IGEM:IMPERIAL/2008/New/Chassis 2

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{| cellpadding="5" style="background:#66aadd; border: 4px solid #66aadd; color:black" align="center"
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|style="background:#66aadd" width=50%|<font size=4px><font color=white><center>'''Benefits'''</center>
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|style="background:#66aadd" width=50%|<font size=4px><font color=white><center>'''Challenges'''</center>
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!width="200"|
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<font size=4px><font color=white><center>'''Benefits'''</center>
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!width="200"|<font size=4px><font color=white><center>'''Challenges'''</center>
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|style="background:#99BBFF" width=50%|<font size=3px><font color=white><center>'''Protein Expression'''</center>
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|width="15" style="background:#99BBFF"|
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|style="background:#99BBFF" width=50%|
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|width="200" style="background:#99BBFF"|<font size=3px><font color=white><center>'''Protein Expression'''</center>
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|style="background:#FFFFFF"| '''Single Membrane''' - ''B.subtilis'' is a gram-positive bacterium and contains only a single membrane. This makes ''B.subtilis'' an ideal organism for secretion of proteins (in our case, peptides for the biomaterials) in high amounts.
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|style="background:#FFFFFF"| [[Image:Secretion.PNG| 150px]]
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|style="background:#FFFFFF"| '''Peptidase activity''' - ''B.subtilis'' possesses a stringent protein folding checking system that may reject our biomaterials. Proteins expressed in ''B.subtilis'' may not fold correctly, causing a build up inside the cell. ''B.subtilis'' responds to this problem by expressing exopeptidases, which digest the protein. There is a risk that our biomaterial may be cleaved up before it can be secreted.
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|style="background:#FFFFFF"| '''Single Membrane''' - ''B.subtilis'' is a gram-positive bacterium and contains only a single membrane. This makes ''B.subtilis'' an ideal chassis for secretion of biomaterials.
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|style="background:#FFFFFF"| '''Peptidase activity''' - ''B.subtilis'' express exopeptidases and so there is a risk that our biomaterial may be cleaved up before it can be secreted.
|-
|-
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|style="background:#99BBFF" width=50%|<font size=3px><font color=white><center>'''Foundational Technology'''</center>
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|style="background:#99BBFF"|
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|style="background:#99BBFF" width=50%|
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|style="background:#99BBFF"|<font size=3px><font color=white><center>'''Foundational Technology'''</center>
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|style="background:#99BBFF"|
|-
|-
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| rowspan=2 style="background:#FFFFFF"| '''Availability of Potential Parts''' - ''B.subtilis'' is a highly studied organism. Its genome has been fully sequenced and many of these genes have been functionally annotated. As a result, ''B.subtilis'' provides many useful potential parts that we could take advantage of. For example within our project, potential parts for control of motility, light sensing and secretion pathways.
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|rowspan=2 style="background:#FFFFFF" |[[Image:Gene.PNG| 150px]]
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| rowspan=2 style="background:#FFFFFF"| '''Availability of Potential Parts''' - ''B.subtilis'' is a highly studied organism, with a fully sequenced genome. As a result, ''B.subtilis'' provides many useful potential parts.
|style="background:#FFFFFF"| '''Biobricking''' - Although there is a huge number of potential parts, these still have to be manipulated to conform to existing Biobrick standards.
|style="background:#FFFFFF"| '''Biobricking''' - Although there is a huge number of potential parts, these still have to be manipulated to conform to existing Biobrick standards.
|-
|-
|style="background:#FFFFFF"| '''Starting from scratch''' - Although previous iGEM teams have looked at ''B.subtilis'' as a potential chassis, there are very few working ''B.subtilis'' parts available in the Registry. As a result, we will have to design a variety of promoter, ribosome binding sites and protein coding regions.
|style="background:#FFFFFF"| '''Starting from scratch''' - Although previous iGEM teams have looked at ''B.subtilis'' as a potential chassis, there are very few working ''B.subtilis'' parts available in the Registry. As a result, we will have to design a variety of promoter, ribosome binding sites and protein coding regions.
