Difference between revisions of "Team:UChile OpenBio-CeBiB/Notebook"

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<button class="accordion"><p id="panelTitle">Week 33 [05/29/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 33 [05/29/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Reunión with the team to determinate the list of protocols that we are going to get for the posterior lab work.
+
<p>Meeting with the team in order to determinate the list of protocols that we were going to get for the later lab work.
 
</p>
 
</p>
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 35 [06/12/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 35 [06/12/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>It is possible to elaborate a first document with the experimental strategy and the most of the protocols. It is presented and evaluated in front of professor ÁLvaro, who suggested us correct some details and make  contact Dr. Tomás egaña, Engineer in Biotechnology molecular , expert working with the microalgae Chlamydomonas reinhardtii.
+
<p>It is possible to elaborate a first document with the experimental strategy and most of the protocols. It was presented to professor Álvaro, who suggested us to correct some details and contact Dr. Tomás egaña, Engineer in Molecular Biotechnology, expert working with the microalgae <i>Chlamydomonas reinhardtii</i>.
 
</p>
 
</p>
 
<p>Reunion with the team to find the answers of the doubts about the document with the elaborated protocols.</p>  
 
<p>Reunion with the team to find the answers of the doubts about the document with the elaborated protocols.</p>  
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<button class="accordion"><p id="panelTitle">Week 36 [06/19/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 36 [06/19/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Reunion with Dr. Tomás Egaña, who, kindly, help us to solve our doubts about our experimental strategy and some protocols related with Chlamydomonas reinhardtii. Finally, he talk us about Myra Chávez, a postdoc and an expert in work in lab with Chlamydomonas reinhardtii, who can share with us transformation plasmid, and other materials.  
+
<p>Meeting with Dr. Tomás Egaña, who kindly helped us solve our doubts about our experimental strategy and some protocols related to <i>Chlamydomonas reinhardtii</i>. Finally, he talked us about Myra Chávez, a postdoc and an expert working with <i>Chlamydomonas reinhardtii</i>, who could share with us transformation plasmids, and other materials.  
 
</p>
 
</p>
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 37 [06/26/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 37 [06/26/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>We accomplished to have contact with Myra Chávez, who offered help solving some doubts and she accepted give us pBC1-CrGFP. From now, Myra became a big help and support for our team and we nicknamed her as Maymi.
+
<p>We achieved to make contact with Myra Chávez, who offered us help to solve some problems and she kindly gave us pBC1-CrGFP. From now on, Myra became a big help and support for our team and we nicknamed her as Maymi.
 
</p>
 
</p>
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 39 [07/10/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 39 [07/10/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Reunion to work in the sequences that must be sent to print, define them, analysis them, and search the tools of optimization of codons for chlamydomonas reinhardtii to make the first order to IDT.
+
<p>Meeting to work in the sequences that must be sent to print, define, and analyze. We also searched the tools of optimization of codons for <i>Chlamydomonas reinhardtii</i> to make the first order to IDT.
 
</p>
 
</p>
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 40 [07/17/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 40 [07/17/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Improve of the genetic circuit. Maymi accept be part of the team.
+
<p>We improved the genetic circuit. Maymi accepted to be part of the team.
 
</p>
 
</p>
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 41 [07/24/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 41 [07/24/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Use the IDT tool to make the codon’s optimization.
+
<p>Usage of the IDT tool to make the codon’s optimization.
 
</p>
 
</p>
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 42 [07/31/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 42 [07/31/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Collaboration from Germany: LMU München (Ludwig Maximilians Universität München), they help us checking our experimental strategy and sequences design. </p>
+
<p>Collaboration from Germany: LMU München (Ludwig Maximilians Universität München), they helped us check our experimental strategy and sequences design. </p>
 
</div>
 
</div>
  
 
<button class="accordion"><p id="panelTitle">Week 43 [08/07/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 43 [08/07/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Reunion with Jose Duguet, who give us information about how to make the iGEM parts and help us with some doubts. Work in the parts design.</p>
+
<p>Meeting with Jose Duguet, who give us information about how to make the iGEM parts and helped us with some questions. We then worked in the parts design.</p>
 
</div>
 
</div>
  
 
<button class="accordion"><p id="panelTitle">Week 44 [08/14/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 44 [08/14/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Reunion with professor Álvaro, design of the primers, and consultation
+
<p>Meeting with professor Álvaro, design of the primers, and consultations.
 
