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Linares-Alvelais JAR, Figueroa-Cavazos JO, Chuck-Hernandez C, Siller HR, Rodríguez CA, Martínez-López JI. Hydrostatic High-Pressure Post-Processing of Specimens Fabricated by DLP, SLA, and FDM: An Alternative for the Sterilization of Polymer-Based Biomedical Devices. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E2540. [PMID: 30551631 PMCID: PMC6316578 DOI: 10.3390/ma11122540] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 11/16/2022]
Abstract
In this work, we assess the effects of sterilization in materials manufactured using additive manufacturing by employing a sterilization technique used in the food industry. To estimate the feasibility of the hydrostatic high-pressure (HHP) sterilization of biomedical devices, we have evaluated the mechanical properties of specimens produced by commercial 3D printers. Evaluations of the potential advantages and drawbacks of Fused Deposition Modeling (FDM), Digital Light Processing (DLP) technology, and Stereolithography (SLA) were considered for this study due to their widespread availability. Changes in mechanical properties due to the proposed sterilization technique were compared to values derived from the standardized autoclaving methodology. Enhancement of the mechanical properties of samples treated with Hydrostatic high-pressure processing enhanced mechanical properties, with a 30.30% increase in the tensile modulus and a 26.36% increase in the ultimate tensile strength. While traditional autoclaving was shown to systematically reduce the mechanical properties of the materials employed and damages and deformation on the surfaces were observed, HHP offered an alternative for sterilization without employing heat. These results suggest that while forgoing high-temperature for sanitization, HHP processing can be employed to take advantage of the flexibility of additive manufacturing technologies for manufacturing implants, instruments, and other devices.
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Affiliation(s)
- José A Robles Linares-Alvelais
- Department of Mechanical Engineering and Advanced Materials, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico.
- Laboratorio Nacional de Manufactura Aditiva y Digital (MADiT), Apodaca 66629, NL, Mexico.
| | - J Obedt Figueroa-Cavazos
- Department of Mechanical Engineering and Advanced Materials, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico.
| | - C Chuck-Hernandez
- Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico.
| | - Hector R Siller
- Department of Engineering Technology, University of North Texas, 3940 N. Elm. St., Denton, TX 76207, USA.
| | - Ciro A Rodríguez
- Department of Mechanical Engineering and Advanced Materials, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico.
- Laboratorio Nacional de Manufactura Aditiva y Digital (MADiT), Apodaca 66629, NL, Mexico.
| | - J Israel Martínez-López
- Department of Mechanical Engineering and Advanced Materials, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico.
- Laboratorio Nacional de Manufactura Aditiva y Digital (MADiT), Apodaca 66629, NL, Mexico.
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52
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Perez Calderon LJ, Gontikaki E, Potts LD, Shaw S, Gallego A, Anderson JA, Witte U. Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments. Microbiologyopen 2018; 8:e00768. [PMID: 30444300 PMCID: PMC6562134 DOI: 10.1002/mbo3.768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/24/2022] Open
Abstract
The Hatton-Rockall Basin (North-East Atlantic) is an area with potential for deep-sea (2,900 m) hydrocarbon exploration. Following the Deepwater Horizon oil spill, many investigations into the responses of sediment microbial communities to oil pollution have been undertaken. However, hydrostatic pressure is a parameter that is often omitted due to the technical difficulties associated with conducting experiments at high pressure (>10 MPa). In this study, sediments from 2,900 m in the Hatton-Rockall Basin, following a one-week decompression period in a temperature-controlled room at 5°C, were incubated in factorial combinations of 0.1 and 30 MPa, 5 and 20°C, and contamination with a hydrocarbon mixture or uncontaminated controls to evaluate the effect of these environmental variables on the bacterial community composition. Our results revealed varying effects of pressure, temperature, and oil contamination on the composition of the bacterial community within the sediment. Temperature was the strongest determinant of differences in the bacterial community structure between samples followed by pressure. Oil contamination did not exert a strong change in the sediment bacterial community structure when pressure and temperature conditions were held at in situ levels (30 MPa and 5°C). The γ-proteobacteria Pseudomonas and Colwellia, and several Bacteroidetes dominated communities at 30 MPa. In contrast, hydrocarbon degraders such as Halomonas, Alcanivorax, and Marinobacter decreased in relative abundance at the same pressure. This study highlights the importance of considering hydrostatic pressure in ex situ investigations into hydrocarbon-degrading deepwater microbial communities.
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Affiliation(s)
- Luis J Perez Calderon
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK.,Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK.,Marine Laboratory Aberdeen, Marine Scotland Science, Aberdeen, UK
| | - Evangelia Gontikaki
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
| | - Lloyd D Potts
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK.,Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK
| | - Sophie Shaw
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | | | - James A Anderson
- Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK
| | - Ursula Witte
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
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53
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Bucur FI, Grigore-Gurgu L, Crauwels P, Riedel CU, Nicolau AI. Resistance of Listeria monocytogenes to Stress Conditions Encountered in Food and Food Processing Environments. Front Microbiol 2018; 9:2700. [PMID: 30555426 PMCID: PMC6282059 DOI: 10.3389/fmicb.2018.02700] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/23/2018] [Indexed: 12/17/2022] Open
Abstract
Listeria monocytogenes is a human food-borne facultative intracellular pathogen that is resistant to a wide range of stress conditions. As a consequence, L. monocytogenes is extremely difficult to control along the entire food chain from production to storage and consumption. Frequent and recent outbreaks of L. monocytogenes infections illustrate that current measures of decontamination and preservation are suboptimal to control L. monocytogenes in food. In order to develop efficient measures to prevent contamination during processing and control growth during storage of food it is crucial to understand the mechanisms utilized by L. monocytogenes to tolerate the stress conditions in food matrices and food processing environments. Food-related stress conditions encountered by L. monocytogenes along the food chain are acidity, oxidative and osmotic stress, low or high temperatures, presence of bacteriocins and other preserving additives, and stresses as a consequence of applying alternative decontamination and preservation technologies such high hydrostatic pressure, pulsed and continuous UV light, pulsed electric fields (PEF). This review is aimed at providing a summary of the current knowledge on the response of L. monocytogenes toward these stresses and the mechanisms of stress resistance employed by this important food-borne bacterium. Circumstances when L. monocytogenes cells become more sensitive or more resistant are mentioned and existence of a cross-resistance when multiple stresses are present is pointed out.
