Team:UC Chile2/SpiderColi/Notepad

From 2012.igem.org

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{{Beerdragons}}
{{Beerdragons}}
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March, 5-11, 2012
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The whole team met for the first time after the vacations of February. We discussed our scheduling and divided ourselves in two groups: Cyanolux and Bactomythril. The leaders of each group were elected: Carla (Cyanolux) and Claudia (Bactomithril).
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Cyanolux: Wetlab: Simon, Seba / Drylab: Carla, Tamara, Isaac
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Bactomithril: Wetlab: Ulises, Bryon / Drylab: Claudia, Emilia, Max
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Carla and Max were chosen to maintain the wiki updated.
 +
Bernardo and Rolando are going to collaborate with both groups.
 +
Also, we scheduled meetings of the whole team every Friday or Tuesday (depending on the availability of the majority of the team), and meetings with the whole team and our advisor, Professor Rodrigo Gutierrez, every other Thursday. Likewise, each group should have their own meetings.
 +
Finally, we decided to work based on delivery dates. Each member should compromise to complete a task in specific time intervals.
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March, 12-18, 2012
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== '''March''' ==
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We registered our team in iGEM. Now we are officially part of iGEM 2012! Also we began to learn how to use our wiki.
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</div>
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Our Bactomithril project is still in its initial stage, so we began to read as many papers about recombinant spider silk and protein modeling as we could.
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Some of the most relevant papers we found are
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Xia et al. 2010 - “Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber”
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'''Week 1: 5-9 march'''
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Widmaier et al. - 2009 - “Engineering the Salmonella type III secretion system to export spider silk monomers”
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We learnt about interesting protein modeling and simulation software (e.g. Rosetta, Foldit), and some protein visualization software  (PyMOL, VMD, Chimera)
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'''Tu:'''The whole team met for the first time after the vacations of february. We discussed our scheduling and divided ourselves in two groups: Cyano and Bactomythril. The leaders of each group were elected: Carla (Cyano) and Claudia (Bactomithril).
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Additionally, we began to send emails requesting genetic sequences from spider silk to scientists from other countries. According to what we know, in Chile nobody works with natural or recombinant spider silk proteins or its genetic sequences. So that this is a real challenge to us.
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<br/>
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March, 19-25, 2012
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The iGEM team Slovenia 2009 had a project potentially useful for our own project. For that reason, we sent an email to them asking if they could share their biobricks Bba_K245005 and Bba_K245113 with us.  
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'''Cyano:''' Wetlab: Simon, Seba / Drylab: Carla, Tamara, Isaac
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They answered us and offered their help. But their shipment never arrived. Anyway, later we realized that those parts are not fully suitable for our needs.  
-
 
+
Also, some of us had the privilege to assist to a lecture of Andrew Hessel, an authority in Synthetic Biology from USA. Unexpectedly, he had a slide about us! (He found out about us in Internet). He said he was surprised that Chile had an iGEM team working in a forefront discipline such as Synthetic Biology.
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'''Biomithril:''' Wetlab: Ulises, Bryon / Drylab: Claudia, Emilia, Max
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But most importantly, we designed our first secretion constructs, consisting of a GFP Reporter Plasmid, a Protease Producer Plasmid (see section constructs for more information) and a working plasmid. This last plasmid is used as an intermediate plasmid to build the other two plasmids. We ordered the primers that we need (it takes about two weeks until they arrive!)
-
 
+
March 26 – April 11, 2012
-
Carla and Max were chosen to maintain the wiki updated.
+
We met with Ignacio Ibarra, an undergrad student of the group of Dr. Francisco Melo. He is willing to advise us in the area of protein modeling.
-
 
+
-
Bernardo and Rolando are going to collaborate with both groups.
+
-
 
+
-
 
+
-
Also, we scheduled meetings of the whole team every Friday or Tuesday (depending on the availability of the majority of the team), and meetings with the whole team and our advisor, Professor Rodrigo Gutierrez, every other Thursday. Likewise, each group should have their own meetings.
+
-
 
+
-
 
+
-
Finally, we decided to work based on delivery dates. Each member should compromise to complete a task in specific time intervals.
+
-
 