</p>
 
</p>
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 45 [08/21/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 45 [08/21/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Collaboration from England, Dra Allison Smith from the Cambridge University. She shared us the promoter MetE sequence, 5’UTR and its terminator. Also, gave us some advices for the construction of our construct.
+
<p>Collaboration from England, Dr. Allison Smith from the Cambridge University. She shared us the promoter MetE sequence, 5’UTR and its terminator. She also gave us some advices for the elaboration of our construct.</p>
 +
<p>
 
Finished the primers design.  
 
Finished the primers design.  
 
</p>
 
</p>
−
<p>The sequences are finally ready to be sent to IDT.</p>
+
<p>The sequences were finally ready to be sent to IDT.</p>
−
<p>Is made the shipment of the sequences to IDT.</p>
+
<p>The shipment of the sequences was made to IDT.</p>
  
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 46 [08/28/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 46 [08/28/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Reunion with Maymi and professor Álvaro, to specify the experimental strategy, materials and required methods. </p>
+
<p>Meeting with Maymi and professor Álvaro to specify the experimental strategy, materials and required methods. </p>
 
</div>
 
</div>
  
 
<button class="accordion"><p id="panelTitle">Week 47 [09/04/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 47 [09/04/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Amplification of pBC1-CrGFP in e. coli DH10B chemically competent. </p>
+
<p>Amplification of pBC1-CrGFP in <i> E. coli </i> DH10B chemically competent. </p>
−
<p>Repetition of the last lab. Because there was not growth on the plate, was repeated the amplification, however, now the transformation is made in the e coli top 10 chemi competent strains and with more care and caution. After a thermic shock and the incubating in TB medium for an hour and a half, the cell were plated in several plates with LB and ampicillin, and they are left incubating at 37°C.</p>
+
<p>Repetition of the last lab. Because there was no growth on the plate, the amplification was repeated. However, now the transformation was made in the <i>E. coli</i> top 10 chemically competent strains with more care and caution. After a thermic shock and incubation TB medium for an hour and a half, the cells were transfered to several plates with LB and ampicillin, and they were left incubating at 37°C.</p>
−
<p>The plates are checked and if there is presence of transformants colonies with resistance to ampicillin, two of them are inoculated in Falcon tubes with Lb and ampicillin medium at 37°C.</p>
+
<p>The plates were checked and there actually was presence of transformant colonies with resistance to ampicillin, two of them were inoculated in Falcon tubes with LB and ampicillin medium at 37°C.</p>
 
<p>Miniprep of the transformants colonies in Falcon. Isolation of the plasmid pBC1-CrGFP.</p>
 
<p>Miniprep of the transformants colonies in Falcon. Isolation of the plasmid pBC1-CrGFP.</p>
  
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<button class="accordion"><p id="panelTitle">Week 48 [09/11/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 48 [09/11/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Test transformation of the chlamydomonas reinhardtii by the method of glass beads with pBC1-CrGFP. Also was learnt the cell counting on a Neubauer camera. After the transformation the cells were left incubating in Falcon tubes with TAPS medium in dark during the night at ambient temperature with agitation.
+
<p>Test transformation of the <i>Chlamydomonas reinhardtii</i> by method of glass beads with pBC1-CrGFP. We also learnt to cell count on a Neubauer camera. After the transformation the cells were left incubating in Falcon tubes with TAPS medium in dark during the night at room temperature with agitation.
 