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Affiliation(s)
- Florentina Ionela Bucur
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | - Leontina Grigore-Gurgu
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | - Peter Crauwels
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany
| | | | - Anca Ioana Nicolau
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
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Sreedevi P, Rao PS. Microbial destruction kinetics of high-pressure-processed sugarcane juice (Saccharum officinarum). J FOOD PROCESS ENG 2018. [DOI: 10.1111/jfpe.12850] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- P. Sreedevi
- Department of Agricultural and Food Engineering; Indian Institute of Technology; Kharagpur, West Bengal India
| | - P. Srinivasa Rao
- Department of Agricultural and Food Engineering; Indian Institute of Technology; Kharagpur, West Bengal India
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Roobab U, Aadil RM, Madni GM, Bekhit AED. The Impact of Nonthermal Technologies on the Microbiological Quality of Juices: A Review. Compr Rev Food Sci Food Saf 2018; 17:437-457. [DOI: 10.1111/1541-4337.12336] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/07/2017] [Accepted: 12/18/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Ume Roobab
- Natl. Inst. of Food Science and Technology; Univ. of Agriculture; Faisalabad Pakistan
| | - Rana Muhammad Aadil
- Natl. Inst. of Food Science and Technology; Univ. of Agriculture; Faisalabad Pakistan
| | - Ghulam Muhammad Madni
- Natl. Inst. of Food Science and Technology; Univ. of Agriculture; Faisalabad Pakistan
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56
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Nishiyama M. High-pressure microscopy for tracking dynamic properties of molecular machines. Biophys Chem 2017; 231:71-78. [DOI: 10.1016/j.bpc.2017.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/24/2017] [Accepted: 03/27/2017] [Indexed: 01/29/2023]
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57
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Aguirre A, Karwe MV, Borneo R. Effect of high pressure processing on sugar-snap cookie dough preservation and cookie quality. J FOOD PROCESS PRES 2017. [DOI: 10.1111/jfpp.13407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- A. Aguirre
- Facultad Ciencias Exactas, Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
- Intituto de Ciencia y Tecnología de Alimentos Córdoba (ICYTAC)-CONICET; Córdoba Argentina
| | - M. V. Karwe
- Department of Food Science, School of Environmental and Biological Sciences Rutgers; The State University of New Jersey; 65 Dudley Road, New Brunswick New Jersey
| | - R. Borneo
- Facultad Ciencias Exactas, Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
- Intituto de Ciencia y Tecnología de Alimentos Córdoba (ICYTAC)-CONICET; Córdoba Argentina
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58
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Otero L, Pérez-Mateos M, López-Caballero M. Hyperbaric cold storage versus conventional refrigeration for extending the shelf-life of hake loins. INNOV FOOD SCI EMERG 2017. [DOI: 10.1016/j.ifset.2017.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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59
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Mota MJ, Lopes RP, Koubaa M, Roohinejad S, Barba FJ, Delgadillo I, Saraiva JA. Fermentation at non-conventional conditions in food- and bio-sciences by the application of advanced processing technologies. Crit Rev Biotechnol 2017; 38:122-140. [PMID: 28423948 DOI: 10.1080/07388551.2017.1312272] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The interest in improving the yield and productivity values of relevant microbial fermentations is an increasingly important issue for the scientific community. Therefore, several strategies have been tested for the stimulation of microbial growth and manipulation of their metabolic behavior. One promising approach involves the performance of fermentative processes during non-conventional conditions, which includes high pressure (HP), electric fields (EF) and ultrasound (US). These advanced technologies are usually applied for microbial inactivation in the context of food processing. However, the approach described in this study focuses on the use of these technologies at sub-lethal levels, since the aim is microbial growth and fermentation under these stress conditions. During these sub-lethal conditions, microbial strains develop specific genetic, physiologic and metabolic stress responses, possibly leading to fermentation products and processes with novel characteristics. In some cases, these modifications can represent considerable improvements, such as increased yields, productivities and fermentation rates, lower accumulation of by-products and/or production of different compounds. Although several studies report the successful application of these technologies during the fermentation processes, information on this subject is still scarce and poorly understood. For that reason, the present review paper intends to assemble and discuss the main findings reported in the literature to date, and aims to stimulate interest and encourage further developments in this field.
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Affiliation(s)
- Maria J Mota
- a Chemistry Department, QOPNA , University of Aveiro, Campus Universitário de Santiago , Aveiro , Portugal
| | - Rita P Lopes
- a Chemistry Department, QOPNA , University of Aveiro, Campus Universitário de Santiago , Aveiro , Portugal
| | - Mohamed Koubaa
- b Sorbonne Universités , Université de Technologie de Compiègne, Laboratoire Transformations Intégrées de la Matière Renouvelable (UTC/ESCOM, EA 4297 TIMR), Centre de Recherche de Royallieu , Compiegne France
| | - Shahin Roohinejad
- c Department of Food Technology and Bioprocess Engineering , Max Rubner-Institut, Federal Research Institute of Nutrition and Food , Karlsruhe , Germany.,d Burn and Wound Healing Research Center, Division of Food and Nutrition , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Francisco J Barba
- e Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Faculty of Pharmacy , Universitat de València , València , Spain
| | - Ivonne Delgadillo
- a Chemistry Department, QOPNA , University of Aveiro, Campus Universitário de Santiago , Aveiro , Portugal
| | - Jorge A Saraiva
- a Chemistry Department, QOPNA , University of Aveiro, Campus Universitário de Santiago , Aveiro , Portugal
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60
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Lemos ÁT, Ribeiro AC, Fidalgo LG, Delgadillo I, Saraiva JA. Extension of raw watermelon juice shelf-life up to 58days by hyperbaric storage. Food Chem 2017; 231:61-69. [PMID: 28450024 DOI: 10.1016/j.foodchem.2017.03.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
Hyperbaric storage (HS) of raw watermelon juice, at 50, 62.5 and 75MPa, at temperatures of 10, 15 and ≈25°C (room temperature, RT), was studied to evaluate shelf-life comparatively to refrigeration (RF, 4°C). Generally, RF caused an increase of microbial loads to values ≥6.0logCFU/mL after 7days of storage. Contrarily, HS at 62.5/75MPa (15°C) showed a reduction of initial loads, by at least 2.5logCFU/mL, up to 58days, while pH and colour values did not changed under these HS conditions. Additionally, the combination of a lower temperature with HS has beneficial effects to control microbial development, particularly for the lower pressure studied (50MPa/10°C). In conclusion, HS increased watermelon juice shelf-life for at least 58days, indicating a great potential for future RF replacement.
