Browsing by Author "Divya Pandey"

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A Trust-based Security Aware Congestion Control Algorithm for Wireless Sensor Networks
(Old City Publishing, 2022) Divya Pandey; Vandana Kushwaha
Congestion in the network may result from natural causes or selfish nodes acting as catalysts. It is possible for malicious sensor nodes in Wireless Sensor Networks (WSNs) to create congestion-like situations by sending redundant fake packets or throwing away data packets. As a result, relying solely on congestion control techniques is insufficient to assure fair delivery. It is, therefore, necessary to first prevent this adversity by separating these types of nodes from the network. Existing congestion control strategies in the literature make the erroneous assumption that all the nodes are authentic and act appropriately which is impractical. For this purpose, a Security-Aware Congestion Control (SACC) algorithm has been proposed that would not only take care of the natural mode of congestion occurrence but would also consider the case in which hostile nodes intentionally try to block packets from reaching their destination. A collaborative effort has been undertaken in this study to alleviate congestion and security challenges utilizing the lightweight energy-efficient trust-based model method. The residual energy of nodes, buffer occupancy, and packet delivery ratio of nodes these network parameters have been taken for setting up trust metrics as they play a vital role in identifying malicious behaviour as well as preventing congestion occurrence. We have also explained the strategic way of how to give weights to these metrics so as to get more accurate trust values. The proposed approach beats existing related solutions in terms of energy efficiency, congestion control, and security due to its strong capacity to withstand numerous internal attacks. © 2022 Old City Publishing, Inc. Published by license under the OCP Science imprint, a member of the Old City Publishing Group.
An exploratory study of congestion control techniques in Wireless Sensor Networks
(Elsevier B.V., 2020) Divya Pandey; Vandana Kushwaha
Congestion is one of the pervasive issues for Wireless Sensor Networks(WSNs) because of its bounded resources with respect to data processing, storage, transmission capacity and most importantly energy supply. A multitude of survey operations have been carried out over the previous decade to investigate and address multiple congestion-oriented problems and issues that are still unresolved. Various review articles published in the literature concentrated mainly on classical techniques for congestion control such as traffic-based, resource-based, and hybrid techniques, etc. In this survey article, an attempt has been made to present a systematic review of recent efforts assisted at refining the congestion control methodologies in WSNs by considering classical approaches as well as soft computing based approaches. It is a practicable idea to take a holistic view and study both approaches together. Finally, this article discusses design difficulties, various optimization models and future directions for the mechanism of congestion control in the domain of wireless sensor networks. © 2020 Elsevier B.V.
An Exploratory Study of Optimization Techniques for Congestion Control in Wireless Sensor Networks
(Old City Publishing, 2024) Divya Pandey; Vandana Kushwaha
Wireless Sensor Network (WSN) is an engrossing area of research due to its various applications and the adaptability into increasingly sophis-ticated system frameworks. The challenges experienced in WSN con-figuration, are mostly related to it’s stringent constraints, which incor-porate energy, transmission capacity, memory, computational abilities and to the necessities of the specific application. Over the last decade, a substantial number of attempts have been made to examine and address congestion-oriented problems using a range of methods. Owing to the high energy utilization and data processing needs, the use of traditional algorithms has usually been degraded. In this sense, contemporary researchers have begun using optimization approaches in the field of wireless sensor networks. However, efforts for congestion control technique in sensor networks using optimization model has not yet been done to any great extent in the literature. The goal of this study is to explore various prevalent optimization method that have been used for congestion control in WSNs. We have also analyzed the multifaceted nature inborn in various optimization problems, which would also sug-gest future directions to the researchers working in this ambit. © 2023 Old City Publishing, Inc.
