Team:UNAM Genomics Mexico/Parts

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<center><h1>'''Our Parts'''</h1></center>
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<groupparts>iGEM012 UNAM_Genomics_Mexico</groupparts>
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This is a template page. READ THESE INSTRUCTIONS.
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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
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You <strong>MUST</strong> have all of the pages listed in the menu below with the names specified.  PLEASE keep all of your pages within your teams namespace. 
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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<center><h1>'''Characterization'''</h1></center>
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!align="center"|[[Team:UNAM_Genomics_Mexico|Home]]
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!align="center"|[[Team:UNAM_Genomics_Mexico/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=UNAM_Genomics_Mexico Official Team Profile]
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!align="center"|[[Team:UNAM_Genomics_Mexico/Project|Project]]
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!align="center"|[[Team:UNAM_Genomics_Mexico/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:UNAM_Genomics_Mexico/Modeling|Modeling]]
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!align="center"|[[Team:UNAM_Genomics_Mexico/Notebook|Notebook]]
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!align="center"|[[Team:UNAM_Genomics_Mexico/Safety|Safety]]
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!align="center"|[[Team:UNAM_Genomics_Mexico/Attributions|Attributions]]
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_K851004 <h1>'''Aminoglycoside antibiotic resistance Sm+ Spc+'''</h1>]
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The aminoglycoside antibiotic resistance gene (aadA +)of pHP45Ω was originally carried on a 1.7-kb PvuII-HindIII fragment from the R100.1 plasmid. Plasmid pHP45Ω was constructed in Pierre Prentki and Henry M. Krisch, as stated in NCBI with this fragment. The addA sequence can be found in, it is confirmed to be the one contained in pHP45Ω and the complete sequence of pHP45Ω plasmid can be found in the registry references.
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Hawaii 2008 iGEM team attempted before to construct a similar cassette but didn’t succeed. For iGEM UNAM Genomics México 2012 project, the Ω Cassette was used in the design of an OR logic gate using a recently described new type of communication system between ''Bacillus Subtilis'' cells called Nanotubes.
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An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" 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.
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Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for  users who wish to know more.
 
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<groupparts>iGEM012 UNAM_Genomics_Mexico</groupparts>
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Second Repetition <br>
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<td id="contentcolumnwhite" align= "center"><br />[[File:Unamgenomicsomegacassete2.png|400px]]<br /><br /><p>
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_K851002 <h1>'''pBAD/pXyl promoter'''</h1>]<br/>
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The characterization of this construction was made on an E.coli strain in a semi quantitative attempt. In that way, we expected that only araC was repressing the promoter because the xylR binding sites corresponds to xylR of B. subtilis. Since it requires sugars for its expression, and the system is repressed by a metabolite from the pentose metabolism pathway, we used a minimal medium, M9 (Sambrook, 1989), but we changed the glucose for arginine as carbon source in order to get the lowest interference in the expression of GFP from another monosaccharides species in the medium. We use a gradient for both, xylose and arabinose on cultures at 0.1 O.D (540 nm). We could see that the expression of GFP increases as the amount of sugars added also increases. An amount of 0.01% (g/ml) of arabinose is enough for an increase of 4 times the basal expression, and the maximum production is approximately 5 times greater for the downstream genes with 0.1%(g/ml) of arabinose. Xylose gradient had a small contribution on the expression of GFP, which could be attributed to the partial similarity of the binding sites between xylR from B. subtilis and E. coli. The measurements were made with a filter fluorometer based in three different measures for each condition.<br/>
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<td id="contentcolumnwhite" align= "center"><br />[[File:UGM Pbadxyl.png|600px]]<br /><br /><p>Expression of GFP in the sugars gradient measured in fluorescence units
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Latest revision as of 02:29, 27 October 2012


UNAM-Genomics_Mexico


Our Parts





<groupparts>iGEM012 UNAM_Genomics_Mexico</groupparts>



Characterization



[http://partsregistry.org/wiki/index.php?title=Part:BBa_K851004

Aminoglycoside antibiotic resistance Sm+ Spc+

]



The aminoglycoside antibiotic resistance gene (aadA +)of pHP45Ω was originally carried on a 1.7-kb PvuII-HindIII fragment from the R100.1 plasmid. Plasmid pHP45Ω was constructed in Pierre Prentki and Henry M. Krisch, as stated in NCBI with this fragment. The addA sequence can be found in, it is confirmed to be the one contained in pHP45Ω and the complete sequence of pHP45Ω plasmid can be found in the registry references.

Hawaii 2008 iGEM team attempted before to construct a similar cassette but didn’t succeed. For iGEM UNAM Genomics México 2012 project, the Ω Cassette was used in the design of an OR logic gate using a recently described new type of communication system between Bacillus Subtilis cells called Nanotubes.


Unamgenomicsomegacassete1.png




Second Repetition


Unamgenomicsomegacassete2.png



[http://partsregistry.org/wiki/index.php?title=Part:BBa_K851002

pBAD/pXyl promoter

]


The characterization of this construction was made on an E.coli strain in a semi quantitative attempt. In that way, we expected that only araC was repressing the promoter because the xylR binding sites corresponds to xylR of B. subtilis. Since it requires sugars for its expression, and the system is repressed by a metabolite from the pentose metabolism pathway, we used a minimal medium, M9 (Sambrook, 1989), but we changed the glucose for arginine as carbon source in order to get the lowest interference in the expression of GFP from another monosaccharides species in the medium. We use a gradient for both, xylose and arabinose on cultures at 0.1 O.D (540 nm). We could see that the expression of GFP increases as the amount of sugars added also increases. An amount of 0.01% (g/ml) of arabinose is enough for an increase of 4 times the basal expression, and the maximum production is approximately 5 times greater for the downstream genes with 0.1%(g/ml) of arabinose. Xylose gradient had a small contribution on the expression of GFP, which could be attributed to the partial similarity of the binding sites between xylR from B. subtilis and E. coli. The measurements were made with a filter fluorometer based in three different measures for each condition.


UGM Pbadxyl.png

Expression of GFP in the sugars gradient measured in fluorescence units



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