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Affiliation(s)
- Álvaro T Lemos
- QOPNA, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana C Ribeiro
- QOPNA, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Liliana G Fidalgo
- QOPNA, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ivonne Delgadillo
- QOPNA, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Jorge A Saraiva
- QOPNA, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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61
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Wang L, Xu C, Huang P, Li Y. Single- and multi-cycle high hydrostatic pressure treatment on microbiological quality of mud snail (Bullacta exarata) during refrigerated storage. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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62
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Scoma A, Boon N. Osmotic Stress Confers Enhanced Cell Integrity to Hydrostatic Pressure but Impairs Growth in Alcanivorax borkumensis SK2. Front Microbiol 2016; 7:729. [PMID: 27242746 PMCID: PMC4870253 DOI: 10.3389/fmicb.2016.00729] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/02/2016] [Indexed: 01/13/2023] Open
Abstract
Alcanivorax is a hydrocarbonoclastic genus dominating oil spills worldwide. While its presence has been detected in oil-polluted seawaters, marine sediment and salt marshes under ambient pressure, its presence in deep-sea oil-contaminated environments is negligible. Recent laboratory studies highlighted the piezosensitive nature of some Alcanivorax species, whose growth yields are highly impacted by mild hydrostatic pressures (HPs). In the present study, osmotic stress was used as a tool to increase HP resistance in the type strain Alcanivorax borkumensis SK2. Control cultures grown under standard conditions of salinity and osmotic pressure with respect to seawater (35.6 ppt or 1136 mOsm kg-1, respectively) were compared with cultures subjected to hypo- and hyperosmosis (330 and 1720 mOsm kg-1, or 18 and 62 ppt in salinity, equivalent to brackish and brine waters, respectively), under atmospheric or increased HP (0.1 and 10 MPa). Osmotic stress had a remarkably positive impact on cell metabolic activity in terms of CO2 production (thus, oil bioremediation) and O2 respiration under hyperosmosis, as acclimation to high salinity enhanced cell activity under 10 MPa by a factor of 10. Both osmotic shocks significantly enhanced cell protection by reducing membrane damage under HP, with cell integrities close to 100% under hyposmosis. The latter was likely due to intracellular water-reclamation as no trace of the piezolyte ectoine was found, contrary to hyperosmosis. Notably, ectoine production was equivalent at 0.1 MPa in hyperosmosis-acclimated cells and at 10 MPa under isosmotic conditions. While stimulating cell metabolism and enhancing cell integrity, osmotic stress had always a negative impact on culture growth and performance. No net growth was observed during 4-days incubation tests, and CO2:O2 ratios and pH values indicated that culture performance in terms of hydrocarbon degradation was lowered by the effects of osmotic stress alone or combined with increased HP. These findings confirm the piezosensitive nature of A. borkumensis, which lacks proper resistance mechanisms to improve its metabolic efficiency under increased HP, thus explaining its limited role in oil-polluted deep-sea environments.
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Affiliation(s)
- Alberto Scoma
- Center for Microbial Ecology and Technology, Department of Biochemical and Microbial Technology, University of Ghent Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Department of Biochemical and Microbial Technology, University of Ghent Ghent, Belgium
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63
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Scoma A, Barbato M, Hernandez-Sanabria E, Mapelli F, Daffonchio D, Borin S, Boon N. Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria? Sci Rep 2016; 6:23526. [PMID: 27020120 PMCID: PMC4810429 DOI: 10.1038/srep23526] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/08/2016] [Indexed: 01/19/2023] Open
Abstract
Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10 MPa, corresponding to a depth of 0, 500 and 1000 m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10 MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10 MPa CO2 production per cell was not affected, cell integrity was preserved and PO4(3-) uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential.
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Affiliation(s)
- Alberto Scoma
- Laboratory of Microbial Ecology and Technology (LabMET), University of Gent, Coupure Links 653, B 9000 Gent, Belgium
| | - Marta Barbato
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, 20133, Milano, Italy
| | - Emma Hernandez-Sanabria
- Laboratory of Microbial Ecology and Technology (LabMET), University of Gent, Coupure Links 653, B 9000 Gent, Belgium
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, 20133, Milano, Italy
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, Thuwal 23955-6900, Kingdom of Saudi Arabia.,Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, 20133, Milano, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, 20133, Milano, Italy
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), University of Gent, Coupure Links 653, B 9000 Gent, Belgium
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Itävaara M, Salavirta H, Marjamaa K, Ruskeeniemi T. Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 94:1-77. [PMID: 26917241 DOI: 10.1016/bs.aambs.2015.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities.
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Affiliation(s)
- M Itävaara
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - H Salavirta
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - K Marjamaa
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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Hyperbaric storage at room temperature: Effect of pressure level and storage time on the natural microbiota of strawberry juice. INNOV FOOD SCI EMERG 2016. [DOI: 10.1016/j.ifset.2015.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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66
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Ragon M, Nguyen Thi Minh H, Guyot S, Loison P, Burgaud G, Dupont S, Beney L, Gervais P, Perrier-Cornet JM. Innovative High Gas Pressure Microscopy Chamber Designed for Biological Cell Observation. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:63-70. [PMID: 26810277 DOI: 10.1017/s1431927615015639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An original high-pressure microscopy chamber has been designed for real-time visualization of biological cell growth during high isostatic (gas or liquid) pressure treatments up to 200 MPa. This new system is highly flexible allowing cell visualization under a wide range of pressure levels as the thickness and the material of the observation window can be easily adapted. Moreover, the design of the observation area allows different microscope objectives to be used as close as possible to the observation window. This chamber can also be temperature controlled. In this study, the resistance and optical properties of this new high-pressure chamber have been tested and characterized. The use of this new chamber was illustrated by a real-time study of the growth of two different yeast strains - Saccharomyces cerevisiae and Candida viswanathii - under high isostatic gas pressure (30 or 20 MPa, respectively). Using image analysis software, we determined the evolution of the area of colonies as a function of time, and thus calculated colony expansion rates.
