Work Area
Papers to cite
biosensors
- 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 |
- 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 |
- 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 |
- 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
- 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 |
- 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
The need for alternative fuels has increased considerably in the recent years due to rising fossil fuel prices and worldwide attention towards environmental sustainability. While battery technology has steadily progressed, electrochemical energy storage still cannot (and may never) compete with liquid or gaseous fuels on energy density.
Among the promising candidates for alternative fuels are biofuels and hydrogen. Biofuels -- fuels produced from crop-based carbohydrates -- include bioethanol from fermentable corn or switchgrass sugars and biodiesel from plant oils (torney). Numerous groups have employed recombinant and metabolic engineering to develop microorganisms that produce biofuels. For example, a recombinant Saccharomyces yeast strain has been engineered to break down cellulose and ferment ethanol from xylose, a pentose commonly found in renewable lignocellulosic biomass such as waste paper. This was achieved by introducing genes from P. stipitis and S. cerevisiae for their xylose-fermenting ability, and displaying on the cell surface a cellooligosaccharide-degrading fusion protein from an A. aculeatus gene and α-agglutinin (Katahira). Commercial entities pursuing biofuel applications of synthetic biology include California startups Amyris Biotechnologies, LS9, and Synthetic Genomics.
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- Bro C, Regenberg B, Förster J, and Nielsen J. In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng. 2006 Mar;8(2):102-11. DOI:10.1016/j.ymben.2005.09.007 |
- Hill J, Nelson E, Tilman D, Polasky S, and Tiffany D. Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11206-10. DOI:10.1073/pnas.0604600103 |
- Zhang YH, Evans BR, Mielenz JR, Hopkins RC, and Adams MW. High-yield hydrogen production from starch and water by a synthetic enzymatic pathway. PLoS One. 2007 May 23;2(5):e456. DOI:10.1371/journal.pone.0000456 |
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Papers baby wants
- 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
- 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
- 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 |
- 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
1990
1991
1992
1993
1994
Pentachlorophenol
- 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 |
1995
1996
1997
1998
1999
2000
2001
2002
Endocrine disrupting chemicals (EDCs)
- 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
- 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
- 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 |
2003
2004
2005
Chlorinated aliphatic hydrocarbons (CAHs) -- trichloroethene (TCE) in ground water
- 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
- 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 |
2007
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.
- 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