Index indicates a reasonable fidelity of the model in predicting heavy to very heavy rainfall. The continuous ranked probability score for NEPS-G is much lower than the mean absolute error of the CNTL forecast. The Relative Operating Characteristic curve of the ensemble distribution relative to CNTL further illustrates the value-addition by NEPS-G model to forecasts at longer lead times. Thus, through this study, the use of large computational resources for running the high-resolution NEPS-G is proved to be justified as it produces more reliable forecasts with longer lead times. � 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.Publication Induction of Iron Stress in Hepatocellular Carcinoma Cell Lines by Siderophore of Aspergillus nidulans Towards Promising Anticancer Effect(Humana Press Inc., 2022) Khan, Azmi; Singh, Pratika; Chaudhary, Archana; Haque, Rizwanul; Singh, Prashant; Mishra, Arun Kumar; Sarkar, Abhijit; Srivastava, AmritaHepatocellular carcinoma is among the leading causes of cancer-related deaths worldwide and needs efficient and feasible approach of treatment. Present study focuses on exploring the anticancer activity of a secondary metabolite called siderophore of Aspergillus nidulans against hepatocellular carcinoma cell line HepG2. These small peptides are produced by microorganisms including fungi for scavenging iron from its surroundings. Fungi including Aspergillus spp. are known to produce siderophores under iron-limited conditions. Siderophores have high affinity towards iron and are classified into various types. In the present study, siderophore isolated and purified from fungal cultures was confirmed to be of hydroxamate type by chrome azurol sulfonate and Atkin�s assay. HPLC analysis confirmed purity while LC�ESI�MS revealed that the siderophore is triacetyl fusigen. Cancerous cells, HepG2, grown under siderophore treatment showed inhibition in growth and proliferation in a dose- and time-dependent manner. Reduction in viability and metabolic activity was evident upon treatment as seen in trypan blue, MTT and WST assay. Fluorescent staining using PI and DAPI confirmed the same while DCFDA staining revealed increased reactive oxygen species production which might have led to cell death and deterioration. Such increase in ROS has been correlated with iron accumulation by assessing intracellular iron level through ICP-MS. To assess the effect of siderophore treatment on normal cells, WRL-68, same assays were carried out but the effect was mostly non-significant up to 48�h. Thus, present work suggests that an optimum dose of siderophore purified from A. nidulans culture might prove a useful anticancer agent. � 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Publication Metabarcoding analysis of the bacterial succession during vermicomposting of municipal solid waste employing the earthworm Eisenia fetida(Elsevier B.V., 2021) Srivastava, Vaibhav; Squartini, Andrea; Masi, Antonio; Sarkar, Abhijit; Singh, Rajeev PratapA culture-independent DNA metabarcoding analysis of the bacterial communities was carried out throughout a complete vermicomposting cycle of municipal solid waste material using the earthworm Eisenia fetida. 16S rRNA amplicons from the initial material (0 days), an intermediate (42 days), and a final stage (84 days) were sequenced in an Illumina NGS platform and compared. A steady increase in community diversity was observed corresponding to a 2.5-fold higher taxa richness and correspondingly risen values of the Shannon and Simpson ecological indexes and the evenness parameter. A total of 49,665 operational taxonomic units (OTUs) were counted. From the qualitative standpoint, a clear successional shift was observed with an initial community dominated by putatively plant-associated groups belonging to the Rhizobiales order within the Alphaproteobacteria class, regressively leaving the scores of relative abundance (RA) to the Firmicutes phylum and in particular to the Bacilli. Vermistabilization of municipal solid waste (MSW) increased (p < 0.001) the TKN and total P content in the final vermicompost, while pH, TOC, and C/N ratio declined (p < 0.001) in the process. Likewise, a progressive decrease was noticed in ?-glucosidase, acid phosphatase, and urease activity while protease and dehydrogenase showed a slight increase, followed by a steep fall. A strong positive correlation was observed among the canonical functions of physico-chemical attributes and enzyme activities. The canonical correspondence analysis (CCA) revealed that significant families did not change on the temporal scale; however, their abundance was influenced by the abiotic environmental factors. In comparison to prior studies on vermicomposting that used different earthworm species (Eisenia andrei) and different substrates, results reflect a considerable degree of substrate specificity for the earthworm species used. The results offer clues to optimize the vermistabilization of MSW along with its potential use in agriculture, to foster improved levels of the circular economy. � 2020 Elsevier B.V.
