Difference between revisions of "Team:Arizona State/Notebook"

This week, I added the menu bar to the Wiki, created the team logo, and designed the layout of the main page. I also added to the Project Description.

9/1 Thursday

This week, I added to the Project Description, added 6 protocols to the Protocols tab, and created the Safety tab. I also edited the AubI and BjaI parts pages.

9/8 Thursday

This week, I helped Jiaqi with psB1C3 cloning, doing a gel extraction on the digested plasmid. For the Wiki, I finished the Protocols tab, while also adding information to the About the Team tab. I also added information to the BraI and CerI parts pages.

9/15 Thursday

This week, I helped Jiaqi with psB1C3 cloning, making liquid culture for Aub, Bja, Bra and Cer inserts. I also retransformed all 10 systems in BL21 for OD600 and mCherry test next week. For the Wiki, the Team description page was updated, as well as the Basic Parts, Composite Parts, and Part Collection tables. Also, I helped work on the presentation for a practice presentation next Monday.

9/22 Thursday

This week, I ran a 96-well plate over an 8-hour read to test OD600 and mCherry absorbance over time. This proof-of-concept experiment was done in order to demonstrate that it is likely that the AHL is being produced in E. coli. This is because the AHL gene is located upstream of the mCherry gene, so the production of mCherry should also mean AHL production.

For the wiki, I worked on the Project Description, added Attributions, and more Safety information. The Human Practices page was also started.

9/29 Thursday

This week, I retransformed the 10 systems and re-ran the OD tests over an 8 hour period, because the previous run had produced a negative trend of mCherry production over time. The results were more promising, but the Esa, Lux, Rhl, and Rpa systems will be rerun next week in order to produce reasonable data.

For the wiki, I finished Attributions, worked on Human Practices and the Parts Overview tab, while also finishing up the Team description. I also added a graphic to the front page.

10/6 Thursday

This week, I reran the OD test for the Esa, Lux, Rhl, and Rpa systems. These produced positive growth curves for mCherry over time, which is a good indicator of successful AHL production in E. coli.

For the wiki, I set up the Sin and Modular Sender Vector parts pages. I also added to the Aub, Bja, Bra, and Cer parts pages. I added to the Project Description, and Parts Overview tabs.

10/13 Thursday

This week, I added to the Parts Pages in the registry and finished the Attributions tab.

10/19 Wednesday

This week is the Wiki Freeze. I finished up the Wiki, with additions to Results, Parts Overview, Project Description, Notebook, and Human Practices. Template:Arizona State Footer

