Difference between revisions of "Team:Rotterdam HR/Notebook"
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Created the first prototype for the team page</div> | + | <div class="description">b'Created the first prototype for the team page'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Social media created</div> | + | <div class="description">b'Social media created'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Social media buttons same color and fixed iGEM style issues</div> | + | <div class="description">b'Social media buttons same color and fixed iGEM style issues'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Multiple week summary styles created for the notes</div> | + | <div class="description">b'Multiple week summary styles created for the notes'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Added the header with mobile compatibility als resized logos and readded them to the header</div> | + | <div class="description">b'Added the header with mobile compatibility als resized logos and readded them to the header'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Added template header and footer with 'under construction' content</div> | + | <div class="description">b"Added template header and footer with 'under construction' content"</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Small fixes and menu adjustments</div> | + | <div class="description">b'Small fixes and menu adjustments'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Added a PI list with the secondary PI</div> | + | <div class="description">b'Added a PI list with the secondary PI'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Designed and added content holders to the index Page</div> | + | <div class="description">b'Designed and added content holders to the index Page'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Added myself to the teammember Page and did some bugfixing</div> | + | <div class="description">b'Added myself to the teammember Page and did some bugfixing'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Started working on a better looking menubar</div> | + | <div class="description">b'Started working on a better looking menubar'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Added the ability to add sub-menus to items in the menu bar. Integration into the website and added indication for which Page you are on</div> | + | <div class="description">b'Added the ability to add sub-menus to items in the menu bar. Integration into the website and added indication for which Page you are on'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Updated all Pages to the new style with an under construction sign</div> | + | <div class="description">b'Updated all Pages to the new style with an under construction sign'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Added a way to recognise Pages under construction using the menubar</div> | + | <div class="description">b'Added a way to recognise Pages under construction using the menubar'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Updated the content containers so that they are responsive</div> | + | <div class="description">b'Updated the content containers so that they are responsive'</div> |
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<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">The first draft of the architecture design for the temperature controller was made.</div> | + | <div class="description">b'The first draft of the architecture design for the temperature controller was made.'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Content added to the human practices page</div> | + | <div class="description">b'Content added to the human practices page'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Content created and added to the main page</div> | + | <div class="description">b'Content created and added to the main page'</div> |
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<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">Today a few changes have been made to the architecture design of the temperature controller. The choice was made to use a premade power supply as opposed to a self-made one, because this was considering the time left to finish this device the best choice. A few alterations were made to make the architecture design better readable.</div> | + | <div class="description">b'Today a few changes have been made to the architecture design of the temperature controller. The choice was made to use a premade power supply as opposed to a self-made one, because this was considering the time left to finish this device the best choice. A few alterations were made to make the architecture design better readable.'</div> |
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<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">A 3d drawing was made for the casing that will hold the temperature controller. The first prototype was printed, but was determent to be inadequate due to the lack of enough space for the cooler block.</div> | + | <div class="description">b'A 3d drawing was made for the casing that will hold the temperature controller. The first prototype was printed, but was determent to be inadequate due to the lack of enough space for the cooler block.'</div> |
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<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Added the remaining instructors to the team</div> | + | <div class="description">b'Added the remaining instructors to the team'</div> |
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<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">In the drawing space was added to fit the cooler block for the temperature controller. Slits were added to the drawing for the nuts to slide into. The altered drawing was printed. The newly printed parts, cooler block, fan and Peltier element were assembled. Everything fit together.</div> | + | <div class="description">b'In the drawing space was added to fit the cooler block for the temperature controller. Slits were added to the drawing for the nuts to slide into. The altered drawing was printed. The newly printed parts, cooler block, fan and Peltier element were assembled. Everything fit together.'</div> |
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<div class="attendees">Dustin van der Meulen</div> | <div class="attendees">Dustin van der Meulen</div> | ||
| − | <div class="description">To start testing the production of CooA, we firstly resuspended and transformed the BioBricks from the kit witch we wanted to use (Table 1). This has been done using the iGEM Kit plate instructions (Protocol 1, step 1 - 3) and the NEB 10 | + | <div class="description">b'To start testing the production of CooA, we firstly resuspended and transformed the BioBricks from the kit witch we wanted to use (Table 1). This has been done using the iGEM Kit plate instructions (Protocol 1, step 1 - 3) and the NEB 10 b\xc3\xa9ta transformation protocol adapted New England Biolabs (Protocol 2), using bought cells with a reported transformation efficienty of 1-3 10^9 cfu/\xc2\xb5g pUC19. Inucbation was at 37\xc2\xb0C.<br>\n<br>\nTable 1 : Resuspended BioBricks from the iGEM 2018 Distribution kit and their uses.\n<table border="1" cellpadding="1" cellspacing="1" style="width: 500px;">\n\t<tbody>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_K592009</td>\n\t\t\t<td style="text-align: center; width: 365px;">Blue Chromoprotein AmilCP</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_B0031</td>\n\t\t\t<td style="text-align: center; width: 365px;">Ribosomal binding site (strong), derived from BBa_B0030</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_B0032</td>\n\t\t\t<td style="text-align: center; width: 365px;">Ribosomal binding site (medium), derived from BBa_B0030</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_B0030</td>\n\t\t\t<td style="text-align: center; width: 365px;">Ribosomal binding site (weak)</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_B0015</td>\n\t\t\t<td style="text-align: center; width: 365px;">Double terminator (BBa_B0010 & BBa_B0012)</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_J23100</td>\n\t\t\t<td style="text-align: center; width: 365px;">Strong Constitutive Anderson Promotor</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_J23105</td>\n\t\t\t<td style="text-align: center; width: 365px;">Medium Constitutive Anderson Promotor</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_J23113</td>\n\t\t\t<td style="text-align: center; width: 365px;">Weak Constitutive Anderson Promotor</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_J45199</td>\n\t\t\t<td style="text-align: center; width: 365px;">Banana odor enzyme (ATF1) generator</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_K1184000</td>\n\t\t\t<td style="text-align: center; width: 365px;">Killer Red</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_K352001</td>\n\t\t\t<td style="text-align: center; width: 365px;">CooA</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="text-align: center; width: 122px;">BBa_K352011</td>\n\t\t\t<td style="text-align: center; width: 365px;">CooA responsive system</td>\n\t\t</tr>\n\t</tbody>\n</table>\n<br>\nAfter checking the plates on the 28th of June, we recieved the following results (Table 2):<br>\n<br>\nTable 2 : Kolonies found after overnight growth.