Browsing by Author "Deepanker Yadav"

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Advancement in bioinformatics and microarray-based technologies for genome sequence analysis and its application in bioremediation of soil and water pollutants
(Elsevier, 2020) Jyoti Singh; Madhuri Gupta; Kaushalendra Kumar Singh; Ajay Kumar; Deepanker Yadav; Wang Wenjing; Prashant Kumar Singh
The microarray is an excellent platform for the understanding of complex regulatory as well as functional mechanisms operating in various cellular processes and, hence, microarray significantly contributing to human welfare. However, voluminous data generated following to microarray, requiring a series of consecutive-analyses to extract useful information to draw any conclusion. Moreover, bioinformatics is an emerging tool advocated for the generation of valuable information’s from large datasets, such as microarray, RNA sequencing, next-generation sequencing, proteomics, transcriptomics. Therefore, to make these experiments interpretable, a series of algorithms must be applied. Thus, in recent decades, microarray in combination with bioinformatics has transformed the field of biology by enhancing our fundamental understanding of how genome shapes the organism. In this chapter, we discuss key concepts, tools, software, and databases used in bioinformatics for the interpretation of large datasets. Furthermore, some fundamental issues associated with sequence analyses, transcriptomic studies, computational proteomics and metabolomics, bioontologies, and biological databases covered to gain our fundamental understanding of the general approaches and algorithms currently employed in the microarray. Today’s world is suffering from various environmental pollutants that impose a negative impact on our lifestyles. Therefore an economical and eco-friendly way is urgently calling the attention of scientists. Recently, bioremediation emerges as a hopeful tool, which utilizes microbes to clean our environment. The microarray and bioinformatics approach could be applied for the identification and characterization of novel microbes, which will serve as an inoculum in wastes bioremediation. However, this field is remaining elusive because of the complex biological activities of these microbes, and a better knowledge of their interactions could only be possible through microarray and bioinformatics. Several molecular and bioinformatic tools such as genomics, transcriptomics, translatomics, proteomics, evogenimics, metagenomics, metabolomics are used to gather information on such interaction. In this chapter, we discuss the role of microarray-based technologies and bioinformatics in the bioremediation of wastes. © 2021 Elsevier Inc.
Cyanobacteria: Potential and role for environmental remediation
(Elsevier, 2019) Priyanka; Cash Kumar; Antra Chatterjee; Wang Wenjing; Deepanker Yadav; Prashant Kumar Singh
In recent decades, rapid industrialization has significantly increased the level of toxic and hazardous chemicals in the environment which further adversely affects human health and the other organisms as well in one hand. While on the other, a rapidly mounting human population and their demand for food, fuel, and other necessities have remarkably increased the complexity of toxic effluents in the air, soil, and water. Conventional approaches to remove these contaminants from the environment are time- and cost-consuming. Recent understating of microbial metabolism, their occurrence in a diverse environment, cost-effectiveness, and eco-friendly nature has made them suitable for remediation of the environmental pollutants. Among these cyanobacteria are common phototropic microorganisms which play a distinct role in the ecosystem and can survive in a variety of environment. Diazotrophic cyanobacteria are capable of fixing atmospheric nitrogen and carbon and thus increase the fertility of the contaminated soil, and they are being used for reclamation of usar/alkali soil in one way, while on other contributes to a significant proportion in global carbon fixation. Additionally, they are capable enough to remove/degrade the heavy metals from the contaminated sites by modifying their metabolic activities. Desirable traits of these microbes can be obtained by genetic engineering with increased efficiency to degrade the organic pollutants. In this chapter, the contribution of cyanobacteria to environmental remediation has been discussed. © 2020 Elsevier Inc. All rights reserved.
Cyanobacterial genome editing toolboxes: recent advancement and future projections for basic and synthetic biology researches
(Elsevier, 2020) Sandeep Kumar Singh; Alok Kumar Shrivastava; Ajay Kumar; Vipin Kumar Singh; Deepanker Yadav; Arpan Modi; Wenjing Wang; Avinash Singh; Toolika Singh; Viji Sitther; Prashant Kumar Singh
Cyanobacteria are ancient photosynthetic prokaryotes and serve as a model organism for studies such as photosynthesis and earth elements cycling. Cyanobacteria also termed microbial cell factories, because of their ability to utilize carbon dioxide, as well as sunlight absorption in one way, act as primary producers of the aquatic ecosystem while on the other way the diazotrophic forms fix atmospheric nitrogen in paddy fields. Moreover, the successful invention of several fuels as well as fine chemicals from cyanobacteria is indicative of the advancement in synthetic cyanobacteriology in one hand while on the other knocking the door of the augmented application shortly. Unfortunately, the limited availability of genetic manipulation tools for either at single-gene level or pathway to the whole genome in cyanobacteria compared to other organisms handicaps the fundamental biology researches as well as further application and advancement in synthetic cyanobacteriology. However, the role of genetic tools in tuning gene expression, genome-wide manipulations, and carbon flux redirections is available in cyanobacteria. Furthermore, recently a noteworthy headway evolving to familiarizing novel and efficient genetic manipulations tools such as riboswitches, promoters, ribosome-binding site engineering, small RNA regulatory tools, genome-scale modeling strategies, and clustered regularly interspaced short palindromic repeats-associated nuclease has revolutionized the cyanobacteriology. The present chapter disapprovingly recapitulates the recent advancement on the applications and development as well as technical limitations also for the future projections of the toolboxes for genetic manipulation of cyanobacterial genes/genomes. Besides this, the chapter also briefly discusses the toolkits feasible for large-scale cultivation of cyanobacteria. © 2020 Elsevier Inc. All rights reserved.