|-
|-
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|style="background:#99BBFF" width=50%|<font size=3px><font color=white><center>'''Biobrick Assembly</center>
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|style="background:#99BBFF" |
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|style="background:#99BBFF" width=50%|
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|style="background:#99BBFF" |<font size=3px><font color=white><center>'''Biobrick Assembly</center>
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|style="background:#99BBFF"|
|-
|-
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|style="background:#FFFFFF"| '''Natural Competency and Integration''' - ''B. subtilis'' has been noted for its ease and efficieny of transformation. Plasmids can be naturally taken up by ''B. subtilis'' cells. In addition to the use of vectors to carry exogenous DNA, we can integrate directly into the ''B.subtilis'' chromosome. This has the advantage of a greater control of copy number and potential greater stability of genetic devices.
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|style="background:#FFFFFF"|[[Image:Integration.PNG| 150px]]
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|style="background:#FFFFFF"| '''Natural Competency and Integration''' - ''B. subtilis'' has been noted for its ease and efficieny of transformation. In addition, inegration of exogenous DNA into the chromosome has been wel studied and provides an alternative to using traditional plasmids.    
|style="background:#FFFFFF"| '''Vector Degradation''' - ''B.subtilis'' does not use all the same vectors as ''E.coli''. One reason for this is that ''B.subtilis'' often recognises vectors grown in ''E.coli'' and digests them. This will (judging by the approach of previous iGEM teams) include the biobrick itself.
|style="background:#FFFFFF"| '''Vector Degradation''' - ''B.subtilis'' does not use all the same vectors as ''E.coli''. One reason for this is that ''B.subtilis'' often recognises vectors grown in ''E.coli'' and digests them. This will (judging by the approach of previous iGEM teams) include the biobrick itself.
|-
|-
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|style="background:#99BBFF" width=50%|<font size=3px><font color=white><center>'''Chassis Properties'''</center>
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|style="background:#99BBFF"|
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|style="background:#99BBFF" width=50%|
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|style="background:#99BBFF"|<font size=3px><font color=white><center>'''Chassis Properties'''</center>
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|style="background:#99BBFF"|
|-
|-
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| rowspan=3 style="background:#FFFFFF"| [[Image:Chassis.PNG| 150px]]
|style="background:#FFFFFF"| '''Non-pathogenicity''' - ''B. subtilis'' is a non-pathogenic organism that is commonly found in soil. As a result, ''B. subtilis'' has a biological harzardous level of 1 and offers a useful non-pathogenic chassis for synthetic biologists.
|style="background:#FFFFFF"| '''Non-pathogenicity''' - ''B. subtilis'' is a non-pathogenic organism that is commonly found in soil. As a result, ''B. subtilis'' has a biological harzardous level of 1 and offers a useful non-pathogenic chassis for synthetic biologists.
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| rowspan=3 style="background:#EEEEEE" width=50%|
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| rowspan=3 style="background:#FFFFFF"|
|-
|-
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|style="background:#FFFFFF"|'''High Motility''' - ''B.subtilis'' is often referred to as a highly motile organsim. Quoted velocity range from 60 - 100 μm per second. In comparison to ''E.coli'' which has an average velocity of .... ''B.subtilis'' is much more motile.  
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|style="background:#FFFFFF"|'''High Motility''' - ''B.subtilis'' is often referred to as a highly motile organsim in comparison to other bacterium.
|-
|-
|style="background:#FFFFFF"|'''Sporulation: Transport''' - Under stress conditions, ''B.subtilis'' will form spores. These spores are highly resistant versions of single cells, able to withstand extreme temperatures and pH. These spores are capable of growing into new cells once favourable growing conditions are restored. Due to the resistance of spores, there is a great potential for manipulating them for transporting ''B.subtilis'' devices and constructs.
|style="background:#FFFFFF"|'''Sporulation: Transport''' - Under stress conditions, ''B.subtilis'' will form spores. These spores are highly resistant versions of single cells, able to withstand extreme temperatures and pH. These spores are capable of growing into new cells once favourable growing conditions are restored. Due to the resistance of spores, there is a great potential for manipulating them for transporting ''B.subtilis'' devices and constructs.