\n<table border="1" cellpadding="1" cellspacing="1" style="width: 500px;">\n\t<tbody>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_K592009</td>\n\t\t\t<td style="width: 277px; text-align: center;">20 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_B0031</td>\n\t\t\t<td style="width: 277px; text-align: center;">4 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_B0032</td>\n\t\t\t<td style="width: 277px; text-align: center;">5 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_B0030</td>\n\t\t\t<td style="width: 277px; text-align: center;">1 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_B0015</td>\n\t\t\t<td style="width: 277px; text-align: center;">6 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_J23100</td>\n\t\t\t<td style="width: 277px; text-align: center;">1 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_J23105</td>\n\t\t\t<td style="width: 277px; text-align: center;">98 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_J23113</td>\n\t\t\t<td style="width: 277px; text-align: center;">19 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_J45199</td>\n\t\t\t<td style="width: 277px; text-align: center;">0 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_K1184000</td>\n\t\t\t<td style="width: 277px; text-align: center;">4 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_K352001</td>\n\t\t\t<td style="width: 277px; text-align: center;">2 colonies</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 210px; text-align: center;">BBa_K352011</td>\n\t\t\t<td style="width: 277px; text-align: center;">4 colonies</td>\n\t\t</tr>\n\t</tbody>\n</table>\n'</div> |
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<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">A short test run was done with the newly assembled cooler. The test concluded that the temperature controller could cool a water droplet to the point of freezing and heat it back up to its boiling point.</div> | + | <div class="description">b'A short test run was done with the newly assembled cooler. The test concluded that the temperature controller could cool a water droplet to the point of freezing and heat it back up to its boiling point.'</div> |
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<div class="attendees">Dustin van der Meulen</div> | <div class="attendees">Dustin van der Meulen</div> | ||
| − | <div class="description"><p>After making a 20 mL overnight culture of our NEB 10 | + | <div class="description">b'<p>After making a 20 mL overnight culture of our NEB 10 b\xc3\xa9ta cells containing our BioBricks, we performed a mini prep (Protocol 3). Using our nanodrop spectrophotometer which gave us the following DNA concentrations:<br>\n </p>\n\n<table border="1" cellpadding="1" cellspacing="1" style="width: 500px;">\n\t<tbody>\n\t\t<tr>\n\t\t\t<td>BBa_K592009</td>\n\t\t\t<td>72,5 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_B0031</td>\n\t\t\t<td>118,9 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_B0032</td>\n\t\t\t<td>52,5 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_B0030</td>\n\t\t\t<td>488,6 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_B0015</td>\n\t\t\t<td>53,5 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_J23100</td>\n\t\t\t<td>148,3 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_J23105</td>\n\t\t\t<td>96,3 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_J23113</td>\n\t\t\t<td>151,8 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_K118400</td>\n\t\t\t<td>140,4 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_K352001</td>\n\t\t\t<td>77,7 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td>BBa_K352011</td>\n\t\t\t<td>76,8 ng/\xc2\xb5L</td>\n\t\t</tr>\n\t</tbody>\n</table>\n<br>\nAfter assessign our results, in the future we will perform the ethanol carry-over steps.<br>\n<br>\nAlso from the previously mentioned overnight culture 1 mL has been used to make Glycerol Stock (Protocol 4)'</div> |
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<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">The choice to use a computer PSU as a power supply was made. The choice was made on the grounds, that computer PSU have a standard 12, 5 and 3.3V output. This is beneficial because these are the voltages necessary for the selected components.</div> | + | <div class="description">b'The choice to use a computer PSU as a power supply was made. The choice was made on the grounds, that computer PSU have a standard 12, 5 and 3.3V output. This is beneficial because these are the voltages necessary for the selected components.'</div> |
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</div> | </div> | ||
<div class="attendees">Dustin van der Meulen</div> | <div class="attendees">Dustin van der Meulen</div> | ||
| − | <div class="description"><p>Today we performed a digestion, dephosphorilation and ligation (following protocols 4 and 5) of a few promotor and RBS BioBricks. Because of administrative compliations only the variants with J23113 and a RBS could be made.</p> | + | <div class="description">b'<p>Today we performed a digestion, dephosphorilation and ligation (following protocols 4 and 5) of a few promotor and RBS BioBricks. Because of administrative compliations only the variants with J23113 and a RBS could be made.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 1,590: | Line 1,424: | ||
</div> | </div> | ||
<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">Changes were made to the architecture design of the temperature controller. Different voltage regulators were selected to fit the newly chosen power supply. To better readability of the architecture design a legend was added.</div> | + | <div class="description">b'Changes were made to the architecture design of the temperature controller. Different voltage regulators were selected to fit the newly chosen power supply. To better readability of the architecture design a legend was added.'</div> |
</div> | </div> | ||
| Line 1,631: | Line 1,465: | ||
</div> | </div> | ||
<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">Custom footprints were made for multiple components and added to the parts library in the PCB design software.</div> | + | <div class="description">b'Custom footprints were made for multiple components and added to the parts library in the PCB design software.'</div> |
</div> | </div> | ||
| Line 1,672: | Line 1,506: | ||
</div> | </div> | ||
<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">The provisional electronic circuit design for the temperature controller was made.</div> | + | <div class="description">b'The provisional electronic circuit design for the temperature controller was made.'</div> |
</div> | </div> | ||
| Line 1,713: | Line 1,547: | ||
</div> | </div> | ||
<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">The electronic circuit design for the temperature controller was finished. Measuring point were added to the electronic circuit design.</div> | + | <div class="description">b'The electronic circuit design for the temperature controller was finished. Measuring point were added to the electronic circuit design.'</div> |
</div> | </div> | ||
| Line 1,754: | Line 1,588: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Loraine Nelson | Paul Reusink</div> | <div class="attendees">Elise Grootscholten | Loraine Nelson | Paul Reusink</div> | ||
| − | <div class="description">To have some basic biobricks ready, we stocked them by doing a plasmid isolation and freeze the DNA. </div> | + | <div class="description">b'To have some basic biobricks ready, we stocked them by doing a plasmid isolation and freeze the DNA. '</div> |
</div> | </div> | ||
| Line 1,795: | Line 1,629: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Loraine Nelson | Paul Reusink</div> | <div class="attendees">Elise Grootscholten | Loraine Nelson | Paul Reusink</div> | ||
| − | <div class="description">To start on a basic construct we did a digestion and ligation with the parts we isolated earlier. To prevent original constructs we did a defosphorylation after the digestion. We controlled the digestion by doing a gelelktroforeses. </div> | + | <div class="description">b'To start on a basic construct we did a digestion and ligation with the parts we isolated earlier. To prevent original constructs we did a defosphorylation after the digestion. We controlled the digestion by doing a gelelktroforeses. '</div> |
</div> | </div> | ||
| Line 1,836: | Line 1,670: | ||
</div> | </div> | ||
<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">Started working on the board layout for the PCB of the temperature controller.</div> | + | <div class="description">b'Started working on the board layout for the PCB of the temperature controller.'</div> |
</div> | </div> | ||
| Line 1,877: | Line 1,711: | ||
</div> | </div> | ||
<div class="attendees">Tom van Dijk | Randall de Waard</div> | <div class="attendees">Tom van Dijk | Randall de Waard</div> | ||