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Affiliation(s)
- Mélanie Ragon
- 1UMR A 02.102 Procédés Alimentaires et Microbiologiques,Université Bourgogne Franche-Comté/AgroSup Dijon,1 Esplanade Erasme,21000 Dijon,France
| | - Hue Nguyen Thi Minh
- 1UMR A 02.102 Procédés Alimentaires et Microbiologiques,Université Bourgogne Franche-Comté/AgroSup Dijon,1 Esplanade Erasme,21000 Dijon,France
| | - Stéphane Guyot
- 1UMR A 02.102 Procédés Alimentaires et Microbiologiques,Université Bourgogne Franche-Comté/AgroSup Dijon,1 Esplanade Erasme,21000 Dijon,France
| | - Pauline Loison
- 1UMR A 02.102 Procédés Alimentaires et Microbiologiques,Université Bourgogne Franche-Comté/AgroSup Dijon,1 Esplanade Erasme,21000 Dijon,France
| | - Gaëtan Burgaud
- 2Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (EA3882),IFR 148,Université Européenne de Bretagne/Université de Brest/ESMISAB,Technopole Brest-Iroise,29280 Plouzané,France
| | - Sébastien Dupont
- 1UMR A 02.102 Procédés Alimentaires et Microbiologiques,Université Bourgogne Franche-Comté/AgroSup Dijon,1 Esplanade Erasme,21000 Dijon,France
| | - Laurent Beney
- 1UMR A 02.102 Procédés Alimentaires et Microbiologiques,Université Bourgogne Franche-Comté/AgroSup Dijon,1 Esplanade Erasme,21000 Dijon,France
| | - Patrick Gervais
- 1UMR A 02.102 Procédés Alimentaires et Microbiologiques,Université Bourgogne Franche-Comté/AgroSup Dijon,1 Esplanade Erasme,21000 Dijon,France
| | - Jean-Marie Perrier-Cornet
- 1UMR A 02.102 Procédés Alimentaires et Microbiologiques,Université Bourgogne Franche-Comté/AgroSup Dijon,1 Esplanade Erasme,21000 Dijon,France
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67
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Sheen S, Cassidy J, Scullen B, Sommers C. Inactivation of a diverse set of shiga toxin-producing Escherichia coli in ground beef by high pressure processing. Food Microbiol 2015; 52:84-7. [DOI: 10.1016/j.fm.2015.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/25/2015] [Accepted: 07/02/2015] [Indexed: 11/29/2022]
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69
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Fichtel K, Logemann J, Fichtel J, Rullkötter J, Cypionka H, Engelen B. Temperature and pressure adaptation of a sulfate reducer from the deep subsurface. Front Microbiol 2015; 6:1078. [PMID: 26500624 PMCID: PMC4594026 DOI: 10.3389/fmicb.2015.01078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/21/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment-basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure.
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Affiliation(s)
- Katja Fichtel
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jörn Logemann
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jörg Fichtel
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jürgen Rullkötter
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Heribert Cypionka
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
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70
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A Continuous Culture System for Assessing Microbial Activities in the Piezosphere. Appl Environ Microbiol 2015. [PMID: 26209666 DOI: 10.1128/aem.01215-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Continuous culture under elevated pressures is an important technique for expanding the exploration of microbial growth and survival in extreme environments associated with the deep biosphere. Here we present a benchtop stirred continuous culture bioreactor capable of withstanding temperatures ranging from 25 to 120°C and pressures as high as 69 MPa. The system is configured to allow the employment of media enriched in dissolved gases, under oxic or anoxic conditions, while permitting periodic sampling of the incubated organisms with minimal physical/chemical disturbance inside the reactor. In a pilot experiment, the fermentative growth of the thermopiezophilic bacterium Marinitoga piezophila was investigated continuously for 382 h at 65°C and at pressures ranging from 0.1 to 40 MPa while the medium flow rate was varied from 2 to 0.025 ml/min. The enhanced growth observed at 30 and 40 MPa and 0.025 ml/min supports the pressure preferences of M. piezophila when grown fermentatively. This assay successfully demonstrates the capabilities of the bioreactor for continuous culturing at a variety of dilution rates, pressures, and temperatures. We anticipate that this technology will accelerate our understanding of the physiological and metabolic status of microorganisms under temperature, pressure, and energy regimes resembling those of the Earth's piezosphere.
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71
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Hsu H, Sheen S, Sites J, Cassidy J, Scullen B, Sommers C. Effect of High Pressure Processing on the survival of Shiga Toxin-Producing Escherichia coli (Big Six vs. O157:H7) in ground beef. Food Microbiol 2015; 48:1-7. [DOI: 10.1016/j.fm.2014.12.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 11/17/2014] [Accepted: 12/03/2014] [Indexed: 11/28/2022]
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72
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Abstract
Movement is a fundamental characteristic of all living things. This biogenic function is carried out by various nanometer-sized molecular machines. Molecular motor is a typical molecular machinery in which the characteristic features of proteins are integrated; these include enzymatic activity, energy conversion, molecular recognition and self-assembly. These biologically important reactions occur with the association of water molecules that surround the motors. Applied pressures can alter the intermolecular interactions between the motors and water. In this chapter we describe the development of a high-pressure microscope and a new motility assay that enables the visualization of the motility of molecular motors under conditions of high-pressure. Our results demonstrate that applied pressure dynamically changes the motility of molecular motors such as kinesin, F1-ATPase and bacterial flagellar motors.
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Affiliation(s)
- Masayoshi Nishiyama
- The Hakubi Center for Advanced Research/Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan,
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73
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Abstract
The deep biosphere is composed of very different biotopes located in the depth of the oceans, the ocean crust or the lithosphere. Although very different, deep biosphere biotopes share one common feature, high hydrostatic pressure. The deep biosphere is colonized by specific organisms, called piezophiles, that are able to grow under high hydrostatic pressure. Bacterial piezophiles are mainly psychrophiles belonging to five genera of γ-proteobacteria, Photobacterium, Shewanella, Colwellia, Psychromonas and Moritella, while piezophilic Archaea are mostly (hyper)thermophiles from the Thermococcales. None of these genera are specific for the deep biosphere. High pressure deeply impacts the activity of cells and cellular components, and reduces the activity of numerous key processes, eventually leading to cell death of piezosensitive organisms. Biochemical and genomic studies yield a fragmented view on the adaptive mechanisms in piezophiles. It is yet unclear whether piezophilic adaptation requires the modification of a few genes, or metabolic pathways, or a more profound reorganization of the genome, the fine tuning of gene expression to compensate the pressure-induced loss of activity of the proteins most affected by high pressure, or a stress-like physiological cell response. In contrast to what has been seen for thermophily or halophily, the adaptation to high pressure is diffuse in the genome and may concern only a small fraction of the genes.
