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| In this page we shall write what is being done and what remains to be done. <- (yeah, right) | | In this page we shall write what is being done and what remains to be done. <- (yeah, right) |
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| + | <html> |
| + | <head> |
| + | <title>notebook</title> |
| | | |
- | [[#Tasks | Tasks]]
| + | <style type="text/css"> |
| + | #navbar2 ul{ |
| + | list-style-type: none; |
| + | text-align: left; |
| + | } |
| + | #navbar2 li{ |
| + | display: inline; |
| + | text-align: center; |
| + | margin: 0 0 0 0; |
| + | } |
| | | |
- | <div id="Tasks">
| + | #navbar2 li a { |
- | == Tasks ==
| + | padding: 2px 7px 2px 7px; |
- | </div>
| + | color: #000000; |
- | | + | background-color: #52D017; |
- | <li>Task 1
| + | text-decoration: none; |
- | <li>Task 2
| + | } |
- | <li>Task 3
| + | #navbar2 li a:hover{ |
- | <li>Task 4
| + | background-color: #333333; |
- | <li>Task 5 | + | color: #ffffff; |
- | <br /> | + | } |
- | <br /> | + | </style> |
| + | </head> |
| + | <body> |
| | | |
- | [[#Week 1 | Week 1]]
| |
- | <br />
| |
- | [[#Week 2 | Week 2]]
| |
- | <br />
| |
- | [[#Week 6 | Week 6]]
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- | <br />
| |
- | [[#Week 7 | Week 7]]
| |
- | <br />
| |
- | [[#Week 8 | Week 8]]
| |
- | <br />
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- | [[#Week 9 | Week 9]]
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- | <br />
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- | [[#Week 10 | Week 10]]
| |
- | <br />
| |
| | | |
- | <div id="Week 1"> | + | <div id="navbar2"> |
| + | <ul>Quest to destroy the ring : |
| + | <li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad">0</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week1">1</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week2">2</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week3">3</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week4">4</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week5">5</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week6">6</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week7">7</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week8">8</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week9">9</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week10">10</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week11">11</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week12">12</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week13">13</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week14">14</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week15">15</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week16">16</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week17">17</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week18">18</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week19">19</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week20">20</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week21">21</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week22">22</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week23">23</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week24">24</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week25">25</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week26">26</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week27">27</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week28">28</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week29">29</a></li><li><a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/week30">30</a></li> |
| | | |
- | == Week 1 ==
| + | </ul> |
| </div> | | </div> |
| | | |
- | Check out our constructs!!!
| + | </body> |
| + | </html> |
| | | |
- | <div id="Week 2">
| |
| | | |
- | == Week 2 ==
| + | <html> |
- | </div> | + | |
| | | |
- | Hey, it's just me at SJ library.
| + | <p><font size="5">Brainstorming, dragons and a summer that never ended (Before week 1)</font></p><br><br> |
| | | |
- | Monday: weekly meeting. We came up with three solutions for the sustentability problem. The formal proposal must be ready next Tuesday afternoon. Also, we designed primers for the integration biobrick experiment.
| + | <img src = "https://static.igem.org/mediawiki/2012/1/1f/Dragon1.jpg" width= "300" align="left"> |
| | | |
- | Tuesday: we prepared synechocystis culture media and lots of other pretty things :) I ate ice cream and pizza for example (seriously, need some help here!).
| + | <h1> January </h1><br><br> |
| | | |
- | Wednesday: I am supposed to be studying proba instead of doing this. Can't concentrate though, too boring for me still.
| + | Well, after everyone had already recevied their iGEM acceptance e-mails and confirmed being on the team, we had our first official meeting on January 2nd. The plan was to define a project before the month was over, take february off and return on March to work full time on wet lab and other tasks. As we have parallel college classes, the full time means: all the time we are not in class! <br><br> |
| | | |
- | <div id="Week 6">
| |
- | == Week 6 ==
| |
- | </div>
| |
| | | |
- | Sat 04.14
| + | First day was odd. The campus was almost empty save for us and the construction workers, January is extremely hot in Santiago and as the team members were all from differenet areas, we did not knew each other at all. We took as headquarters the undergraduate labs of the biological sciences faculty. By 11 am we already had briefly introduced ourselves . So the count was: 6 engineers, 2 biochemists, 1 agricultural scientist, 1 architect and 1 chemist. Once that was settled, we did our first brainstorming ever: we managed to fill the board with ideas (check brainstorming section for more details). The day continue to move on, we found a nice place to have lunch (the only one opened actually) and then we were done by the day. We agreed that everyone would do research on interesting iGEM projects and then he/ she was going to present them to the rest of the team. The idea was to find the common characteristics of the successful projects and apply them to our creation. <br><br> |
| | | |
- | Horrible day. Nothing worked.
