Work Area

Papers to cite

biosensors

1. Daunert S, Barrett G, Feliciano JS, Shetty RS, Shrestha S, and Smith-Spencer W. Genetically engineered whole-cell sensing systems: coupling biological recognition with reporter genes. Chem Rev. 2000 Jul 12;100(7):2705-38. DOI:10.1021/cr990115p |
2. Yagi K. Applications of whole-cell bacterial sensors in biotechnology and environmental science. Appl Microbiol Biotechnol. 2007 Jan;73(6):1251-8. DOI:10.1007/s00253-006-0718-6 |
3. Harms H, Wells MC, and van der Meer JR. Whole-cell living biosensors--are they ready for environmental application?. Appl Microbiol Biotechnol. 2006 Apr;70(3):273-80. DOI:10.1007/s00253-006-0319-4 |
4. Gu MB, Min J, and Kim EJ. Toxicity monitoring and classification of endocrine disrupting chemicals (EDCs) using recombinant bioluminescent bacteria. Chemosphere. 2002 Jan;46(2):289-94. DOI:10.1016/s0045-6535(01)00081-9 |

Papers cited by Forrest's writings

5. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, and O'Shea EK. Global analysis of protein localization in budding yeast. Nature. 2003 Oct 16;425(6959):686-91. DOI:10.1038/nature02026 |
6. Pajot-Augy E, Crowe M, Levasseur G, Salesse R, and Connerton I. Engineered yeasts as reporter systems for odorant detection. J Recept Signal Transduct Res. 2003;23(2-3):155-71. DOI:10.1081/rrs-120025196 |

Biofuel

5. Torney F, Moeller L, Scarpa A, and Wang K. Genetic engineering approaches to improve bioethanol production from maize. Curr Opin Biotechnol. 2007 Jun;18(3):193-9. DOI:10.1016/j.copbio.2007.03.006 |
7. Prasad D, Arun S, Murugesan M, Padmanaban S, Satyanarayanan RS, Berchmans S, and Yegnaraman V. Direct electron transfer with yeast cells and construction of a mediatorless microbial fuel cell. Biosens Bioelectron. 2007 May 15;22(11):2604-10. DOI:10.1016/j.bios.2006.10.028 |
8. Okuda N, Ninomiya K, Takao M, Katakura Y, and Shioya S. Microaeration enhances productivity of bioethanol from hydrolysate of waste house wood using ethanologenic Escherichia coli KO11. J Biosci Bioeng. 2007 Apr;103(4):350-7. DOI:10.1263/jbb.103.350 |
9. Henstra AM, Sipma J, Rinzema A, and Stams AJ. Microbiology of synthesis gas fermentation for biofuel production. Curr Opin Biotechnol. 2007 Jun;18(3):200-6. DOI:10.1016/j.copbio.2007.03.008 |
10. Katahira S, Mizuike A, Fukuda H, and Kondo A. Ethanol fermentation from lignocellulosic hydrolysate by a recombinant xylose- and cellooligosaccharide-assimilating yeast strain. Appl Microbiol Biotechnol. 2006 Oct;72(6):1136-43. DOI:10.1007/s00253-006-0402-x |

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Papers baby wants

12. Lu TK and Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11197-202. DOI:10.1073/pnas.0704624104 |

Used in paper already

13. Keane A, Phoenix P, Ghoshal S, and Lau PC. Exposing culprit organic pollutants: a review. J Microbiol Methods. 2002 Apr;49(2):103-19. DOI:10.1016/s0167-7012(01)00382-7 |

Bacterial plastics

14. Ward PG, Goff M, Donner M, Kaminsky W, and O'Connor KE. A two step chemo-biotechnological conversion of polystyrene to a biodegradable thermoplastic. Environ Sci Technol. 2006 Apr 1;40(7):2433-7. DOI:10.1021/es0517668 |
15. Liu SJ and Steinbüchel A. A novel genetically engineered pathway for synthesis of poly(hydroxyalkanoic acids) in Escherichia coli. Appl Environ Microbiol. 2000 Feb;66(2):739-43. DOI:10.1128/AEM.66.2.739-743.2000 |

Chronology of biosensors

1994

Pentachlorophenol

16. Van Dyk TK, Majarian WR, Konstantinov KB, Young RM, Dhurjati PS, and LaRossa RA. Rapid and sensitive pollutant detection by induction of heat shock gene-bioluminescence gene fusions. Appl Environ Microbiol. 1994 May;60(5):1414-20. DOI:10.1128/aem.60.5.1414-1420.1994 |

2002

Endocrine disrupting chemicals (EDCs)

4. Gu MB, Min J, and Kim EJ. Toxicity monitoring and classification of endocrine disrupting chemicals (EDCs) using recombinant bioluminescent bacteria. Chemosphere. 2002 Jan;46(2):289-94. DOI:10.1016/s0045-6535(01)00081-9 |

