http://2010.igem.org/wiki/index.php?title=Special:Contributions/Tmiller&feed=atom&limit=50&target=Tmiller&year=&month=2010.igem.org - User contributions [en]2024-03-28T20:51:24ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Team:Purdue/Oxygen_Sequestration_to_Inhibit_Photorespiration_in_C3_PlantsTeam:Purdue/Oxygen Sequestration to Inhibit Photorespiration in C3 Plants2010-06-25T16:37:13Z<p>Tmiller: Undo revision 12556 by Tmiller (Talk)</p>
<hr />
<div>[https://2010.igem.org/Team:Purdue HOMEPAGE]<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/Oxygen_Sequestration_to_Inhibit_Photorespiration_in_C3_PlantsTeam:Purdue/Oxygen Sequestration to Inhibit Photorespiration in C3 Plants2010-06-25T16:35:40Z<p>Tmiller: Removing all content from page</p>
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==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
====Arabidopsis Metabolism====<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Collaboration|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
====External Links====<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
<br />
[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}</div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T16:30:21Z<p>Tmiller: </p>
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==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
====Arabidopsis Metabolism====<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
====External Links====<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
<br />
[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}</div>Tmillerhttp://2010.igem.org/Team:PurdueTeam:Purdue2010-06-25T16:29:01Z<p>Tmiller: </p>
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'''Purdue Wiki users: Be certain to include "Team:Purdue/" before any pages you create to avoiding causing conflicts with other teams' pages. If you are confused, contact me, or temporarily store your content on your user page. I've created a template that should ease linking to internal pages.''' --[[User:Jmason|Jmason]]<br />
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==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
====Arabidopsis Metabolism====<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
====External Links====<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
<br />
[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T16:27:24Z<p>Tmiller: /* The solution */</p>
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==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
====Arabidopsis Metabolism====<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:PurdueTeam:Purdue2010-06-25T16:26:00Z<p>Tmiller: </p>
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==Purdue University iGEM 2010==<br />
<br />
'''Purdue Wiki users: Be certain to include "Team:Purdue/" before any pages you create to avoiding causing conflicts with other teams' pages. If you are confused, contact me, or temporarily store your content on your user page. I've created a template that should ease linking to internal pages.''' --[[User:Jmason|Jmason]]<br />
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UPDATE: Any information regarding our project has been moved to the "The Project" Link. <br />
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{{Team:Purdue/link|Metabolism & Cancer}}<br />
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{{Team:Purdue/link|A crash-course in Wiki editing}}<br />
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<br />
===Arabidopsis Metabolism===<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===External Links===<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
<br />
[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
<br />
{|align="justify"</div>Tmillerhttp://2010.igem.org/Team:Purdue/CollaborationTeam:Purdue/Collaboration2010-06-25T16:25:30Z<p>Tmiller: </p>
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==Collaboration & Faculty==<br />
<br />
Purdue Faculty<br />
<br />
[http://www.ag.purdue.edu/biochem/Pages/fgimble.aspx Frederick S. Gimble, Associate Professor of Biochemistry]<br />
<br />
[http://www.ag.purdue.edu/hla/Pages/drhodes.aspx David Rhodes, Professor Horticulture (Horticulture/BioChem)]<br />
<br />
[https://engineering.purdue.edu/ChE/People/ptProfile?id=11220 John Morgan, Associate Prof. ChemE (Plant Metabolism)]<br />
<br />
[https://engineering.purdue.edu/ABE/People/ptProfile?resource_id=7374 Martin Okos, Prof. ABE/Biochem]<br />
<br />
[http://www.ag.purdue.edu/biochem/Pages/chapple.aspx Clint CS Chapple, Head/Distinguished Prof. Biochem]<br />
<br />
[https://engineering.purdue.edu/BME/People/viewPersonById?resource_id=7380 Marshall Porterfield, Prof. Biomed Eng, ABE, Horticulture]<br />
<br />
<br />
DOW <br />
<br />
Dr. Evans (need info)<br />
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Algae Resources<br />
<br />
[http://www.phycotransgenics.com/standard/index.html Richard E. Wagner: Phycotransgenics]<br />
Dr. Wagner is a researcher in Bloomington, IN and could possibly be a link with the IU team.</div>Tmillerhttp://2010.igem.org/Team:Purdue/CollaborationTeam:Purdue/Collaboration2010-06-25T16:25:15Z<p>Tmiller: </p>
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<br />
==Collaboration==<br />
<br />
Purdue Faculty<br />
<br />
[http://www.ag.purdue.edu/biochem/Pages/fgimble.aspx Frederick S. Gimble, Associate Professor of Biochemistry]<br />
<br />
[http://www.ag.purdue.edu/hla/Pages/drhodes.aspx David Rhodes, Professor Horticulture (Horticulture/BioChem)]<br />
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[https://engineering.purdue.edu/ChE/People/ptProfile?id=11220 John Morgan, Associate Prof. ChemE (Plant Metabolism)]<br />
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[https://engineering.purdue.edu/ABE/People/ptProfile?resource_id=7374 Martin Okos, Prof. ABE/Biochem]<br />
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[http://www.ag.purdue.edu/biochem/Pages/chapple.aspx Clint CS Chapple, Head/Distinguished Prof. Biochem]<br />
