Pressure cycling technology in systems biology

Methods in Molecular Biology

Volumn 881, Issue , 2012, Pages 27-62

  Powell, Bradford S ^a   Lazarev, Alexander V ^b   Carlson, Greta ^b   Ivanov, Alexander R ^c   Rozak, David A ^a  

^a UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

^b Pressure BioSciences Inc   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Barocycling; Biological threat agent inactivation; Biomolecule extraction; Pressure cycling technology; Sample preparation; Sample processing; Sterilization; Systems biology; Ultra high pressure

Indexed keywords

ARTICLE; ATMOSPHERIC PRESSURE; BIOGEOCHEMISTRY; COVALENT BOND; HYDROGEN BOND; HYDROSTATIC PRESSURE; HYPERBARISM; MOLECULAR WEIGHT; NONHUMAN; PHYSICAL CHEMISTRY; PRESSURE CYCLING TECHNOLOGY; PRIORITY JOURNAL; PROTEIN PROCESSING; SOLUBILIZATION; SYSTEMS BIOLOGY; ANIMAL; CELL FRACTIONATION; CHEMISTRY; GENETICS; HUMAN; INSTRUMENTATION; ISOLATION AND PURIFICATION; METHODOLOGY;

BACTERIAL DNA; MITOCHONDRIAL DNA; OLIGOPEPTIDE; PROTEKTIN;

ANIMALS; CELL FRACTIONATION; DNA, BACTERIAL; DNA, MITOCHONDRIAL; HUMANS; OLIGOPEPTIDES; SYSTEMS BIOLOGY;

EID: 84866444879     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-827-6_2     Document Type: Article

References (76)

