Browsing by Author "Sanjiv Kumar"

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Acute cadmium toxicity and post-stress recovery: Insights into coordinated and integrated response/recovery strategies of Anabaena sp. PCC 7120
(Elsevier B.V., 2021) Akanksha Srivastava; Subhankar Biswas; Sandhya Yadav; Sanjiv Kumar; Vaibhav Srivastava; Yogesh Mishra
Cyanobacteria, the first photoautotrophs have remarkable adaptive capabilities against most abiotic stresses, including Cd. A model cyanobacterium, Anabaena sp. PCC 7120 has been commonly used to understand cyanobacterial plasticity under different environmental stresses. However, very few studies have focused on the acute Cd toxicity. In this context, Anabaena was subjected to 100 μM Cd for 48 h (acute Cd stress, ACdS) and then transferred into the fresh medium for post-stress recovery (PSR). We further investigated the dynamics of morpho-ultrastructure, physiology, cytosolic proteome, thylakoidal complexes, chelators, and transporters after ACdS, as well as during early (ER), mid (MR), and late (LR) phases of PSR. The findings revealed that ACdS induced intracellular Cd accumulation and ROS production, altered morpho-ultrastructure, reduced photosynthetic pigments, and affected the structural organization of PSII, which subsequently hindered photosynthetic efficiency. Anabaena responded to ACdS and recovered during PSR by reprogramming the expression pattern of proteins/genes involved in cellular defense and repair; CO2 access, Calvin-Benson cycle, glycolysis, and pentose phosphate pathway; protein biosynthesis, folding, and degradation; regulatory functions; PSI-based cyclic electron flow; Cd chelation; and efflux. These modulations occurred in an integrated and coordinated manner that facilitated Anabaena to detoxify Cd and repair ACdS-induced cellular damage. © 2021 Elsevier B.V.
Biochemical and proteomic analysis reveals oxidative stress tolerance strategies of Scenedesmus abundans against allelochemicals released by Microcystis aeruginosa
(Elsevier B.V., 2019) Simranjeet Kaur; Akanksha Srivastava; Sanjiv Kumar; Vaibhav Srivastava; Amrik Singh Ahluwalia; Yogesh Mishra
We studied the possible survival strategies of a green alga, Scenedesmus abundans, against allelochemicals secreted by Microcystis aeruginosa. We exposed the monoculture of S. abundans to a cell free-filtrate (allelochemicals)of M. aeruginosa at the start of our experiment and measured the growth behaviour, morphological changes and oxidative stress markers. The results suggest that exposure to allelochemicals induced oxidative stress in S. abundans, which had significantly reduced the growth of green alga with certain morphological changes. However, after seven days, S. abundans found ways to reduce oxidative stress by recovering its morphology and growth close to that of control. To understand possible survival strategies of test alga, we measured biochemical as well as protein level changes in S. abundans. Biochemical response of the green alga clearly showed that as a response to allelochemicals, enzymatic and non-enzymatic antioxidants were induced. Proteomic analysis showed that exposure to allelochemicals induced accumulation of 13 proteins on the 2-DE gel of S. abundans, which falls in three functional categories, i.e., (i)energy metabolism (photosynthesis, carbon fixation and respiration), (ii)ROS scavenging enzymes and molecular chaperones, and (iii)amino acid and protein biosynthesis. After chronic oxidative stress, these proteins presumably retained glycolysis, pentose phosphate pathway and turnover rate of the Calvin-Benson cycle. Moreover, these proteins assisted in the adequate detoxification of ROS and played an important role in the damage removal and repair of oxidized proteins, lipids and nucleic acids. Therefore, our study anticipates that S. abundans embraces biochemical and proteomic reprogramming to thrives against allelochemicals released by M. aeruginosa. © 2019
Comparison and optimization of protein extraction and two-dimensional gel electrophoresis protocols for liverworts
(BioMed Central Ltd., 2020) Sandhya Yadav; Akanksha Srivastava; Subhankar Biswas; Neha Chaurasia; Sushil Kumar Singh; Sanjiv Kumar; Vaibhav Srivastava; Yogesh Mishra
Objective: Liverworts possess historical adaptive strategies for abiotic stresses because they were the first plants that shifted from water to land. Proteomics is a state-of-the-art technique that can capture snapshots of events occurring at the protein level in many organisms. Herein, we highlight the comparison and optimization of an effective protein extraction and precipitation protocol for two-dimensional gel electrophoresis (2-DE) of liverworts. Results: We compared three different protein extraction methods, i.e.,1.5 M Tris-HCl (pH 8.8), 50 mM Tris-HCl (pH 7.5), and polyvinylpolypyrrolidone (PVPP) extraction, followed by three precipitation methods, i.e., 80% ethanol, 80% acetone, and 20% tricholoroacetic acid (TCA)-acetone, in a liverwort Dumortiera hirsuta. Among these methods, 50 mM Tris-HCl (pH 7.5) extraction, followed by 20% TCA-acetone precipitation, appeared to be more suitable for 2-DE. Furthermore, we performed modifications during protein washing, re-solubilization in rehydration buffer and isoelectric focusing (IEF). The modifications provided us better results in terms of protein yield, resolution, spot numbers, and intensities for 2-DE gels of D. hirsuta and other two liverworts, i.e., Marchantia paleacea and Plagiochasma appendiculatum. Furthermore, we randomly selected spots from the 2-DE gel of D. hirsuta and identified using mass spectrometry, which confirms the applicability of this protocol for liverworts proteomics. © 2020 The Author(s).
