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<br><br>
= Chassis 2 - Other pros, cons and information... =
&nbsp; <font size=6px color=#E5EBFF><b>Benefits vs Challenges</b></font>
 
<br><br>
http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Project
{| cellpadding="5" style="background:#66aadd; border: 4px solid #66aadd; color:black" align="center" width=95%
 
!width="150px" |
Authors: Chris, James
!width="50%"|
 
<font size=4px color=white><center>'''Benefits'''</center></font>
Editors: Wiki team
!width="50%"|<font size=4px color=white><center>'''Challenges'''</center></font>
 
'''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!
 
 
{| width="100%" cellpadding="5" style="background:#66aadd; border: 4px solid #66aadd; color:black" align="center"
|style="background:#66aadd" width=50%|<font size=5px><font color=white><center>'''Benefits'''</center>
|style="background:#66aadd" width=50%|<font size=5px><font color=white><center>'''Challenges'''</center>
|-
|-
|style="background:#99BBFF" width=50%|<font size=3px><font color=white><center>'''Protein Expression'''</center>
|style="background:#99BBFF"|
|style="background:#99BBFF" width=50%|
|style="background:#99BBFF" colspan="2"|<font size=3px color=white><center>'''Protein Expression'''</center></font>
|-
|-
|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"| [[Image:Secretion.PNG| 150px]]
|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.
|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.
|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.
|-
|-
|style="background:#99BBFF" width=50%|<font size=3px><font color=white><center>'''Foundational Technology'''</center>
|style="background:#99BBFF"|
|style="background:#99BBFF" width=50%|
|style="background:#99BBFF" colspan="2"|<font size=3px color=white><center>'''Foundational Technology'''</center></font>
|-
|-
|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.
|rowspan=2 style="background:#FFFFFF" |[[Image:Gene.PNG| 150px]]
|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.
| 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:#99BBFF" width=50%|<font size=3px><font color=white><center>'''Biobrick Assembly</center>
|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:#99BBFF" width=50%|
|-
|-
|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.
|style="background:#99BBFF"|
|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:#99BBFF" colspan="2"|<font size=3px color=white><center>'''BioBrick Assembly'''</center></font>
|-
|-
|style="background:#FFFFFF"|
|style="background:#FFFFFF"|[[Image:Integration.PNG| 150px]]
|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
|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.   
|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.
|-
|-
|style="background:#99BBFF" width=50%|<font size=3px><font color=white><center>'''Chassis Properties'''</center>
|style="background:#99BBFF"|
|style="background:#99BBFF" width=50%|
|style="background:#99BBFF" colspan="2"|<font size=3px color=white><center>'''Chassis Properties'''</center></font>
|-
|-
|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.
| rowspan=3 style="background:#FFFFFF"| [[Image:Chassis.PNG| 150px]]
|style="background:#FFFFFF" width=50%|
|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.
| rowspan=3 style="background:#FFFFFF"|
|-
|-
|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"|
|-
|-
|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.
|style="background:#FFFFFF" width=50%|
|}
|}
<br>
<br clear="all"><hr>
{{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 >>>''']]}}
{{Imperial/EndPage|Chassis_1|Wet_Lab}}

Latest revision as of 07:14, 27 September 2008

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       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Chassis_1">Why B. subtilis?</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Chassis_2">B. subtilis: Benefits vs Challenges</a>
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</td><td align="center" width="17%" valign="bottom"><ul id="sddm"><a href="http://2008.igem.org/Team:Imperial_College/Notebook"> Notebook </a></ul> </td><td align="center" width="17%" valign="bottom"><ul id="sddm"><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Team"> Our Team </a></ul> </td></tr></table></html>

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  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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