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[https://engineering.purdue.edu/BME/People/viewPersonById?resource_id=7380 Marshall Porterfield, Prof. Biomed Eng, ABE, Horticulture]<br />
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DOW <br />
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Dr. Evans (need info)<br />
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Algae Resources<br />
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[http://www.phycotransgenics.com/standard/index.html Richard E. Wagner: Phycotransgenics]<br />
Dr. Wagner is a researcher in Bloomington, IN and could possibly be a link with the IU team.</div>Tmillerhttp://2010.igem.org/Team:Purdue/SafetyTeam:Purdue/Safety2010-06-25T16:24:01Z<p>Tmiller: </p>
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==Safety Training==<br />
# '''Safety Training Opportunity''' offered by BME: Tuesday, '''May 25, 2010'''. MJIS 2001 at 10:30 AM. will include basic lab safety and bloodborne pathogen training<br />
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==Safety==<br />
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Please use this page to answer the safety questions posed on the [[Safety | safety page]].</div>Tmillerhttp://2010.igem.org/Team:Purdue/NotebookTeam:Purdue/Notebook2010-06-25T16:23:40Z<p>Tmiller: </p>
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==Notebook==<br />
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===6/16/10===<br />
Prepared nine pots of wildtype (Col-0) ''A. thaliana'' and moved to cold storage for stratification. Pots intended for use in ''Agrobacterium'' flower-dip. Seeds were sewn in soilless media and the pot was covered with a wide meshing to retain the soil.<br />
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===6/21/10===<br />
Transfered pots from cold storage to greenhouse. Prepared 0.5 MS agar media and sterilized seeds for sterile growth, to be sewn on 6/23. Seeds left in dilute agar solution in fridge to stratify.<br />
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===6/23/10===<br />
Agar plates poured. Seeds to be sewn on 6/24 to give time for the media to solidify.<br />
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===6/24/10===<br />
Seeds sown onto agar. Five large culture plates and two small plates were then transfered into horticulture growth chamber. Seeds in soil media forecasted to germinate by 6/26.<br />
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===6/25/10===<br />
A. thaliana expirement mapping: Testing low oxygen response in WT and Transgenic using atmospheric chamber in Purdue Agronomy department. Using sensors to measure ethanol, oxygen, auxin response in control and in hypoxic conditions.<br />
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===6/25/10===<br />
Communicating with IU iGEM team concerning synergies including arabidopsis transformation workshop.<br />
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Communicating with Naperville, Ill high school student as part of community outreach experience.<br />
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Planning Purdue University campus poster session to involve public in forum discussion on genetic engineering.</div>Tmillerhttp://2010.igem.org/Team:Purdue/ModelingTeam:Purdue/Modeling2010-06-25T16:23:19Z<p>Tmiller: </p>
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===Parts===<br />
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New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
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<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:22:44Z<p>Tmiller: </p>
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UNDER CONSTRUCTION.... <br />
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{|align="justify"<br />
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===Parts===<br />
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New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
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<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T16:22:04Z<p>Tmiller: </p>
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==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
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===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
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===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
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===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
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====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
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====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
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===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
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[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
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[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
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====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
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[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
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[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
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[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
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Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
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Purdue-Home:<br />
[[Team:Purdue]]<br />
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===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
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Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
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Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
