Pub Date : 2021-10-13DOI: 10.5772/intechopen.96706
Sudhesh Dev Sareshma, B. Subha
RNA sequencing is a valuable tool brought about by advances in next generation sequencing (NGS) technology. Initially used for transcriptome mapping, it has grown to become one of the ‘gold standards’ for studying molecular changes that occur in niche environments or within and across infections. It employs high-throughput sequencing with many advantages over previous methods. In this chapter, we review the experimental approaches of RNA sequencing from isolating samples all the way to data analysis methods. We focus on a number of NGS platforms that offer RNA sequencing with each having their own strengths and drawbacks. The focus will also be on how RNA sequencing has led to developments in the field of host-pathogen interactions using the dual RNA sequencing technique. Besides dual RNA sequencing, this review also explores the application of other RNA sequencing techniques such as single cell RNA sequencing as well as the potential use of newer techniques like ‘spatialomics’ and ribosome-profiling in host-pathogen interaction studies. Finally, we examine the common challenges faced when using RNA sequencing and possible ways to overcome these challenges.
{"title":"Assessing Host-Pathogen Interaction Networks via RNA-Seq Profiling: A Systems Biology Approach","authors":"Sudhesh Dev Sareshma, B. Subha","doi":"10.5772/intechopen.96706","DOIUrl":"https://doi.org/10.5772/intechopen.96706","url":null,"abstract":"RNA sequencing is a valuable tool brought about by advances in next generation sequencing (NGS) technology. Initially used for transcriptome mapping, it has grown to become one of the ‘gold standards’ for studying molecular changes that occur in niche environments or within and across infections. It employs high-throughput sequencing with many advantages over previous methods. In this chapter, we review the experimental approaches of RNA sequencing from isolating samples all the way to data analysis methods. We focus on a number of NGS platforms that offer RNA sequencing with each having their own strengths and drawbacks. The focus will also be on how RNA sequencing has led to developments in the field of host-pathogen interactions using the dual RNA sequencing technique. Besides dual RNA sequencing, this review also explores the application of other RNA sequencing techniques such as single cell RNA sequencing as well as the potential use of newer techniques like ‘spatialomics’ and ribosome-profiling in host-pathogen interaction studies. Finally, we examine the common challenges faced when using RNA sequencing and possible ways to overcome these challenges.","PeriodicalId":416299,"journal":{"name":"Applications of RNA-Seq in Biology and Medicine","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130848539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-10-13DOI: 10.5772/intechopen.96449
R. Priyadarshini, K. Krishnan, R. Niranjan
Oral cavity is an ecologically complex environment and hosts a diverse microbial community. Most of these organisms are commensals, however, on occasion, some have the potential to become pathogenic causing damage to the human host. Complex interactions between pathogenic bacteria, the microbiota, and the host can modify pathogen physiology and behavior. Most bacteria in the environment do not exist in free-living state but are found as complex matrix enclosed aggregates known as biofilms. There has been research interest in microbial biofilms because of their importance in industrial and biomedical settings. Bacteria respond to environmental cues to fine-tune the transition from planktonic growth to biofilm by directing gene expression changes favorable for sessile community establishment. Meta-approaches have been used to identify complex microbial associations within human oral cavity leading to important insights. Comparative gene expression analysis using deep sequencing of RNA and metagenomics studies done under varying conditions have been successfully used in understanding and identifying possible triggers of pathogenicity and biofilm formation in oral commensals.
{"title":"Insights into Oropharyngeal Microbiota, Biofilms and Associated Diseases from Metagenomics and Transcriptomic Approaches","authors":"R. Priyadarshini, K. Krishnan, R. Niranjan","doi":"10.5772/intechopen.96449","DOIUrl":"https://doi.org/10.5772/intechopen.96449","url":null,"abstract":"Oral cavity is an ecologically complex environment and hosts a diverse microbial community. Most of these organisms are commensals, however, on occasion, some have the potential to become pathogenic causing damage to the human host. Complex interactions between pathogenic bacteria, the microbiota, and the host can modify pathogen physiology and behavior. Most bacteria in the environment do not exist in free-living state but are found as complex matrix enclosed aggregates known as biofilms. There has been research interest in microbial biofilms because of their importance in industrial and biomedical settings. Bacteria respond to environmental cues to fine-tune the transition from planktonic growth to biofilm by directing gene expression changes favorable for sessile community establishment. Meta-approaches have been used to identify complex microbial associations within human oral cavity leading to important insights. Comparative gene expression analysis using deep sequencing of RNA and metagenomics studies done under varying conditions have been successfully used in understanding and identifying possible triggers of pathogenicity and biofilm formation in oral commensals.","PeriodicalId":416299,"journal":{"name":"Applications of RNA-Seq in Biology and Medicine","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121620944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-10-13DOI: 10.5772/intechopen.99882
I. Vlasova-St Louis
{"title":"Introductory Chapter: Applications of RNA-Seq Diagnostics in Biology and Medicine","authors":"I. Vlasova-St Louis","doi":"10.5772/intechopen.99882","DOIUrl":"https://doi.org/10.5772/intechopen.99882","url":null,"abstract":"<jats:p />","PeriodicalId":416299,"journal":{"name":"Applications of RNA-Seq in Biology and Medicine","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127524596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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