| − | <div class="description">We continued with the ligated DNA by transformating it to Neb10Beta. This was plated onto agarplates and incubated for 1 day. </div> | + | <div class="description">b'We continued with the ligated DNA by transformating it to Neb10Beta. This was plated onto agarplates and incubated for 1 day. '</div> |
</div> | </div> | ||
| Line 1,918: | Line 1,752: | ||
</div> | </div> | ||
<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">Further work was done to the board layout for the temperature controller.</div> | + | <div class="description">b'Further work was done to the board layout for the temperature controller.'</div> |
</div> | </div> | ||
| Line 1,959: | Line 1,793: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description">The results of 7/12/2018 were collected, in action of this we decided to plate some ligated and transferred DNA from 7/12/2018 again. This we did because there wasn't a clear grow of colonies on the plates.</div> | + | <div class="description">b"The results of 7/12/2018 were collected, in action of this we decided to plate some ligated and transferred DNA from 7/12/2018 again. This we did because there wasn't a clear grow of colonies on the plates."</div> |
</div> | </div> | ||
| Line 2,000: | Line 1,834: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description">We tried to let bacteria grow on paper, therefore we used our own buisnesscards. We let the buisnesscards absorb some LB-medium and put them inside petridishes. </div> | + | <div class="description">b'We tried to let bacteria grow on paper, therefore we used our own buisnesscards. We let the buisnesscards absorb some LB-medium and put them inside petridishes. '</div> |
</div> | </div> | ||
| Line 2,041: | Line 1,875: | ||
</div> | </div> | ||
<div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | <div class="attendees">Tom van Dijk | Mike Vrieswijk</div> | ||
| − | <div class="description">Work has been done on the board layout for the temperature controller. The board layout is now finished.</div> | + | <div class="description">b'Work has been done on the board layout for the temperature controller. The board layout is now finished.'</div> |
</div> | </div> | ||
| Line 2,082: | Line 1,916: | ||
</div> | </div> | ||
<div class="attendees">Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Randall de Waard</div> | <div class="attendees">Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Randall de Waard</div> | ||
| − | <div class="description">To know if the ligation was succesfull we will controll the DNA, therefor we ented the bacteria's with DNA in LB-medium to grow overnight. We also plated the used bacteria's onto new plates to use for further experiments. </div> | + | <div class="description">b"To know if the ligation was succesfull we will controll the DNA, therefor we ented the bacteria's with DNA in LB-medium to grow overnight. We also plated the used bacteria's onto new plates to use for further experiments. "</div> |
</div> | </div> | ||
| Line 2,123: | Line 1,957: | ||
</div> | </div> | ||
<div class="attendees">Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Randall de Waard</div> | <div class="attendees">Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Randall de Waard</div> | ||
| − | <div class="description">We did a blue white screening on our buisnesscards to see if bacteria had grew on them. We transferred the buisnesscards to new petrydishes and added ITPG and X-gal to the petrydishes. </div> | + | <div class="description">b'We did a blue white screening on our buisnesscards to see if bacteria had grew on them. We transferred the buisnesscards to new petrydishes and added ITPG and X-gal to the petrydishes. '</div> |
</div> | </div> | ||
| Line 2,164: | Line 1,998: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Frontend design for the notebook</div> | + | <div class="description">b'Frontend design for the notebook'</div> |
</div> | </div> | ||
| Line 2,205: | Line 2,039: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard</div> | <div class="attendees">Rens Boeser | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard</div> | ||
| − | <div class="description">The resulst of 7/16/2018 showed that the DNA didnt ligate as planned. To be able to digest enough DNA we did a plasmid isolation again. We digested this DNA and froze it for further use. </div> | + | <div class="description">b'The resulst of 7/16/2018 showed that the DNA didnt ligate as planned. To be able to digest enough DNA we did a plasmid isolation again. We digested this DNA and froze it for further use. '</div> |
</div> | </div> | ||
| Line 2,246: | Line 2,080: | ||
</div> | </div> | ||
<div class="attendees">Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Mike Vrieswijk | Randall de Waard</div> | <div class="attendees">Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Mike Vrieswijk | Randall de Waard</div> | ||
| − | <div class="description">We did another round of plasmid isolation for stocking. </div> | + | <div class="description">b'We did another round of plasmid isolation for stocking. '</div> |
</div> | </div> | ||
| Line 2,287: | Line 2,121: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Designed a way to follow experiments that take up multiple days and eventually designed a notebook entry page and made it a responsive page</div> | + | <div class="description">b'Designed a way to follow experiments that take up multiple days and eventually designed a notebook entry page and made it a responsive page'</div> |
</div> | </div> | ||
| Line 2,328: | Line 2,162: | ||
</div> | </div> | ||
<div class="attendees">Dustin van der Meulen | Mei Ju Goemans| Randall de Waard </div> | <div class="attendees">Dustin van der Meulen | Mei Ju Goemans| Randall de Waard </div> | ||
| − | <div class="description">We digested all DNA we have in stock to test for our basic construct. We tested the DNA by doing a gelelktroforeses. </div> | + | <div class="description">b'We digested all DNA we have in stock to test for our basic construct. We tested the DNA by doing a gelelktroforeses. '</div> |
</div> | </div> | ||
| Line 2,369: | Line 2,203: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Created a one page notebook. Made the notebook entry page more suited for the entry length</div> | + | <div class="description">b'Created a one page notebook. Made the notebook entry page more suited for the entry length'</div> |
</div> | </div> | ||
| Line 2,410: | Line 2,244: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Transformations of the biobricks K133071, K173003 and I13453 are performed. K133071 will produce CO2 if there's pyruvate present and K173003 will produce CO2 if urea is present. I13453 is a promotor which will work if there's arabinose present. <br> | + | <div class="description">b"<p>Transformations of the biobricks K133071, K173003 and I13453 are performed. K133071 will produce CO2 if there's pyruvate present and K173003 will produce CO2 if urea is present. I13453 is a promotor which will work if there's arabinose present. <br>\nThe biobricks were transformed first into electrocometent cells and later into chemical competent cells from the strain NEb10Beta. After transformations the culture was plated on agar plates with antibiotics. The first transformations didn't work out, but the second did, because then the right competent cells were used. </p>\n"</div> |
| − | + | ||
| − | </div> | + | |
</div> | </div> | ||
| Line 2,453: | Line 2,285: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser | Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard</div> | <div class="attendees">Rens Boeser | Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard</div> | ||
| − | <div class="description">New biobricks, used to make an ATP sensor, were transformed into NEB10Beta. The culture was than plated onto agar and incubated for 1 day. </div> | + | <div class="description">b'New biobricks, used to make an ATP sensor, were transformed into NEB10Beta. The culture was than plated onto agar and incubated for 1 day. '</div> |
</div> | </div> | ||
| Line 2,494: | Line 2,326: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser | Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard</div> | <div class="attendees">Rens Boeser | Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard</div> | ||
| − | <div class="description">New biobricks, which produces gasses, were transformed into NEB10Beta. The culture was than plated onto agar and incubated for 1 day. </div> | + | <div class="description">b'New biobricks, which produces gasses, were transformed into NEB10Beta. The culture was than plated onto agar and incubated for 1 day. '</div> |
</div> | </div> | ||
| Line 2,535: | Line 2,367: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Started working on an automatic notebook creator</div> | + | <div class="description">b'Started working on an automatic notebook creator'</div> |
</div> | </div> | ||
| Line 2,576: | Line 2,408: | ||
</div> | </div> | ||