Effect of concentration of molecular crowder on the unfolding force distribution: Emergence of a long tail
(Institute of Physics Publishing, 2017) Sanjiv Kumar; Amit Raj Singh; Debaprasad Giri; Sanjay Kumar
We investigate the force induced unfolding transitions of a polymer in presence of crowding particles over a wide range of conditions. The polymer conformations are specified by the reaction coordinate i.e. end-to-end distance and the quality of the solvent. Crowding distribution is obtained through the percolation process, which gives rise to a distribution of clusters of different shapes and sizes starting from isolated disorder sites up to clusters with an extent spanning the entire system. It was shown here that the polymer structures are altered by such distributions and induces an array of structural changes in the form of intermediate states. It was found that the mechanical stability of polymer was insensitive at lower concentration, but increases at higher concentration. This is in accordance with experiments. Exact results based on a short polymer revealed that there is emergence of a long tail in the unfolding force distributions. This is less visible at lower concentration, but has significant contribution at higher concentration. This important feature either was overlooked or not explored so far, and therefore, needs further investigation. © 2017 IOP Publishing Ltd and SISSA Medialab srl.
Grafted polymer under shear flow
(Institute of Physics Publishing, 2016) Sanjiv Kumar; Damien P. Foster; Debaprasad Giri; Sanjay Kumar
A self-attracting-self-avoiding walk model of polymer chain on a square lattice has been used to gain an insight into the behaviour of a polymer chain under shear flow in a slit of width L. Using exact enumeration technique, we show that at high temperature, the polymer acquires the extended state continuously increasing with shear stress. However, at low temperature the polymer exhibits two transitions: a transition from the coiled to the globule state and a transition to a stem-flower like state. For a chain of finite length, we obtained the exact monomer density distributions across the layers at different temperatures. The change in density profile with shear stress suggests that the polymer under shear flow can be used as a molecular gate with potential application as a sensor. © 2016 IOP Publishing Ltd and SISSA Medialab srl.
Polymer in a pore: Effect of confinement on the free energy barrier
(Elsevier B.V., 2018) Sanjiv Kumar; Sanjay Kumar
We investigate the transfer of a polymer chain from cis- side to trans- side through two types of pores: cone-shaped channel and flat-channel. Using the exact enumeration technique, we obtain the free energy landscapes of a polymer chain for such systems. We have also calculated the free-energy barrier of a polymer chain attached to the edge of the pore. The model system allows us to calculate the force required to pull polymer from the pore and stall-force to confine polymer within the pore. © 2018 Elsevier B.V.
Statistical mechanics of a polymer chain attached to the interface of a cone-shaped channel
(Institute of Physics Publishing, 2017) Sanjay Kumar; Sanjiv Kumar; Debaprasad Giri; Shesh Nath
A polymer chain confined in nano-scale geometry has been used to investigate the underlying mechanism of Nuclear Pore Complex (NPC), where transport of cargoes is directional. It was shown here that depending on the solvent quality (good or poor) across the channel, a polymer chain can be either inside or outside the channel or both. Exact results based on the short chain revealed that a slight variation in the solvent quality can drag the polymer chain inside the pore and vice versa similarly to one seen in NPC. Furthermore, we also report the absence of crystalline (highly dense) state when the pore size is less than a certain value, which may have potential application in packaging of DNA inside the preformed viral proheads. © CopyrightEPLA, 2017.