</p>
 
</p>
 
<p>Continuing with the last lab. The cells were incubated in TAPS, then they were centrifuged and sowed in plates with TAPS medium with agar and paromomycin. They were left incubating at ambient temperature.</p>
 
<p>Continuing with the last lab. The cells were incubated in TAPS, then they were centrifuged and sowed in plates with TAPS medium with agar and paromomycin. They were left incubating at ambient temperature.</p>
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<button class="accordion"><p id="panelTitle">Week 50 [09/25/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 50 [09/25/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Due to was informed that some of the sequences that were sent could not be printed, a second order was made to IDT with the correct sequences.  
+
<p>Due to that we were informed that some of the sequences that were sent could not be printed, a second order was made to IDT with the correct sequences.  
 
</p>
 
</p>
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 51 [10/02/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 51 [10/02/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Arrived the first order from IDT.</p>
+
<p>Arrival of the first order from IDT.</p>
 
<p>Resuspension of the lyophilized gBlocks.</p>
 
<p>Resuspension of the lyophilized gBlocks.</p>
−
<p>Was informed to us that one of the sequences from the second order can not be synthesized again.</p>
+
<p>It was informed to us that one of the sequences from the second order could not be synthesized again.</p>
  
 
</div>
 
</div>
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<button class="accordion"><p id="panelTitle">Week 53 [10/16/17]</p></button>
 
<button class="accordion"><p id="panelTitle">Week 53 [10/16/17]</p></button>
 
<div class="panel">
 
<div class="panel">
−
<p>Extraction and purification of DNA from the agarose bands gels.</p>
+
<p>Extraction and purification of DNA from the agarose gel bands.</p>
 
<p>Digestion of the standard sequences and the igem vector pSB1C3. Ligation with the standard sequences.</p>
 
<p>Digestion of the standard sequences and the igem vector pSB1C3. Ligation with the standard sequences.</p>
−
<p>Transformation by electroporation of the vectors and sequences in BL21DE3 E. coli strain. Sow in selective mediums, they were left incubating at 37°C until 2 p.m. of the next day.</p>
+
<p>Transformation by electroporation of the vectors and sequences in BL21DE3 E. coli strain. Seeding in selective mediums, they were left incubating at 37°C until 2 p.m. of the next day.</p>
−
<p>Rescue of the colonies and growth in LB liquid medium with antibiotic. Left at 4°C</p>
+
<p>Isolation of the colonies and growth in LB liquid medium with antibiotic. Left at 4°C</p>
  
 
</div>
 
</div>
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<p>Miniprep of the colonies and generation of a glycerol inventory.</p>
 
<p>Miniprep of the colonies and generation of a glycerol inventory.</p>
 
<p>First test of miniprep digestion. The samples were saved at -20°C.</p>
 
<p>First test of miniprep digestion. The samples were saved at -20°C.</p>
−
<p>Preparation of visualization gel of the miniprep digestion. Was not observed bands on the gel.</p>
+
<p>Preparation of visualization gel of the miniprep digestion. Bands on the gel were not observed.</p>
−
<p>Was repeated the visualization gel and again was not observed the bands on the gel. The part was sent.</p>
+
<p>The visualization gel was repeated and again bands on the gel were not observed. The part was sent.</p>
−
<p>Was decided to repeat the test of miniprep digestion and was made the electrophoresis. Finally, was observed the bands, which validated the construct with the part that is going to be sent.</p>
+
<p>We decided to repeat the test of miniprep digestion and electrophoresis was carried out. Finally, we were able to observe the bands, which validated the construct with the part that was sent.</p>
  
  

Revision as of 23:25, 31 October 2017

Document

Notebook


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Meeting with the team in order to determinate the list of protocols that we were going to get for the later lab work.

No activity in lab this week

It is possible to elaborate a first document with the experimental strategy and most of the protocols. It was presented to professor Álvaro, who suggested us to correct some details and contact Dr. Tomás egaña, Engineer in Molecular Biotechnology, expert working with the microalgae Chlamydomonas reinhardtii.