1. Powell BS, Cybulski R (2011) Inactivation and extraction of bacterial spores for systems biological analysis. In: Ivanov AR, Lazarev A (eds) Sample preparation in biological mass spectrometry. Springer, New York
2. Banerjee S, Smallwood A, Chambers AE, Nicolaides K (2003) Quantitative recovery of immunoreactive proteins from clinical samples following RNA and DNA isolation. Biotechniques 35:450-452, 454, 456
3. Hummon AB, Lim SR, Difilippantonio MJ, Ried T (2007) Isolation and solubilization of proteins after TRIzol extraction of RNA and DNA frompatient material following prolonged storage. Biotechniques 42:467-470, 472
4. Nolan RL, Teller JK (2006) Diethylamine extraction of proteins and peptides isolated with a mono-phasic solution of phenol and guanidine isothiocyanate. J Biochem Biophys Methods 68:127-131
5. Riol H, Jeune B, Moskovic A, Bathum L,Wang E (1999) Optimized lymphocyte protein extraction performed simultaneously with DNA and RNA isolation: application to the study of factors affecting DNA, RNA, and protein recovery from lymphocytes of the oldest individuals. Anal Biochem 275:192-201
6. Tolosa JM, Schjenken JE, Civiti TD, Clifton VL, Smith R (2007) Column-based method to simultaneously extract DNA, RNA, and proteins from the same sample. Biotechniques 43:799-804
7. Bradley DW, Hess RA, Tao F, Sciaba-Lentz L, Remaley AT, Laugharn JA Jr, ManakM(2000) Pressure cycling technology: a novel approach to virus inactivation in plasma. Transfusion 40:193-200
8. Gross V, Carlson G, Kwan AT, Smejkal G, Freeman E, Ivanov AR, Lazarev A (2008) Tissue fractionation by hydrostatic pressure cycling technology: the unified sample preparation technique for systems biology studies. J Biomol Tech 19:189-199
9. Ringham H, Bell RL, Smejkal GB, Behnke J, Witzmann FA (2007) Application of pressure cycling technology to tissue sample preparation for 2-DE. Electrophoresis 28:1022-1024
10. Smejkal GB, Robinson MH, Lawrence NP, Tao F, Saravis CA, Schumacher RT (2006) Increased protein yields from Escherichia coli using pressure-cycling technology. J Biomol Tech 17:173-175
11. Smejkal GB, Witzmann FA, Ringham H, Small D, Chase SF, Behnke J, Ting E (2007) Sample preparation for two-dimensional gel electrophoresis using pressure cycling technology. Anal Biochem 363:309-311
12. Chesnick IE, Mason JT, OLeary TJ, Fowler CB (2010) Elevated pressure improves the rate of formalin penetration while preserving tissue morphology. J Cancer 1:178-183
13. Fowler CB, Chesnick IE, Moore CD, OLeary TJ, Mason JT (2010) Elevated pressure improves the extraction and identification of proteins recovered from formalin-fixed, paraffin- embedded tissue surrogates. PLoS One 5: e14253
14. Fowler CB, Cunningham RE, Waybright TJ, Blonder J, Veenstra TD, OLeary TJ, Mason JT (2008) Elevated hydrostatic pressure promotes protein recovery from formalin-fixed, paraffinembedded tissue surrogates. Lab Invest 88:185-195
15. Smejkal GB, Poinar GO, Righetti PG (2009) Will amber inclusions provide the first glimpse of a Mesozoic proteome? Expert Rev Proteomics 6:1-4
16. Okubara PA, Li C, Schroeder KL, Schumacher RT, Lawrence NP (2007) Improved extraction of Rhizoctonia and Pythium DNA from wheat roots and soil samples using pressure cycling technology. Can J Plant Pathol 29:304-310
17. Tao F, Behnke J, Li C, Schumacher R, Lawrence NP (2006) Applications of pressure cycling technology (PCT) in proteomics. In: Smejkal GB, Lazarev A (eds) Separation methods in proteomics. CRC Taylor and Francis, Boca Raton, pp 3-18
18. Gross VS, Greenberg HK, Baranov SV, Carlson G, Stavrovskaya IG, Lazarev AV, Kristal BS (2011) Isolation of functional mitochondria from rat kidney and skeletal muscle without manual homogenization. Anal Biochem 418 (2):213-223
19. Fourme R, Kahn R, Mezouar M, Girard E, Hoerentrup C, Prange T, Ascone I (2001) High-pressure protein crystallography (HPPX): instrumentation, methodology and results on lysozyme crystals. J Synchrotron Radiat 8:1149-1156
20. Visuri K, Kaipainen E, Kivimaki J, Niemi H, Leisola M, Palosaari S (1990) A new method for protein crystallization using high pressure. Biotechnology (N Y) 8:547-549
21. Hess RA, Reinhard LA (1999) Unusual properties of highly charged buffers: large ionization volumes and low barrier hydrogen bonds. JACS 121:9867-9870
22. Laugharn JA Jr, Tao F, Sciaba-Lentz L, Bradley DW, Hess RA (1998) Sample preparation for molecular diagnostics by pressure cycling. In: Ludwig H (ed) High pressure bioscience and biotechnology. Springer, New York
23. Dreier GH, Tao F, Hess RA, Cheung CY, Sciaba LE, Green DJ, Laugharn JA Jr (1999) A bioseparation apparatus with high-pressure fluid injection and fluid sampling. Anal Biochem 269:223-229
24. Cheung CY, Green DJ, Litt GJ, Laugharn JA Jr (1998) High-pressure- mediated dissociation of immune complexes demonstrated in model systems. Clin Chem 44:299-303
25. Dusing S,Li C,Behnke J,ManakM, Schumacher R (2001) Inactivation of viruses in plasma by cycled pulses of high pressure. In: Hayashi R (ed) Trends in high pressure bioscience and biotechnology. Elsevier Science B.V., Amsterdam, pp 355-359