<div class="attendees">Loraine Nelson | Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Loraine Nelson | Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>Today we did a transformation with new biobricks. The biobricks were built into chemically competent cells from the strain NEb10Beta. After transformation the culture was plated on agar plates with antibiotics. The results were checked the next day. </p> | + | <div class="description">b'<p>Today we did a transformation with new biobricks. The biobricks were built into chemically competent cells from the strain NEb10Beta. After transformation the culture was plated on agar plates with antibiotics. The results were checked the next day. </p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 2,618: | Line 2,449: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>To be able to always get the necessary biobricks, there have been made glycerolstocks of the transformed biobricks K133071, K173003 and I13453. The glycerolstocks are stored at -80 degrees Celsius. If needed, they can be retrieved from this storage to use for experiments. </p> | + | <div class="description">b'<p>To be able to always get the necessary biobricks, there have been made glycerolstocks of the transformed biobricks K133071, K173003 and I13453. The glycerolstocks are stored at -80 degrees Celsius. If needed, they can be retrieved from this storage to use for experiments. </p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 2,660: | Line 2,490: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Automatic generation of entries completed</div> | + | <div class="description">b'Automatic generation of entries completed'</div> |
</div> | </div> | ||
| Line 2,701: | Line 2,531: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Used the Google drive REST API to download the entries from drive</div> | + | <div class="description">b'Used the Google drive REST API to download the entries from drive'</div> |
</div> | </div> | ||
| Line 2,742: | Line 2,572: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Used the igemwiki API to update pages using software</div> | + | <div class="description">b'Used the igemwiki API to update pages using software'</div> |
</div> | </div> | ||
| Line 2,783: | Line 2,613: | ||
</div> | </div> | ||
<div class="attendees">Loraine Nelson | Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Loraine Nelson | Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>To be able to always get the necessary biobricks, we made an glycerol stock after every transformation. The glycerol stocks are stored at -80 degrees Celsius. If needed, they can retrieved from this storage to use for experiments. </p> | + | <div class="description">b'<p>To be able to always get the necessary biobricks, we made an glycerol stock after every transformation. The glycerol stocks are stored at -80 degrees Celsius. If needed, they can retrieved from this storage to use for experiments. </p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 2,825: | Line 2,654: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>For further experiments there is isolated DNA needed of the biobricks J23100, K133071, K173003 and I134353. The DNA is isolated out of the bacteria with the help of a plasmid purifaction kit. After isolation this DNA can be used for digestion and ligation or other experiments. <span style="font-size:12px;">J23100 (from the glycerolstock): 325,59 ng/ul, K173003: 217,06 ng/ul, K133071: 186,79 ng/ul, </span>I13453: 88,18 ng/ul</p> | + | <div class="description">b'<p>For further experiments there is isolated DNA needed of the biobricks J23100, K133071, K173003 and I134353. The DNA is isolated out of the bacteria with the help of a plasmid purifaction kit. After isolation this DNA can be used for digestion and ligation or other experiments. <span style="font-size:12px;">J23100 (from the glycerolstock): 325,59 ng/ul, K173003: 217,06 ng/ul, K133071: 186,79 ng/ul, </span>I13453: 88,18 ng/ul</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 2,867: | Line 2,695: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Connected the page uploader to the notebook generator</div> | + | <div class="description">b'Connected the page uploader to the notebook generator'</div> |
</div> | </div> | ||
| Line 2,908: | Line 2,736: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Created a program that uploads all updated pages</div> | + | <div class="description">b'Created a program that uploads all updated pages'</div> |
</div> | </div> | ||
| Line 2,949: | Line 2,777: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Built a page builder that automatically adds the header and footer before uploading</div> | + | <div class="description">b'Built a page builder that automatically adds the header and footer before uploading'</div> |
</div> | </div> | ||
| Line 2,990: | Line 2,818: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Redone the google API handler for reusability and readability and made the google API handler generic</div> | + | <div class="description">b'Redone the google API handler for reusability and readability and made the google API handler generic'</div> |
</div> | </div> | ||
| Line 3,031: | Line 2,859: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">revamped the main program</div> | + | <div class="description">b'revamped the main program'</div> |
</div> | </div> | ||
| Line 3,072: | Line 2,900: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Finished redoing the application for generating and uploading pages</div> | + | <div class="description">b'Finished redoing the application for generating and uploading pages'</div> |
</div> | </div> | ||
| Line 3,113: | Line 2,941: | ||
</div> | </div> | ||
<div class="attendees">Rens Boeser</div> | <div class="attendees">Rens Boeser</div> | ||
| − | <div class="description">Added month categorization to the page</div> | + | <div class="description">b'Added month categorization to the page'</div> |
</div> | </div> | ||
| Line 3,154: | Line 2,982: | ||
</div> | </div> | ||
<div class="attendees">Loraine Nelson | Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Loraine Nelson | Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>For further experiments we needed isolated DNA. The DNA is isolated out of the bacteria with the help of a plasmid purifaction kit. After isolation this DNA can be used for digestion and ligation or other experiments.</p> | + | <div class="description">b'<p>For further experiments we needed isolated DNA. The DNA is isolated out of the bacteria with the help of a plasmid purifaction kit. After isolation this DNA can be used for digestion and ligation or other experiments.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 3,196: | Line 3,023: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>The biobricks J23100, K133071, K173003 and I134353 were sucessfully digested after the second time. After the digestions the biobricks K133071 and K173003 were dephosphorylated and ligated with the inserts J23100 and I13453. This was done in the original backbone of K133071 and K173003, and not another control backbone. To know if the biobricks were right ligated this was done by testing practically. See the experiments: <em>Testing gas production.</em> </p> | + | <div class="description">b'<p>The biobricks J23100, K133071, K173003 and I134353 were sucessfully digested after the second time. After the digestions the biobricks K133071 and K173003 were dephosphorylated and ligated with the inserts J23100 and I13453. This was done in the original backbone of K133071 and K173003, and not another control backbone. To know if the biobricks were right ligated this was done by testing practically. See the experiments: <em>Testing gas production.</em> </p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 3,238: | Line 3,064: | ||
</div> | </div> | ||
<div class="attendees">Randall de Waard | Elise Grootscholten</div> | <div class="attendees">Randall de Waard | Elise Grootscholten</div> | ||
| − | <div class="description"><p><span style="font-size:14px;">Testing different amounts of urea and sodiumpyruvate to know which concentrations the bacteria survive.</span></p> | + | <div class="description">b'<p><span style="font-size:14px;">Testing different amounts of urea and sodiumpyruvate to know which concentrations the bacteria survive.</span></p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 3,280: | Line 3,105: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Transformations of the biobricks (K133071 + J23100), (K13071 + I1345), (K173003 + J23100) and (K173003 + I13453) in | + | <div class="description">b'<p>Transformations of the biobricks (K133071 + J23100), (K13071 + I1345), (K173003 + J23100) and (K173003 + I13453) in NEB10B\xc3\xa8ta. There was no grow except for the biobrick combination K133071 + J23100.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 3,322: | Line 3,146: | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>A colony PCR is done for the | + | <div class="description">b"<p>A colony PCR is done for the NEB10B\xc3\xa8ta E.coli cells with expected the biobrick combination of K133071 with J23100. Nevertheless, on a gel the difference with and without promotor couldn't be seen. So there must be another way of proving the right biobricks are there.</p>\n"</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description">The ligations and transformations of the biobricks K173003 + J23100, K173003 + I13453, and K133071 + I13453 has been performed again. There was a lot of grow on the agar plates. To know if the biobricks were right ligated this was done by testing practically. See the experiments: <em>Testing gas production.</em> </div> | + | <div class="description">b'The ligations and transformations of the biobricks K173003 + J23100, K173003 + I13453, and K133071 + I13453 has been performed again. There was a lot of grow on the agar plates. To know if the biobricks were right ligated this was done by testing practically. See the experiments: <em>Testing gas production.</em>\xe2\x80\x8b '</div> |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>Making a set up for the gas production testing and testing it with | + | <div class="description">b'<p>Making a set up for the gas production testing and testing it with NEB10B\xc3\xa8ta with the expected biobricks in it (K133071 + J23100) and a negative control.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
