Biochemistry And Microbial Sciences - Research Publications

Permanent URI for this collectionhttps://kr.cup.edu.in/handle/32116/27

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Author: search.filters.author.Ramakrishna, Wusirika

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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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    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.
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    MicroRNAs Involved in Nutritional Regulation During Plant�Microbe Symbiotic and Pathogenic Interactions with Rice as a Model
    (Springer, 2023-07-19T00:00:00) Yadav, Radheshyam; Ramakrishna, Wusirika
    Plants are constantly challenged with numerous adverse environmental conditions, including biotic and abiotic stresses. Coordinated regulation of plant responses requires crosstalk between regulatory pathways initiated by different external cues. Stress induced by excessiveness or deficiency of nutrients has been shown to positively or negatively interact with pathogen-induced immune responses. Also, colonization by arbuscular mycorrhizal (AM) fungi can improve plant nutrition, mainly phosphorus and resistance to pathogen infection. The proposed review addresses these issues about a new question that integrates adaptation to nutrient stress and disease resistance. The main goal of the current review is to provide insights into the interconnected regulation between nutrient signaling and immune signaling pathways in rice, focusing on phosphate, potassium and iron signaling. The underpinnings of plant/pathogen/AM fungus interaction concerning rice/M. oryzae/R. irregularis is highlighted. The role of microRNAs (miRNAs) involved in Pi (miR399, miR827) and Fe (miR7695) homeostasis in pathogenic/symbiotic interactions in rice is discussed. The intracellular dynamics of membrane proteins that function in nutrient transport transgenic rice lines expressing fluorescent protein fusion genes are outlined. Integrating functional genomic, nutritional and metal content, molecular and cell biology approaches to understand how disease resistance is regulated by nutrient status leading to novel concepts in fundamental processes underlying plant disease resistance will help to devise novel strategies for crop protection with less input of pesticides and fertilizers. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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    Soil Diseases Suppressiveness Conferred by Organic Farming, Practices and Microbial Metabolites
    (Taylor and Francis Ltd., 2023-05-08T00:00:00) Yadav, Radheshyam; Beniwal, Rahul; Ramakrishna, Wusirika
    A major obstacle to the creation of efficient biobased disease management practices continues to be the poor integration of traditional agricultural practices and cutting-edge technical approaches. The present review will expand the understanding of organic amendments and metabolites-mediated microbial community metabolism and their mechanistic aspects in disease-suppressive soil (DSS). Organic amendments have been shown to promote the biocontrol potential of resident soil microbiota. Organic amendments positively affect the labile carbon, cation exchange content (CEC) and microbial enzymatic activity. DSS is considered a rich source of beneficial soil microbial community that produces a plethora of antibacterial metabolites. Multiple gene clusters associated with known metabolites offer mechanistic insights associated with disease-suppressive phenotypes. Organic amended soil has higher abundance of chemotaxis genes. Several strains of Bacillus and Pseudomonas produce key metabolites, phenazines, 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, cyclic lipopeptides and volatile organic compounds in DSS. High-resolution metagenomics combined with bioinformatics tools would be instrumental in the identification of biomarkers associated with suppressive soils. The integration of traditional and genomic approaches can be employed to infer the untapped potential of resident soil microbiomes. � 2023 Informa UK Limited, trading as Taylor & Francis Group.
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    Multifarious Effects of Arsenic on Plants and Strategies for Mitigation
    (MDPI, 2023-02-09T00:00:00) Beniwal, Rahul; Yadav, Radheshyam; Ramakrishna, Wusirika
    Arsenic contamination in soil and water is a major problem worldwide. Inorganic arsenic is widely present as arsenate and arsenite. Arsenic is transferred to crops through the soil and irrigation water. It is reported to reduce crop production in plants and can cause a wide array of diseases in humans, including different types of cancers, premature delivery, stillbirth, and spontaneous abortion. Arsenic methyltransferase (AS3MT) in the human body converts inorganic arsenic into monomethylarsonic acid and dimethylarsinic acid, which are later excreted from the body. Arsenic transfer from the soil to grains of rice involves different transporters such as Lsi1, Lsi2, and Lsi6. These transporters are also required for the transfer of silicate, which makes them important for the plant. Different mitigation strategies have been used to mitigate arsenic from crops, such as plant growth-promoting bacteria, fungi, and nanoparticles, as well as using different plant genotypes and plant extracts. Different factors such as nitric oxide, Fe, and jasmonate also affect the response of a plant to the oxidative stress caused by arsenic. This review highlights the various effects of arsenic on plants with respect to their biochemical, molecular, and physiological aspects and the employment of classical and innovative methods for their mitigation. The current review is expected to initiate further research to improve As remediation to mitigate the effect of heavy metal pollution on the environment. � 2023 by the authors.
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    Endophytes as nature's gift to plants to combat abiotic stresses
    (Oxford University Press, 2022-12-20T00:00:00) Godara, Himanshi; Ramakrishna, Wusirika
