Browsing by Author "Nidhi Kumari"

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A single gene all3940 (Dps) overexpression in Anabaena sp. PCC 7120 confers multiple abiotic stress tolerance via proteomic alterations
(Springer Verlag, 2016) Om Prakash Narayan; Nidhi Kumari; Poonam Bhargava; Hema Rajaram; Lal Chand Rai
DNA-binding proteins (Dps) induced during starvation play an important role in gene regulation and maintaining homeostasis in bacteria. The nitrogen-fixing cyanobacterium, Anabaena PCC7120, has four genes annotated as coding for Dps; however, the information on their physiological roles is limiting. One of the genes coding for Dps, ‘all3940’ was found to be induced under different abiotic stresses in Anabaena and upon overexpression enhanced the tolerance of Anabaena to a multitude of stresses, which included salinity, heat, heavy metals, pesticide, and nutrient starvation. On the other hand, mutation in the gene resulted in decreased growth of Anabaena. The modulation in the levels of All3940 in Anabaena, achieved either by overexpression of the protein or mutation of the gene, resulted in changes in the proteome, which correlated well with the physiological changes observed. Proteins required for varied physiological activities, such as photosynthesis, carbon-metabolism, oxidative stress alleviation, exhibited change in protein profile upon modulation of All3940 levels in Anabaena. This suggested a direct or an indirect effect of All3940 on the expression of the above stress-responsive proteins, thereby enhancing tolerance in Anabaena PCC7120. Thus, All3940, though categorized as a Dps, is possibly a general stress protein having a global role in regulating tolerance to multitude of stresses in Anabaena. © 2015, Springer-Verlag Berlin Heidelberg.
Cyanobacterial diversity: molecular insights under multifarious environmental conditions
(Elsevier, 2020) Nidhi Kumari; Lal Chand Rai
Cyanobacteria are the first oxygenic photoautotrophs, which are widely distributed in aquatic and terrestrial environments, including extreme habitats such as deserts, hot springs, and polar regions. This chapter presents an overview of recent advancements in cyanobacterial diversity using molecular techniques under various environmental conditions, for example, stromatolites, marine, and freshwater, dry valleys, rice fields, natural and artificial microbial mats, and hot and cold springs. The molecular techniques applied for cyanobacterial diversity assessment range from specific gene (16S ribosomal RNA, nif, rpo, its, etc.)-based PCR, sequencing, and phylogeny, denaturing gradient gel electrophoresis, microarray to metagenomics. It is pertinent to mention here that, nowadays, the polyphasic approach is considered as an indispensable method to register the overall existence of cyanobacteria that a single method is not sufficient to highlight. Microarray and metagenomics may positively contribute in deciphering and amplifying the horizon of cyanobacterial diversity in various natural milieus. © 2020 Elsevier Inc. All rights reserved.
Ethical, societal issues, and future challenges of plant CRISPR technologies
(Elsevier, 2025) Aman Prakash; Sayanti Mandal; Shashi Ranjan; Nishtha Sood; Raj Bahadur Singh; S. Dasaratha Kumar; Nidhi Kumari
The gene editing tools, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas,) have brought about a revolutionary shift in the field of plant breeding and molecular biology. In prokaryotes, it is a component of the adaptive immune system for providing defense against viruses. It has been modified to act in plants, thus representing an excellent, programmable endonuclease enzyme with target specificity, simplicity of use, and cost-effectiveness, allowing for precise genetic modification of crop species, which opens the door for the development of improved germplasm. Its rapid development has led to widespread applications in research, biomedicine, and agriculture, but also poses new regulatory challenges worldwide due to ethical, safety, and technical concerns. Moreover, genome editing (GE) with engineered nucleases is increasingly utilized in agricultural crop development for gene discovery and trait enhancement. While traditional concerns about GM foods have been extensively debated, CRISPR-Cas9 technology introduces new ethical and regulatory dilemmas related to its impact on health, the environment, and society. This technology is at the forefront of GE, with growing use in academic research for gene function studies and in creating improved crop varieties. The global debate continues on the policies and regulations surrounding CRISPR-edited crops. © 2026 Elsevier Inc. All rights reserved.
Heterologous expression of Anabaena PCC 7120 all3940 (a Dps family gene) protects Escherichia coli from nutrient limitation and abiotic stresses
(2010) Om Prakash Narayan; Nidhi Kumari; Lal Chand Rai
This study presents first hand data on the cloning and heterologous expression of Anabaena PCC 7120 all3940 (a dps family gene) in combating nutrients limitation and multiple abiotic stresses. The Escherichia coli transformed with pGEX-5X-2-all3940 construct when subjected to iron, carbon, nitrogen, phosphorus limitation and carbofuron, copper, UV-B, heat, salt and cadmium stress registered significant increase in growth over the cells transformed with empty vector under iron (0%), carbon (0.05%), nitrogen (3.7 mM) and phosphorus (2 mM) limitation and carbofuron (0.025 mg ml-1), CuCl2 (1 mM), UV-B (10 min), heat (47 °C), NaCl (6% w/v) and CdCl2 (4 mM) stress. Enhanced expression of all3940 gene measured by semi-quantitative RT-PCR at different time points under above mentioned treatments clearly demonstrates its role in tolerance against aforesaid abiotic stresses. This study opens the gate for developing transgenic cyanobacteria capable of growing successfully under above mentioned stresses. © 2010 Elsevier Inc. All rights reserved.