+
-
 
+
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'''Week 2: 12-16 march'''
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'''Week 3: 19-23 march'''
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'''Week 4: 26-30 march'''
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<div id="April">
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== '''April''' ==
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</div>
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'''Week 1: 2-6 april'''
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'''Week 2: 9-13 april'''
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'''We:''' We have lunch-meeting where we decide to change our responsabilities.
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Wetlab: Brion y Max
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Modelation: Emilia y Ulises
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Wiki: Claudia
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Our task for next week are:
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Wetlab: Work with the new material that arrived, primer and plasmid.
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Modelation: Read paper Hayashi 1999, Hypotheses that correlate the sequence, structure, and mechanical properties  of spider silk proteins.  
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Learn how to use the software.
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'''Week 3: 16-20 april'''
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'''We:''' We have our regular lunch-meeting.
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Gibson Assembly of Working Plasmid Construct and transformation.
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'''Th:''' Meeting with Rodrigo Gutierrez
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We have a colony after the transformation!!! :D
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a) Removing the parts that deal to make the construct (Working Plasmid) and transforming them into Colis.
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b) Miniprep of all constructs that transform and obtain DNA
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c) Constructs were amplified in the thermocycler. We did PCR, but wasn’t in good condition, running buffer was weird was going very slow so we decided to leave it for next week.
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'''Week 4: 23-27 april'''
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'''Tu:''' Meeting with Rodrigo
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'''We:''' We have a stand in ''Feria Ingenia''
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'''Th:''' We participate in a conversation table in ''Feria Ingenia''. [http://twitcam.livestream.com/9pslw Livestream]
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a) PCR amplification of the constructs. Of the 7 constructs to amplify, we can only see 5 in gel electrophoresis. Is due in large part because one of them is 42kb (HIV cleavage site) and a 2 kb (vector backbone; psB1K3) and the gel was not as resolute (1%) to observe clearly.
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b) The gel was run with the 2 constructs mentioned. This time, add more of them (4UL template in PCR) to ensure that they were present in our tubes.
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c) We observed 2 bands for both constructs.
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d) We made the decision to leave the Gibson for next week.
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<div id="May">
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== May ==
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</div>
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'''Week 1: 1-4 may'''
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a) It was made at 7 Gibson parts, to obtain finally the Working Plasmid (see section constructs).
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b) Transform E. coli and then in culture plates (LB + KanR), we expect to grow overnight.
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c) There are red plates; we don’t expect that, we think is a contamination. So again we held the Gibson plasmid construct working (on two different plates). In one observed 2 colonies grow in the other about 10 (:D!).
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d) In the wake of the red colonies, we believe that Gibson could not have come out quite right. To ensure that our construct was made in good way, we construct colony PCR assembly (with / without taking into account the vector backbone). When you run the gel, we realized that our construct actually corresponded to the expected product (hence the Gibson worked OK, :D).
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e) As our work Gibson, Gibson performed another to generate our second and third construct (HIV protease sfGFP reporter and producer, respectively).
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f) Competent bacteria were transformed with the products of previous Gibson.
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'''Week 2: 7-11 may'''
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'''Week 3: 14-18 may'''
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'''Week 4: 21-25 may'''
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'''Week 5: 28 may-1 june'''
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== June ==
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</div>
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Revision as of 03:44, 15 August 2012

Cyanolux & Bactomithril - Pontificia Universidad Católica de Chile, iGEM 2012

March, 5-11, 2012 The whole team met for the first time after the vacations of February. We discussed our scheduling and divided ourselves in two groups: Cyanolux and Bactomythril. The leaders of each group were elected: Carla (Cyanolux) and Claudia (Bactomithril). Cyanolux: Wetlab: Simon, Seba / Drylab: Carla, Tamara, Isaac Bactomithril: Wetlab: Ulises, Bryon / Drylab: Claudia, Emilia, Max Carla and Max were chosen to maintain the wiki updated. Bernardo and Rolando are going to collaborate with both groups. Also, we scheduled meetings of the whole team every Friday or Tuesday (depending on the availability of the majority of the team), and meetings with the whole team and our advisor, Professor Rodrigo Gutierrez, every other Thursday. Likewise, each group should have their own meetings. Finally, we decided to work based on delivery dates. Each member should compromise to complete a task in specific time intervals.

March, 12-18, 2012 We registered our team in iGEM. Now we are officially part of iGEM 2012! Also we began to learn how to use our wiki. Our Bactomithril project is still in its initial stage, so we began to read as many papers about recombinant spider silk and protein modeling as we could. Some of the most relevant papers we found are Xia et al. 2010 - “Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber” Widmaier et al. - 2009 - “Engineering the Salmonella type III secretion system to export spider silk monomers” We learnt about interesting protein modeling and simulation software (e.g. Rosetta, Foldit), and some protein visualization software (PyMOL, VMD, Chimera) Additionally, we began to send emails requesting genetic sequences from spider silk to scientists from other countries. According to what we know, in Chile nobody works with natural or recombinant spider silk proteins or its genetic sequences. So that this is a real challenge to us. March, 19-25, 2012 The iGEM team Slovenia 2009 had a project potentially useful for our own project. For that reason, we sent an email to them asking if they could share their biobricks Bba_K245005 and Bba_K245113 with us. They answered us and offered their help. But their shipment never arrived. Anyway, later we realized that those parts are not fully suitable for our needs. Also, some of us had the privilege to assist to a lecture of Andrew Hessel, an authority in Synthetic Biology from USA. Unexpectedly, he had a slide about us! (He found out about us in Internet). He said he was surprised that Chile had an iGEM team working in a forefront discipline such as Synthetic Biology. But most importantly, we designed our first secretion constructs, consisting of a GFP Reporter Plasmid, a Protease Producer Plasmid (see section constructs for more information) and a working plasmid. This last plasmid is used as an intermediate plasmid to build the other two plasmids. We ordered the primers that we need (it takes about two weeks until they arrive!) March 26 – April 11, 2012 We met with Ignacio Ibarra, an undergrad student of the group of Dr. Francisco Melo. He is willing to advise us in the area of protein modeling.

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