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Microbial Biofilm in Remediation of Environmental Contaminants from Wastewater
Published in Vineet Kumar, Vinod Kumar Garg, Sunil Kumar, Jayanta Kumar Biswas, Omics for Environmental Engineering and Microbiology Systems, 2023
Pallavi Singh, Akshita Maheshwari, Varsha Dharmesh, Vandana Anand, Jasvinder Kaur, Sonal Srivastava, Satish Kumar Verma, Suchi Srivastava
Next-generation sequencing is a revolutionized DNA sequencing technology, where sequencing by synthesis principle is applied. In NGS, sequencing of millions of small fragments of DNA occurs. This technology provides an insight into microbial ecology with exploration of deeper layers of communities of microbes and gives impartial outlook of diversities and composition of communities. The steps involved in NGS are (1) DNA extraction from the sample biofilms; (2) checking the extracted DNA’s purity and quantity using NanoDrop spectrophotometer; (3) PCR amplification of the samples using 16SrRNA gene along with universal primers, i.e. 28F and 519R, with the different barcodes incorporated between the forward primer and 454 adaptor; (4) PCR products which are purified are further used for pyrosequencing and then short adaptors are ligated to both ends for sequence segregation; (5) modified products are attached to the DNA beads; (6) clonal amplification; (7) pyrosequencing for 16S rRNA gene sequence, pre-processing at Ribosomal Database Project (RDP) for trimming of barcodes and primers are removed from the partial ribo tags along with discarding short and low-quality sequences; (8) generation of the FASTA file data sets; (9) analysis of these sequence through analysis pipeline (MOTHUR) and R-Scripts. The NGS technique has the potential utility in confirming the sequencing and removing the conventional technique of characterizing of microbes because it has the advantages of flexibility, accuracy, and easy automation (Ronaghi, 2001).
Role of Artificial Intelligence-Based Technologies in Healthcare to Combat Critical Diseases
Published in Chinmay Chakraborty, Digital Health Transformation with Blockchain and Artificial Intelligence, 2022
Dlamini et al. (2020) highlighted next-generation sequencing (NGS) platforms that have transformed precision oncology’s prospects. They discovered that NGS has various clinical uses, including risk prediction, early disease monitoring, genomic and medical imaging diagnosis, precise prediction, biomarker discovery, and therapeutic target acquisition for innovative drug discovery. NGS generates huge datasets that necessitate the use of sophisticated bioinformatics tools to examine the therapeutically useful data. Cancer diagnosis and prognosis prediction are improved using NGS and high-resolution medical imaging due to these AI applications. With recent technological advancements, it is projected that NGS systems would have lower costs, better sensitivity, and faster high throughput data available for diagnostic and therapeutic applications. AI has had a substantial influence on healthcare and precise chemotherapy, and it will continue to do so.
Recent Advancement and Combination of Different Molecular Tools and Techniques for Applications in Wastewater Treatment
Published in Maulin P. Shah, Wastewater Treatment, 2022
Ritwija Bhattacharya, Indraneel Rakshit, Aniruddha Mukhopadhyay, Pritha Bhattacharjee
The recent development of next-generation sequencing (NGS) has created a great impact on the identification of microorganisms found in different environmental samples. In 1987, Fredrick Sanger first developed the sequencing technique (Sanger sequencing) which was based on a chain termination method using dNTPs. This is considered the “first-generation sequencing.” Due to the high effort and use of radioactive materials for Sanger sequencing, scientists thought of building new sequencing techniques for better output. Newly developed NGS has different aspects from Sanger sequencing as it has high-throughput output and reduced cost (Sidhu 2005).
Advancements of next generation sequencing in the field of Rheumatoid Arthritis
Published in Egyptian Journal of Basic and Applied Sciences, 2023
Ankita Pati, Dattatreya Kar, Jyoti Ranjan Parida, Ananya Kuanar
NGS technology has been associated with the working principle of determining the condition for addressing high-throughput sequencing developed through the parallel genome sequencing. Moreover, it is important to understand that the workflow of the NGS process is related to the Sanger’s genome sequencing. NGS technology has been associated with the three major steps such as library preparation for the genome, amplification and sequencing process. The first step for the NGS process has been associated with the library preparation through the ligation of random fragmented DNA sequences [46]. Therefore, using the NGS techniques, the RA disease can be diagnosed at an early stage and can be prevented using proper treatments [47].
Pathogen contamination of groundwater systems and health risks
Published in Critical Reviews in Environmental Science and Technology, 2023
Yiran Dong, Zhou Jiang, Yidan Hu, Yongguang Jiang, Lei Tong, Ying Yu, Jianmei Cheng, Yu He, Jianbo Shi, Yanxin Wang
The emergence of high-throughput next-generation sequencing (NGS) has enabled the recovery of millions of nucleic acid sequences from environmental samples. Based on the complexity of the microorganisms and types of nucleic acids, the applications of NGS technologies are classified into whole genome sequencing (WGS), metagenomic sequencing, and metatranscriptomic sequencing (Garner et al., 2021). Compared with WGS and metagenomics that generate the genetic information from the DNA of isolated organisms and bulk microbial communities, respectively, metatranscriptomics targets the RNA transcripts and thus obtain insight into microbial activity (Franzosa et al., 2014). These NGS-based methods have been increasingly applied to monitor and analyze pathogens as well as pathogen-associated environmental and clinical samples. For example, by using metagenomic sequencing, Cui et al. (2019) screened 303 pathogenic species in the water samples and demonstrated an abundance of pathogens in urban rivers (Cui et al., 2019). Gu et al. (2021) developed a metagenomic next-generation sequencing (mNGS) test by using cell-free DNA in the body fluids from patients with acute illnesses to identify pathogenic bacteria and fungi. In this study, utilization of the Illumina® (Illumina, Inc., CA, U. S.) and Nanopore® (Oxford Nanopore Technologies Limited, Oxford, U. K.) sequencing platforms significantly improved the sensitivities and specificities of pathogen detection. In addition, combined nanopore sequencing and real-time computational analyses enabled rapid mNGS testing with a median 50 min of sequencing and 6 h of sample-to-answer time (Gu et al. 2021). Although NGS technologies have shown promise in pathogen detection, screening and analyses, their application is still challenged by relatively high costs, false negatives, lack of standardized methods, and the requirement for specialized expertise and equipment.