Assessment of soil quality under different tillage practices during wheat cultivation: soil enzymes and microbial biomass
(Taylor and Francis Ltd., 2015) Divya Pandey; Madhoolika Agrawal; Jitendra Singh Bohra
Microbial processes, particularly enzyme activities, play crucial functional roles in soil ecology, hence serving as sensitive indicators of soil quality. We assessed the temporal dynamics of microbial biomass and selected soil enzymes (β-d-glucosidase, cellobiohydrolase, polyphenol oxidase, urease, glycine-aminopeptidase and alkaline phosphatase) during wheat cultivation, under four different tillage practices in the rice–wheat system. The four practices involved conventional tilling of soil before cultivating each crop (CTR-CTW); no tilling before cultivating rice but conventional tillage before wheat (NTR-CTW); conventional tilling before cultivating rice but no tilling before wheat (CTR-NTW) and no tilling before cultivation of each crop (NTR-NTW). Microbial biomass and activities of hydrolytic enzymes increased under NTR-NTW followed by CTR-NTW and NTR-CTW with respect to the conventional practice CTR-CTW, thus reflecting improvement in microbial activities with reduced tillage frequency. Enzyme activities generally depended on soil moisture and temperature, but nature of relationships varied among different practices. Nutrient demand appeared to be the strongest driver of alkaline phosphatase and urease, and soil temperature for glycine-aminopeptidase. Under CTR-CTW, activities of most of the extracellular enzymes were related with β-d-glucosidase or urease, but such relations altered under rest of the practices. The study showed that extracellular soil enzymes respond sensitively to tillage practices as well as environmental variables, particularly soil temperature and moisture and hence can serve as a sensitive indicator of changes in soil processes. Considering improvement in microbial biomass and enzymatic activities as indicators of better soil quality, adoption of no tillage apparently improved soil quality. Still, more number of field studies are required under tillage managements to explore the relationships between different enzyme activities and environmental factors. © 2015 Taylor & Francis.
Bioprocessing of Metals from Packaging Wastes
(Springer, 2016) Meenu Gautam; Divya Pandey; Madhoolika Agrawal
Packaging refers to the covering used to protect the product inside. Metals—such as iron, copper, and their alloys, i.e., brass and bronze, have been used for the packaging and storage of goods since ancient times. Unique properties of metals, particularly the ease of fabrication, strength, thermal and electrical conductivities, and ability to hold diverse materials securely in different states, make them an essential packaging material either as such or as composites with materials such as polymers, fibers, plastics, and ceramics. Boxes, cans, cylinders, and foils made from iron, aluminum, tin, copper, etc., are the most common and everyday examples of metal-based packaging; however, specialized packaging requirements, e.g., for electronic parts, composites based on different metals are preferred. After its end use, discarded packaging becomes a major contributor to waste generation. Completely metal-based packages can be recycled; however, this becomes expensive for composites. In such cases, landfilling is the most common disposal method, which may cause adverse impacts on human health through the contamination of groundwater and soil. This calls for effective and better alternate metal waste-management options that can help metal recycling and recovery. In this chapter, we present a brief introduction of metal-based packaging, their various methods of disposal, and recovery and recycling options with particular focus on biotechnological approaches. With the help of different examples and recent developments in the recovery and reuse of waste metals, potential sustainable and cost-effective solutions in managing metallic or metal-based packaging waste are discussed. © 2016, Springer Science+Business Media Singapore.
Carbon footprint: Current methods of estimation
(2011) Divya Pandey; Madhoolika Agrawal; Jai Shanker Pandey
Increasing greenhouse gaseous concentration in the atmosphere is perturbing the environment to cause grievous global warming and associated consequences. Following the rule that only measurable is manageable, mensuration of greenhouse gas intensiveness of different products, bodies, and processes is going on worldwide, expressed as their carbon footprints. The methodologies for carbon footprint calculations are still evolving and it is emerging as an important tool for greenhouse gas management. The concept of carbon footprinting has permeated and is being commercialized in all the areas of life and economy, but there is little coherence in definitions and calculations of carbon footprints among the studies. There are disagreements in the selection of gases, and the order of emissions to be covered in footprint calculations. Standards of greenhouse gas accounting are the common resources used in footprint calculations, although there is no mandatory provision of footprint verification. Carbon footprinting is intended to be a tool to guide the relevant emission cuts and verifications, its standardization at international level are therefore necessary. Present review describes the prevailing carbon footprinting methods and raises the related issues. © 2010 Springer Science+Business Media B.V.
