Department Of Biochemistry And Microbial Sciences

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    Bioinformatics insights into CENP-T and CENP-W protein-protein interaction disruptive amino acid substitution in the CENP-T-W complex
    (John Wiley and Sons Inc, 2023-11-09T00:00:00) Mohanty, Suryakanta; Bhadane, Rajendra; Kumar, Shashank
    Kinetochores are multi-protein assemblies present at the centromere of the human chromosome and play a crucial role in cellular mitosis. The CENP-T and CENP-W chains form a heterodimer, which is an integral part of the inner kinetochore, interacting with the linker DNA on one side and the outer kinetochore on the other. Additionally, the CENP-T-W dimer interacts with other regulatory proteins involved in forming inner kinetochores. The specific roles of different amino acids in the CENP-W at the protein-protein interaction (PPI) interface during the CENP-T-W dimer formation remain incompletely understood. Since cell division goes awry in diseases like cancer, this CENP-T-W partnership is a potential target for new drugs that could restore healthy cell division. We employed molecular docking, binding free energy calculations, and molecular dynamics (MD) simulations to investigate the disruptive effects of amino acids substitutions in the CENP-W chain on CENP-T-W dimer formation. By conducting a molecular docking study and analysing hydrogen bonding interactions, we identified key residues in CENP-W (ASN-46, ARG-53, LEU-83, SER-86, ARG-87, and GLY-88) for further investigation. Through site-directed mutagenesis and subsequent binding free energy calculations, we refined the selection of mutant. We chose four mutants (N46K, R53K, L83K, and R87E) of CENP-W to assess their comparative potential in forming CENP-T-W dimer. Our analysis from 250 ns long revealed that the substitution of LEU83 and ARG53 residues in CENP-W with the LYS significantly disrupts the formation of CENP-T-W dimer. In conclusion, LEU83 and ARG53 play a critical role in CENP-T and CENP-W dimerization which is ultimately required for cellular mitosis. Our findings not only deepen our understanding of cell division but also hint at exciting drug-target possibilities. � 2023 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals LLC.
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    Immunodominant conserved moieties on spike protein of SARS-CoV-2 renders virulence factor for the design of epitope-based peptide vaccines
    (Springer, 2023-11-23T00:00:00) Mohapatra, Subhashree; Kumar, Santosh; Kumar, Shashank; Singh, Atul Kumar; Nayak, Bismita
    The outbreak of novel SARS-CoV-2 virion has wreaked havoc with a high prevalence of respiratory illness and high transmission due to a vague understanding of the viral antigenicity, augmenting the dire challenge to public health globally. This viral member necessitates the expansion of diagnostic and therapeutic tools to track its transmission and confront it through vaccine development. Therefore, prophylactic strategies are mandatory. Virulent spike proteins can be the most desirable candidate for the computational design of vaccines targeting SARS-CoV-2, followed by the meteoric development of immune epitopes. Spike protein was characterized using existing bioinformatics tools with a unique roadmap related to the immunological profile of SARS-CoV-2 to predict immunogenic virulence epitopes based on antigenicity, allergenicity, toxicity, immunogenicity, and population coverage. Applying in silico approaches, a set of twenty-four B lymphocyte-based epitopes and forty-six T lymphocyte-based epitopes were selected. The predicted epitopes were evaluated for their intrinsic properties. The physico-chemical characterization of epitopes qualifies them for further in vitro and in vivo analysis and pre-requisite vaccine development. This study presents a set of screened epitopes that bind to HLA-specific allelic proteins and can be employed for designing a peptide vaccine construct against SARS-CoV-2 that will confer vaccine-induced protective immunity due to its structural stability. � 2023, The Author(s), under exclusive licence to Indian Virological Society.