Reunion with the team to find the answers of the doubts about the document with the elaborated protocols.

Meeting with Dr. Tomás Egaña, who kindly helped us solve our doubts about our experimental strategy and some protocols related to Chlamydomonas reinhardtii. Finally, he talked us about Myra Chávez, a postdoc and an expert working with Chlamydomonas reinhardtii, who could share with us transformation plasmids, and other materials.

We achieved to make contact with Myra Chávez, who offered us help to solve some problems and she kindly gave us pBC1-CrGFP. From now on, Myra became a big help and support for our team and we nicknamed her as Maymi.

No activity in lab this week

Meeting to work in the sequences that must be sent to print, define, and analyze. We also searched the tools of optimization of codons for Chlamydomonas reinhardtii to make the first order to IDT.

We improved the genetic circuit. Maymi accepted to be part of the team.

Usage of the IDT tool to make the codon’s optimization.

Collaboration from Germany: LMU München (Ludwig Maximilians Universität München), they helped us check our experimental strategy and sequences design.

Meeting with Jose Duguet, who give us information about how to make the iGEM parts and helped us with some questions. We then worked in the parts design.

Meeting with professor Álvaro, design of the primers, and consultations.

Collaboration from England, Dr. Allison Smith from the Cambridge University. She shared us the promoter MetE sequence, 5’UTR and its terminator. She also gave us some advices for the elaboration of our construct.

Finished the primers design.

The sequences were finally ready to be sent to IDT.

The shipment of the sequences was made to IDT.

Meeting with Maymi and professor Álvaro to specify the experimental strategy, materials and required methods.

Amplification of pBC1-CrGFP in E. coli DH10B chemically competent.

Repetition of the last lab. Because there was no growth on the plate, the amplification was repeated. However, now the transformation was made in the E. coli top 10 chemically competent strains with more care and caution. After a thermic shock and incubation TB medium for an hour and a half, the cells were transfered to several plates with LB and ampicillin, and they were left incubating at 37°C.

The plates were checked and there actually was presence of transformant colonies with resistance to ampicillin, two of them were inoculated in Falcon tubes with LB and ampicillin medium at 37°C.

Miniprep of the transformants colonies in Falcon. Isolation of the plasmid pBC1-CrGFP.

Test transformation of the Chlamydomonas reinhardtii by method of glass beads with pBC1-CrGFP. We also learnt to cell count on a Neubauer camera. After the transformation the cells were left incubating in Falcon tubes with TAPS medium in dark during the night at room temperature with agitation.

Continuing with the last lab. The cells were incubated in TAPS, then they were centrifuged and sowed in plates with TAPS medium with agar and paromomycin. They were left incubating at ambient temperature.

No activity in lab this week

Due to that we were informed that some of the sequences that were sent could not be printed, a second order was made to IDT with the correct sequences.

Arrival of the first order from IDT.

Resuspension of the lyophilized gBlocks.

It was informed to us that one of the sequences from the second order could not be synthesized again.

Resuspension of the universal primers and PCR of the gBlock of the first order from IDT.

Preparation of gel extraction of amplified sequences cut DNA bands.

Extraction and purification of DNA from the agarose gel bands.

Digestion of the standard sequences and the igem vector pSB1C3. Ligation with the standard sequences.

Transformation by electroporation of the vectors and sequences in BL21DE3 E. coli strain. Seeding in selective mediums, they were left incubating at 37°C until 2 p.m. of the next day.

Isolation of the colonies and growth in LB liquid medium with antibiotic. Left at 4°C

Miniprep of the colonies and generation of a glycerol inventory.

First test of miniprep digestion. The samples were saved at -20°C.

Preparation of visualization gel of the miniprep digestion. Bands on the gel were not observed.

The visualization gel was repeated and again bands on the gel were not observed. The part was sent.

We decided to repeat the test of miniprep digestion and electrophoresis was carried out. Finally, we were able to observe the bands, which validated the construct with the part that was sent.

No activity in lab this week

ono

ono