| |
| | | |
- | The one good thing:
| + | Later during the week, we became more familiarized with the iGEM environment. Besides checking on winner projects, we read and re read the competition bases and the requirements for medals. Also, the very first transformation was done using nitrate and tetracyclin reporters. Truth to be told, we were only practicing our wet lab skills and were not really looking forward to do something with the amplified parts. |
| + | There was generalized interest to support our project with the Arduino microcontroller as a way to complement biology and electronics. <br><br> |
| | | |
| | | |
- | [[File:flyingpig.jpg]]
| + | On wednesday (3rd day) Dani Restovic came to the lab. She is a undergraduate sicology student who kindly agreed to help us with guidance on forming work teams. This was the first instance the team members had to talk and share more personal thoughts with each other. Pollak told each person why was chosen: everyone had different characteristics that together made awesome investigation teams. We finished the evening defining our major goal:<br><br> |
| + | |
| + | "Enjoy daily work and make the most of our potentials in order to develop a creative, fantastic and innovative project able to revolutionize our academic and proffesional skills. Along with that, start a paradigm change in our country by stablishing a precedent in synthetic biology research. Last but not least: to win the iGEM competition. "<br><br> |
| | | |
- | FLYIIIIIIIIIIIIIIIIIIIIIIIIIIIIIING PIIIIIIIIIIIIIIIIIIIIIIIIIIIIG!!!!!!!!!!!!!!!!!!!!!!
| + | <span style="padding-left:250px"><img src = "https://static.igem.org/mediawiki/2012/0/01/Majorgoal_uc_chile.jpg" width= "500" align="center"><br><br></span> |
| | | |
| + | We decided to have a proper brainstorming on Saturday at Pollak's with the help of Dani.<br><br> |
| | | |
- | <div id="Week 7">
| + | The first working week ended with the visit of our international advisor Fernán Federici(from now on "the Argentinian"). And actually it was not a visit, he happened to show up in the lab just before we were leaving and took a horrible photograph of us (all record of that material has been erased) and commented a bit about our ideas: they were ok. Rodrigo (big boss, from now on Rodrigo) on the other hand, expected more development of the potential projects but as there was no real brainstorming yet, he gave us another week to think. <br><br> |
| | | |
- | == Week 7 == | + | Brainstorming at Pollak's turned out very productive :) Cool ideas came up. Check on <a href="https://2012.igem.org/Team:UC_Chile/Cyano/Notepad/brainstorming" target="_blank"> brainstorming section.</a><br><br> |
| | | |
- | Tuesday 04.17
| + | <img src = "https://static.igem.org/mediawiki/2012/1/1d/Asomao_uc_chile.jpg" style ="margin:15px" width= "300" align="right"> |
| | | |
- | We purified parts for Construct 1 and then assembled them by Gibson. Hope everythings works out. Simon was wearing his Gibson Les Paul T-shirt so we kinda hope that the power of rock leads us through the good side of the force. | + | The next two weeks it was all about defining a winner awesome project. Unfortunately, Newton's apple did not seem to fall on us. We had many many many ideas, but were not specially mad about any. The lab environment started exhausting us (really, artificial light, no windows and 30 C are not a good combination to boost creativity). In the meantime meetings were scheduled with different faculty proffesors in other to find out more about the state of the art and unexplored opportunites. People who helped us out in at this stage: Mónica Vasquez (research on cyanobacteria), Francisco Melo (bioinformatics), Loreto Valenzuela (biopolymers) and Ignacio Vargas (microbial fuel cells). <br><br> |
| | | |
- | Also, have you ever seen a centrifuge dance? It's pretty funny actually.In one step of the purification, the protocol stated "centrifuge with lid open"
| |
| | | |
- | So we did...and it danced...