Carbon footprints of rice cultivation under different tillage practices in rice-wheat system
(Springer International Publishing, 2015) Divya Pandey; Madhoolika Agrawal; Jitendra Singh Bohra
Continually rising concentration of greenhouse gases (GHGs) in the atmosphere is increasing concerns over how to manage global warming. Quantification of sources and sinks of these gases have been carried out, but there remains incoherence among the estimates due to different nature of sources and processes related therewith. This renders inter-comparison and further utilization of available assessments quite incomparable. Except major point sources like thermal power plants, cement manufacturing, etc. which have been quantified confidently (Matthews et al., 2008), fugitive and sensitive sources/sinks still need proper quantification. Agriculture is one such system which plays dominating role in the global fluxes of CH4 and N2O, as their biggest emitter. Substantial inputs of energy, machinery, synthetic fertilizers and pesticides in the modern agriculture bear embodied emissions in addition to much focused direct emissions from soil (Lal, 2004a). At the same time, agricultural soils may reportedly act as considerable carbon sink (Lal, 2004b). Therefore it becomes essential to integrate all inputs-outputs to estimate the actual impact. © Capital Publishing Company 2015.
Deterioration of rhizospheric soil health due to elevated ultraviolet-B
(2013) Krishna Kumar Choudhary; Divya Pandey; S.B. Agrawal
Enhancements in ultraviolet-B radiation (UV-B) due to stratospheric ozone depletion affect biological forms directly and indirectly. To investigate how belowground processes are affected under increased UV-B, a field experiment with mung bean cultivars (HUM-1 and HUM-12) was conducted. The responses of selected soil enzymes (β-glucosidase, cellobiohydrolase, polyphenol oxidase, glycine aminopeptidase, and phosphatase), microbial biomass C and N were assessed in rhizospheric and non-rhizospheric zones, along with measurements of phenol and flavanoid contents in roots and leaves. Test plants were exposed to two UV-B levels: (1) UVB, simulating 20% stratospheric O3 depletion; and (2) UV0, the ambient UV-B. Elevated UV-B depressed shoot biomass by 24.8 and 15.9% and root biomass by 43.7 and 38.4% in cv. HUM-1 and HUM-12 compared with UV0. Although elevated UV-B caused an increase in phenol and flavonoid contents in leaves and roots, a reduction in the number of root nodules (32.4 and 24% in HUM-1 and HUM-2, respectively) and their fresh weight (27 and 23% in HUM-1 and HUM-2, respectively) was observed. Elevated UV-B caused microbial activity to shift from the rhizosphere to non-rhizosphere as indicated by increased microbial biomass N and soil enzyme activities in this zone. © 2013 Copyright Taylor and Francis Group, LLC.
Effects of conventional tillage and no tillage permutations on extracellular soil enzyme activities and microbial biomass under rice cultivation
(2014) Divya Pandey; Madhoolika Agrawal; Jitendra Singh Bohra
Extracellular soil enzymes hold a cardinal position in nutrient dynamics by regulating bioavailability of elements, and hence are linked with soil health. The present study aimed to analyze the responses of extracellular enzymes involved in mineralization of carbon (β- d-glucosidase (BG), cellobiohydrolase (CBH), polyphenol oxidase (PPO)), nitrogen (urease (UR), glycine-amino peptidase (GAP)) and phosphorous (alkaline phosphatase (ALP)) under four permutations of conventional tillage and no tillage under rice-wheat system in eastern Indo-gangetic plains during rice cultivation period. The permutations were: tillage before sowing/transplantation of each crop (RCT-WCT), tillage before transplantation of rice and no tillage before sowing of wheat (RCT-WNT), tillage before sowing wheat and no tillage before sowing of rice (RNT-WCT) and no tillage before sowing of each crop (RNT-WNT). Microbial biomass carbon and nitrogen and activities of BG, CBH, ALP and UR increased with reduction in tillage frequency, becoming the highest under RNT-WNT and the lowest under RCT-WCT. Principal component analyses (PCA) condensed the variables in to two components, apparently described by soil temperature and moisture content under all the tillage permutations. Most of the enzymes and soil properties identified to be associated under PCA followed linear relationships. Under RCT-WCT, CBH, UR and ALP were related with BG. Different orders of residue incorporation and tillage under RCT-WNT, RNT-WCT and RNT-WNT masked these relations. Results indicated that reduction in tillage frequency made the soil healthier. Relationship of BG with other enzymes appeared as a probable indicator to reflect deviations from the conventional cultivation practice in the study region. © 2013 Elsevier B.V.