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Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/TeamTeam:Purdue/Team2010-06-25T16:21:36Z<p>Tmiller: </p>
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|-<br />
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|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
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== '''Who we are''' ==<br />
{|border = "0"<br />
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'''Advisors:'''<br />
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*''' Advisor 1''': Mentor for all<br />
*'''Advisor 2''': Our favorite<br />
*'''Grad Student 1''': Our leader <br />
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'''Undergrads:'''<br />
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*'''Student 1''': Sleepyhead <br />
*'''Student 2''': Math nerd<br />
*'''Student 3''': Michael, Is going to save the world<br />
*'''Student 4''': Loves iGEM<br />
*'''Student 5''': A normal student... or(r) am I?<br />
*'''Student 6''': Table football fan<br />
*'''Student 7''':<br />
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|<br />
<gallery><br />
Image:Purdue_Team_member_1.png|Team member 1<br />
Image:Purdue_Team_member_2.png|Team member 2<br />
Image:Purdue_Team_member_3.png|Team member 3<br />
Image:Purdue_Team_member_4.png|Team member 4<br />
Image:Purdue_Team_member_5.png|Team member 5<br />
Image:Purdue_Team_member_6.png|Team member 6<br />
Image:Purdue_Team_member_7.png|Team member 7<br />
Image:JennaRickusphoto2.jpg|Super Cool Advisor, Prof R<br />
</gallery><br />
|}<br />
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== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
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== '''Where we're from''' ==</div>Tmillerhttp://2010.igem.org/Team:PurdueTeam:Purdue2010-06-25T16:21:11Z<p>Tmiller: </p>
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<div>[[Image:Purdue Banner.png]]<br />
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<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
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<span style="background:#98FB98"><br />
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==Purdue University iGEM 2010==<br />
<br />
'''Purdue Wiki users: Be certain to include "Team:Purdue/" before any pages you create to avoiding causing conflicts with other teams' pages. If you are confused, contact me, or temporarily store your content on your user page. I've created a template that should ease linking to internal pages.''' --[[User:Jmason|Jmason]]<br />
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UPDATE: Any information regarding our project has been moved to the "The Project" Link. <br />
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{{Team:Purdue/link|Metabolism & Cancer}}<br />
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{{Team:Purdue/link|Potential Partners and Collaborators}}<br />
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{{Team:Purdue/link|A crash-course in Wiki editing}}<br />
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===Arabidopsis Metabolism===<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
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[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
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===External Links===<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
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[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
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{|align="justify"</div>Tmillerhttp://2010.igem.org/Team:Purdue/CollaborationTeam:Purdue/Collaboration2010-06-25T16:20:48Z<p>Tmiller: </p>
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<div>[[Image:Purdue Banner.png]]<br />
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<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|Collaboration]]</span></div>Tmillerhttp://2010.igem.org/Team:Purdue/CollaborationTeam:Purdue/Collaboration2010-06-25T16:20:37Z<p>Tmiller: </p>
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<div>[[Image:Purdue Banner.png]]<br />
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<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|Collaboration]]</span></div>Tmillerhttp://2010.igem.org/Team:Purdue/CollaborationTeam:Purdue/Collaboration2010-06-25T16:20:06Z<p>Tmiller: New page: Image:Purdue Banner.png <span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:gre...</p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
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<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|Collaboration]]</span></div>Tmillerhttp://2010.igem.org/Team:Purdue/SafetyTeam:Purdue/Safety2010-06-25T16:19:27Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
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<br />
<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|Safety]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
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==Safety Training==<br />
# '''Safety Training Opportunity''' offered by BME: Tuesday, '''May 25, 2010'''. MJIS 2001 at 10:30 AM. will include basic lab safety and bloodborne pathogen training<br />
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==Safety==<br />
<br />
Please use this page to answer the safety questions posed on the [[Safety | safety page]].</div>Tmillerhttp://2010.igem.org/Team:Purdue/NotebookTeam:Purdue/Notebook2010-06-25T16:18:15Z<p>Tmiller: </p>
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<div>[[Image:Purdue Banner.png]]<br />
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<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style= "color:green;">Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|Notebook]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
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==Notebook==<br />
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===6/16/10===<br />
