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Pressure Cycling Technology in Systems Biology

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Book cover Microbial Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 881))

Abstract

Systems biologists frequently seek to integrate complex data sets of diverse analytes into a comprehensive picture of an organism’s biological state under defined environmental conditions. Although one would prefer to collect these data from the same sample, technical limitations with traditional sample preparation methods often commit the investigator to extracting one type of analyte at the expense of losing all others. Often, volume further constrains the range of experiments that can be collected from a single sample. The practical solution employed to date has been to rely on information collected from multiple replicate experiments and similar historical or reported data. While this approach has been popular, the integration of information collected from disparate single-analyte sample preparation streams increases uncertainty due to nonalignment during comparative analysis, and such gaps accumulate quickly when combining multiple data sets. Regrettably, discontinuities between separate data streams can confound a whole understanding of the biological system being investigated. This difficulty is further compounded for researchers handling highly pathogenic samples, in which it is often necessary to use harsh chemicals or high-energy sterilization procedures that damage the target analytes. Ultra-high pressure cycling technology (PCT), also known as barocycling, is an emerging sample preparation strategy that has distinct advantages for systems biology studies because it neither commits the researcher to pursuing a specific analyte nor leads to the degradation of target material. In fact, samples prepared under pressure cycling conditions have been shown to yield a more complete set of analytes due to uniform disruption of the sample matrix coupled with an advantageous high pressure solvent environment. Fortunately, PCT safely sterilizes and extracts complex or pathogenic viral, bacterial, and spore samples without adversely affecting the constituent biomolecules valued as informative and meaningful analytes. This chapter provides procedures and findings associated with incorporating PCT into systems biology as a new and enabling approach to preanalytical sample treatment.

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Abbreviations

BSL:

Biological safety level

cfu:

Colony forming units

FEP:

Fluorinated ethylene propylene

MMIB:

Muscle Mitochondria Isolation Buffer

PBI:

Pressure BioSciences, Inc.

PCT:

Pressure cycling technology, also Barocycling

SPS:

Sample preparation system

TSB:

Tryptone Soy Broth

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Acknowledgments

This work was funded in part by a grant from the United States Defense Threat Reduction Agency (TMTI0049_09_RD_T). The spore inactivation and spore proteome specific work was performed under NIAID/MRMC interagency agreement Y1-AI-2663-01 A120 B.9 and OSD SBIR Phase I grant W81XWH-10-C-0175 to Pressure BioSciences, Inc. Opinions, interpretations, conclusions, and recommendations are those of the authors and are not necessarily endorsed by the United States Army.

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Authors and Affiliations

  1. Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA

    Bradford S. Powell & David A. Rozak

  2. Pressure BioSciences, Inc., South Easton, MA, USA

    Alexander V. Lazarev & Greta Carlson

  3. Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA

    Alexander R. Ivanov

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  1. Bradford S. Powell
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  2. Alexander V. Lazarev
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  3. Greta Carlson
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  4. Alexander R. Ivanov
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  5. David A. Rozak
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Correspondence to David A. Rozak .

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Editors and Affiliations

  1. Physics & Life Sciences Directorate, Biosciences & Biotechnology Div., Lawrence Livermore National Laboratory, East Avenue 7000, Livermore, 94551, California, USA

    Ali Navid

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Powell, B.S., Lazarev, A.V., Carlson, G., Ivanov, A.R., Rozak, D.A. (2012). Pressure Cycling Technology in Systems Biology. In: Navid, A. (eds) Microbial Systems Biology. Methods in Molecular Biology, vol 881. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-827-6_2

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  • DOI: https://doi.org/10.1007/978-1-61779-827-6_2

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