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    Genome-wide identification of NAC transcription factors in Avena sativa under salinity stress
    (Elsevier B.V., 2023-10-29T00:00:00) Bokolia, Muskan; Singh, Baljinder; Kumar, Avneesh; Goyal, Nandni; Singh, Kashmir; Chhabra, Ravindresh
    Background: NAC (NAM, ATAF1/2, and CUC2) is one of the most prominent family of plant-specific transcription factors that play diverse roles in plant growth and development as well as in abiotic stress responses in plants. The members of this family are recognized by presence of typical conserved NAC domain at the N-terminal and diverse C-terminal region. Results: In this study, we have identified 101 Avena sativa NAC (AsNAC) genes from the available Avena genome database. Genes were analyzed for their physicochemical properties, conserved motifs, gene structure, chromosomal localization, phylogenetic relationship, and cis-acting elements. The phylogenetic analysis illustrated that there were 15 subgroups in both Avena sativa and Arabidopsis thaliana. Mainly four types of cis-acting regulatory elements were present in the promoter regions of NAC genes, including hormone-responsive, light-responsive, stress-responsive and growth and developmental responsive elements. The chromosomal mapping analysis concluded that 101 NAC genes of Avena sativa were unevenly distributed on 21 chromosomes. Expression analysis identified 27 Avena NAC genes that respond to salt stress based on transcriptomic data analysis available on the NCBI SRA database. Significance: The genome-wide identification and molecular analysis of NAC TFs involved in environmental stress responses have the ability to overcome the limitations that came across in producing the transgenic crops with superior quality and improved production under abiotic stressed conditions. Future prospectives: These NAC genes may be considered as potential candidates for further explorations of functional analysis and could be used to develop stress tolerant lines in Avena sativa. � 2023 The Author(s)
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    Synthesis, In silico mapping for anti-cancer proviso, hardness studies of D-gluconic acid monohydrate crystals for usage in electronic, mechanical and biological sectors
    (Elsevier Ltd, 2023-10-17T00:00:00) B, Padmanaban; Nikolova, Maria P.; Kumar, Shashank; K, SenthilKannan
    D-Gluconic acid monohydrate - DGAMH crystals are grown in a period of 61 days by using the customary slow evaporation method with a, b and c as 8.4309, 5.409 and 10.4071 in � units; ? as 96.87�; monoclinic system, space group as P21. The material is an anticancer stipulation to inhibit them with the docked score of the DGAMH as ?6.0 and ?7.1 for both cases. Considering the mechanic behaviour of the DGAMH; the n as 7.57 of the DGAMH � work hardening coefficient value as Reverse ISE (indentation size effect) response for DGAMH. The computational structural info of DGAMH provides the supercell proviso, VanderWaal's impact with the nano-tubular proviso of DGAMH for cell impacting, weak type of interactions and devices with nano-tube impact. The electronic fluxing is in microns for macro-DGAMH; micro-DGAMH; thin-film DGAMH and nano-DGAMH for filtering property confirmations. The frequency by IC741 is twice over the input values with DGAMH crystal. � 2023 The Authors
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    Combing of picogram level DNA equivalent to genomic DNA present in single human cell by self propelled droplet motion over a stable gradient surface
    (Academic Press Inc., 2023-11-08T00:00:00) Yadav, Hemendra; Algaonkar, Prashant S.; Chakraborty, Sudip; Ramakrishna, Wusirika
    DNA combing is a powerful technique for studying replication profile, fork-directionality and fork velocity. At present, there is requirement of a methodology to comb DNA present in a single human cell for studying replication dynamics at early embryonic stage. In our study, a surface having dual characteristics i.e., affinity towards negatively charged single DNA molecules and a hydrophobic gradient for self propelled droplet motion of combing solution was developed. The surface was made by coating of TCOS (trichloro-octylsilane) by vapor diffusion on APTES (Aminopropyl-triethoxysilane) coated glass slides. A gradient surface having high deposition efficiency (DE) was developed on which 5 picogram DNA equivalent to genomic DNA present in one single human cell can be combed. The gradient surface was thermostable in nature having the ability to sustain boiling temperature for two hours and sustain anisotropy in 70 % ethanol for 80 h. Applicability for multiple runs was enhanced such that the surface can be used for 13�14 times. Factors associated with gradient surface are unidirectional movement of combing solution droplet over the gradient surface for combing straight DNA molecules and a longer gradient surface of more than 1 cm such that long size DNA molecules can be combed. Ellipsometry and contact angle hysteresis confirmed the presence of hydrophobic gradient. XPS (X-ray photoelectron spectroscopy) and FTIR (Fourier Transform Infrared Spectroscopy) confirmed the presence of characteristic affinity towards negatively charged DNA molecules on the gradient surface. Combing solution was optimized for increasing deposition efficiency and for increasing the applicability of gradient surface for multiple runs. High temperature of combing solution was found to increase Deposition Efficiency. Combing solution was also optimized for combing single DNA molecules over the gradient surface. Single DNA molecules were combed by reducing pH and lowering concentration of triton-X in the combing solution. Dye: bp ratio was optimized for high fluorescent intensity and low surface background. � 2023 Elsevier Inc.
