IGEM:IMPERIAL/2008/New/Chassis 2

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<br><br>
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= Chassis 2 - Other pros, cons and information... =
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&nbsp; <font size=6px color=#E5EBFF><b>Benefits vs Challenges</b></font>
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<br><br>
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http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Project
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{| cellpadding="5" style="background:#66aadd; border: 4px solid #66aadd; color:black" align="center" width=95%
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!width="150px" |
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Authors: Chris, James
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!width="50%"|
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<font size=4px color=white><center>'''Benefits'''</center></font>
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Editors: Wiki team
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!width="50%"|<font size=4px color=white><center>'''Challenges'''</center></font>
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'''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!
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{| width="100%" cellpadding="5" style="background:#66aadd; border: 4px solid #66aadd; color:black" align="center"
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|style="background:#99BBFF" width=50%|<center>'''Benefits'''</center>
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|style="background:#99BBFF" width=50% width=50%|<center>'''Challenges'''</center>
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|-
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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:#99BBFF"|
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|style="background:#FFFFFF"| '''Starting from scratch''' - Although previous iGEM teams have looked at ''B.subtilis'' as a potential chassis, there are few working ''B.subtilis'' parts. As a result we will have to design a vaerity of promoter, ribosome binding sites and protein coding regions.
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|style="background:#99BBFF" colspan="2"|<font size=3px color=white><center>'''Protein Expression'''</center></font>
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|-
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|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 functionaly 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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|style="background:#FFFFFF"| [[Image:Secretion.PNG| 150px]]
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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"| '''Biobricking''' - Even though some of the parts for our project are potentially available, we still have to manipulate them carefully such that they conform to existing Biobrick standards.
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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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|-
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|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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|style="background:#99BBFF"|
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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:#99BBFF" colspan="2"|<font size=3px color=white><center>'''Foundational Technology'''</center></font>
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|-
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|style="background:#FFFFFF"| '''Natural Competency''' - ''B. subtilis'' has been noted for its ease and efficieny of transformation. Plasmids can be naturally taken up by ''B. subtilis'' cells.
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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.
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|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:#FFFFFF"| '''BioBricking''' - Although there is a huge number of potential parts, these still have to be manipulated to conform to existing BioBrick standards.
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|-
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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"| '''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:#FFFFFF"|
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|-
|-
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|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.
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|style="background:#99BBFF"|
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|style="background:#99BBFF" colspan="2"|<font size=3px color=white><center>'''BioBrick Assembly'''</center></font>
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|}
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<br>
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{| width="100%" cellpadding="5" style="background:#66aadd; border: 4px solid #66aadd; color:black" align="center"
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|style="background:#99BBFF" width=50%|<center>'''Benefits'''</center>
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-
|style="background:#99BBFF" width=50% width=50%|<center>'''Challenges'''</center>
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|-
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|style="background:#99BBFF" width=50%|<center>'''Protein Expression'''</center>
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-
|-
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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.
+
-
|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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|-
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|style="background:#99BBFF" width=50%|<center>'''Foundational Technology'''</center>
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-
|-
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|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 functionaly 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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|style="background:#FFFFFF"| '''Biobricking''' - Even though some of the parts for our project are potentially available, we still have to manipulate them carefully such that they conform to existing Biobrick standards.
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|-
|-
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|style="background:#99BBFF" width=50%|<center>'''Chassis Properties'''</center>
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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, integration of exogenous DNA into the chromosome has been well studied and provides an alternative to using traditional plasmids.   
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|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'' as foreign and digests them. Vectors and shuttle vectors are thus not reliable carriers of genetic information.
|-
|-
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|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:#99BBFF"|
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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:#99BBFF" colspan="2"|<font size=3px color=white><center>'''Chassis Properties'''</center></font>
|-
|-
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|style="background:#FFFFFF"| '''Natural Competency''' - ''B. subtilis'' has been noted for its ease and efficieny of transformation. Plasmids can be naturally taken up by ''B. subtilis'' cells.
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| rowspan=3 style="background:#FFFFFF"| [[Image:Chassis.PNG| 150px]]
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|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"| '''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.
+
| 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.  
+
|style="background:#FFFFFF"|'''High Motility''' - ''B.subtilis'' is often referred to as a highly motile organism in comparison to other bacterium.
-
|style="background:#FFFFFF"|
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|-
|-
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|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.
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|}
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<br>
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<br clear="all"><hr>
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{{Imperial/Box1||Having decided what we're doing and how we plan to do it, the next step is to get started! To see how our lab work went please start with the [[IGEM:IMPERIAL/2008/New/Wet_Lab | '''>>> Wet Lab Hub >>>''']]}}
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{{Imperial/EndPage|Chassis_1|Wet_Lab}}

Current revision






  Benefits vs Challenges

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, integration of exogenous DNA into the chromosome has been well 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 as foreign and digests them. Vectors and shuttle vectors are thus not reliable carriers of genetic information.
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 organism 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.


Having decided what we're doing and how we plan to do it, the next step is to get started! To see how our lab work went please start with the >>> Wet Lab Hub >>>



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