Herbicides

17. Shao CY, Howe CJ, Porter AJ, and Glover LA. Novel cyanobacterial biosensor for detection of herbicides. Appl Environ Microbiol. 2002 Oct;68(10):5026-33. DOI:10.1128/AEM.68.10.5026-5033.2002 |

Genotoxic agents -- MMC, MNNG, NA

18. Weisweiler P and Schwandt P. Biological action of the lipotrophic peptides A and B from pig pituitary glands. Acta Endocrinol (Copenh). 1975 May;79(1):34-42. DOI:10.1530/acta.0.0790034 |

2005

Chlorinated aliphatic hydrocarbons (CAHs) -- trichloroethene (TCE) in ground water

19. Bhattacharyya J, Read D, Amos S, Dooley S, Killham K, and Paton GI. Biosensor-based diagnostics of contaminated groundwater: assessment and remediation strategy. Environ Pollut. 2005 Apr;134(3):485-92. DOI:10.1016/j.envpol.2004.09.002 |

2006

Heavy metals

20. Shao CY, Howe CJ, Porter AJ, and Glover LA. Novel cyanobacterial biosensor for detection of herbicides. Appl Environ Microbiol. 2002 Oct;68(10):5026-33. DOI:10.1128/AEM.68.10.5026-5033.2002 |

Figures

Example of Abstraction Hierarchy. The oscillator system is composed of three inverter devices, each of which is composed of a ribosome binding site part, a protein coding part, terminator parts, and a regulatory part. DNA-level researchers need only be concerned with creating a specific DNA sequence; part-level researchers need only be concerned with designing DNA sequences with a certain functionality; device-level researchers need only be concerned with combining existing parts to achieve a certain input-output response; and system-level researchers need only be concerned with combining existing devices to build a system with certain behaviors.

21. Sørensen SJ, Burmølle M, and Hansen LH. Making bio-sense of toxicity: new developments in whole-cell biosensors. Curr Opin Biotechnol. 2006 Feb;17(1):11-6. DOI:10.1016/j.copbio.2005.12.007 |

Text

How 'Synthetic' is Environmental Synthetic Biology?

The current state of knowledge in biology has enabled researchers to work principally within one level of the abstraction hierarchy to engineer novel organisms. For example, a biological input-output device can be created by taking an output part from one organism (e.g. the GFP gene from jellyfish [Nature425]), and input part from another (e.g. an olfactory receptor from a mammalian cell [Pajot-Augy03]), and integrating those parts into a chassis of choice (e.g. yeast cells). This sort of genetic plug-and-play can in some cases be done without fully understanding the operational mechanisms of all the parts.

However, the lack of standardization of biological parts and devices has impeded research progress by requiring researchers to devote a significant portion of their efforts to interface engineering -- that is, assembling the many parts and getting them to function together predictably. Standardization would reduce costly inefficiencies by simplifying both the design and construction stages of bioengineering and minimizing the amount of experimental guesswork needed.

Furthermore, as bioconstruction technologies advance, synthetic biology research activities can be expected to progress at higher rates and become much more widespread. While researchers today can purchase made-to-order DNA cheaply, most of the necessary bioengineering steps (e.g. making fusion proteins,XXXXXXXXXXXX) must still be done laboriously by hand. Decoupling design and construction in bioengineering would allow individuals to innovate without having to work in expensive wet lab facilities at all times. Just as online machine shop services have enabled individuals to order custom-designed parts to create innovative products from their home, the further decoupling of biological design and construction (e.g. providing the ability to order custom-designed organisms rather than just fragments its DNA) will allow synthetic biologist to create and experiment with useful biological systems at lower costs. Perhaps more importantly, the decoupling would enable a greater number of individuals (of various levels of experience) to utilize synthetic biology for solving a variety of real world problems.

In the following sections, the current state of environmental synthetic biology is summarized. It shall be apparent that most of the work involve creating whole cell sensors that contain a reporter (e.g. coding for GFP or luciferase) and a promoter inducible by environmental toxins. These projects can be considered device-level engineering, as the resulting product is usually a simple input-output device. Examples of system-level engineering for environmental applications is only starting to appear...

Non-relevant

Calculating relative centrifugal force (RCF)

Relative centrifugal force is the measurement of the force applied to a sample within a centrifuge. This can be calculated from the speed (RPM) and the rotational radius (cm) using the following calculation.

g = RCF = 0.00001118 × r × N²

where

g = Relative centrifuge force

r = rotational radius (centimetre, cm)

N = rotating speed (revolutions per minute, r/min)

Links

Title:

Selective Fractionation of Nanowire Diameter by Centrifugation 

Authors:

Trammell, T. E. 

Publication:

American Physical Society, APS March Meeting, March 21-25, 2005, abstract #V25.005 

Publication Date:

03/2005

http://www.coleparmer.com/techinfo/techinfo.asp?htmlfile=basic-centrifugation.htm&ID=30

http://homepages.gac.edu/~cellab/appds/appd-f.html