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    SUMO and SUMOylation in Plants: Ignored Arsenal to Combat Abiotic Stress
    (Springer, 2023-10-11T00:00:00) Yadav, Radheshyam; Chaudhary, Shivam; Ramakrishna, Wusirika
    Plants being fixed in one place are exposed to various episodes of different abiotic stresses such as drought, salinity, cold, and heat. SUMOylation is one of the ignored arsenals that help plants to develop tolerance to these external abiotic stresses. SUMOylation of target protein generally leads to changes in its transportation, transcriptional regulation, apoptosis, stability, and response to different stresses. de-SUMOylation of substrate proteins by SUMO proteases also play a crucial role in maintaining the cellular pool of SUMO. This review highlights different components of SUMOylation and their role in different abiotic stresses and their ability to contribute to plant abiotic stress tolerance. Furthermore, the current perspective of SUMOylation in phytochrome signaling, nutrient and ROS homeostasis is discussed. The full potential of SUMOylation in combination with other molecular approaches to combat abiotic stresses in plants is not yet realized. As research in this area continues to advance, it is crucial to explore the interplay between SUMOylation and other signaling networks, as well as the crosstalk with different stress-responsive pathways. Additionally, understanding the specificity and dynamics of SUMOylation in response to specific stressors can provide valuable insights for designing targeted interventions to enhance plant stress tolerance. In conclusion, the review highlights the emerging significance of SUMOylation in plant stress responses and its potential in contributing to plant resilience against abiotic stresses. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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    Preparation, Characterization, and Biological Potential of Nanoemulsion from Rosmarinus officinalis L. Essential Oil
    (Springer, 2023-10-02T00:00:00) Sharma, Arun Dev; Chhabra, Ravindresh; Jain, Puneet; Kaur, Inderjeet; Chauhan, Amrita; Rani, Retika
    Essential oil from Rosmarinus officinalis (also known as rosemary essential oil) is used as traditional medicine and used as therapeutic in medicine, food, and cosmetic sectors. However, this oil is highly unstable, volatile, and prone to oxidation which limits its use. Thus, encapsulation is the better way to protect this oil from adverse conditions. The objective of this study was synthesis of rosemary essential oil (REO) based O/W (oil/water) nanoemulsions (designated as RNE) and evaluation of its biological potential. Physiological characterization was carried out using, UV, fluorescent, and FT-IR techniques. Various biological activities such as anticancerous, antidiabetic, and anti-inflammatory were also estimated. Pharmacokinetics studies on RNE were carried out. Encapsulation efficiency of RNE was found to be 92%. RNE nanoemulsions were spherical in shape with globule size, Z-Average (nm) size 220 nm, zeta potential ?11.33 mV, and polydispersity index was 0.47. RNE nanoemulsions were stable even after 50 days of storage at different temperatures. Antioxidant potential of RNE was conducted by various assays and IC50 were DPPH free radical scavenging activity: 21.53, nitric oxide radical scavenging activity: 26.66, hydroxyl radical scavenging activity: 32.69, ABTS radical scavenging activity: 33.05, and iron chelating assay: 38.78. Notable anticancer activity was observed with the percent cell viability of HeLa cells after treatment with RNE was 23% at higher concentration of 5 ?g. Antidiabetic study revealed that RNE inhibited ?-amylase in a concentration dependent manner, with 71% inhibition at its higher concentration of 250 ?g. RNE depicted maximum antibacterial activity against Bacillus subtilis at higher concentration of 300 ?g. Drug kinetic study revealed that nanoemulsions exhibited Korsmeyer�Peppas model. Based on this, the possible role of R. officinalis oil-based nanoemulsions in food, cosmetic, and pharma sectors has been discussed. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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    Piper chaba, an Indian spice plant extract, inhibits cell cycle G1/S phase transition and induces intrinsic apoptotic pathway in luminal breast cancer cells
    (John Wiley and Sons Ltd, 2023-09-15T00:00:00) Prajapati, Kumari Sunita; Kumar, Shashank