Electrophoretic Separation of Humic Acids Isolated from Tropical Soils Through Modified Denaturing Polyacrylamide Gel Electrophoresis
(Springer India, 2017) Divya Pandey; Abhijit Sarkar; S.B. Agrawal; Madhoolika Agrawal
Electrophoretic separation of humic acids obtained from soil was attempted through denaturing polyacrylamide gel electrophoresis (dn-PAGE) by modifying the known methods. The modifications of sample preparation and gel composition led to significant improvement in both visibility and intensity of humic acid profile. The comparative profile showed a similar nature of humic acid components in all the samples and the commercial standard. The Fourier transform infrared spectroscopy (FTIR) spectra indicated the presence of carboxyl and carbonyl functional groups and aliphatic chains in humic acid samples. The modified method facilitated better separation of humic acid. The results of the present study indicate the potential of dn-PAGE for electrophoretic separation of different components of humic acids. © 2017, NAAS (National Academy of Agricultural Sciences).
Global warming potential and sustainable management of three land uses in Varanasi
(Emerald Group Publishing Ltd., 2016) Shikha Sharma; Divya Pandey; Madhoolika Agrawal
Purpose – Varanasi, an ancient city has witnessed the conversion of forest into agricultural lands. The high urbanization rate along with affluent lifestyle is adding another category of land use, i.e. landfill. Such land use changes significantly affect the fluxes of greenhouse gases (GHGs) from soil thus contributing to global warming. The purpose of this paper is to quantify the global warming potential (GWP) of the three land uses in Varanasi city taking into consideration CH4 and CO2.The paper also highlights the land use pattern of Varanasi. Design/methodology/approach – Sites representing land uses under forest, agriculture and landfill were identified in and around the city and measurements of GHG fluxes were conducted periodically using closed static chambers. The GWP from each land use was calculated using the standard formula of IPCC (2007). Findings – Landfill was found to be the land use with the highest GWP followed by agriculture. GWP from forest was negative. The study indicated that conversion of natural ecosystems into man made ecosystems contributed significantly to GHGs emissions. Research limitations/implications – The present research is a seasonal study with inherent uncertainties. To reduce the uncertainties long-term monitoring covering wider spatial area is required. Practical implications – The sustainable use of land along with the increment of forest cover will not only reduce the contribution in GHGs emission, but will also increase the carbon sequestrations thus limiting the implication of climate change. Originality/value – This study is the first of its kind comparing the soil borne emissions from three different land uses in a rapidly urbanizing ancient city, suggesting if there is rapid conversion of forested land into other two land uses there will be considerable increase in global warming. No similar studies could be found in the literature. © Emerald Group Publishing Limited.