| Line 3,447: | Line 3,269: | ||
</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>Making a set up for the gas production testing and testing it with | + | <div class="description">b'<p>Making a set up for the gas production testing and testing it with NEB10B\xc3\xa8ta with the expected biobricks in it (K133071 + I13453), (K173003 + J23100), (K173003 + I13453) and a negative control.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>Gasproduction testing for the biobricks (K173003 + I13453), (K133071 + I13453) and negative controls (B0015 and K133071 without urea and arabinose).<br> | + | <div class="description">b'<p>Gasproduction testing for the biobricks (K173003 + I13453), (K133071 + I13453) and negative controls (B0015 and K133071 without urea and arabinose).<br>\nK173003 + I13453 is tested with sodiumpyruvate and arabinose for gasproduction and K133071 + I13453 is tested with urea and arabinose for gasproduction.<br>\nThe negative control also produces a little bit gas.</p>\n'</div> |
| − | + | ||
| − | + | ||
| − | </div> | + | |
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<div class="attendees">Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>Testing the gasproduction of the colonies 9 and 10 of biobricks (K173003 + J23100), colonies 5 and 7 of biobricks (K173003 + I13453) and colony 4 of biobricks (K133071 + I13453) with and without centrifuging the bacteria. There is also a negative control (J04450 pSB1K3) with Kanamycine. The negative contol started with a lot of gas inside the tube. We can not see wether there is produced more after a day or not. This have to be tested later.</p> | + | <div class="description">b'<p>Testing the gasproduction of the colonies 9 and 10 of biobricks (K173003 + J23100), colonies 5 and 7 of biobricks (K173003 + I13453) and colony 4 of biobricks (K133071 + I13453) with and without centrifuging the bacteria. There is also a negative control (J04450 pSB1K3) with Kanamycine. The negative contol started with a lot of gas inside the tube. We can not see wether there is produced more after a day or not. This have to be tested later.</p>\n'</div> |
| − | </div> | + | |
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Minipreps are made of colonies 11 and 19 of biobrick combination K133071 + J23100. Results: 11. 270,57 ng/ul 19. 253,59 ng/ul.</p> | + | <div class="description">b'<p>Minipreps are made of colonies 11 and 19 of biobrick combination K133071 + J23100. Results: 11. 270,57 ng/ul 19. 253,59 ng/ul.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>A miniprep of the biobrick K352002 is made. The concentration is 69,77 ng/ul.</p> | + | <div class="description">b'<p>A miniprep of the biobrick K352002 is made. The concentration is 69,77 ng/ul.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Randall de Waard | Elise Grootscholten</div> | <div class="attendees">Randall de Waard | Elise Grootscholten</div> | ||
| − | <div class="description"><p><span style="font-size:14px;">Testing different amounts of urea and sodiumpyruvate to know which concentrations the bacteria survive.</span></p> | + | <div class="description">b'<p><span style="font-size:14px;">Testing different amounts of urea and sodiumpyruvate to know which concentrations the bacteria survive.</span></p>\n'</div> |
| − | </div> | + | |
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<div class="attendees">None</div> | <div class="attendees">None</div> | ||
| − | <div class="description"><p></p></div> | + | <div class="description">b'<p></p>'</div> |
</div> | </div> | ||
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</div> | </div> | ||
<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Digestions, gelelectrophoresis, dephosphorylations and ligations of different biobrick combinations. These biobrick combinations are 4 different promotors (J23100, I13453, K352002, K352003) with 4 different gasproduction biobricks (k173003, K173013, K133071, K133116). J23100 is about 1 kb to long. The rest seems likely to be right digested. The ligations will be transformed in | + | <div class="description">b'<p>Digestions, gelelectrophoresis, dephosphorylations and ligations of different biobrick combinations. These biobrick combinations are 4 different promotors (J23100, I13453, K352002, K352003) with 4 different gasproduction biobricks (k173003, K173013, K133071, K133116). J23100 is about 1 kb to long. The rest seems likely to be right digested. The ligations will be transformed in NEB10b\xc3\xa8ta and digested again as control.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Transformations of the biobrick combinations in | + | <div class="description">b'<p>Transformations of the biobrick combinations in NEB10b\xc3\xa8ta. The transformations are plated on kanamycine agar plates, because all the ligations were done in pSB1K3 (kanamycine resistence) backbone. Pink and with colonies appeared after incubation by 37 degrees Celcius for about 12h. The white colonies will be used for further experiments.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Plasmid DNA was isolated of 20 different colonies. The first time something went wrong. The second time we had good concentrations of isolated plasmid DNA. After this we will digest the DNA to see if the plasmids all have the required biobricks. The tube have a code from now on, see table 1.<br> | + | <div class="description">b'<p>Plasmid DNA was isolated of 20 different colonies. The first time something went wrong. The second time we had good concentrations of isolated plasmid DNA. After this we will digest the DNA to see if the plasmids all have the required biobricks. The tube have a code from now on, see table 1.<br>\n </p>\n\n<table border="1" cellpadding="1" cellspacing="1" style="width: 500px;">\n\t<tbody>\n\t\t<tr>\n\t\t\t<td style="width: 122px;"><strong>Number</strong></td>\n\t\t\t<td style="width: 131px;"><strong>Promotor</strong></td>\n\t\t\t<td style="width: 118px;"><strong>Gene</strong></td>\n\t\t\t<td style="width: 106px;"><strong>Backbone</strong></td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">A</td>\n\t\t\t<td style="width: 131px;">K352002 (CooF)</td>\n\t\t\t<td style="width: 118px;">K173013</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">B</td>\n\t\t\t<td style="width: 131px;">K352002 (CooF)</td>\n\t\t\t<td style="width: 118px;">K133071</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">C</td>\n\t\t\t<td style="width: 131px;">K352002 (CooF)</td>\n\t\t\t<td style="width: 118px;">K173003</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">D</td>\n\t\t\t<td style="width: 131px;">K352003 (CooM)</td>\n\t\t\t<td style="width: 118px;">K133071</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">E</td>\n\t\t\t<td style="width: 131px;">K352003 (CooM)</td>\n\t\t\t<td style="width: 118px;">K173003</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">F</td>\n\t\t\t<td style="width: 131px;">K352003 (CooM)</td>\n\t\t\t<td style="width: 118px;">K173013</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">H</td>\n\t\t\t<td style="width: 131px;">I13453</td>\n\t\t\t<td style="width: 118px;">K173013</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">I</td>\n\t\t\t<td style="width: 131px;">I13453</td>\n\t\t\t<td style="width: 118px;">K173003</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 122px;">J</td>\n\t\t\t<td style="width: 131px;">II13453</td>\n\t\t\t<td style="width: 118px;">K133071</td>\n\t\t\t<td style="width: 106px;">pSB1K3</td>\n\t\t</tr>\n\t</tbody>\n</table>\n\n<p><em>Table 1: list of biobricks of abbreviations</em></p>\n'</div> |
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| − | </table> | + | |
| − | + | ||