Revision as of 06:13, 11 September 2008




Benefits vs Challenges

http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Project

Authors: Chris, James

Editors: Wiki team

James - Here is a table of potential advantages and disadvatages of using B.subtilis for our project and some more general chassis ad/disad. We may wish to think about chassis ad/dis seperatly, for example, in the registry the we will want to put the chassis info up!


Benefits
Challenges
Protein Expression
Single Membrane - B.subtilis is a gram-positive bacterium and contains only a single membrane. This makes B.subtilis an ideal chassis for secretion of biomaterials. Peptidase activity - B.subtilis express exopeptidases and so there is a risk that our biomaterial may be cleaved up before it can be secreted.
Foundational Technology
Availability of Potential Parts - B.subtilis is a highly studied organism, with a fully sequenced genome. As a result, B.subtilis provides many useful potential parts. Biobricking - Although there is a huge number of potential parts, these still have to be manipulated to conform to existing Biobrick standards.
Starting from scratch - Although previous iGEM teams have looked at B.subtilis as a potential chassis, there are very few working B.subtilis parts available in the Registry. As a result, we will have to design a variety of promoter, ribosome binding sites and protein coding regions.
Biobrick Assembly
Natural Competency and Integration - B. subtilis has been noted for its ease and efficieny of transformation. In addition, inegration of exogenous DNA into the chromosome has been wel studied and provides an alternative to using traditional plasmids. Vector Degradation - B.subtilis does not use all the same vectors as E.coli. One reason for this is that B.subtilis often recognises vectors grown in E.coli and digests them. This will (judging by the approach of previous iGEM teams) include the biobrick itself.
Chassis Properties
Non-pathogenicity - B. subtilis is a non-pathogenic organism that is commonly found in soil. As a result, B. subtilis has a biological harzardous level of 1 and offers a useful non-pathogenic chassis for synthetic biologists.
High Motility - B.subtilis is often referred to as a highly motile organsim in comparison to other bacterium.
Sporulation: Transport - Under stress conditions, B.subtilis will form spores. These spores are highly resistant versions of single cells, able to withstand extreme temperatures and pH. These spores are capable of growing into new cells once favourable growing conditions are restored. Due to the resistance of spores, there is a great potential for manipulating them for transporting B.subtilis devices and constructs.



Benefits
Challenges
Protein Expression
Single Membrane - B.subtilis is a gram-positive bacterium and contains only a single membrane. This makes B.subtilis an ideal organism for secretion of proteins (in our case, peptides for the biomaterials) in high amounts. Peptidase activity - B.subtilis possesses a stringent protein folding checking system that may reject our biomaterials. Proteins expressed in B.subtilis may not fold correctly, causing a build up inside the cell. B.subtilis responds to this problem by expressing exopeptidases, which digest the protein. There is a risk that our biomaterial may be cleaved up before it can be secreted.
Foundational Technology
Availability of Potential Parts - B.subtilis is a highly studied organism. Its genome has been fully sequenced and many of these genes have been functionally annotated. As a result, B.subtilis provides many useful potential parts that we could take advantage of. For example within our project, potential parts for control of motility, light sensing and secretion pathways. Biobricking - Although there is a huge number of potential parts, these still have to be manipulated to conform to existing Biobrick standards.
Starting from scratch - Although previous iGEM teams have looked at B.subtilis as a potential chassis, there are very few working B.subtilis parts available in the Registry. As a result, we will have to design a variety of promoter, ribosome binding sites and protein coding regions.
Biobrick Assembly
Natural Competency and Integration - B. subtilis has been noted for its ease and efficieny of transformation. Plasmids can be naturally taken up by B. subtilis cells. In addition to the use of vectors to carry exogenous DNA, we can integrate directly into the B.subtilis chromosome. This has the advantage of a greater control of copy number and potential greater stability of genetic devices. Vector Degradation - B.subtilis does not use all the same vectors as E.coli. One reason for this is that B.subtilis often recognises vectors grown in E.coli and digests them. This will (judging by the approach of previous iGEM teams) include the biobrick itself.
Chassis Properties
Non-pathogenicity - B. subtilis is a non-pathogenic organism that is commonly found in soil. As a result, B. subtilis has a biological harzardous level of 1 and offers a useful non-pathogenic chassis for synthetic biologists.
High Motility - B.subtilis is often referred to as a highly motile organsim. Quoted velocity range from 60 - 100 μm per second. In comparison to E.coli which has an average velocity of .... B.subtilis is much more motile.
Sporulation: Transport - Under stress conditions, B.subtilis will form spores. These spores are highly resistant versions of single cells, able to withstand extreme temperatures and pH. These spores are capable of growing into new cells once favourable growing conditions are restored. Due to the resistance of spores, there is a great potential for manipulating them for transporting B.subtilis devices and constructs.


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