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74
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Mota CR, Head MA, Williams JC, Eland L, Cheng JJ, de los Reyes FL. Structural integrity affects nitrogen removal activity of granules in semi-continuous reactors. Biodegradation 2014; 25:923-34. [DOI: 10.1007/s10532-014-9712-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/05/2014] [Indexed: 10/24/2022]
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75
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Abstract
Covering: 2009 to 2013. This review covers the 188 novel marine natural products described since 2008, from deep-water (50->5000 m) marine fauna including bryozoa, chordata, cnidaria, echinodermata, microorganisms, mollusca and porifera. The structures of the new compounds and details of the source organism, depth of collection and country of origin are presented, along with any relevant biological activities of the metabolites. Where reported, synthetic studies on the deep-sea natural products have also been included. Most strikingly, 75% of the compounds were reported to possess bioactivity, with almost half exhibiting low micromolar cytotoxicity towards a range of human cancer cell lines, along with a significant increase in the number of microbial deep-sea natural products reported.
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Affiliation(s)
- Danielle Skropeta
- School of Chemistry, University of Wollongong, Wollongong, NSW 2500, Australia
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76
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Huang HW, Lung HM, Yang BB, Wang CY. Responses of microorganisms to high hydrostatic pressure processing. Food Control 2014. [DOI: 10.1016/j.foodcont.2013.12.007] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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77
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Duarte-Gómez E, Graham D, Budzik M, Paxson B, Csonka L, Morgan M, Applegate B, San Martín-González M. High hydrostatic pressure effects on bacterial bioluminescence. Lebensm Wiss Technol 2014. [DOI: 10.1016/j.lwt.2013.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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78
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Abstract
Review of deep-sea natural products covering the five-year period 2009–2013.
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Affiliation(s)
| | - Liangqian Wei
- Centre of Medicinal Chemistry
- University of Wollongong
- Wollongong, Australia
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79
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Novel psychropiezophilic Oceanospirillales species Profundimonas piezophila gen. nov., sp. nov., isolated from the deep-sea environment of the Puerto Rico trench. Appl Environ Microbiol 2013; 80:54-60. [PMID: 24123740 DOI: 10.1128/aem.02288-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The diversity of deep-sea high-pressure-adapted (piezophilic) microbes in isolated monoculture remains low. In this study, a novel obligately psychropiezophilic bacterium was isolated from seawater collected from the Puerto Rico Trench at a depth of ∼6,000 m. This isolate, designated YC-1, grew best in a nutrient-rich marine medium, with an optimal growth hydrostatic pressure of 50 MPa (range, 20 to 70 MPa) at 8°C. Under these conditions, the maximum growth rate was extremely slow, 0.017 h(-1), and the maximum yield was 3.51 × 10(7) cells ml(-1). Cell size and shape changed with pressure, shifting from 4.0 to 5.0 μm in length and 0.5 to 0.8 μm in width at 60 MPa to 0.8- to 1.0-μm diameter coccoid cells under 20 MPa, the minimal pressure required for growth. YC-1 is a Gram-negative, facultatively anaerobic heterotroph. Its predominant cellular fatty acids are the monounsaturated fatty acids (MUFAs) C16:1 and C18:1. Unlike many other psychropiezophiles, YC-1 does not synthesize any polyunsaturated fatty acids (PUFAs). Phylogenetic analysis placed YC-1 within the family of Oceanospirillaceae, closely related to the uncultured symbiont of the deep-sea whale bone-eating worms of the genus Osedax. In common with some other members of the Oceanospirillales, including those enriched during the Deepwater Horizon oil spill, YC-1 is capable of hydrocarbon utilization. On the basis of its characteristics, YC-1 appears to represent both a new genus and a new species, which we name Profundimonas piezophila gen. nov., sp. nov.
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81
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Kanda N, Abe F. Structural and functional implications of the yeast high-affinity tryptophan permease Tat2. Biochemistry 2013; 52:4296-307. [PMID: 23768406 DOI: 10.1021/bi4004638] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Tryptophan is hydrophobic, bulky, and the rarest amino acid found in nutrients. Accordingly, the import machinery can be specialized evolutionarily. Our previous study in Saccharomyces cerevisiae demonstrated that tryptophan import by the high-affinity tryptophan permease Tat2 is accompanied by a large volume increase during substrate import. Nevertheless, the mechanisms by which the permease mediates tryptophan recognition and permeation remain to be elucidated. Here we determined amino acid residues essential for Tat2-mediated tryptophan import. By means of random mutagenesis in combination with site-directed mutagenesis based on crystallographic studies of the Escherichia coli arginine/agmatine antiporter AdiC, we identified 15 amino acid residues in the Tat2 transmembrane domains (TMDs) 1, -3, -5, -8, and -10, which are responsible for tryptophan uptake. T98, Y167, and E286 were assumed to form the central cavity in Tat2. G97/T98 and E286 were located within the putative α-helix break in TMD1 and TMD6, respectively, which are highly conserved among yeast amino acid permeases and bacterial solute transporters. Given the conformational change in AdiC upon substrate binding, G97/T98 and E286 of Tat2 were assumed to mediate a structural shift from an outward-open to a tryptophan-bound-occluded structure upon tryptophan binding, and T320, V322, and F324 became stabilized in TMD7. Such dynamic structural changes may account for the large volume increase associated with tryptophan import occurring concomitantly with a movement of water molecules from the tryptophan binding site. We also propose the working hypothesis that E286 mediates the proton influx that is coupled to tryptophan import.