| − | <p><em>Table 1: list of biobricks of abbreviations</em></p> | + | |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>The minipreps of experiment 12 are digested with the restriction enzymes: SmaI and ScaI. Only Sca and Sma are both incubated at 37 degrees Celcius. Sma has to be incubated at 25 degrees Celcius. This is done in experiment 15.</p> | + | <div class="description">b'<p>The minipreps of experiment 12 are digested with the restriction enzymes: SmaI and ScaI. Only Sca and Sma are both incubated at 37 degrees Celcius. Sma has to be incubated at 25 degrees Celcius. This is done in experiment 15.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Digestions have been done of the biobrickcombinations K352002 +K133116 + pSB1K3 and K352003 + K133116 + pSB1K3 with restriction-enzymes ScaI and SmaI</p> | + | <div class="description">b'<p>Digestions have been done of the biobrickcombinations K352002 +K133116 + pSB1K3 and K352003 + K133116 + pSB1K3 with restriction-enzymes ScaI and SmaI</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>All the digestions of experiment 13 have digested again with SmaI for an our at 25 degrees Celcius. Because earlier the digestions have been put immediately bt 37 degrees Celcius. It looks like H1, J1 and D2 include the right biobricks. </p> | + | <div class="description">b'<p>All the digestions of experiment 13 have digested again with SmaI for an our at 25 degrees Celcius. Because earlier the digestions have been put immediately bt 37 degrees Celcius. It looks like H1, J1 and D2 include the right biobricks. </p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Minipreps of the biobrick combinations: K352002+K133116+pSB1K3 (1) and K352003+K133116+pSB1K3 (2) are done. The DNA concentration is for 1:189,3 ng/ | + | <div class="description">b'<p>Minipreps of the biobrick combinations: K352002+K133116+pSB1K3 (1) and K352003+K133116+pSB1K3 (2) are done. The DNA concentration is for 1:189,3 ng/\xc2\xb5l and for 2: 355,3 ng/\xc2\xb5l.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>Different strains of E.coli are tested as negative control. Those strains were: | + | <div class="description">b"<p>Different strains of E.coli are tested as negative control. Those strains were: NEB10B\xc3\xa8ta, BL21 (DE3), BL21, HB101, DH5alpha and JM109. NEB10B\xc3\xa8ta produced the most gas. BL21, HB101 and JM101 produced none/almost none gas. Because BL21 isn't a K12 strain we can not use that one. That is why we will test further gasproduction in HB101 and JM109. And maybe those will be our final E.coli strains.</p>\n"</div> |
| − | </div> | + | |
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description">32 minipreps have been performed. A lot of them have a low concentration nucleic acid and/or have a high 260/280 and 260/230 rate. Therefore those will be done again.</div> | + | <div class="description">b'32 minipreps have been performed. A lot of them have a low concentration nucleic acid and/or have a high 260/280 and 260/230 rate. Therefore those will be done again.'</div> |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Making overnight cultures of the numbers: A1, A4, A5, A6, B1, B5, B6 C1, C2, C3, C4, C5, C6, E1, E2, E5, E6, F4, F5 with Kanamycin. These biobrick combinations can be found in experiment 12. Also the first digestions with XbaI, Eco0109I, HindIII and SspI-HF have been done.</p> | + | <div class="description">b'<p>Making overnight cultures of the numbers: A1, A4, A5, A6, B1, B5, B6 C1, C2, C3, C4, C5, C6, E1, E2, E5, E6, F4, F5 with Kanamycin. These biobrick combinations can be found in experiment 12. Also the first digestions with XbaI, Eco0109I, HindIII and SspI-HF have been done.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Minipreps have been made of the numbers: A1, A4, A5, A6, B1, B5, B6 C1, C2, C3, C4, C5, C6, E1, E2, E5, E6, F4, F5.</p> | + | <div class="description">b'<p>Minipreps have been made of the numbers: A1, A4, A5, A6, B1, B5, B6 C1, C2, C3, C4, C5, C6, E1, E2, E5, E6, F4, F5.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>From 27-09 until 04-10 more than 200 digestions and 17 gelelectrophoresis have been performed. This was done as a control for our composite parts. We digested with XbaI, Eco01019 and SspI-HF/HindIII. Every restriction-enzyme has an unique place to cut in our constructs. With this we could test if the promoter, backbone and gas production gene was present. However, the digestions didn't show us very good results. After this we started with PCR.</p> | + | <div class="description">b"<p>From 27-09 until 04-10 more than 200 digestions and 17 gelelectrophoresis have been performed. This was done as a control for our composite parts. We digested with XbaI, Eco01019 and SspI-HF/HindIII. Every restriction-enzyme has an unique place to cut in our constructs. With this we could test if the promoter, backbone and gas production gene was present. However, the digestions didn't show us very good results. After this we started with PCR.</p>\n"</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p></p></div> | + | <div class="description">b'<p></p>'</div> |
</div> | </div> | ||
| Line 4,354: | Line 4,089: | ||
</div> | </div> | ||
<div class="attendees">Randall de Waard | Elise Grootscholten</div> | <div class="attendees">Randall de Waard | Elise Grootscholten</div> | ||
| − | <div class="description"><p></p></div> | + | <div class="description">b'<p></p>'</div> |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Randall de Waard</div> | <div class="attendees">Elise Grootscholten | Randall de Waard</div> | ||
| − | <div class="description"><p>Digestions with EcoRI-HF and PstI are done for the biobrick numbers A2, B1, B5, B6, D1, E1, E3, I1, J1, J1.2, CooA (8) and pSB1C3. This is done because now the Kanamycin backbone can be replaced for the Chloramphenicol backbone. This is done by dephosphorylation and ligation.</p> | + | <div class="description">b'<p>Digestions with EcoRI-HF and PstI are done for the biobrick numbers A2, B1, B5, B6, D1, E1, E3, I1, J1, J1.2, CooA (8) and pSB1C3. This is done because now the Kanamycin backbone can be replaced for the Chloramphenicol backbone. This is done by dephosphorylation and ligation.</p>\n'</div> |
| − | </div> | + | |
</div> | </div> | ||
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<div class="attendees">Elise Grootscholten | Paul Reusink</div> | <div class="attendees">Elise Grootscholten | Paul Reusink</div> | ||
| − | <div class="description"><p>Overnight cultures made of the following strains with the right plasmid:</p> | + | <div class="description">b'<p>Overnight cultures made of the following strains with the right plasmid:</p>\n\n<table border="1" cellpadding="1" cellspacing="1" style="width: 322px;">\n\t<tbody>\n\t\t<tr>\n\t\t\t<td style="width: 88px;"><strong>Number</strong></td>\n\t\t\t<td style="width: 105px;"><strong>HB101</strong></td>\n\t\t\t<td style="width: 113px;"><strong>JM109</strong></td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 88px;">J1</td>\n\t\t\t<td style="width: 105px;">1x</td>\n\t\t\t<td style="width: 113px;">1x</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 88px;">I1</td>\n\t\t\t<td style="width: 105px;">3x</td>\n\t\t\t<td style="width: 113px;">3x</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 88px;">D1</td>\n\t\t\t<td style="width: 105px;">2x</td>\n\t\t\t<td style="width: 113px;">2x</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 88px;">B1</td>\n\t\t\t<td style="width: 105px;">1x</td>\n\t\t\t<td style="width: 113px;">1x</td>\n\t\t</tr>\n\t\t<tr>\n\t\t\t<td style="width: 88px;">B6</td>\n\t\t\t<td style="width: 105px;">1x</td>\n\t\t\t<td style="width: 113px;">1x</td>\n\t\t</tr>\n\t</tbody>\n</table>\n\n<p><em>Table 1: Overnight culture scheme.</em></p>\n'</div> |
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| − | <p><em>Table 1: Overnight culture scheme.</em></p> | + | |
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</div> | </div> | ||
Revision as of 10:46, 12 October 2018
Notebook
Notebook
show wetlab entriesshow hardware entries
show software entries
Rens Boeser
b'Created the first prototype for the team page'
01
Team page
May 10
Rens Boeser
b'Social media created'
01
Footer
May 20
Rens Boeser
b'Social media buttons same color and fixed iGEM style issues'
02
Footer
May 21
Rens Boeser
b'Multiple week summary styles created for the notes'
01
Notebook
May 24
Rens Boeser
b'Added the header with mobile compatibility als resized logos and readded them to the header'
01
Header
May 27
Rens Boeser
b"Added template header and footer with 'under construction' content"
01
Main template
May 28
Rens Boeser
b'Small fixes and menu adjustments'
02
Header
May 28
Rens Boeser
b'Added a PI list with the secondary PI'
02
Team
May 29
Rens Boeser
b'Designed and added content holders to the index Page'
01
Main page
June 7
Rens Boeser
b'Added myself to the teammember Page and did some bugfixing'
03
Team
June 9
Rens Boeser
b'Started working on a better looking menubar'
03
Header
June 9
Rens Boeser
b'Added the ability to add sub-menus to items in the menu bar. Integration into the website and added indication for which Page you are on'
04
Header
June 10
Rens Boeser
b'Updated all Pages to the new style with an under construction sign'
01
Construction pages
June 13
Rens Boeser
b'Added a way to recognise Pages under construction using the menubar'
05
Header
June 14
Rens Boeser
b'Updated the content containers so that they are responsive'
02
Main page
June 14
Tom van Dijk | Mike Vrieswijk
b'The first draft of the architecture design for the temperature controller was made.'