| + | By third week we could not take it being in lab anymore, so Simon offered his place for a last wrap up of ideas. And yes, finally that awaited struck of enlightment dawn on us: why not couple lux brick in synechocystis and express it only by night? Our biolamp was born. Another cool project was to create mithril coats made from mithril. However, as mithril is a bit expensive, scarce and unreal the material was replaced by spider silk fibers secreted by E. coli's. |
| | | |
- | Pic of the day
| |
| | | |
- | [[File:proudresize.jpg]]
| + | </html> |
| | | |
- | | + | {{UC_Chilefooter}} |
- | | + | |
- | | + | |
- | Thursday 04.19
| + | |
- | | + | |
- | Construct 1 is ready!!!
| + | |
- | | + | |
- | [[File:freddie.jpg]]
| + | |
- | | + | |
- | | + | |
- | Conclusion: absolutely nothing is more powerful than rock!
| + | |
- | | + | |
- | | + | |
- | Friday 04.20
| + | |
- | | + | |
- | | + | |
- | Seven a.m., waking up in the morning. Gotta be fresh, gotta go downstairs...
| + | |
- | | + | |
- | hahaha i'm just messing with your head
| + | |
- | | + | |
- | | + | |
- | | + | |
- | Sat 04.21
| + | |
- | | + | |
- | Started preparing parts for Construct 2 by PCR.
| + | |
- | | + | |
- | Here is Simon heroically diminishing his life span for the success of Construct2.
| + | |
- | | + | |
- | [[File: lifespan.jpg]]
| + | |
- | | + | |
- | Although he actually seems to be enjoying it...
| + | |
- | | + | |
- | [[File:enjoys.jpg]]
| + | |
- | | + | |
- | | + | |
- | | + | |
- | To do:
| + | |
- | | + | |
- | Assemble C2.1 and C2.2. Characterization of psAB and psbA2 promoters.
| + | |
- | | + | |
- | | + | |
- | <div id="Week 8">
| + | |
- | | + | |
- | == Week 8 ==
| + | |
- | | + | |
- | Tuesday 04.24
| + | |
- | | + | |
- | Did a restriction digest of construct 1 to check if it is really what we wanted to assemble. We believe it's not.
| + | |
- | We are strongly considering to start work from scratch. (Order primers again and so on).
| + | |
- | | + | |
- | Simon confessed that he didn't like classic rock, Bernardo tried to fix his headphones with a soldering gun and Carla quit Proba.
| + | |
- | | + | |
- | Getting ready for Ingenia fair at engineering faculty tomorrow!!!
| + | |
- | | + | |
- | | + | |
- | Wednesday 04.25
| + | |
- | | + | |
- | Spent the morning talking about our project at engineering faculty. At least 30 people are interested in participating next year. For details check out our human practices section.
| + | |
- | | + | |
- | Today is Carla's birthday. In the spirit of celebration, we ordered pizza-cake and she could blow out her candles. Happy 20 years!
| + | |
- | | + | |
- | | + | |
- | [[File:bday.jpg]]
| + | |
- | | + | |
- | | + | |
- | Finally, run 42 PCR's to check if the parts assembled by gibson were correct. We included the digested contructs. Waiting for tomorrow's results.
| + | |
- | | + | |
- | | + | |
- | Thursday 04.26
| + | |
- | | + | |
- | Weird things are happening. The desired parts have wrong weights so clearly they are not what we want. The constructs don't have all the parts. Some have two or three and none is complete.
| + | |
- | | + | |
- | Second day at Ingenia fair.
| + | |
- | | + | |
- | Had a few gourmet drinks to cheer up the team!
| + | |
- | | + | |
- | | + | |
- | [[File:drinks.jpg]]
| + | |
- | | + | |
- | | + | |
- | Friday 04.27
| + | |
- | | + | |
- | Did one last PCR run with parts that correctly assembled. We are going to build our desired construct from the good parts of the former ones. Frankenson is on! (Frankenstein Gibson).
| + | |
- | | + | |
- | First rainny day of the season! Brace yourselves, winter is coming.
| + | |
- | | + | |
- | | + | |
- | Saturday 04.28
| + | |
- | | + | |
- | Checked the PCR results and they are not what we expected. Parts that supposedly were together are not in the right weight. Still, we did the corresponding Frankenson.
| + | |
- | | + | |
- | | + | |
- | <div id="Week 9">
| + | |
- | | + | |
- | == Week 9 ==
| + | |
- | </div>
| + | |
- | | + | |
- | Monday 04.30
| + | |
- | | + | |
- | Did a massive PCR run. We amplified every part of Construct 1 using as template old PCR purifications and PCR products. We'll build C1 from scratch. Hoping everything works out well this time.