Greenhouse gas emissions from rice crop with different tillage permutations in rice-wheat system
(2012) Divya Pandey; Madhoolika Agrawal; Jitendra Singh Bohra
Global agriculture lies in intersection of two inescapable issues of the present times, viz. keeping pace with growing food demand and participating in climate change mitigation efforts. Rice cultivation is a major emitter of greenhouse gases (GHGs) and no tillage of soil is becoming popular due to low economic investments with improved soil conditions. However, how these arrangements will affect GHG emissions need to be quantified. Therefore, monitoring over diverse agricultural practices is essential for optimum utilization of cultivable land and resources, while identifying the chances of emission reductions. We assessed the impacts of four tillage practices in rice-wheat cultivation system on fluxes of GHGs (CH 4, N 2O and CO 2) and yield of rice. The tillage practices were tilling of soil before sowing of every crop (RCT-WCT), tillage before sowing of rice but no tillage before sowing of wheat (RCT-WNT), tillage before sowing of wheat but no tillage before sowing of rice (RNT-WCT), and no tillage before sowing of rice as well as wheat (RNT-WNT). Reduction in tillage frequency led to significant reductions in fluxes of CH 4 and N 2O, but increased CO 2 while permutations of tillage and no tillage influenced grain yield. RNT-WCT produced next to or comparable to the most yielding RCT-WCT. Although it is difficult to select the best performer since no single tillage permutation showed consistent increment in yield with accompanied emission reductions, RNT-WCT, however may be considered as better agricultural practice for the study region. Long term and extensive spatio-temporal monitoring is still required before making any recommendation. It is also essential for understanding the factors that cause declination in yields under no tillage. © 2012 Elsevier B.V.
Greenhouse Gas Fluxes from Sugarcane and Pigeon Pea Cultivated Soils
(Springer India, 2015) Divya Pandey; Madhoolika Agrawal
Quantification of greenhouse gas (GHG) emissions from agricultural lands is essential for strategic planning towards GHG efficient development in India. We measured the fluxes of CH4, N2O and CO2 during cultivation of two important crops; sugarcane and pigeon pea following the closed chamber technique. Both the soils acted as net CH4 sinks, but sources of N2O and CO2. Pigeon pea soil acted as a weak sink, removing 0.054 ± 0.002 kg CH4 ha−1 from the atmosphere, while sugarcane soil removed 11.061 ± 0.093 kg CH4 ha−1. Urea application in sugarcane field increased the fluxes of N2O, but the total N2O emission over growth period of sugarcane (355 days) was similar to the total emissions during pigeon pea cultivation (245 days); 2.69 ± 0.09 and 2.07 ± 0.17 kg N2O ha−1, respectively. CO2 fluxes from pigeon pea cultivation were higher than sugarcane cultivation. Pigeon pea cultivation was a low input farming, but its global warming potential was higher than that of sugarcane cultivation. This study presents the GHG estimates from cultivation of the two important crops in India for which GHG estimates are lacking. © 2015, NAAS (National Academy of Agricultural Sciences).
Impact of four tillage permutations in rice-wheat system on GHG performance of wheat cultivation through carbon footprinting
(2013) Divya Pandey; Madhoolika Agrawal; Jitendra Singh Bohra
The world which is facing dual challenges of global warming and food insecurity warrants critical assessment of cultivation practices to improve yield and reduce greenhouse gas (GHG) emissions. No tillage is gaining popularity, but responses of GHG fluxes associated with soil, farm activities and other agricultural inputs under different tillage managements need to be explored. In the present study, spatial and yield scaled carbon footprints of wheat cultivation were calculated under four permutations of tillage and no tillage practices in rice-wheat system covering all direct and indirect emissions. The practices were tillage of soil before sowing of every crop (RCT-WCT), tillage before transplanting of rice, but no tillage before sowing of wheat (RCT-WNT), tillage before sowing of wheat, but no tillage before sowing of rice (RNT-WCT), and no tillage before sowing of rice as well as wheat (RNT-WNT). Direct emissions were the most prominent contributor to carbon footprint with CH4 fluxes from soil having the largest individual share. RCT-WCT acting as a CH4 sink left negative spatial carbon footprints, however, it was positive for rest of the practices. N2O fluxes were negligible compared to CH4 and CO2 under all the practices. Although carbon sequestration in soil under RCT-WNT, RNT-WCT and RNT-WNT could offset indirect emissions completely, its impact on overall spatial carbon footprints ranged from 3.2 to 6.0%. Yield scaled carbon footprints ranged from -8.11 to 23.82kgCO2-ekg-1. Improvement in yield occurred only under RNT-WNT. Footprint analysis recognized RCT-WCT as the most GHG efficient practice and RCT-WNT as the least efficient. The study further suggested that reducing CH4 and CO2 emissions will reduce spatial carbon footprints of wheat cultivation. RCT-WCT practice not only provided higher yield but also reduced GHG intensity of wheat production in the study region. © 2013 Elsevier B.V.
