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Omics Approaches for the Production of the Microbial Enzymes and Applications
Published in Pankaj Bhatt, Industrial Applications of Microbial Enzymes, 2023
Heena Parveen, Anuj Chaudhary, Parul Chaudhary, Rabiya Sultana, Govind Kumar, Priyanka Khati, Meenakshi Rana, Pankaj Bhatt
Transcriptome includes the transcribed subset of genes of an organism, which interlinks the cellular phenotype, the genome, and the proteome. Gene expression regulation acts as the prime key for adaptation to changes in the environment leading to survival. Transcriptomics portrays the method in a genome-wide range. In transcriptomics, one of the powerful platforms that facilitate the expression of mRNA level determination of each gene of an organism is the DNA microarrays [70–71]. The crucial phase in microarray experiments is data elucidation. A large amount of data may evolve in a specific stress condition due to the upregulation and downregulation of a wide range of genes. Hence, it becomes tremendously complex in statistical matters in addition to systemic and random errors.
Recent Advancements in Microbial Degradation of Xenobiotics by Using Proteomics Approaches
Published in Vineet Kumar, Vinod Kumar Garg, Sunil Kumar, Jayanta Kumar Biswas, Omics for Environmental Engineering and Microbiology Systems, 2023
Neha Sharma, Smriti Shukla, Kartikeya Shukla, Ajit Varma, Vineet Kumar, Menaka Devi Salam, Arti Mishra
The transcriptome is the set of all RNA transcripts that include the coding and noncoding RNA. Microarray is one of the important tools. It gives information about the mRNA expression of every gene of an organism. DNA microarray has been used for determining bacterial species and their quantitative analysis of genes, which are upregulated or downregulated in stressed environments (Muffler et al. 2002; Singh and Nagaraj 2006). This tool can be used for the screening of bacterial expression in various stress conditions. Advancements in multiomics approaches enabled researchers to extract mRNA from bacterial, archaeal, and eukaryotic microbial cells. It also enabled researchers to obtain the complete profile of gene expression of microbial communities. It is known as “meta-transcriptome”. cDNA microarray offers an important tool for monitoring the transcriptional activities of the microbial communities (Urich et al. 2008). Meta-transcriptomic approaches have been employed by researchers to get information regarding the function and structure of microbial communities of rhizospheric soil (Urich et al. 2008).
Omics Approach to Understanding Microbial Diversity
Published in Jyoti Ranjan Rout, Rout George Kerry, Abinash Dutta, Biotechnological Advances for Microbiology, Molecular Biology, and Nanotechnology, 2022
Shilpee Pal, Arijit Jana, Keshab Chandra Mondal, Suman Kumar Halder
A transcriptome is the entire set of RNA transcribed from the genome of an organism under a particular physiological condition. Transcriptomics comprises high-throughput methods to comprehend the expression of genes that resides in the genome at the transcription level. Thus, it provides the information on genome dynamics of an organism, that is, gene structure, regulation of gene expression, and gene product function at specific physiological, developmental, and/orpathologicalprocesses. Transcriptomics can also reveal the regulation network of biological processes, which further helps in proteomics research. Moreover, transcriptomics has now been applied to explore the structure and function of nonprotein-coding RNA (ncRNA), which has essential roles in gene regulation (Eddy, 2001).
Plant responses to per- and polyfluoroalkyl substances (PFAS): a molecular perspective
Published in International Journal of Phytoremediation, 2023
Ayesha Karamat, Rouzbeh Tehrani, Gregory D. Foster, Benoit Van Aken
The development of -omics technologies have revolutionized biological sciences, including plant biology. Although the entire genetic material of an organism is referred to as the genome, the expression of genes generates transcripts (messenger RNAs–mRNAs), which together constitute the transcriptome. Transcripts are then translated into proteins, which together constitute the proteome. Proteins, mostly enzymes, mediate biochemical reactions of the metabolism, resulting in the synthesis of a multitude of small molecules forming the metabolome (Abdullah-Zawawi et al. 2022). Studying the transcriptome, proteome, and metabolome constitutes therefore a powerful approach for understanding the molecular mechanisms of the plant response to stress, including toxic chemicals, such as PFAS.
Incorporation of chemical and toxicological availability into metal mixture toxicity modeling: State of the art and future perspectives
Published in Critical Reviews in Environmental Science and Technology, 2022
Bing Gong, Hao Qiu, Ana Romero-Freire, Cornelis A. M. Van Gestel, Erkai He
Genetic responses upon chemical exposure are commonly regulated at the transcriptional level. Transcriptomics can quantify the levels of nearly all the transcriptional profiles to stress conditions. Microarrays are used to measure expression profiles of mRNA, which can help to generate a wide impression of how environmental stressors affect organisms. High-throughput RNA-sequencing (RNA-Seq) technology opens research opportunities for collecting transcriptomic data from any species of interest (Trapp et al., 2016). In addition, quantitative PCR (qPCR) is becoming more important for in-depth gene expression analysis as it allows to quantify a particular fragment in a sample (Altenburger et al., 2012). Recently, transcriptome analysis has become a useful tool to unravel the role of differential expression induced by different gene-related aspects during biological processes (Shi & He, 2014).