Prepared nine pots of wildtype (Col-0) ''A. thaliana'' and moved to cold storage for stratification. Pots intended for use in ''Agrobacterium'' flower-dip. Seeds were sewn in soilless media and the pot was covered with a wide meshing to retain the soil.<br />
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===6/21/10===<br />
Transfered pots from cold storage to greenhouse. Prepared 0.5 MS agar media and sterilized seeds for sterile growth, to be sewn on 6/23. Seeds left in dilute agar solution in fridge to stratify.<br />
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===6/23/10===<br />
Agar plates poured. Seeds to be sewn on 6/24 to give time for the media to solidify.<br />
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===6/24/10===<br />
Seeds sown onto agar. Five large culture plates and two small plates were then transfered into horticulture growth chamber. Seeds in soil media forecasted to germinate by 6/26.<br />
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===6/25/10===<br />
A. thaliana expirement mapping: Testing low oxygen response in WT and Transgenic using atmospheric chamber in Purdue Agronomy department. Using sensors to measure ethanol, oxygen, auxin response in control and in hypoxic conditions.<br />
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===6/25/10===<br />
Communicating with IU iGEM team concerning synergies including arabidopsis transformation workshop.<br />
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Communicating with Naperville, Ill high school student as part of community outreach experience.<br />
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Planning Purdue University campus poster session to involve public in forum discussion on genetic engineering.</div>Tmillerhttp://2010.igem.org/Team:Purdue/ModelingTeam:Purdue/Modeling2010-06-25T16:17:18Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
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<br />
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<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span>Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:16:11Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
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<br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
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<br />
<br />
UNDER CONSTRUCTION.... <br />
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<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
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<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:15:29Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
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<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:15:04Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
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<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:9px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:15px; font-family:georgia; border:2px solid black; padding: 6px; margin: 3px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:14:36Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:14px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:9px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:14px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:14px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:14px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:14px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:14px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:14px; font-family:georgia; border:2px solid black; padding: 6px; margin: 3px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:13:36Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:9px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted<br> to the Registry</br></span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 3px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:12:52Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:9px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 3px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:11:47Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 3px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:11:09Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:10:49Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:10:13Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left: 13px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span>Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/PartsTeam:Purdue/Parts2010-06-25T16:09:37Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
<br />
<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span>Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
===Parts===<br />
<br />
New for iGEM 2010 is the ''groupparts'' tag. This tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
<groupparts>iGEM010 Purdue</groupparts></div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T16:07:57Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
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<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span>The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
<br />
<br />
==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T16:07:29Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
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<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green";>Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span>The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
<br />
<br />
<br />
==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/TeamTeam:Purdue/Team2010-06-25T16:06:07Z<p>Tmiller: </p>
<hr />
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<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|<span style="color:green;">Home</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span>The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
<br />