    In recent decades, scientists have recognized that plants' distinct and immensely dynamic microbial communities are more than just "passengers,"but instead, play an important role in their development, and shielding against abiotic and biotic stresses. Endophytes comprise fungi and bacteria that live within plant tissues and support growth when plants are under stress. All plants in nature are considered to have symbiotic association with endophytes. A comprehensive review of the accessible data suggests that mobility, cell-wall degradation capacity, and reactive oxygen species scavenging are critical attributes for the successful colonization of endophytes. Plants encounter several abiotic stresses caused by climate change and global warming, which have an effect on their growth and production. Abiotic stress like high temperature, salinity, and high precipitation can severely affect plants compared to biotic stress. This review aims to highlight what role endophytes play to aid plant growth under abiotic stress conditions like heat, salinity, and drought. In the current review, we discuss how endophytic microbes can be efficiently used for the improvement and promotion of plant growth and crop production under abiotic stress conditions. � 2022 The Author(s). Published by Oxford University Press on behalf of Applied Microbiology International.
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    Synergistic Effect of Azotobacter nigricans and Nitrogen Phosphorus Potassium Fertilizer on Agronomic and Yieldtraits of Maize (Zea mays L.)
    (Frontiers Media S.A., 2022-08-03T00:00:00) Sagar, Alka; Sayyed, R.Z.; Ramteke, Pramod W.; Ramakrishna, Wusirika; Poczai, Peter; Al Obaid, Sami; Ansari, Mohammad Javed
    Plant growth-promoting bacteria (PGPB) Azotobacter spp. is the most promising bacteria among all microorganisms. It is an aerobic, free-living, and N2-fixing bacterium that commonly lives in soil, water, and sediments. It can be used as a biofertilizer for plant growth and nutrient utilization efficiency. Maize is the highly consumed cereal food crop of the cosmopolitan population, and the sustainable maize productivity achieved by applying bacteria in combination with nitrogen phosphorus potassium (NPK) is promising. In the present study, a bacterial isolate (PR19). Azotobacter nigricans, obtained from the soil of an organic farm was evaluated for its plant growth promoting potential alone and in combination with an inorganic fertilizer (NPK) included. The bacterial cultue (PR19) was screened for its morphological, biochemical, and plant growth-promoting characteristics, sequenced by the 16S rDNA method, and submitted to NCBI for the confirmation of strain identification. Further, the inoculation effect of the bacterial culture (PR19) in combination with NPK on growth and yield parameters of maize under pot were analyzed. Based on phenotypic and molecular characteristics, PR19 was identified as Azotobacter nigricans it was submitted to NCBI genbank under the accession No. KP966496. The bacterial isolate possessed multiple plant growth-promoting (MPGP) traits such as the production of ammonia, siderophore, indole-3-acetic acid (IAA), and ACC Deaminase (ACCD). It showed phosphate solubilization activity and tolerance to 20% salt, wide range of pH 5�9, higher levels of trace elements and heavy metals, and resistance to multiple antibiotics. PR19 expressed significantly increased (p < 0.001) antioxidant enzyme activities (SOD, CAT, and GSH) under the abiotic stress of salinity and pH. In vitro condition, inoculation of maize with the PR19 showed a significant increase in seed germination and enhancement in elongation of root and shoot compared to untreated control. The combined application of the PR19 and NPK treatments showed similar significant results in all growth and yield parameters of maize variety SHIATS-M S2. This study is the first report on the beneficial effects of organic farm isolated PR19-NPK treatment combinations on sustainable maize productivity. Copyright � 2022 Sagar, Sayyed, Ramteke, Ramakrishna, Poczai, Al Obaid and Ansari.
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    Pseudomonas citronellolis alleviates arsenic toxicity and maintains cellular homeostasis in chickpea (Cicer arietinum L.)
    (Elsevier Masson s.r.l., 2022-05-19T00:00:00) Adhikary, Arindam; Saini, Rashmi; Kumar, Rashpal; Singh, Inderjit; Ramakrishna, Wusirika; Kumar, Sanjeev
    Arsenic is a hazardous metalloid that causes detrimental effects on plant growth and metabolism. Plants accumulate arsenic in edible parts that consequently enter the food chain leading to many health problems. Metal tolerant plant growth-promoting bacteria (PGPB) ameliorate heavy metal toxicity. In this study, the effect of arsenic (As5+) and the role of PGPB Pseudomonas citronellolis (PC) in mitigating As5+ toxicity and associated metabolic alterations in chickpea were assessed. Five chickpea varieties (PBG1, GPF2, PDG3, PDG4 and PBG5) were evaluated for arsenic accumulation, translocation, and its interference with metabolic and defense processes. As5+ (40 mg kg?1) interfered with plant metabolism and enhanced the antioxidative and carbohydrate metabolizing enzyme's activity but PC treatment maintained the activity at par with control. PC also facilitated the accumulation of As5+ in the root system and restricted its translocation to the shoot. Further, to map the metabolic changes, Gas chromatography Mass Spectroscopy (GC-MS) based metabolite profiling and gene expression analysis (qRT-PCR) were performed in the best and worst-performing chickpea varieties (PBG1 and PBG5). 48 metabolites of various metabolic pathways (amino acid, carbohydrate, and fatty acid) were altered in As5+ and PC treatment. Gene expressions showed correlation with biochemical analysis of the antioxidative enzymes and carbohydrate metabolizing enzymes while PC treatment improved chlorophyll biosynthesis enzyme CaDALA expression in As5+ treated plants. Therefore, PC mitigates As5+ toxicity by restricting it in the roots thereby maintaining the cellular homeostasis under As5+ stress in chickpeas. � 2022 Elsevier Masson SAS