Iron starvation-induced proteomic changes in Anabaena (Nostoc) sp. PCC 7120: Exploring survival strategy
(2011) Narayan; Om Prakash; Nidhi Kumari; Lal Chand Rai
This study provides first-hand proteomic data on the survival strategy of Anabaena sp. PCC 7120 when subjected to long-term iron-starvation conditions. 2D-gel electrophoresis followed by MALDI-TOF/MS analysis of iron-deficient Anabaena revealed significant and reproducible alterations in ten proteins, of which six are associated with photosynthesis and respiration, three with the antioxidative defense system, and the last, hypothetical protein all1861, conceivably connected with iron homeostasis. Iron-starved Anabaena registered a reduction in growth, photosynthetic pigments, PSI, PSII, whole-chain electron transport, carbon and nitrogen fixation, and ATP and NADPH content. The kinetics of hypothetical protein all1861 expression, with no change in expression until day 3, maximum expression on the 7 th day, and a decline in expression from the 15 th day onward, coupled with in silico analysis, suggested its role in iron sequestration and homeostasis. Interestingly, the up-regulated FBP-aldolase, Mn/Fe-SOD, and all1861 all appear to assist the survival of Anabeana subjected to iron-starvation conditions. Furthermore, the N th-fixation capabilities of the iron-starved Anabaena encourage us to recommend its application as a biofertilizer, particularly in iron-limited paddy soils. © 2009 by the Korean Society for Microbiology and Biotechnology.
Molecular approaches towards assessment of cyanobacterial biodiversity
(2009) Nidhi Kumari; Ashish Kumar Srivastava; Poonam Bhargava; Lal Chand Rai
Cyanobacteria, a diverse group of photosynthetic prokaryotes, often play central roles in carbon and nitrogen assimilation which makes their environment productive. Despite their significant agronomic values, biodiversity assessment and conservation of these important microbes have not been given much attention by researchers. This review tries to bring together the important aspects of molecular approaches being used for cyanobacterial biodiversity assessment. Molecular approaches have been divided into 2 classes: PCR independent and PCR based approaches. While the former includes guanine plus cytosine (G+C) content, nucleic acid re-association and hybridization and DNA microarrays, the latter basically uses DNA cloning and sequencing, DGGE (denaturing gradient gel electrophoresis), TGGE (temperature gradient gel electrophoresis), SSCP (single strand conformation polymorphism), RFLP (restriction fragment length polymorphism), ARDRA (amplified ribosomal DNA restriction analysis), T-RFLP (terminal restriction fragment length polymorphism), RISA (ribosomal intergenic spacer analysis), ARISA (automated ribosomal intergenic spacer analysis) and RAPD (random amplified polymorphic DNA). Molecular assessment of cyanobacterial biodiversity frequently uses markers like 16S rDNA, phycocyanin locus, nif gene, rpo gene, ITS region etc. This article examines and compares various conventional and modern methods and their short comings, if any. It attempts to provide a general overview of biodiversity assessment, molecular techniques and markers used for biodiversity assessment and also recommends combinatorial approach with different molecular markers. It is likely to improve the degree of resolution and provide as possible the broadest picture and indepth information about biodiversity documentation. © 2009 Academic Journals.
Molecular characterization of local cyanobacterial isolates using 16S rRNA, rpoB, and nif H biomarkers
(Elsevier, 2022) Nidhi Kumari; Lal Chand Rai
Cyanobacteria, the first oxygenic photosynthetic prokaryotes, are designated as architects of the earth’s atmosphere. These organisms are an important, agronomically significant, and integral component of water-logged paddy fields. These autotrophs contribute to soil fertility via their dual capacity to fix atmospheric nitrogen and carbon. Despite of rich biodiversity of India, data available on molecular assessment of cyanobacterial diversity of paddy fields are scarce. The present chapter intends to describe a general overview of the molecular biomarkers used to assess cyanobacterial diversity with a specific focus on molecular characterization of the local cyanobacterial isolates of Eastern Uttar Pradesh and Western Bihar, India using three biomarkers, that is, 16S rRNA, RNA polymerase, and nifH gene. In this way, a total of 69 new sequences of 16S rRNA, rpoB, and nifH gene (23 for each gene) of cyanobacterial isolates were successfully deposited in the GenBank database. Hence, we look forward to the state-of-the-art polyphasic approach as a unique, unambiguous, and comprehensive procedure for cyanobacterial characterization. © 2022 Elsevier Inc. All rights reserved.