26. Green DJ, Litt GJ, Laugharn JA Jr (1998) Use of high pressure to accelerate antibody: antigen binding kinetics demonstrated in an HIV-1 p24: anti-HIV-1 p24 assay. Clin Chem 44:341-342
27. Laugharn J, Dreier G, Rudd E, Green D (2000) Pressure cycling reactor and methods of controlling reactions using pressure. BBI BioSeq, Inc., US Patent 6,036,923
28. Laugharn JA Jr, Hess RA, Tao F (2000) Nucleic acid isolation and purification. BBI BioSeq, Inc., US Patent 6,111,096
29. Laugharn JA Jr, Hess RA, Tao F (2000) Pressure- enhanced extraction and purification. BBI BioSeq, Inc., US Patent 6,120,985 and 6,274,726
30. Remaley A, Hess R, Fischer S, Sampson M, Manak M (2000) Pre-analytical sterilization of serum by pressure cycling treatment: a novel procedure to prevent laboratory acquired infections. Clin Chem 46:A39
31. Rudd EA (1997) Reversible inhibition of lambda exonuclease with high pressure. Biochem Biophys Res Commun 230:140-142
32. Balasubramanian S, Balasubramaniam VM (2003) Compression heating influence of pressure transmitting fluids on bacteria inactivating during high pressure processing. Food Res Int 36:661-668
33. Rasanayagam Vet al (2003) Compression heating of selected fatty food materials during highpressure processing. J Food Sci 68:254
34. Fatima S, Mishra A, Sen P, Khan RH (2008) Characterization of fluoroalcohols-induced intermediates of Mucor miehei lipase at low pH. Protein Pept Lett 15:346-352
35. Gross V, Lazarev A, Lawrence N, Schumacher R (2008) Isolation of mitochondria from cell cultures by PCT for proteomic analysis. Biotechniques 45:99-100
36. Yao H, Stuart RA, Cai S, Sem DS (2008) Structural characterization of the transmembrane domain from subunit e of yeast F1Fo- ATP synthase: a helical GXXXG motif located just under the micelle surface. Biochemistry 47:1910-1917
37. Chicon R, Belloque J, Recio I, Lopez-Fandino R (2006) Influence of high hydrostatic pressure on the proteolysis of beta-lactoglobulin A by trypsin. J Dairy Res 73:121-128
38. Chicon R, Lopez-Fandino R, Quiros A, Belloque J (2006) Changes in chymotrypsin hydrolysis of beta-lactoglobulin A induced by high hydrostatic pressure. J Agric Food Chem 54:2333-2341
39. Penas E, Restani P, Ballabio C, Prestamo G, Fiocchi A, Gomez R (2006) Evaluation of the residual antigenicity of dairy whey hydrolysates obtained by combination of enzymatic hydrolysis and high-pressure treatment. J Food Prot 69:1707-1712
40. Lopez-Ferrer D, Petritis K, Hixson KK, Heibeck TH, Moore RJ, Belov ME, Camp DG II, Smith RD (2008) Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly. J Proteome Res 7:3276-3281
41. Freeman E, Margolin E, Ivanov AR (2011) Pressure-assisted lysis of mammalian cell cultures prior to proteomic analysis. In: Ivanov AR, Lazarev A (eds) Sample preparation in biological mass spectrometry. Springer, New York
42. Getie-Kebtie M, Lazarev A, Eichelberger M, Alterman M (2010) Label-free mass spectrometry- based relative quantification of proteins separated by one-dimensional gel electrophoresis. Anal Biochem 409:202-212
43. Lee B, Lopez-Ferrer D, Kim BC, Na HB, Park YI, Weitz KK, Warner MG, Hyeon T, Lee SW, Smith RD, Kim J (2011) Rapid and efficient protein digestion using trypsin-coated magnetic nanoparticles under pressure cycles. Proteomics 11:309-318
44. Lopez-Ferrer D, Petritis K, Robinson EW, Hixson KK, Tian Z, Lee JH, Lee SW, Tolic N, Weitz KK, Belov ME, Smith RD, Pasa-Tolic L (2011) Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics. Mol Cell Proteomics 10:M110.001479
45. Courtney JW, Kostelnik LM, Zeidner NS, Massung RF (2004) Multiplex real-time PCR for detection of Anaplasma phagocytophilum and Borrelia burgdorferi. J Clin Microbiol 42:3164-3168
46. Black WC IV, Piesman J (1994) Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences. Proc Natl Acad Sci U S A 91:10034-10038
47. Clements RT, Smejkal G, Sodha NR, Ivanov AR, Asara JM, Feng J, Lazarev A, Gautam S, Senthilnathan V, Khabbaz KR, Bianchi C, Sellke FW (2008) Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass. Circulation 118:S24-S31
48. Tao F, Li C, Smejkal G, Lazarev A, Lawrence NP, Schumacher RT (2007) Pressure cycling technology (PCT) applications in extraction of biomolecules from challenging biological samples. In: Abe F, Suzuki A (eds) Fourth international conference on high-pressure biosciences and biotechnology, J-STAGE, Tsukuba, pp 166-173
49. Crowder CD, Matthews HE, Schutzer S, Rounds MA, Luft BJ, Nolte O, Campbell SR, Phillipson CA, Li F, Sampath R, Ecker DJ, Eshoo MW (2010) Genotypic variation and mixtures of Lyme Borrelia in Ixodes ticks from North America and Europe. PLoS One 5: e10650
50. Rijpkema SG, Herbes RG, Verbeek-De Kruif N, Schellekens JF (1996) Detection of four species of Borrelia burgdorferi sensu lato in Ixodes ricinus ticks collected from roe deer (Capreolus capreolus) in The Netherlands. Epidemiol Infect 117:563-566