01
Architecture design [TC]
June 18
Rens Boeser
b'Content added to the human practices page'
01
Human Practices page
June 22
Rens Boeser
b'Content created and added to the main page'
03
Main page
June 23
Tom van Dijk | Mike Vrieswijk
b'Today a few changes have been made to the architecture design of the temperature controller. The choice was made to use a premade power supply as opposed to a self-made one, because this was considering the time left to finish this device the best choice. A few alterations were made to make the architecture design better readable.'
02
Architecture design [TC]
June 24
Tom van Dijk | Mike Vrieswijk
b'A 3d drawing was made for the casing that will hold the temperature controller. The first prototype was printed, but was determent to be inadequate due to the lack of enough space for the cooler block.'
01
First prototype [TC]
June 25
Rens Boeser
b'Added the remaining instructors to the team'
04
Team
June 26
Tom van Dijk | Mike Vrieswijk
b'In the drawing space was added to fit the cooler block for the temperature controller. Slits were added to the drawing for the nuts to slide into. The altered drawing was printed. The newly printed parts, cooler block, fan and Peltier element were assembled. Everything fit together.'
02
Second prototype [TC]
June 26
Dustin van der Meulen
b'To start testing the production of CooA, we firstly resuspended and transformed the BioBricks from the kit witch we wanted to use (Table 1). This has been done using the iGEM Kit plate instructions (Protocol 1, step 1 - 3) and the NEB 10 b\xc3\xa9ta transformation protocol adapted New England Biolabs (Protocol 2), using bought cells with a reported transformation efficienty of 1-3 10^9 cfu/\xc2\xb5g pUC19. Inucbation was at 37\xc2\xb0C.
\n
\nTable 1 : Resuspended BioBricks from the iGEM 2018 Distribution kit and their uses.\n\n\t\n\t\t
\n
\nAfter checking the plates on the 28th of June, we recieved the following results (Table 2):
\n
\nTable 2 : Kolonies found after overnight growth.\n\n\t\n\t\t
\n'
\n
\nTable 1 : Resuspended BioBricks from the iGEM 2018 Distribution kit and their uses.\n
| BBa_K592009 | \n\t\t\tBlue Chromoprotein AmilCP | \n\t\t
| BBa_B0031 | \n\t\t\tRibosomal binding site (strong), derived from BBa_B0030 | \n\t\t
| BBa_B0032 | \n\t\t\tRibosomal binding site (medium), derived from BBa_B0030 | \n\t\t
| BBa_B0030 | \n\t\t\tRibosomal binding site (weak) | \n\t\t
| BBa_B0015 | \n\t\t\tDouble terminator (BBa_B0010 & BBa_B0012) | \n\t\t
| BBa_J23100 | \n\t\t\tStrong Constitutive Anderson Promotor | \n\t\t
| BBa_J23105 | \n\t\t\tMedium Constitutive Anderson Promotor | \n\t\t
| BBa_J23113 | \n\t\t\tWeak Constitutive Anderson Promotor | \n\t\t
| BBa_J45199 | \n\t\t\tBanana odor enzyme (ATF1) generator | \n\t\t
| BBa_K1184000 | \n\t\t\tKiller Red | \n\t\t
| BBa_K352001 | \n\t\t\tCooA | \n\t\t
| BBa_K352011 | \n\t\t\tCooA responsive system | \n\t\t
\nAfter checking the plates on the 28th of June, we recieved the following results (Table 2):
\n
\nTable 2 : Kolonies found after overnight growth.\n
| BBa_K592009 | \n\t\t\t20 colonies | \n\t\t
| BBa_B0031 | \n\t\t\t4 colonies | \n\t\t
| BBa_B0032 | \n\t\t\t5 colonies | \n\t\t
| BBa_B0030 | \n\t\t\t1 colonies | \n\t\t
| BBa_B0015 | \n\t\t\t6 colonies | \n\t\t
| BBa_J23100 | \n\t\t\t1 colonies | \n\t\t
| BBa_J23105 | \n\t\t\t98 colonies | \n\t\t
| BBa_J23113 | \n\t\t\t19 colonies | \n\t\t
| BBa_J45199 | \n\t\t\t0 colonies | \n\t\t
| BBa_K1184000 | \n\t\t\t4 colonies | \n\t\t
| BBa_K352001 | \n\t\t\t2 colonies | \n\t\t
| BBa_K352011 | \n\t\t\t4 colonies | \n\t\t
1
Assessing CooA Production
June 26
Tom van Dijk | Mike Vrieswijk
b'A short test run was done with the newly assembled cooler. The test concluded that the temperature controller could cool a water droplet to the point of freezing and heat it back up to its boiling point.'
03
Testrun [TC]
June 27
Dustin van der Meulen
b'\n\t\n\t\t
\n
\nAfter assessign our results, in the future we will perform the ethanol carry-over steps.
\n
\nAlso from the previously mentioned overnight culture 1 mL has been used to make Glycerol Stock (Protocol 4)'
After making a 20 mL overnight culture of our NEB 10 b\xc3\xa9ta cells containing our BioBricks, we performed a mini prep (Protocol 3). Using our nanodrop spectrophotometer which gave us the following DNA concentrations:
\n
| BBa_K592009 | \n\t\t\t72,5 ng/\xc2\xb5L | \n\t\t
| BBa_B0031 | \n\t\t\t118,9 ng/\xc2\xb5L | \n\t\t
| BBa_B0032 | \n\t\t\t52,5 ng/\xc2\xb5L | \n\t\t
| BBa_B0030 | \n\t\t\t488,6 ng/\xc2\xb5L | \n\t\t
| BBa_B0015 | \n\t\t\t53,5 ng/\xc2\xb5L | \n\t\t
| BBa_J23100 | \n\t\t\t148,3 ng/\xc2\xb5L | \n\t\t
| BBa_J23105 | \n\t\t\t96,3 ng/\xc2\xb5L | \n\t\t
| BBa_J23113 | \n\t\t\t151,8 ng/\xc2\xb5L | \n\t\t
| BBa_K118400 | \n\t\t\t140,4 ng/\xc2\xb5L | \n\t\t
| BBa_K352001 | \n\t\t\t77,7 ng/\xc2\xb5L | \n\t\t
| BBa_K352011 | \n\t\t\t76,8 ng/\xc2\xb5L | \n\t\t
\nAfter assessign our results, in the future we will perform the ethanol carry-over steps.