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Affiliation(s)
- Naoko Kanda
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
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82
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Pressure-induced endocytic degradation of the Saccharomyces cerevisiae low-affinity tryptophan permease Tat1 is mediated by Rsp5 ubiquitin ligase and functionally redundant PPxY motif proteins. EUKARYOTIC CELL 2013; 12:990-7. [PMID: 23666621 DOI: 10.1128/ec.00049-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cells of Saccharomyces cerevisiae express two tryptophan permeases, Tat1 and Tat2, which have different characteristics in terms of their affinity for tryptophan and intracellular localization. Although the high-affinity permease Tat2 has been well documented in terms of its ubiquitin-dependent degradation, the low-affinity permease Tat1 has not yet been characterized fully. Here we show that a high hydrostatic pressure of 25 MPa triggers a degradation of Tat1 which depends on Rsp5 ubiquitin ligase and the EH domain-containing protein End3. Tat1 was resistant to a 3-h cycloheximide treatment, suggesting that it is highly stable under normal growth conditions. The ubiquitination of Tat1 most likely occurs at N-terminal lysines 29 and 31. Simultaneous substitution of arginine for the two lysines prevented Tat1 degradation, but substitution of either of them alone did not, indicating that the roles of lysines 29 and 31 are redundant. When cells were exposed to high pressure, Tat1-GFP was completely lost from the plasma membrane, while substantial amounts of Tat1(K29R-K31R)-GFP remained. The HPG1-1 (Rsp5(P514T)) and rsp5-ww3 mutations stabilized Tat1 under high pressure, but any one of the rsp5-ww1, rsp5-ww2, and bul1Δ bul2Δ mutations or single deletions of genes encoding arrestin-related trafficking adaptors did not. However, simultaneous loss of 9-arrestins and Bul1/Bul2 prevented Tat1 degradation at 25 MPa. The results suggest that multiple PPxY motif proteins share some essential roles in regulating Tat1 ubiquitination in response to high hydrostatic pressure.
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83
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High hydrostatic pressure induces counterclockwise to clockwise reversals of the Escherichia coli flagellar motor. J Bacteriol 2013; 195:1809-14. [PMID: 23417485 DOI: 10.1128/jb.02139-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The bacterial flagellar motor is a reversible rotary machine that rotates a left-handed helical filament, allowing bacteria to swim toward a more favorable environment. The direction of rotation reverses from counterclockwise (CCW) to clockwise (CW), and vice versa, in response to input from the chemotaxis signaling circuit. CW rotation is normally caused by binding of the phosphorylated response regulator CheY (CheY-P), and strains lacking CheY are typically locked in CCW rotation. The detailed mechanism of switching remains unresolved because it is technically difficult to regulate the level of CheY-P within the concentration range that produces flagellar reversals. Here, we demonstrate that high hydrostatic pressure can induce CW rotation even in the absence of CheY-P. The rotation of single flagellar motors in Escherichia coli cells with the cheY gene deleted was monitored at various pressures and temperatures. Application of >120 MPa pressure induced a reversal from CCW to CW at 20°C, although at that temperature, no motor rotated CW at ambient pressure (0.1 MPa). At lower temperatures, pressure-induced changes in direction were observed at pressures of <120 MPa. CW rotation increased with pressure in a sigmoidal fashion, as it does in response to increasing concentrations of CheY-P. Application of pressure generally promotes the formation of clusters of ordered water molecules on the surfaces of proteins. It is possible that hydration of the switch complex at high pressure induces structural changes similar to those caused by the binding of CheY-P.
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84
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Pradel N, Ji B, Gimenez G, Talla E, Lenoble P, Garel M, Tamburini C, Fourquet P, Lebrun R, Bertin P, Denis Y, Pophillat M, Barbe V, Ollivier B, Dolla A. The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus. PLoS One 2013; 8:e55130. [PMID: 23383081 PMCID: PMC3559428 DOI: 10.1371/journal.pone.0055130] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 12/18/2012] [Indexed: 01/19/2023] Open
Abstract
Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle.
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Affiliation(s)
- Nathalie Pradel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
- * E-mail: (NP); (AD)
| | - Boyang Ji
- Aix-Marseille Université, CNRS, LCB, UMR 7283, Marseille, France
| | | | - Emmanuel Talla
- Aix-Marseille Université, CNRS, LCB, UMR 7283, Marseille, France
| | - Patricia Lenoble
- Laboratoire de Finition C.E.A., Institut de Génomique – Genoscope, Evry, France
| | - Marc Garel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | - Christian Tamburini
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | | | - Régine Lebrun
- Plate-formes Protéomique et Transcriptomique FR3479, IBiSA Marseille-Protéomique. IMM - CNRS, Marseille, France
| | - Philippe Bertin
- UMR 7156, CNRS, Université Louis Pasteur, Strasbourg, France
| | - Yann Denis
- Plate-formes Protéomique et Transcriptomique FR3479, IBiSA Marseille-Protéomique. IMM - CNRS, Marseille, France
| | | | - Valérie Barbe
- Laboratoire de Finition C.E.A., Institut de Génomique – Genoscope, Evry, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB, UMR 7283, Marseille, France
- * E-mail: (NP); (AD)
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85
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Davydov DR, Sineva EV, Davydova NY, Bartlett DH, Halpert JR. CYP261 enzymes from deep sea bacteria: a clue to conformational heterogeneity in cytochromes P450. Biotechnol Appl Biochem 2013; 60:30-40. [PMID: 23586990 DOI: 10.1002/bab.1083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 12/14/2012] [Indexed: 11/12/2022]
Abstract
We have explored the adaptation of the cytochromes P450 (P450) of deep-sea bacteria to high hydrostatic pressures. Strict conservation of the protein fold and functional importance of protein-bound water make P450 a unique subject for the studies of high-pressure adaptation. Earlier, we expressed and purified a fatty-acid binding P450 from the deep-sea bacteria Photobacterium profundum SS9 (CYP261C1). Here, we report purification and initial characterization of its mesophilic ortholog from the shallow-water P. profundum 3TCK (CYP261C2), as well as another piezophilic enzyme, CYP261D1, from deep-sea Moritella sp. PE36. Comparison of the three enzymes revealed a striking peculiarity of the piezophilic enzymes. Both CYP261C1 and CYP261D1 possess an apparent pressure-induced conformational toggle actuated at the pressures commensurate with the physiological pressure of habitation of the host bacteria. Furthermore, in contrast to CYP261C2, the piezophilic CYP261 enzymes may be chromatographically separated into two fractions with different properties, and different thermodynamic parameters of spin equilibrium in particular. According to our concept, the changes in the energy landscape that evolved in pressure-tolerant enzymes must stabilize the less-hydrated, closed conformers, which may be transient in the catalytic mechanisms of nonpiezophilic enzymes. The studies of enzymes of piezophiles should help unravel the mechanisms that control water access during the catalytic cycle.