We are the team from Purdue. We have many cool project ideas. Yay!<br />
<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
<br />
'''Advisors:'''<br />
<br />
*''' Advisor 1''': Mentor for all<br />
*'''Advisor 2''': Our favorite<br />
*'''Grad Student 1''': Our leader <br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student 1''': Sleepyhead <br />
*'''Student 2''': Math nerd<br />
*'''Student 3''': Michael, Is going to save the world<br />
*'''Student 4''': Loves iGEM<br />
*'''Student 5''': A normal student... or(r) am I?<br />
*'''Student 6''': Table football fan<br />
*'''Student 7''':<br />
<br />
<br />
|<br />
<gallery><br />
Image:Purdue_Team_member_1.png|Team member 1<br />
Image:Purdue_Team_member_2.png|Team member 2<br />
Image:Purdue_Team_member_3.png|Team member 3<br />
Image:Purdue_Team_member_4.png|Team member 4<br />
Image:Purdue_Team_member_5.png|Team member 5<br />
Image:Purdue_Team_member_6.png|Team member 6<br />
Image:Purdue_Team_member_7.png|Team member 7<br />
Image:JennaRickusphoto2.jpg|Super Cool Advisor, Prof R<br />
</gallery><br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
<br />
== '''Where we're from''' ==</div>Tmillerhttp://2010.igem.org/Team:Purdue/TeamTeam:Purdue/Team2010-06-25T16:04:33Z<p>Tmiller: </p>
<hr />
<div>[[Image:Purdue Banner.png]]<br />
<br />
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<br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px; margin-left:15px;">[[Team:Purdue|Home]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Team|<span style="color:green;">The Team</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Project|<span style="color:green;">The Project</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Parts|<span style="color:green;">Parts Submitted to the Registry</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Modeling|<span style="color:green;">Modeling</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Notebook|<span style="color:green;">Notebook</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Safety|<span style="color:green;">Safety</span>]]</span><br />
<span style="font-size:16px; font-family:georgia; border:2px solid black; padding: 6px; margin: 5px;">[[Team:Purdue/Collaboration|<span style="color:green;">Collaboration</span>]]</span><br />
<br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
<br />
We are the team from Purdue. We have many cool project ideas. Yay!<br />
<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
<br />
'''Advisors:'''<br />
<br />
*''' Advisor 1''': Mentor for all<br />
*'''Advisor 2''': Our favorite<br />
*'''Grad Student 1''': Our leader <br />
<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Student 1''': Sleepyhead <br />
*'''Student 2''': Math nerd<br />
*'''Student 3''': Michael, Is going to save the world<br />
*'''Student 4''': Loves iGEM<br />
*'''Student 5''': A normal student... or(r) am I?<br />
*'''Student 6''': Table football fan<br />
*'''Student 7''':<br />
<br />
<br />
|<br />
<gallery><br />
Image:Purdue_Team_member_1.png|Team member 1<br />
Image:Purdue_Team_member_2.png|Team member 2<br />
Image:Purdue_Team_member_3.png|Team member 3<br />
Image:Purdue_Team_member_4.png|Team member 4<br />
Image:Purdue_Team_member_5.png|Team member 5<br />
Image:Purdue_Team_member_6.png|Team member 6<br />
Image:Purdue_Team_member_7.png|Team member 7<br />
Image:JennaRickusphoto2.jpg|Super Cool Advisor, Prof R<br />
</gallery><br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
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== '''Where we're from''' ==</div>Tmillerhttp://2010.igem.org/Team:Purdue/TeamTeam:Purdue/Team2010-06-25T16:04:08Z<p>Tmiller: </p>
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== '''Who we are''' ==<br />
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Image:Purdue_Team_member_1.png|Team member 1<br />
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Image:JennaRickusphoto2.jpg|Super Cool Advisor, Prof R<br />
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== '''What we did''' ==<br />
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(Provide proper attribution for all work)<br />
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== '''Where we're from''' ==</div>Tmillerhttp://2010.igem.org/Team:PurdueTeam:Purdue2010-06-25T16:02:13Z<p>Tmiller: </p>
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==Purdue University iGEM 2010==<br />
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'''Purdue Wiki users: Be certain to include "Team:Purdue/" before any pages you create to avoiding causing conflicts with other teams' pages. If you are confused, contact me, or temporarily store your content on your user page. I've created a template that should ease linking to internal pages.''' --[[User:Jmason|Jmason]]<br />
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{{Team:Purdue/link|Metabolism & Cancer}}<br />
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===Arabidopsis Metabolism===<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===External Links===<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
<br />
[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
<br />
{|align="justify"</div>Tmillerhttp://2010.igem.org/Team:PurdueTeam:Purdue2010-06-25T16:01:33Z<p>Tmiller: </p>
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==Purdue University iGEM 2010==<br />
<br />
'''Purdue Wiki users: Be certain to include "Team:Purdue/" before any pages you create to avoiding causing conflicts with other teams' pages. If you are confused, contact me, or temporarily store your content on your user page. I've created a template that should ease linking to internal pages.''' --[[User:Jmason|Jmason]]<br />
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UPDATE: Any information regarding our project has been moved to the "The Project" Link. <br />
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{{Team:Purdue/link|Metabolism & Cancer}}<br />
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{{Team:Purdue/link|A crash-course in Wiki editing}}<br />
