Limits...
New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview.

Biggar KK, Storey KB - Comput Struct Biotechnol J (2014)

Bottom Line: Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges.Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored.Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.

ABSTRACT
Although much is known about the physiological responses of many environmental stresses in tolerant animals, studies evaluating the regulation of stress-induced mechanisms that regulate the transitions to and from this state are beginning to explore new and fascinating areas of molecular research. Current findings have developed a general, but refined, view of the important molecular pathways contributing to stress-survival. However, studies utilizing newly developed technologies that broadly focus on genomic and proteomic screening are beginning to identify many new targets for future study. This minireview will provide a contextual overview on the use of DNA/RNA sequencing, microRNA annotation and prediction software, protein structure and function prediction tools, as well as methods of high-throughput protein expression analysis. We will also use select examples to highlight the existing use of these technologies in stress biology research. Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges. Although there are many areas of study left to be explored, research in comparative stress biology will always be continuing as new technologies allow the further analysis of cell function, and new paradigms in gene regulation and regulatory molecules (such as microRNAs) are continuing to be discovered. Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored. Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.

No MeSH data available.


Overview of RNAseq transcriptome mapping for gene expression experiments.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4232569&req=5

f0010: Overview of RNAseq transcriptome mapping for gene expression experiments.

Mentions: Recently, the development of high-throughput RNAseq has provided a means to sequencing whole RNA transcripts, allowing the assembly and quantification of transcriptomes. The use of high-throughput RNAseq provides clear advantages over gene microarray studies as the analysis provides both the ability to sequence RNA and measure the dynamic expression of mRNA transcripts. Currently, RNAseq uses deep-sequencing technologies such as 454, illumina, SOLiD and HelicosBiotechnology (see Table 1 for comparison). In general, a population of total RNA is converted into a library of cDNA fragments with adaptors attached to one or both ends. Each adaptor-ligated transcript is then sequenced from one end (single-end sequencing) or both ends (pair-end sequencing), producing reads that are typically 30–400 bp in length [29]. The commonly used illumina sequencing process is similar in principle, but uses a solid phase bridge amplification method to create clusters of a specific gene before sequencing (Fig. 1). RNAseq reads are then aligned and mapped to a reference genome for further analysis, or assembled de novo without the genomic sequence (Fig. 2). Following the release of its genome sequence, RNAseq analysis has been used to determined mRNA expression during anoxia exposure in the Western painted turtle (C. picta bellii) [12]. To explore the transcriptomic basis of its anoxia tolerance, this study assembled an mRNA expression profile by sequencing poly A-enriched RNA isolated from the heart and brain (telencephalon) of normoxic and anoxic turtles. Differential gene expression significantly increased in the brain (19 genes) and heart (23 genes). Highly differentially expressed genes (> 10-fold; APOLD1, FOS, JUNB, ATF3, PTGS2, BTG1/2, and EGR1) were found to encode proteins that have been implicated in the control of cellular proliferation, cancers, and tumor suppression [12]. If a complete genome sequence is not available, a de novo transcriptome assembly may be constructed and used for mRNA expression analysis. However, researchers must consider all of the statistical concerns for this type of experimental design before undertaking this type of study as more reads are typically needed for a de novo assembly (see Box. 2).


New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview.

Biggar KK, Storey KB - Comput Struct Biotechnol J (2014)

Overview of RNAseq transcriptome mapping for gene expression experiments.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4232569&req=5

f0010: Overview of RNAseq transcriptome mapping for gene expression experiments.
Mentions: Recently, the development of high-throughput RNAseq has provided a means to sequencing whole RNA transcripts, allowing the assembly and quantification of transcriptomes. The use of high-throughput RNAseq provides clear advantages over gene microarray studies as the analysis provides both the ability to sequence RNA and measure the dynamic expression of mRNA transcripts. Currently, RNAseq uses deep-sequencing technologies such as 454, illumina, SOLiD and HelicosBiotechnology (see Table 1 for comparison). In general, a population of total RNA is converted into a library of cDNA fragments with adaptors attached to one or both ends. Each adaptor-ligated transcript is then sequenced from one end (single-end sequencing) or both ends (pair-end sequencing), producing reads that are typically 30–400 bp in length [29]. The commonly used illumina sequencing process is similar in principle, but uses a solid phase bridge amplification method to create clusters of a specific gene before sequencing (Fig. 1). RNAseq reads are then aligned and mapped to a reference genome for further analysis, or assembled de novo without the genomic sequence (Fig. 2). Following the release of its genome sequence, RNAseq analysis has been used to determined mRNA expression during anoxia exposure in the Western painted turtle (C. picta bellii) [12]. To explore the transcriptomic basis of its anoxia tolerance, this study assembled an mRNA expression profile by sequencing poly A-enriched RNA isolated from the heart and brain (telencephalon) of normoxic and anoxic turtles. Differential gene expression significantly increased in the brain (19 genes) and heart (23 genes). Highly differentially expressed genes (> 10-fold; APOLD1, FOS, JUNB, ATF3, PTGS2, BTG1/2, and EGR1) were found to encode proteins that have been implicated in the control of cellular proliferation, cancers, and tumor suppression [12]. If a complete genome sequence is not available, a de novo transcriptome assembly may be constructed and used for mRNA expression analysis. However, researchers must consider all of the statistical concerns for this type of experimental design before undertaking this type of study as more reads are typically needed for a de novo assembly (see Box. 2).

Bottom Line: Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges.Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored.Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.

ABSTRACT
Although much is known about the physiological responses of many environmental stresses in tolerant animals, studies evaluating the regulation of stress-induced mechanisms that regulate the transitions to and from this state are beginning to explore new and fascinating areas of molecular research. Current findings have developed a general, but refined, view of the important molecular pathways contributing to stress-survival. However, studies utilizing newly developed technologies that broadly focus on genomic and proteomic screening are beginning to identify many new targets for future study. This minireview will provide a contextual overview on the use of DNA/RNA sequencing, microRNA annotation and prediction software, protein structure and function prediction tools, as well as methods of high-throughput protein expression analysis. We will also use select examples to highlight the existing use of these technologies in stress biology research. Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges. Although there are many areas of study left to be explored, research in comparative stress biology will always be continuing as new technologies allow the further analysis of cell function, and new paradigms in gene regulation and regulatory molecules (such as microRNAs) are continuing to be discovered. Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored. Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.

No MeSH data available.