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Affiliation(s)
- Dmitri R Davydov
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA, USA.
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86
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Soy peptides enhance yeast cell growth at low temperatures. Biotechnol Lett 2012; 35:375-82. [DOI: 10.1007/s10529-012-1088-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
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87
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Singh P, Raghukumar C, Verma AK, Meena RM. Differentially expressed genes under simulated deep-sea conditions in the psychrotolerant yeast Cryptococcus sp. NIOCC#PY13. Extremophiles 2012; 16:777-85. [DOI: 10.1007/s00792-012-0474-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/23/2012] [Indexed: 11/28/2022]
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88
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Bacterial motility measured by a miniature chamber for high-pressure microscopy. Int J Mol Sci 2012; 13:9225-9239. [PMID: 22942763 PMCID: PMC3430294 DOI: 10.3390/ijms13079225] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/03/2012] [Accepted: 07/10/2012] [Indexed: 01/13/2023] Open
Abstract
Hydrostatic pressure is one of the physical stimuli that characterize the environment of living matter. Many microorganisms thrive under high pressure and may even physically or geochemically require this extreme environmental condition. In contrast, application of pressure is detrimental to most life on Earth; especially to living organisms under ambient pressure conditions. To study the mechanism of how living things adapt to high-pressure conditions, it is necessary to monitor directly the organism of interest under various pressure conditions. Here, we report a miniature chamber for high-pressure microscopy. The chamber was equipped with a built-in separator, in which water pressure was properly transduced to that of the sample solution. The apparatus developed could apply pressure up to 150 MPa, and enabled us to acquire bright-field and epifluorescence images at various pressures and temperatures. We demonstrated that the application of pressure acted directly and reversibly on the swimming motility of Escherichia coli cells. The present technique should be applicable to a wide range of dynamic biological processes that depend on applied pressures.
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89
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Segovia-Bravo K, Guignon B, Bermejo-Prada A, Sanz P, Otero L. Hyperbaric storage at room temperature for food preservation: A study in strawberry juice. INNOV FOOD SCI EMERG 2012. [DOI: 10.1016/j.ifset.2012.02.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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90
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Simonin H, Duranton F, de Lamballerie M. New Insights into the High-Pressure Processing of Meat and Meat Products. Compr Rev Food Sci Food Saf 2012. [DOI: 10.1111/j.1541-4337.2012.00184.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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91
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Kish A, Griffin PL, Rogers KL, Fogel ML, Hemley RJ, Steele A. High-pressure tolerance in Halobacterium salinarum NRC-1 and other non-piezophilic prokaryotes. Extremophiles 2012; 16:355-61. [PMID: 22212652 DOI: 10.1007/s00792-011-0418-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 12/13/2011] [Indexed: 01/23/2023]
Abstract
In this study, we examined the high-pressure survival of a range of prokaryotes not found in high-pressure environments to determine the effects of adaptations to osmotic and oxidative stresses on piezo-resistance. The pressure survivals of Halobacterium salinarum NRC-1, Deinococcus radiodurans R1, and Chromohalobacter salexigens were compared to that of Escherichia coli MG1655. C. salexigens, which uses the compatible solute ectoine as an osmolyte, was as piezo-sensitive as E. coli MG1655, suggesting that ectoine is not a piezolyte. D. radiodurans R1 and H. salinarum NRC-1, both resistant to oxidative stress, were found to be highly piezo-resistant. H. salinarum NRC-1 showed nearly full survival after pressurization up to 400 MPa; a survival 3.5 log units higher than E. coli MG1655. This piezo-resistance was maintained in H. salinarum NRC-1 for pressurizations up to 1 h. We hypothesize that the high-pressure resistance of H. salinarum NRC-1 is due to a combination of factors including cell envelope structure and the presence of intracellular salts.
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Affiliation(s)
- Adrienne Kish
- Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Rd., NW, Washington, DC, 20015, USA.
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92
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Bièche C, de Lamballerie M, Chevret D, Federighi M, Tresse O. Dynamic proteome changes in Campylobacter jejuni 81-176 after high pressure shock and subsequent recovery. J Proteomics 2011; 75:1144-56. [PMID: 22079248 DOI: 10.1016/j.jprot.2011.10.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 10/20/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
Abstract
Campylobacter jejuni is one of the most intriguing human foodborne bacterial pathogen. Its survival throughout the food processing chain and its pathogenesis mechanisms in humans remain enigmatic. Living in the animal guts and particularly in avian intestine as a commensal bacterium, this microorganism is frequently isolated from meat products. Ultra high pressure (HP) is a promising alternative to thermal technology for microbial safety of foodstuffs with less organoleptic and nutritional alterations. Its application could be extended to meat products potentially contaminated by C. jejuni. To evaluate the response of Campylobacter to this technological stress and subsequent recovery at a molecular level, a dynamic 2-DE-based proteomic approach has been implemented. After cultivation, C. jejuni cells were conditioned in a high-pressure chamber and transferred to fresh medium for recovery. The protein abundance dynamics at the proteome scale were analyzed by 2-DE during the cellular process of cell injury and recovery. Monitoring protein abundance through time unraveled the basic metabolisms involved in this cellular process. The significance of the proteome evolution modulated by HP and subsequent recovery is discussed in the context of a specific cellular response to stress and recovery of C. jejuni with 69 spots showing significant changes through time.
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93
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Deguchi S, Shimoshige H, Tsudome M, Mukai SA, Corkery RW, Ito S, Horikoshi K. Microbial growth at hyperaccelerations up to 403,627 x g. Proc Natl Acad Sci U S A 2011; 108:7997-8002. [PMID: 21518884 PMCID: PMC3093466 DOI: 10.1073/pnas.1018027108] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well known that prokaryotic life can withstand extremes of temperature, pH, pressure, and radiation. Little is known about the proliferation of prokaryotic life under conditions of hyperacceleration attributable to extreme gravity, however. We found that living organisms can be surprisingly proliferative during hyperacceleration. In tests reported here, a variety of microorganisms, including Gram-negative Escherichia coli, Paracoccus denitrificans, and Shewanella amazonensis; Gram-positive Lactobacillus delbrueckii; and eukaryotic Saccharomyces cerevisiae, were cultured while being subjected to hyperaccelerative conditions. We observed and quantified robust cellular growth in these cultures across a wide range of hyperacceleration values. Most notably, the organisms P. denitrificans and E. coli were able to proliferate even at 403,627 × g. Analysis shows that the small size of prokaryotic cells is essential for their proliferation under conditions of hyperacceleration. Our results indicate that microorganisms cannot only survive during hyperacceleration but can display such robust proliferative behavior that the habitability of extraterrestrial environments must not be limited by gravity.