Impact of resource conservation technologies on carbon emission in major wheat growing regions of India
(2010) O.P. Singh; H.P. Singh; P.S. Badal; Rakesh Singh; Divya Pandey
The demand for food-grains in India is growing very fast due to increase in population coupled with rising economic status of the common people. The prime objective of the present study is to estimate and compare the carbon dioxide and carbon emission by direct use of fossil fuels in farm operations under the conventional and resource conservation systems in major wheat growing regions of India. There is also an urgent need to tackle the problems associated with RCTs and provide incentives to farmers during the initial phase of adoption to compensate for initial yield reduction and financial support and subsidy for procurement of machinery associated with technology should be provided to harness its full potential. The carbon dioxide and carbon emission from burning of fossil fuel would be 1.46 million tons and 0.394 million tons, respectively.
Issues in making food production ghg efficient challenges before carbon footprinting
(CRC Press, 2015) Divya Pandey; Madhoolika Agrawal
[No abstract available]
Metals from mining and metallurgical industries and their toxicological impacts on plants
(Springer Singapore, 2016) Meenu Gautam; Divya Pandey; S.B. Agrawal; Madhoolika Agrawal
The growth of population, increasing urbanization and rising standards of human have contributed to increase in both quantity and variety of solid wastes generated by agricultural, domestic and industrial activities. Industrial wastes contributed more than 85 % of solid waste generation globally. Metals are the major component of almost all the industrial activities but their mining, extraction, purification and various manufacturing processes generate mining and metallurgical wastes having enormous environmental and health impacts. This chapter aims to describe the metals in solid wastes from mining and metallurgical industries and their toxicological impacts on plant community. Industrial wastes are composed of a wide range of essential macro- and micronutrients such as Na, K, Ca, Mg, Mn, Fe, Cu, Zn, Ni, Co, and Mo which are required by plants for their growth and development. But the concentrations of micronutrients in plants when they exceed certain thresholds may interfere with plant metabolic activities leading to the reduction in their productivity. Similarly, non-essential metals and metalloids such as Cd, Pb, As, Al, Bi, Cr, Hg, Ti and Si at elevated concentrations in plants cause phytotoxic effects and lead to food chain contamination. These wastes are generated in huge quantities and discarded without any proper pretreatment; therefore, chances of contamination of environmental components are obvious. This chapter also suggests the possible and better management opportunities including site restoration by rehabilitation and phytoremediation of metal-contaminated sites using native and medicinal plant species to reduce food chain contamination and an ultimate risk to human health. © Springer Nature Singapore Pte Ltd. 2016.
Performance Parameter Analysis of Congestion Control in Wireless Sensor Networks
(Institute of Electrical and Electronics Engineers Inc., 2019) Divya Pandey; Vandana Kushwaha
Congestion control has been witnessed as most pervasive problem in the literature for design and development of Wireless Sensor Networks(WSNs). The most obvious reason of congestion occurrence in WSNs is resource constraints in terms of information processing, storage space, transmission bandwidth and most importantly power supply. To cope effectively with this problem, researchers need to model energy-aware protocols and algorithms along with taking into account different networking parameters such as throughput, reliability, fairness, packet loss ratio, etc. to ensure quality of service. In this research article, we have provided a comprehensive analysis of performance parameters considered by researchers and programmers while designing congestion control algorithms in wireless sensor networks, and their effect on the performance of algorithms. Unlike past studies we have not only considered classical approaches but also analyzed novel soft computing based approaches. It is logical intellection to take a holistic view and study the performance metrics of both the approaches of congestion control so that it would be useful for improving algorithms and further directions in the field of WSNs. © 2019 IEEE.