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-{{Arizona_State}}
+{{Arizona State}}
 <html>
-<div class="column full_size">
-<h1>Notebook</h1>
+<h1>Notebook: Jimmy Xu</h1>
-<h2><ins> Amber Mani </ins> </h2>
+<h2>Wiki Design</h2>
-<h2><ins>Transformation of DH5alpha with PSB1C3 and PSB1A3 backbones</ins></h2>
+<h3>8/25 Thursday</h3>
-<h3>WEDNESDAY, 7/19/2017</h3>
+<p>This week, I added the menu bar to the Wiki, created the team logo, and designed the layout of the main page. I also added to the Project Description.</p>
+<br>
+<h3>9/1 Thursday</h3>
+<p>This week, I added to the Project Description, added 6 protocols to the Protocols tab, and created the Safety tab. I also edited the AubI and BjaI parts pages.</p>
+<h3>9/8 Thursday</h3>
+<p>This week, I helped Jiaqi with psB1C3 cloning, doing a gel extraction on the digested plasmid. For the Wiki, I finished the Protocols tab, while also adding information to the About the Team tab. I also added information to the BraI and CerI parts pages. </p>
+<h3>9/15 Thursday</h3>
+<p>This week, I helped Jiaqi with psB1C3 cloning, making liquid culture for Aub, Bja, Bra and Cer inserts. I also retransformed all 10 systems in BL21 for OD600 and mCherry test next week. For the Wiki, the Team description page was updated, as well as the Basic Parts, Composite Parts, and Part Collection tables. Also, I helped work on the presentation for a practice presentation next Monday.</p>
+<h3>9/22 Thursday</h3>
+<p>This week, I ran a 96-well plate over an 8-hour read to test OD600 and mCherry absorbance over time. This proof-of-concept experiment was done in order to demonstrate that it is likely that the AHL is being produced in E. coli. This is because the AHL gene is located upstream of the mCherry gene, so the production of mCherry should also mean AHL production. </p>
+<p>For the wiki, I worked on the Project Description, added Attributions, and more Safety information. The Human Practices page was also started.</p>
+<h3>9/29 Thursday</h3>
+<p>This week, I retransformed the 10 systems and re-ran the OD tests over an 8 hour period, because the previous run had produced a negative trend of mCherry production over time. The results were more promising, but the Esa, Lux, Rhl, and Rpa systems will be rerun next week in order to produce reasonable data. </p>
+<p>For the wiki, I finished Attributions, worked on Human Practices and the Parts Overview tab, while also finishing up the Team description. I also added a graphic to the front page.</p>
+<h3>10/6 Thursday</h3>
+<p>This week, I reran the OD test for the Esa, Lux, Rhl, and Rpa systems. These produced positive growth curves for mCherry over time, which is a good indicator of successful AHL production in E. coli.</p>
+<p>For the wiki, I set up the Sin and Modular Sender Vector parts pages. I also added to the Aub, Bja, Bra, and Cer parts pages. I added to the Project Description, and Parts Overview tabs.</p>
+<h3>10/13 Thursday</h3>
+<p>This week, I added to the Parts Pages in the registry and finished the Attributions tab.</p>
+<h3>10/19 Wednesday</h3>
+This week is the Wiki Freeze. I finished up the Wiki, with additions to Results, Parts Overview, Project Description, Notebook, and Human Practices.
-<p>In preparation Alyssa and I rehydrated 2 backbones from iGEM, the PSB1C3 and PSB1A3. The C3 was from plate 7 location O,23 and the A3 was from plate 4 location H,2. Will let the plates grow overnight in the incubator and make MP samples, in triplicates of each, tomorrow. </p>
-<p> DNA extraction from kit and rehydration protocol: </p>
-<p> To use the DNA in the Distribution Kit, follow these instructions: </p>
-<p> Note: There is an estimated 2-3ng of DNA in each well, following this protocol, assume that you are transforming with 200- 300pg/µL </p>
-<ol type="1">
-<li> With a pipette tip, punch a hole through the foil cover into the corresponding well of the part that you want. Make sure you have properly oriented the plate. Do not remove the foil cover, as it could lead to cross contamination between the wells </li>
-<li> Pipette 10µL of dH2O (distilled water) into the well. Pipette up and down a few times and let sit for 5 minutes to make sure the dried DNA is fully resuspended. The resuspension will be red, as the dried DNA has cresol red dye. We recommend that you do not use TE to resuspend the dried DNA. </li>
-<li> Transform 1µL of the resuspended DNA into your desired competent cells, plate your transformation with the appropriate antibiotic* and grow overnight. </li>
-<li> Pick a single colony and inoculate broth (again, with the correct antibiotic) and grow for 16 hours </li>
-<li>  Use the resulting culture to miniprep the DNA AND make your own glycerol stock (for further instruction on making a glycerol see this page). We recommend using the miniprepped DNA to run QC tests, such as restriction digests and sequencing. </li>
-</ol>
-<p> <i> * To know which antibiotics to use, look at the plasmid that the part is in. The naming scheme for plasmids is specifically designed to indicate antibiotic resistance. </i> </p>
-<p> <b> 7/20/2017 - something went wrong with the process, the plates to not show sufficient growth. Tests and plating will be redone today. </b> </p>
-<center><img src="https://static.igem.org/mediawiki/2017/6/61/Image_asu.png"style="width:428px;height:428px;/> </center>
-<p> Gathered the available colonies and put in LB with (AMP or CHLOR) to grow overnight and replate for more usable growth to be MP. samples in the shaking incu overnight, was able to grab 3 colonies from the A3 and two from the C3. Put everything in the shaking at 345pm </p>
-<p> Doing the MP on the A3 and C3 growth tubes. Concentrations: </p>
-<p>psb1c3: 80ng/ul </p>
-<p> psb1c3: 40ng/ul </p>
- <p>psb1a3: 50ng/u </p>
- <p>psb1a3: 67ng/ul </p>
-<p>psb1a3: 75ng/ul </p>
-<p><h2><ins>Friday 6/23/17 - Running colony PCR on the AUBr and the BTA3</ins></h2></p>
-<p>From earlier this week the AUBr results showed that number 9 may be a match for the vector we needed but the sequencing was returned and it was an error. Redoing the AUBr today and running the PCR for the BTA3 to try for a result on at least one per receiver.</p>
-<p>Since it is the weekend, instead of placing the new agar plate with the 24 samples of plated AUBr and BTA3 into the 37c incubator, leaving the sample out in room temperature as to not accelerate the growth too much over the weekend. See picture below: </p>
-</div>
 </html>
+{{Arizona_State_Footer}}