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Affiliation(s)
- Shigeru Deguchi
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan.
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94
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Kawamoto J, Sato T, Nakasone K, Kato C, Mihara H, Esaki N, Kurihara T. Favourable effects of eicosapentaenoic acid on the late step of the cell division in a piezophilic bacterium, Shewanella violacea DSS12, at high-hydrostatic pressures. Environ Microbiol 2011; 13:2293-8. [PMID: 21518217 DOI: 10.1111/j.1462-2920.2011.02487.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shewanella violacea DSS12, a deep-sea bacterium, produces eicosapentaenoic acid (EPA) as a component of membrane phospholipids. Although various isolates from the deep sea, such as Photobacterium profundum SS9, Colwellia psychrerythraea 34H and various Shewanella strains, produce EPA- or docosahexaenoic acid-containing phospholipids, the physiological role of these polyunsaturated fatty acids remains unclear. In this article, we illustrate the physiological importance of EPA for high-pressure adaptation in strain DSS12 with the help of an EPA-deficient mutant (DSS12(pfaA)). DSS12(pfaA) showed significant growth retardation at 30 MPa, but not at 0.1 MPa. We also found that DSS12(pfaA) grown at 30 MPa forms filamentous cells. When an EPA-containing phospholipid (sn-1-oleoly-sn-2-eicosapentaenoyl phosphatidylethanolamine) was supplemented, the growth retardation and the morphological defect of DSS12(pfaA) were suppressed, indicating that the externally added EPA-containing phospholipid compensated for the loss of endogenous EPA. In contrast, the addition of an oleic acid-containing phospholipid (sn-1,2-dioleoyl phosphatidylethanolamine) did not affect the growth and the morphology of the cells. Immunofluorescent microscopic analysis with anti-FtsZ antibody revealed a number of Z-rings and separated nucleoids in DSS12(pfaA) grown at 30 MPa. These results demonstrate the physiological importance of EPA for the later step of Z-ring formation of S. violacea DSS12 under high-pressure conditions.
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Affiliation(s)
- Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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95
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Ambily Nath IV, Loka Bharathi PA. Diversity in transcripts and translational pattern of stress proteins in marine extremophiles. Extremophiles 2011; 15:129-53. [DOI: 10.1007/s00792-010-0348-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 12/09/2010] [Indexed: 11/28/2022]
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96
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Oger PM, Jebbar M. The many ways of coping with pressure. Res Microbiol 2010; 161:799-809. [DOI: 10.1016/j.resmic.2010.09.017] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 09/09/2010] [Indexed: 12/14/2022]
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97
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Vass H, Black SL, Herzig EM, Ward FB, Clegg PS, Allen RJ. A multipurpose modular system for high-resolution microscopy at high hydrostatic pressure. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:053710. [PMID: 20515148 DOI: 10.1063/1.3427224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We have developed a modular system for high-resolution microscopy at high hydrostatic pressure. The system consists of a pressurized cell of volume approximately 100 microl, a temperature controlled holder, a ram, and a piston. We have made each of these components in several versions which can be interchanged to allow a wide range of applications. Here, we report two pressure cells with pressure ranges 0.1-700 MPa and 0.1-100 MPa, which can be combined with hollow or solid rams and pistons. Our system is designed to work with fluorescent samples (using a confocal or epifluorescence microscope), but also allows for transmitted light microscopy via the hollow ram and piston. The system allows precise control of pressure and temperature (-20 to 70 degrees C), as well as rapid pressure quenching. We demonstrate its performance and versatility with two applications: time-resolved imaging of colloidal phase transitions caused by pressure changes between 0.1 and 100 MPa, and imaging the growth of Escherichia coli bacteria at 50 MPa. We also show that the isotropic-nematic phase transition of pentyl-cyanobiphenyl (5CB) liquid crystal provides a simple, convenient, and accurate method for calibrating pressure in the range 0.1-200 MPa.
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Affiliation(s)
- Hugh Vass
- SUPA, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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98
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Rivalain N, Roquain J, Demazeau G. Development of high hydrostatic pressure in biosciences: pressure effect on biological structures and potential applications in biotechnologies. Biotechnol Adv 2010; 28:659-72. [PMID: 20398747 DOI: 10.1016/j.biotechadv.2010.04.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 04/01/2010] [Accepted: 04/04/2010] [Indexed: 11/16/2022]
Abstract
Compared to temperature, the development of pressure as a tool in the research field has emerged only recently (at the end of the XIXth century). Following several developments in Physics and Chemistry during the first half of the XXth century (in particular the synthesis of diamond in 1953-1954), high pressures were applied in Food Science, especially in Japan. The main objective was then to achieve the decontamination of foods while preserving their organoleptic properties. Now, a new step is engaged: the biological applications of high pressures, from food to pharmaceuticals and biomedical applications. This paper will focus on three main points: (i) a brief presentation of the pressure parameter and its characteristics, (ii) a description of the pressure effects on biological constituents from simple to more complex structures and (iii) a review of the different domains for which the application of high pressures is able to initiate potential developments in Biotechnologies.
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Affiliation(s)
- Nolwennig Rivalain
- ICMCB-CNRS - Université de Bordeaux - 87, avenue du Dr. Albert Schweitzer, PESSAC Cedex, France
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99
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András CD, Csajági C, Orbán CK, Albert C, Ábrahám B, Miklóssy I. A possible explanation of the germicide effect of carbon dioxide in supercritical state based on molecular-biological evidence. Med Hypotheses 2010; 74:325-9. [DOI: 10.1016/j.mehy.2009.08.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 08/24/2009] [Indexed: 12/01/2022]
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100
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Morozkina EV, Slutskaya ES, Fedorova TV, Tugay TI, Golubeva LI, Koroleva OV. Extremophilic microorganisms: Biochemical adaptation and biotechnological application (review). APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810010011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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