Phytoremediation of metals using lemongrass (Cymbopogon citratus (D.C.) Stapf.) grown under different levels of red mud in soil amended with biowastes
(Taylor and Francis Inc., 2017) Meenu Gautam; Divya Pandey; Madhoolika Agrawal
Due to hostile condition of red mud (RM), its utilization for vegetation is restricted. Therefore, RM with biowastes as soil amendment may offer suitable combination to support plant growth with reduced risk of metal toxicity. To evaluate the effects of RM on soil properties, plant growth performance, and metal accumulation in lemongrass, a study was conducted using different RM concentrations (0, 5, 10, and 15% w/w) in soil amended with biowastes [cow dung manure (CD) or sewage-sludge (SS)]. Application of RM in soil with biowastes improved organic matter and nutrient contents and caused reduction in phytoavailable metal contents. Total plant biomass was increased under all treatments, maximally at 5% RM in soil with SS (91.4%) and CD (51.7%) compared to that in control (no RM and biowastes). Lemongrass acted as a potential metal-tolerant plant as its metal tolerance index is >100%. Based on translocation and bioconcentration factors, lemongrass acted as a potential phytostabilizer of Fe, Mn, and Cu in roots and was found efficient in translocation of Al, Zn, Cd, Pb, Cr, As, and Ni from roots to shoot. The study suggests that 5% RM with biowastes preferably SS may be used to enhance phytoremediation potential of lemongrass. © 2017 Taylor & Francis Group, LLC.
PknB remains an essential and a conserved target for drug development in susceptible and MDR strains of M. Tuberculosis
(BioMed Central Ltd., 2017) Anamika Gupta; Sudhir K. Pal; Divya Pandey; Najneen A. Fakir; Sunita Rathod; Dhiraj Sinha; S. SivaKumar; Pallavi Sinha; Mycal Periera; Shilpa Balgam; Gomathi Sekar; K.R. UmaDevi; Shampa Anupurba; Vijay Nema
Background: The Mycobacterium tuberculosis (M.tb) protein kinase B (PknB) which is now proved to be essential for the growth and survival of M.tb, is a transmembrane protein with a potential to be a good drug target. However it is not known if this target remains conserved in otherwise resistant isolates from clinical origin. The present study describes the conservation analysis of sequences covering the inhibitor binding domain of PknB to assess if it remains conserved in susceptible and resistant clinical strains of mycobacteria picked from three different geographical areas of India. Methods: A total of 116 isolates from North, South and West India were used in the study with a variable profile of their susceptibilities towards streptomycin, isoniazid, rifampicin, ethambutol and ofloxacin. Isolates were also spoligotyped in order to find if the conservation pattern of pknB gene remain consistent or differ with different spoligotypes. The impact of variation as found in the study was analyzed using Molecular dynamics simulations. Results: The sequencing results with 115/116 isolates revealed the conserved nature of pknB sequences irrespective of their susceptibility status and spoligotypes. The only variation found was in one strains wherein pnkB sequence had G to A mutation at 664 position translating into a change of amino acid, Valine to Isoleucine. After analyzing the impact of this sequence variation using Molecular dynamics simulations, it was observed that the variation is causing no significant change in protein structure or the inhibitor binding. Conclusions: Hence, the study endorses that PknB is an ideal target for drug development and there is no pre-existing or induced resistance with respect to the sequences involved in inhibitor binding. Also if the mutation that we are reporting for the first time is found again in subsequent work, it should be checked with phenotypic profile before drawing the conclusion that it would affect the activity in any way. Bioinformatics analysis in our study says that it has no significant effect on the binding and hence the activity of the protein. © 2017 The Author(s).