'Oxygen Pheriwala:' An innovative model for SARS-CoV-2 screening in resource-limited settings
(Wolters Kluwer Medknow Publications, 2022) Vijaya Nath Mishra; Varun Kumar Singh; Abhishek Pathak; Nidhi Kumari; Anand Kumar; Rameshwar Nath Chaurasia
The second wave of SARS-CoV-2 infection came as a hypoxic emergency and situation became worse in rural India, where undiagnosed COVID-19 patients died without any diagnosis or intervention. The primary aim of this innovative model was the early diagnosis of suspected SARS-CoV-2 cases, providing empirical treatment and timely referral to appropriate COVID care facilities. Fever was measured with infrared thermometer and oxygen saturation level with pulse oximeter. A total of 8203 people were screened, of which 274 persons were febrile and 69 (25%) were hypoxic too. Sixty-four out of 69 (93%) patients turned COVID-19 positive on reverse transcription-polymerase chain reaction. At the end of 3 weeks, 48/64 (75%) patients were successfully discharged. This model can be easily implemented in resource-limited regions to identify and prioritize the patients not only in this pandemic but also in outbreak of other communicable diseases. © 2022 Medknow. All right reserved.
Possible Role for Bacteriophages in the Treatment of SARS-CoV-2 Infection
(Hindawi Limited, 2020) Vijaya Nath Mishra; Nidhi Kumari; Abhishek Pathak; Rajnish Kumar Chaturvedi; Arun Kumar Gupta; Rameshwar Nath Chaurasia
An outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan City, China, in December 2019. Since then, the outbreak has grown into a global pandemic, and neither a vaccine nor a treatment for the disease, termed coronavirus disease 2019 (COVID-19), is currently available. The slow translational progress in the field of research suggests that a large number of studies are urgently required. In this context, this review explores the impact of bacteriophages on SARS-CoV-2, especially concerning phage therapy (PT). Bacteriophages are viruses that infect and kill bacterial cells. Several studies have confirmed that in addition to their antibacterial abilities, bacteriophages also show antiviral and antifungal properties. It has also been shown that PT is effective for building immunity against viral pathogens by reducing the activation of NF kappa B; additionally, phages produce the antiviral protein phagicin. The Ganges river in India, which originates from the Himalayan range, is known to harbor a large number of bacteriophages, which are released into the river gradually by the melting permafrost. Water from this river has traditionally been considered a therapeutic agent for several diseases. In this review, we hypothesize that the Ganges river may play a therapeutic role in the treatment of COVID-19. © 2020 Vijaya Nath Mishra et al.
Toxin-induced animal models in Parkinson's disease: Recent updates
(Elsevier, 2025) Vineeta Singh; Arshdeep Kaur Sethi; Shivani Rath; Nidhi Kumari; Damini Shukla; Vijay Nath Mishra
Parkinson's disease (PD) is a prevalent neurodegenerative disorder primarily affecting older adults. It is characterized by motor symptoms such as tremor, rigidity, and bradykinesia, resulting from the degeneration of dopaminergic neurons in the substantia nigra pars compacta. While PD's etiology is multifaceted, toxin-induced models have significantly advanced our understanding of its pathogenesis and potential treatments. Key environmental neurotoxins used in PD research include 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, 6-hydroxydopamine, paraquat, and rotenone. These compounds can cross the blood-brain barrier and selectively damage dopamine neurons, mimicking PD pathology through mechanisms involving mitochondrial dysfunction, oxidative stress, and neuroinflammation. Researchers use various model systems to study toxin-induced PD, including rodents, primates, zebrafish, and invertebrates. The effectiveness of these models depends on the route of administration and concentration of neurotoxins. Understanding these parameters is crucial for accurately reproducing Parkinsonian features in research settings and developing novel therapeutic strategies. © 2026 Elsevier Inc. All rights reserved.
Understanding butachlor toxicity in Aulosira fertilissima using physiological, biochemical and proteomic approaches
(Elsevier Ltd, 2009) Nidhi Kumari; Om Prakash Narayan; Lal Chand Rai
The present study examines butachlor-induced inhibition of growth, photosynthetic pigments such as chlorophyll a, phycocyanin, allophycocyanin, phycoerythrin, photosystems I and II, whole chain electron transport, oxygen evolution, carbon fixation, ATP content, total thiol and glutathione contents of Aulosira fertilissima. For ascertaining if above mentioned changes are due to disturbance in plasma membrane integrity or proteins, fatty acid profiling and proteomics were done. Gas chromatographic (GC) analysis of fatty acid methyl esters (FAME) depicted a decrease in α-linolenic acid (C18:3) which appears responsible for plasma membrane instability. Enhanced lipid peroxidation and electrolyte leakage further attested the butachlor-induced cell damage. Butachlor-treated Aulosira exhibited significant and reproducible alternations in eight proteins as assessed by 2DE and LC-MS analysis of which phycocyanin α-chain, allophycocyanin β-chain, C-phycocyanin α-subunit, ATP synthase β-chain and FBP aldolase were associated with photosynthesis and respiration, peroxiredoxin with antioxidative defense system and GroES and NusB with protein folding and transcription termination respectively. However, a prolonged (15 d) butachlor treatment of Aulosira downregulated all the proteins except NusB. Reverse transcription PCR of the protein genes affirmed that aforesaid proteins were the gene products not artifacts. Downregulated GroES and over expressed NusB are critical proteins for cell death. © 2009 Elsevier Ltd. All rights reserved.