20.109(F09):Alkhairy+Perez: Difference between revisions
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==To Do List== | |||
GO HERE:[http://docs.google.com/Doc?id=dcwgkbhs_241gsq2qhfn] | |||
An Arsenic Biosensor - University of Edinburgh iGEM 2006 team | |||
http://parts.mit.edu/igem07/index.php/Project_Description | |||
E.Chromi | |||
http://www.echromi.com/ | |||
==Project Overview== | ==Project Overview== | ||
Genetically engineering microorganism-based biosensor | Genetically engineering microorganism-based biosensor to detect heavy metals in water. | ||
*Our goal is to develop a simple field test that can warn people or environmental authorities if dangerous levels of toxic metals | *Our goal is to develop a simple, inexpensive field test that can warn people or environmental authorities if dangerous levels of toxic metals are present in the environment, to which they might be exposed. The test could provide vital in helping to tackle one of the world's greatest disasters – the poisoning of tens of millions of people in Bangladesh and West Bengal, India, through naturally–occurring arsenic in their household well water. rather than through long and expensive laboratory testing | ||
Why is this important? : http://www.uq.edu.au/news/?article=12818, http://www.associatedcontent.com/article/366604/researches_develop_new_test_for_contaminated.html | Why is this important? : http://www.uq.edu.au/news/?article=12818, http://www.associatedcontent.com/article/366604/researches_develop_new_test_for_contaminated.html | ||
| Line 7: | Line 18: | ||
==Background Information== | ==Background Information== | ||
-Past heavy metal biosensors | |||
*Heavy Metal BioSensor-BIOMET: http://wwwa.vito.be/english/environment/environmentaltech2d.htm. Currently have E.Coli strain for detecting zinc anc cadmium, or lead or Cr ^+ or nickel or mercury. | |||
*( | *Site some of the papers you listed | ||
*( | |||
* ( | |||
* ( | -Other technologies for detecting heavy metals (accurate but costly) (by decreasing cost) http://www.who.int/water_sanitation_health/dwq/GDW8rev1and2.pdf: look at p16-18 | ||
* ( | *Volumetric method: Our low cost 300 series Karl Fischer titrators are only $4,190 and our low cost potentiometric titrator, the COM-300A is priced at only $5,590 and titrators are in stock for immediate delivery. 110pm-100% off website. | ||
* ( | *Electrode method-The measured potential is proportional to the logarithm of the ion | ||
concentration.- ammiona> 10^-7M - 1M, cadmium-> 10^-1M - 10^-7M | |||
*Ion chromatography- is a process that allows the separation of ions and polar molecules based on their charge.- | |||
*High-performance liquid chromatography (HPLC) | |||
*Flame atomic absorption spectrometry (FAAS) | |||
*Electrothermal atomic absorption spectrometry (EAAS) | |||
*Inductively coupled plasma (ICP)/atomic emission spectrometry (AES) | |||
*ICP/mass spectrometry (MS) | |||
-Field Test detection methods -inaccuarate but cheap | |||
*HPLC | |||
*Gas chromatography (GC) | |||
*GC/MS | |||
*Headspace GC/MS | |||
*Purge-and-trap GC | |||
*Purge-and-trap GC/MS | |||
-Guidelines for Concentrations of Chemicals. (This will be our minimum detection concentration needed) | |||
http://www.who.int/water_sanitation_health/dwq/GDW8rev1and2.pdf (p48-63) | |||
*BAD this about this is that there are so many common chemicals in the environment. Is it useful to look for just metal ions? How common is it that metal ions are the cause for water contamination. However, if we are to find genes regulated by water contaminants, we will only find ones that are regulated by naturally occuring chemicals (metal ions). | |||
-Benefits of this method | -Benefits of this method | ||
- | |||
-Water Standards: | |||
http://www.who.int/water_sanitation_health/dwq/guidelines/en/index.html | |||
==Research Statement and Goals== | ==Research Statement and Goals== | ||
Develop an E. coli system with specific photometric metal detection systems. The system response to concentrations of metal in water would be quantifiable fluorescence at different wavelengths for different metals. The system is intended to combine sensitivity with specificity and also considers bioavailability. | |||
==Specific Aims== | ==Specific Aims== | ||
Specific Aims: | |||
1- Find robust E.Coli with low internal pH to with stand conditions for onsite analysis, and have high binding of metal to promoter for high levels of txn. | |||
2- Find promoters pX, pY, pZ regulated by direct binding of metals mX, mY, mZ, respectively. | |||
3- Fuse each promoter with (G/B/Y)Fluorescent Protein reporter gene, put fusion gene into plasmids then transform into E.Coli. Call this system 'original'. Each metal binding to its respective promoter would give peak fluorescence at a particular lambda. Call the respective wavelengths lamX, lamY, lamZ. | |||
4- To enhance specificity and sensitivity of the system for each metal, we do the following for each promoter: | |||
* Create library of promoter mutations at metal binding site. | |||
* SPR: immobilize mutant promoters and select for tighter binding and specificity of respective metal to find 4 in vitro candidate mutants | |||
* Create vector with candidate mutant promoter fused to its particular fluorescent protein reporter gene. | |||
5- Insert one candidate mutant for each promoter, in different plasmids, into an in vivo system and compare with 'original'. Go through all combinations of promoters mutant candidates (4*4*4) and pick best mutant combination. To compare, we specifically produce graphs w/ (intensity to number of cells ratio) vs. external concentration of mX or mY or mZ for each of lamX, lamY, lamZ. | |||
6- Next, we reproduce graph above with a mixture of metals as opposed to a single metal. Ideally, graph 5 ~= graph 6, for each lambda and therefore our system is very specific. | |||
| Line 51: | Line 89: | ||
==Resources Needed== | ==Resources Needed== | ||
Deleted Info: | |||
-Journal Devoted to created biosensors: http://www.elsevier.com/wps/find/journaldescription.cws_home/405913/description#description | |||
-MicroArray for Heavy Metal Ions: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFC-4X2DCXH-3&_user=501045&_coverDate=12%2F15%2F2009&_alid=1099894232&_rdoc=1&_fmt=high&_orig=search&_cdi=5223&_st=13&_docanchor=&_ct=288&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=a209a6a8e7caf90ef3f7009bfee4705b | |||
Latest revision as of 12:11, 1 December 2009
To Do List
GO HERE:[1]
An Arsenic Biosensor - University of Edinburgh iGEM 2006 team http://parts.mit.edu/igem07/index.php/Project_Description
E.Chromi http://www.echromi.com/
Project Overview
Genetically engineering microorganism-based biosensor to detect heavy metals in water.