51. Canelle L, Bousquet J, Pionneau C, Hardouin J, Choquet-Kastylevsky G, Joubert-Caron R, Caron M (2006) A proteomic approach to investigate potential biomarkers directed against membrane-associated breast cancer proteins. Electrophoresis 27:1609-1616
52. Deshusses JM, Burgess JA, Scherl A,Wenger Y, Walter N, Converset V, Paesano S, Corthals GL, Hochstrasser DF, Sanchez JC (2003) Exploitation of specific properties of trifluoroethanol for extraction and separation of membrane proteins. Proteomics 3:1418-1424
53. Redeby T, Emmer A (2005) Membrane protein and peptide sample handling for MS analysis using a structured MALDI target. Anal Bioanal Chem 381:225-232
54. Redeby T, Roeraade J, Emmer A (2004) Simple fabrication of a structured matrix-assisted laser desorption/ionization target coating for increased sensitivity in mass spectrometric analysis of membrane proteins. Rapid Commun Mass Spectrom 18:1161-1166
55. Wang H, Qian WJ, Mottaz HM, Clauss TR, Anderson DJ, Moore RJ, Camp DG II, Khan AH, Sforza DM, Pallavicini M, Smith DJ, Smith RD (2005) Development and evaluation of a micro- and nanoscale proteomic sample preparation method. J Proteome Res 4:2397-2403
56. Zhang H, Lin Q, Ponnusamy S, Kothandaraman N, Lim TK, Zhao C, Kit HS, Arijit B, Rauff M, Hew CL, Chung MC, Joshi SB, Choolani M (2007) Differential recovery of membrane proteins after extraction by aqueous methanol and trifluoroethanol. Proteomics 7:1654-1663
57. Zuobi-Hasona K, Crowley PJ, Hasona A, Bleiweis AS, Brady LJ (2005) Solubilization of cellular membrane proteins from Streptococcus mutans for two-dimensional gel electrophoresis. Electrophoresis 26:1200-1205
58. Muetzelburg MV, Hoffmann R (2008) Separation of multiphosphorylated peptide isomers by CZE. Electrophoresis 29:4381-4385
59. Mitulovic G, Stingl C, Steinmacher I, Hudecz O, Hutchins JR, Peters JM, Mechtler K (2009) Preventing carryover of peptides and proteins in nano LC-MS separations. Anal Chem 81:5955-5960
60. Apffel A, Chakel JA, Fischer S, Lichtenwalter K, Hancock WS (1997) Analysis of oligonucleotides by HPLC-electrospray ionization mass spectrometry. Anal Chem 69:1320-1325
61. HFIP technical product information. DuPont Chemical Solutions http://www2.dupont.com/Polymer-Specialties/en-US/assets/downloads/ HFIP-Tech-Sheet-jan2012.pdf
62. Lazarev AV, Gross VS (2008) Extraction and partitioning of molecules. US Patent Application 20080300386, filed on 2 June 2008
63. Chatterjee C, Gerig JT (2007) Interactions of trifluroethanol with the Trp-cage peptide. Biopolymers 87:115-123
64. Cort JR, Liu Z, Lee GM, Huggins KN, Janes S, Prickett K, AndersenNH(2009) Solution state structures of human pancreatic amylin and pramlintide. Protein Eng Des Sel 22:497-513
65. Forbes JG, Jin AJ, Ma K, Gutierrez-Cruz G, Tsai WL,Wang K (2005) Titin PEVK segment: charge-driven elasticity of the open and flexible polyampholyte. J Muscle Res Cell Motil 26:291-301
66. Naseem F, Khan RH (2008) Pea lectin in alkaline conditions: formation of molten globulelike intermediate and its structural and thermal studies under the influence of hexafluoroisopropanol. Protein Pept Lett 15:606-611
67. Freeman E, Gross V, Romanovsky I, Ivanov AR (2011) Adipose tissue lysis and protein extraction followed by ms-based proteomic profiling reveals constituents of oxidative stress in obesity. In: Ivanov AR, Lazarev A (eds) Sample preparation in biological mass spectrometry. Springer, New York
68. Rasmussen HN, Andersen AJ, Rasmussen UF (1997) Optimization of preparation of mitochondria from 25-100 mg skeletal muscle. Anal Biochem 252:153-159
69. Carroll JA, Stewart PE, Rosa P, Elias AF, Garon CF (2003) An enhanced GFP reporter system to monitor gene expression in Borrelia burgdorferi. Microbiology 149:1819-1828
70. Dang JL, Heroux K, Kearney J, Arasteh A, Gostomski M, Emanuel PA (2001) Bacillus spore inactivation methods affect detection assays. Appl Environ Microbiol 67:3665-3670
71. Schneider LV, Likhte V, Wright A, Chu F, Cambron E, Baldwin-Burnett A, Krakow J (2012) Recovery and immunoaffinity enrichment of intact membrane proteins from metastatic ovarian cancer tissue. International Journal of Proteomics, August 2012 (in press)
72. Patel N, Solanki E, Picciani R, Cavett V, Caldwell- Busby JA, Bhattacharya SK (2008) Strategies to recover proteins from ocular tissues for proteomics. Proteomics 8:1055-1070
73. Tao F (2008) Challenges and current solutions in proteomic sample preparations. In: Mine Y, Miyashita K, Shahidi F (eds) Nutrigenomics and proteomics in health and disease: food factors and gene interactions. Wiley, New York
74. Yu C, Cohen LH (2004) Tissue sample preparation- not the same old grind. LC GC N Am. 2003;21:1038-1048
75. Szabo Z, Guttman A, Karger BL (2009) Rapid release of N-linked glycans from glycoproteins by pressure-cycling technology. Anal Chem 82:2588-2593
76. McCoy J, Hubbell WL (2011) High-pressure EPR reveals conformational equilibria and volumetric properties of spin-labeled proteins. Proc Natl Acad Sci U S A 108:1331-1336