    Piper chaba (Piperaceae) is a medicinal spice plant that possesses several pharmacological activities. In the present study, we for the first time studied the effect of P. chaba extract on breast cancer cells. P. chaba stem methanolic (PCSM) extract produced time and dose dependent cytotoxicity in luminal breast cancer cells (MCF-7 and T47D) with a minimal toxicity in breast normal cells (MCF-10A) at 10�100 �g/mL concentration. PCSM extract exerts 16.79 and 31.21 �g/mL IC50 for T47D and MCF-7 cells, respectively, in 48 h treatment. PCSM significantly arrests the T47D cells at the G0/G1 phase by reducing the CCND1 and CDK4 expression at mRNA and protein levels. PCSM extract treatment significantly altered nuclear morphology, mitochondria membrane potential, and production of reactive oxygen species in T47D cells at IC50 concentration. Extract treatment significantly altered the Bax/Bcl-2 ratio and altered caspase 8 and 3 mRNA/protein levels in T47D cells. Confocal microscopy showed an increase in late apoptosis in PCSM extract-treated breast cancer cells at IC50. Further, an increased caspase 9 and caspase 3/7 enzymatic activity was observed in test cells compared with nontreated cells. In conclusion, P. chaba phytocompound possesses the potential to induce cell cycle arrest and induce apoptosis in luminal breast cancer cells. � 2023 John Wiley & Sons Ltd.
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    Evolution of Nano-Biofertilizer as a Green Technology for Agriculture
    (Multidisciplinary Digital Publishing Institute (MDPI), 2023-09-24T00:00:00) Patel, Chitranshi; Singh, Jyoti; Karunakaran, Anagha; Ramakrishna, Wusirika
    Agriculture has long been the cornerstone of human civilization, providing sustenance and livelihoods for millennia. However, as the global population continues to burgeon, agriculture faces mounting challenges. Soil degradation, nutrient depletion, environmental pollution, and the need for sustainable farming practices are among the pressing issues that require innovative solutions. In this context, nano-biofertilizers have emerged as a groundbreaking technological advancement with the potential to reshape modern agriculture. nano-biofertilizers are innovative agricultural products that leverage the combined principles of nanotechnology and biotechnology to enhance nutrient uptake by plants, improve soil health, and promote sustainable farming practices. These specialized fertilizers consist of nanoscale materials and beneficial microorganisms. These fertilizers are eco-friendly and cost-effective and have shown promising results in various crop plants. In this review, we discuss the recent advances in the development of eco-friendly nano-biofertilizers along with an overview of the various types of nano-biofertilizers, their formulation, synthesis, and mode of application for next-generation agriculture. The importance of the interaction between nanoparticles and bacterial species and its impact on the effectiveness of nano-biofertilizers has also been discussed along with the potential benefits, challenges, and future perspectives of using eco-friendly nano-biofertilizers for sustainable agriculture, ensuring a greener and healthier future for generations to come. � 2023 by the authors.
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    Biochar as an Environment-Friendly Alternative for Multiple Applications
    (Multidisciplinary Digital Publishing Institute (MDPI), 2023-09-07T00:00:00) Yadav, Radheshyam; Ramakrishna, Wusirika
    The climate crisis and years of unsustainable agricultural practices have reduced soil fertility and crop yield. In addition, agricultural lands contribute more than 10% of greenhouse gases (GHGs). These concerns can be addressed by using biochar for carbon neutralization, environmental restoration, and agricultural management. Biochar has a role in nitrous oxide and methane gas emission mitigation from agricultural soil. New methods are needed to link belowground processes to functioning in multi-species and multi-cultivar agroecosystems. The intricate relationship between biochar and the composition of soil microbial communities, along with its impacts on functions within the rhizosphere, constitutes a highly perplexing and elusive subject within microbial genomics. The present review discusses how biochar can mitigate climate change, enhance carbon sequestration, and support crop productivity. Biochar could be a potential solution to mitigate soil microplastics and heavy metal contamination. Applying a biochar-based microbiome reduces polycyclic aromatic hydrocarbons (PAHs) in soil. The current knowledge and perspectives on biochar�plant�microbial interactions for sustainable agriculture and ameliorating the adverse effects of climate change are highlighted. In this review, a holistic approach was used to emphasize the utility of biochar for multiple applications with positive and negative effects and its role in promoting a functional circular economy. � 2023 by the authors.