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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.


De novo protein modeling and prediction of function. (A) Predicted de novo protein structure of the novel freeze-responsive proteins, FR10 and Li16 from the freeze-tolerant wood frog (Rana sylvatica). Structures were predicted by the QUARK server and optimized by MOE software. (B) Membrane interactions of FR10 and Li16 based on PPM server prediction. Figure modified from [17].
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f0030: De novo protein modeling and prediction of function. (A) Predicted de novo protein structure of the novel freeze-responsive proteins, FR10 and Li16 from the freeze-tolerant wood frog (Rana sylvatica). Structures were predicted by the QUARK server and optimized by MOE software. (B) Membrane interactions of FR10 and Li16 based on PPM server prediction. Figure modified from [17].

Mentions: Occasionally, obtaining protein structure is necessary to determine more specific function information regarding the protein under study. As such, protein structure can be determined through several methods. If the protein is highly homologous to the existing body of protein crystal structures, SWISS-MODEL can be used to determine 3-dimensional (3D) protein structure [68]. Importantly, SWISS-MODEL is currently one of the most commonly used resources and provides information on the quality of prediction. For example, a study on the structural adaptations of aldolase enzyme that helps to drive glycolysis in anoxic turtles (Trachemys scripta elegans) used SWISS-MODEL to generate the structures of aldolase enzymes (ALDOA and ALDOB). These structures were then used to determine the mechanisms involved in substrate interactions compared to rabbit aldolase proteins, stating that differences in substrate binding and heterotetramer formation contribute to the higher activity of turtle aldolase (Fig. 5) [5]. When completely novel proteins are discovered, structures cannot be determined from homology-based methods and be predicted de novo. Several programs currently exist to facilitate de novo predictions, the most commonly used being I-TASSER (for proteins < 1500 amino acids) and QUARK (< 200 amino acids) [69]. To highlight the use of de novo structure prediction for completely novel proteins, a recent study used QUARK to determine the structure of two freeze-response proteins, FR10 and Li16, from the wood frog (Rana sylvatica) (Fig. 6) [17]. The ability to obtain structures for these novel proteins allowed researchers to model membrane interaction (PPM server; http://opm.phar.umich.edu/server.php) [70], leading to the hypothesis that FR10 was an excreted protein and Li16 may have functional roles in membrane-adaptation roles in response to freezing stress.


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)

De novo protein modeling and prediction of function. (A) Predicted de novo protein structure of the novel freeze-responsive proteins, FR10 and Li16 from the freeze-tolerant wood frog (Rana sylvatica). Structures were predicted by the QUARK server and optimized by MOE software. (B) Membrane interactions of FR10 and Li16 based on PPM server prediction. Figure modified from [17].
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4232569&req=5

f0030: De novo protein modeling and prediction of function. (A) Predicted de novo protein structure of the novel freeze-responsive proteins, FR10 and Li16 from the freeze-tolerant wood frog (Rana sylvatica). Structures were predicted by the QUARK server and optimized by MOE software. (B) Membrane interactions of FR10 and Li16 based on PPM server prediction. Figure modified from [17].
Mentions: Occasionally, obtaining protein structure is necessary to determine more specific function information regarding the protein under study. As such, protein structure can be determined through several methods. If the protein is highly homologous to the existing body of protein crystal structures, SWISS-MODEL can be used to determine 3-dimensional (3D) protein structure [68]. Importantly, SWISS-MODEL is currently one of the most commonly used resources and provides information on the quality of prediction. For example, a study on the structural adaptations of aldolase enzyme that helps to drive glycolysis in anoxic turtles (Trachemys scripta elegans) used SWISS-MODEL to generate the structures of aldolase enzymes (ALDOA and ALDOB). These structures were then used to determine the mechanisms involved in substrate interactions compared to rabbit aldolase proteins, stating that differences in substrate binding and heterotetramer formation contribute to the higher activity of turtle aldolase (Fig. 5) [5]. When completely novel proteins are discovered, structures cannot be determined from homology-based methods and be predicted de novo. Several programs currently exist to facilitate de novo predictions, the most commonly used being I-TASSER (for proteins < 1500 amino acids) and QUARK (< 200 amino acids) [69]. To highlight the use of de novo structure prediction for completely novel proteins, a recent study used QUARK to determine the structure of two freeze-response proteins, FR10 and Li16, from the wood frog (Rana sylvatica) (Fig. 6) [17]. The ability to obtain structures for these novel proteins allowed researchers to model membrane interaction (PPM server; http://opm.phar.umich.edu/server.php) [70], leading to the hypothesis that FR10 was an excreted protein and Li16 may have functional roles in membrane-adaptation roles in response to freezing stress.

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.