| + | |
- | | + | |
- | As an inspirational motif:
| + | |
- | | + | |
- | Muchos años después, al frente del pelotón de fusilamiento, el coronel Aureliano Buendía había de recordar aquella remota tarde en que su padre lo llevó a conocer el hielo.
| + | |
- | | + | |
- | | + | |
- | Tuesday 05.01
| + | |
- | | + | |
- | We decided to transform e. coli with the expression plasmid pPMQAK1. Also, as the mentioned plasmid contains ccdb toxin, we took it out by a digestion/ligation procedure and transformed again.
| + | |
- | Transformed e. coli with GFP coding device.
| + | |
- | | + | |
- | During the afternoon, we checked yesterday's PCR's under UV light. Luckily, all parts amplified except for KanR u.u Did a PCR run for KanR alone. We tried with different master mix combinations, some containing GC buffer and some with DMSO.
| + | |
- | | + | |
- | Existential Question: WHAT DO YOU DO WHEN YOU HAVE A GREMLIN PLAGUE IN THE LABORATORY??
| + | |
- | | + | |
- | Got it!! The next protocol can be used,
| + | |
- | | + | |
- | Protocol to get rid of gremlins: http://christalawler.com/2010/06/05/bits-how-to-kill-a-gremlin-as-seen-in-gremlins/
| + | |
- | | + | |
- | *The previous protocol needs to be adapted to laboratory conditions!!!
| + | |
- | | + | |
- | | + | |
- | Wednesday 05.02
| + | |
- | | + | |
- | Talked with one of our advisors today. He gave us interesting input on our failed PCR's.
| + | |
- | | + | |
- | Checked PCR runs. KanR didn't have the strenght we'd have liked, but still we used it. All parts were assembled by Gibson. Also, every part has its neg. control. After Gibson, we transformed coli in kan, chlor and both resistance plates.
| + | |
- | | + | |
- | gel image
| + | |
- | | + | |
- | | + | |
- | Friday 05.04
| + | |
- | | + | |
- | Happy Star Wars day!!!! May the fourth be with you :)
| + | |
- | | + | |
- | | + | |
- | <div id="Week 10">
| + | |
- | == Week 10 ==
| + | |
- | </div>
| + | |
- | | + | |
- | Monday 05.07
| + | |
- | | + | |
- | Well... we believe we have just found the root of all evil: our Gibson master mix. Its efficiency is way lower compared to the master mix used during the introductory course. So, we made new master mix, new competent colis (we ran out of them), tried gibson with new mix and transformed. Hope it works this time!!!!!!
| + | |
- | | + | |
- | | + | |
- | Tuesday 05.08
| + | |
- | | + | |
- | NEW PRIMERS IN DA HOUSE!!!! Made PCR runs for the parts of the new constructs we are going to assemble (with the new primers). Also, digested pPMQAK1 to get rid of the incorporated toxin. We plan to transform coli with new constructs, pPMQAK1 and digested pPMQAK1.
| + | |
- | | + | |
- | Had another pizza orgy!!! Started making plans to buy our own mountain (apparently you can do that in this country u.u).
| + | |
- | | + | |
- | Finished last PCR run at 23.00 (new record).
| + | |
- | | + | |
- | | + | |
- | Wednesday 05.09
| + | |
- | | + | |
- | *tried protocol to ged rid of gremlins in the lab*
| + | |
- | | + | |
- | AHHHHHH POR QUÉ? NOOOOOO MALDITOS GELES (poem by B. Pollak)
| + | |
- | | + | |
- | | + | |
- | Thursday 05.10
| + | |
- | | + | |
- | Reinoculated synechocystis. Getting our bacteria ready for tomorrow's transformation :) Minipreped lux brick, digested pPMQAK1 and pPMQAK1. Transformed future useful parts from the registry. We have not yet transformed tuesday's PCR u.u
| + | |
- | Also, compared (again) old master mixes, failed master mix and fresh master mix with a Gibson assembly for sfGFP.
| + | |
- | | + | |
- | Finished with a measurement of competence for our e. colis using pSB1C3.
| + | |
- | | + | |
- | <div id="Week 11">
| + | |
- | | + | |
- | == Week 11 ==
| + | |
- | </div>
| + | |
- | | + | |
- | <div id="TUESDAY">
| + | |
- | == TUESDAY ==
| + | |
- | </div>
| + | |
In this page we shall write what is being done and what remains to be done. <- (yeah, right)
Ok, let's start by saying that the other guy (the one in charge of bactomithril section) is the serious one. I see myself more like a sort of crazy engineer type of person (thereby my code name is crazyengineer42). While reading the following pages you'll probably stumble on things that don't make much sense and many references to star wars, x files, lost and García Márquez. Oh, and dragons, there's gonna be lots of dragons. But don't despair, some ideas are intelligible if you make the effort to think as I think. If it's impossible for you to do so, well, at least I hope you have some fun (otherwise it may be better for you to stick with bactomithril section and never come back here!).