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===Arabidopsis Metabolism===<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===External Links===<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
<br />
[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
<br />
{|align="justify"</div>Tmillerhttp://2010.igem.org/Team:PurdueTeam:Purdue2010-06-25T16:01:15Z<p>Tmiller: </p>
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==Purdue University iGEM 2010==<br />
<br />
'''Purdue Wiki users: Be certain to include "Team:Purdue/" before any pages you create to avoiding causing conflicts with other teams' pages. If you are confused, contact me, or temporarily store your content on your user page. I've created a template that should ease linking to internal pages.''' --[[User:Jmason|Jmason]]<br />
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UPDATE: Any information regarding our project has been moved to the "The Project" Link. <br />
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{{Team:Purdue/link|Metabolism & Cancer}}<br />
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{{Team:Purdue/link|Potential Partners and Collaborators}}<br />
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{{Team:Purdue/link|A crash-course in Wiki editing}}<br />
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===Arabidopsis Metabolism===<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===External Links===<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
<br />
[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
<br />
{|align="justify"</div>Tmillerhttp://2010.igem.org/Team:PurdueTeam:Purdue2010-06-25T15:59:31Z<p>Tmiller: </p>
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==Purdue University iGEM 2010==<br />
<br />
'''Purdue Wiki users: Be certain to include "Team:Purdue/" before any pages you create to avoiding causing conflicts with other teams' pages. If you are confused, contact me, or temporarily store your content on your user page. I've created a template that should ease linking to internal pages.''' --[[User:Jmason|Jmason]]<br />
<br />
UPDATE: Any information regarding our project has been moved to the "The Project" Link. <br />
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{{Team:Purdue/link|Metabolism & Cancer}}<br />
<br />
{{Team:Purdue/link|Potential Partners and Collaborators}}<br />
<br />
{{Team:Purdue/link|A crash-course in Wiki editing}}<br />
<br />
<br />
<br />
<br />
===Arabidopsis Metabolism===<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]<br />
<br />
[http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]<br />
<br />
===External Links===<br />
[http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]<br />
<br />
[http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]<br />
<br />
{|align="justify"</div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T15:58:02Z<p>Tmiller: </p>
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==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T15:56:47Z<p>Tmiller: </p>
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== '''Overall project''' ==<br />
<br />
Your abstract<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
=== Part 2 ===<br />
<br />
<br />
<br />
<br />
<br />
=== The Experiments ===<br />
<br />
<br />
<br />
<br />
=== Part 3 ===<br />
<br />
<br />
<br />
<br />
== Results ==<br />
<br />
<br />
<br />
==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T15:56:01Z<p>Tmiller: </p>
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<br />
== '''Overall project''' ==<br />
<br />
Your abstract<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
=== Part 2 ===<br />
<br />
<br />
<br />
<br />
<br />
=== The Experiments ===<br />
<br />
<br />
<br />
<br />
=== Part 3 ===<br />
<br />
<br />
<br />
<br />
== Results ==<br />
<br />
<br />
<br />
==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
====Oxygen-Sensitive Promoters====<br />
<br />
====In Arabidopsis====<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
<br />
====In Saccharomyces====<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
<br />
====In Bacteria====<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T15:54:26Z<p>Tmiller: /* The solution */</p>
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{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Purdue_logo.png|200px|right|frame]]<br />
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''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Purdue_team.png|right|frame|Your team picture]]<br />
|-<br />
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|align="center"|[[Team:Purdue | Team Example]]<br />
|}<br />
<br />
<br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
Your abstract<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
=== Part 2 ===<br />
<br />
<br />
<br />
<br />
<br />
=== The Experiments ===<br />
<br />
<br />
<br />
<br />
=== Part 3 ===<br />
<br />
<br />
<br />
<br />
== Results ==<br />
<br />
<br />
<br />
==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
<br />
===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
<br />
===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
<br />
===Oxygen-Sensitive Promoters===<br />
<br />
===In Arabidopsis===<br />
*Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]<br />
*Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]<br />
**Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]<br />
*Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]<br />
**Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]<br />
*The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]<br />
===In Saccharomyces===<br />
*Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]<br />
**Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]<br />
===In Bacteria===<br />
*Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]<br />
* The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]<br />
<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
<br />
[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