- Our goal is to develop a simple, inexpensive field test that can warn people or environmental authorities if dangerous levels of toxic metals are present in the environment, to which they might be exposed. The test could provide vital in helping to tackle one of the world's greatest disasters – the poisoning of tens of millions of people in Bangladesh and West Bengal, India, through naturally–occurring arsenic in their household well water. rather than through long and expensive laboratory testing
Why is this important? : http://www.uq.edu.au/news/?article=12818, http://www.associatedcontent.com/article/366604/researches_develop_new_test_for_contaminated.html
Background Information
-Past heavy metal biosensors
- Heavy Metal BioSensor-BIOMET: http://wwwa.vito.be/english/environment/environmentaltech2d.htm. Currently have E.Coli strain for detecting zinc anc cadmium, or lead or Cr ^+ or nickel or mercury.
- Site some of the papers you listed
-Other technologies for detecting heavy metals (accurate but costly) (by decreasing cost) http://www.who.int/water_sanitation_health/dwq/GDW8rev1and2.pdf: look at p16-18
- Volumetric method: Our low cost 300 series Karl Fischer titrators are only $4,190 and our low cost potentiometric titrator, the COM-300A is priced at only $5,590 and titrators are in stock for immediate delivery. 110pm-100% off website.
- Electrode method-The measured potential is proportional to the logarithm of the ion
concentration.- ammiona> 10^-7M - 1M, cadmium-> 10^-1M - 10^-7M
- Ion chromatography- is a process that allows the separation of ions and polar molecules based on their charge.-
- High-performance liquid chromatography (HPLC)
- Flame atomic absorption spectrometry (FAAS)
- Electrothermal atomic absorption spectrometry (EAAS)
- Inductively coupled plasma (ICP)/atomic emission spectrometry (AES)
- ICP/mass spectrometry (MS)
-Field Test detection methods -inaccuarate but cheap
- HPLC
- Gas chromatography (GC)
- GC/MS
- Headspace GC/MS
- Purge-and-trap GC
- Purge-and-trap GC/MS
-Guidelines for Concentrations of Chemicals. (This will be our minimum detection concentration needed)
http://www.who.int/water_sanitation_health/dwq/GDW8rev1and2.pdf (p48-63)
- BAD this about this is that there are so many common chemicals in the environment. Is it useful to look for just metal ions? How common is it that metal ions are the cause for water contamination. However, if we are to find genes regulated by water contaminants, we will only find ones that are regulated by naturally occuring chemicals (metal ions).
-Benefits of this method
-Water Standards:
http://www.who.int/water_sanitation_health/dwq/guidelines/en/index.html
Research Statement and Goals
Develop an E. coli system with specific photometric metal detection systems. The system response to concentrations of metal in water would be quantifiable fluorescence at different wavelengths for different metals. The system is intended to combine sensitivity with specificity and also considers bioavailability.
Specific Aims
Specific Aims:
1- Find robust E.Coli with low internal pH to with stand conditions for onsite analysis, and have high binding of metal to promoter for high levels of txn.
2- Find promoters pX, pY, pZ regulated by direct binding of metals mX, mY, mZ, respectively.
3- Fuse each promoter with (G/B/Y)Fluorescent Protein reporter gene, put fusion gene into plasmids then transform into E.Coli. Call this system 'original'. Each metal binding to its respective promoter would give peak fluorescence at a particular lambda. Call the respective wavelengths lamX, lamY, lamZ.
4- To enhance specificity and sensitivity of the system for each metal, we do the following for each promoter:
- Create library of promoter mutations at metal binding site.
- SPR: immobilize mutant promoters and select for tighter binding and specificity of respective metal to find 4 in vitro candidate mutants
- Create vector with candidate mutant promoter fused to its particular fluorescent protein reporter gene.
5- Insert one candidate mutant for each promoter, in different plasmids, into an in vivo system and compare with 'original'. Go through all combinations of promoters mutant candidates (4*4*4) and pick best mutant combination. To compare, we specifically produce graphs w/ (intensity to number of cells ratio) vs. external concentration of mX or mY or mZ for each of lamX, lamY, lamZ.
6- Next, we reproduce graph above with a mixture of metals as opposed to a single metal. Ideally, graph 5 ~= graph 6, for each lambda and therefore our system is very specific.
Backup Plan: (Fill in)
Project Methodology
Predicted Outcomes
Resources Needed
Deleted Info: -Journal Devoted to created biosensors: http://www.elsevier.com/wps/find/journaldescription.cws_home/405913/description#description -MicroArray for Heavy Metal Ions: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFC-4X2DCXH-3&_user=501045&_coverDate=12%2F15%2F2009&_alid=1099894232&_rdoc=1&_fmt=high&_orig=search&_cdi=5223&_st=13&_docanchor=&_ct=288&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=a209a6a8e7caf90ef3f7009bfee4705b