I make up for my lack of artistic style with entertaining writing, funny pics and unnecessary smilies.
notebook
Brainstorming, dragons and a summer that never ended (Before week 1)
January
Well, after everyone had already recevied their iGEM acceptance e-mails and confirmed being on the team, we had our first official meeting on January 2nd. The plan was to define a project before the month was over, take february off and return on March to work full time on wet lab and other tasks. As we have parallel college classes, the full time means: all the time we are not in class!
First day was odd. The campus was almost empty save for us and the construction workers, January is extremely hot in Santiago and as the team members were all from differenet areas, we did not knew each other at all. We took as headquarters the undergraduate labs of the biological sciences faculty. By 11 am we already had briefly introduced ourselves . So the count was: 6 engineers, 2 biochemists, 1 agricultural scientist, 1 architect and 1 chemist. Once that was settled, we did our first brainstorming ever: we managed to fill the board with ideas (check brainstorming section for more details). The day continue to move on, we found a nice place to have lunch (the only one opened actually) and then we were done by the day. We agreed that everyone would do research on interesting iGEM projects and then he/ she was going to present them to the rest of the team. The idea was to find the common characteristics of the successful projects and apply them to our creation.
Later during the week, we became more familiarized with the iGEM environment. Besides checking on winner projects, we read and re read the competition bases and the requirements for medals. Also, the very first transformation was done using nitrate and tetracyclin reporters. Truth to be told, we were only practicing our wet lab skills and were not really looking forward to do something with the amplified parts.
There was generalized interest to support our project with the Arduino microcontroller as a way to complement biology and electronics.
On wednesday (3rd day) Dani Restovic came to the lab. She is a undergraduate sicology student who kindly agreed to help us with guidance on forming work teams. This was the first instance the team members had to talk and share more personal thoughts with each other. Pollak told each person why was chosen: everyone had different characteristics that together made awesome investigation teams. We finished the evening defining our major goal:
"Enjoy daily work and make the most of our potentials in order to develop a creative, fantastic and innovative project able to revolutionize our academic and proffesional skills. Along with that, start a paradigm change in our country by stablishing a precedent in synthetic biology research. Last but not least: to win the iGEM competition. "
We decided to have a proper brainstorming on Saturday at Pollak's with the help of Dani.
The first working week ended with the visit of our international advisor Fernán Federici(from now on "the Argentinian"). And actually it was not a visit, he happened to show up in the lab just before we were leaving and took a horrible photograph of us (all record of that material has been erased) and commented a bit about our ideas: they were ok. Rodrigo (big boss, from now on Rodrigo) on the other hand, expected more development of the potential projects but as there was no real brainstorming yet, he gave us another week to think.
Brainstorming at Pollak's turned out very productive :) Cool ideas came up. Check on
brainstorming section.
The next two weeks it was all about defining a winner awesome project. Unfortunately, Newton's apple did not seem to fall on us. We had many many many ideas, but were not specially mad about any. The lab environment started exhausting us (really, artificial light, no windows and 30 C are not a good combination to boost creativity). In the meantime meetings were scheduled with different faculty proffesors in other to find out more about the state of the art and unexplored opportunites. People who helped us out in at this stage: Mónica Vasquez (research on cyanobacteria), Francisco Melo (bioinformatics), Loreto Valenzuela (biopolymers) and Ignacio Vargas (microbial fuel cells).
By third week we could not take it being in lab anymore, so Simon offered his place for a last wrap up of ideas. And yes, finally that awaited struck of enlightment dawn on us: why not couple lux brick in synechocystis and express it only by night? Our biolamp was born. Another cool project was to create mithril coats made from mithril. However, as mithril is a bit expensive, scarce and unreal the material was replaced by spider silk fibers secreted by E. coli's.