<br />
[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
<br />
====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
<br />
[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
<br />
[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
<br />
[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
<br />
Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
<br />
Purdue-Home:<br />
[[Team:Purdue]]<br />
<br />
===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
<br />
Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
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Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
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Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/ProjectTeam:Purdue/Project2010-06-25T15:52:16Z<p>Tmiller: </p>
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{|align="justify"<br />
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== '''Overall project''' ==<br />
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Your abstract<br />
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== Project Details==<br />
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=== Part 2 ===<br />
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=== The Experiments ===<br />
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=== Part 3 ===<br />
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== Results ==<br />
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==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==<br />
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===The problem===<br />
Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.<br />
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===The solution===<br />
Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.<br />
===Resources===<br />
====Photorespiration and Calvin cycle review====<br />
[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]<br />
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[[Team:Purdue/Potential Partners and Collaborators|Potential Partners and Collaborators]]<br />
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[[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]<br />
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====Potentially useful articles====<br />
[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation<br />
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[http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance<br />
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[http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.<br />
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[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]<br />
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Brainstorming Page:<br />
{{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}}<br />
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Purdue-Home:<br />
[[Team:Purdue]]<br />
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===Discussion===<br />
I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]<br />
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Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]<br />
<br />
Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]<br />
<html><br></html><br />
<partinfo>BBa_K258005</partinfo><br />
<br />
Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]</div>Tmillerhttp://2010.igem.org/Team:Purdue/NotebookTeam:Purdue/Notebook2010-06-25T15:50:18Z<p>Tmiller: </p>
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==Notebook==<br />
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===6/16/10===<br />
Prepared nine pots of wildtype (Col-0) ''A. thaliana'' and moved to cold storage for stratification. Pots intended for use in ''Agrobacterium'' flower-dip. Seeds were sewn in soilless media and the pot was covered with a wide meshing to retain the soil.<br />
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===6/21/10===<br />
Transfered pots from cold storage to greenhouse. Prepared 0.5 MS agar media and sterilized seeds for sterile growth, to be sewn on 6/23. Seeds left in dilute agar solution in fridge to stratify.<br />
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===6/23/10===<br />
Agar plates poured. Seeds to be sewn on 6/24 to give time for the media to solidify.<br />
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===6/24/10===<br />
Seeds sown onto agar. Five large culture plates and two small plates were then transfered into horticulture growth chamber. Seeds in soil media forecasted to germinate by 6/26.<br />
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===6/25/10===<br />
A. thaliana expirement mapping: Testing low oxygen response in WT and Transgenic using atmospheric chamber in Purdue Agronomy department. Using sensors to measure ethanol, oxygen, auxin response in control and in hypoxic conditions.<br />
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===6/25/10===<br />
Communicating with IU iGEM team concerning synergies including arabidopsis transformation workshop.<br />
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Communicating with Naperville, Ill high school student as part of community outreach experience.<br />
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Planning Purdue University campus poster session to involve public in forum discussion on genetic engineering.</div>Tmillerhttp://2010.igem.org/Team:Purdue/SafetyTeam:Purdue/Safety2010-06-23T14:50:13Z<p>Tmiller: </p>
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==Safety Training==<br />
# '''Safety Training Opportunity''' offered by BME: Tuesday, '''May 25, 2010'''. MJIS 2001 at 10:30 AM. will include basic lab safety and bloodborne pathogen training<br />
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==Safety==<br />
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Please use this page to answer the safety questions posed on the [[Safety | safety page]].</div>Tmiller