\n
\nAlso from the previously mentioned overnight culture 1 mL has been used to make Glycerol Stock (Protocol 4)'
2
Assessing CooA Production
June 29
Tom van Dijk | Mike Vrieswijk
b'The choice to use a computer PSU as a power supply was made. The choice was made on the grounds, that computer PSU have a standard 12, 5 and 3.3V output. This is beneficial because these are the voltages necessary for the selected components.'
01
Draft decision
July 2
Dustin van der Meulen
b'
Today we performed a digestion, dephosphorilation and ligation (following protocols 4 and 5) of a few promotor and RBS BioBricks. Because of administrative compliations only the variants with J23113 and a RBS could be made.
\n'3
Assessing CooA Production
July 2
Tom van Dijk | Mike Vrieswijk
b'Changes were made to the architecture design of the temperature controller. Different voltage regulators were selected to fit the newly chosen power supply. To better readability of the architecture design a legend was added.'
03
Architecture design [TC]
July 5
Tom van Dijk | Mike Vrieswijk
b'Custom footprints were made for multiple components and added to the parts library in the PCB design software.'
01
Electrical circuit design [TC]
July 8
Tom van Dijk | Mike Vrieswijk
b'The provisional electronic circuit design for the temperature controller was made.'
02
Electrical circuit design [TC]
July 9
Tom van Dijk | Mike Vrieswijk
b'The electronic circuit design for the temperature controller was finished. Measuring point were added to the electronic circuit design.'
03
Electrical circuit design [TC]
July 11
Elise Grootscholten | Loraine Nelson | Paul Reusink
b'To have some basic biobricks ready, we stocked them by doing a plasmid isolation and freeze the DNA. '
01
Stock up
July 11
Elise Grootscholten | Loraine Nelson | Paul Reusink
b'To start on a basic construct we did a digestion and ligation with the parts we isolated earlier. To prevent original constructs we did a defosphorylation after the digestion. We controlled the digestion by doing a gelelktroforeses. '
01
Basic parts
July 11
Tom van Dijk | Mike Vrieswijk
b'Started working on the board layout for the PCB of the temperature controller.'
01
Board layout [TC]
July 12
Tom van Dijk | Randall de Waard
b'We continued with the ligated DNA by transformating it to Neb10Beta. This was plated onto agarplates and incubated for 1 day. '
02
Basic parts
July 12
Tom van Dijk | Mike Vrieswijk
b'Further work was done to the board layout for the temperature controller.'
02
Board layout [TC]
July 13
Elise Grootscholten | Randall de Waard
b"The results of 7/12/2018 were collected, in action of this we decided to plate some ligated and transferred DNA from 7/12/2018 again. This we did because there wasn't a clear grow of colonies on the plates."
03
Basic parts
July 13
Elise Grootscholten | Randall de Waard
b'We tried to let bacteria grow on paper, therefore we used our own buisnesscards. We let the buisnesscards absorb some LB-medium and put them inside petridishes. '
01
Blue White screening on paper
July 13
Tom van Dijk | Mike Vrieswijk
b'Work has been done on the board layout for the temperature controller. The board layout is now finished.'
03
Board layout [TC]
July 15
Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Randall de Waard
b"To know if the ligation was succesfull we will controll the DNA, therefor we ented the bacteria's with DNA in LB-medium to grow overnight. We also plated the used bacteria's onto new plates to use for further experiments. "
04
Basic parts
July 16
Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Randall de Waard
b'We did a blue white screening on our buisnesscards to see if bacteria had grew on them. We transferred the buisnesscards to new petrydishes and added ITPG and X-gal to the petrydishes. '
02
Blue White screening on paper
July 16
Rens Boeser
b'Frontend design for the notebook'
02
Notebook
July 17
Rens Boeser | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard
b'The resulst of 7/16/2018 showed that the DNA didnt ligate as planned. To be able to digest enough DNA we did a plasmid isolation again. We digested this DNA and froze it for further use. '
05
Basic parts
July 17
Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Mike Vrieswijk | Randall de Waard
b'We did another round of plasmid isolation for stocking. '
02
Stock up
July 18
Rens Boeser
b'Designed a way to follow experiments that take up multiple days and eventually designed a notebook entry page and made it a responsive page'
03
Notebook
July 19
Dustin van der Meulen | Mei Ju Goemans| Randall de Waard
b'We digested all DNA we have in stock to test for our basic construct. We tested the DNA by doing a gelelktroforeses. '
06
Basic parts
July 19
Rens Boeser
b'Created a one page notebook. Made the notebook entry page more suited for the entry length'
04
Notebook
July 21
Elise Grootscholten | Randall de Waard
b"
Transformations of the biobricks K133071, K173003 and I13453 are performed. K133071 will produce CO2 if there's pyruvate present and K173003 will produce CO2 if urea is present. I13453 is a promotor which will work if there's arabinose present.
\nThe biobricks were transformed first into electrocometent cells and later into chemical competent cells from the strain NEb10Beta. After transformations the culture was plated on agar plates with antibiotics. The first transformations didn't work out, but the second did, because then the right competent cells were used.
1
Assessing Gas Production BioBricks in E.Coli
July 23
Rens Boeser | Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard
b'New biobricks, used to make an ATP sensor, were transformed into NEB10Beta. The culture was than plated onto agar and incubated for 1 day. '
01
ATP sensor
July 24
Rens Boeser | Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard
b'New biobricks, which produces gasses, were transformed into NEB10Beta. The culture was than plated onto agar and incubated for 1 day. '
01
Gas output
July 24
Rens Boeser
b'Started working on an automatic notebook creator'
01
Notebook generator
July 24
Loraine Nelson | Elise Grootscholten | Paul Reusink
b'
Today we did a transformation with new biobricks. The biobricks were built into chemically competent cells from the strain NEb10Beta. After transformation the culture was plated on agar plates with antibiotics. The results were checked the next day.
\n'1
Transformation
July 24
Elise Grootscholten | Randall de Waard
b'
To be able to always get the necessary biobricks, there have been made glycerolstocks of the transformed biobricks K133071, K173003 and I13453. The glycerolstocks are stored at -80 degrees Celsius. If needed, they can be retrieved from this storage to use for experiments.
\n'2
Assessing Gas Production BioBricks in E.Coli
July 24
Rens Boeser
b'Automatic generation of entries completed'
02
Notebook generator
July 25
Rens Boeser
b'Used the Google drive REST API to download the entries from drive'
01
Google Drive API
July 25
Rens Boeser
b'Used the igemwiki API to update pages using software'
01
Automatic uploader
July 25
Loraine Nelson | Elise Grootscholten | Paul Reusink
b'
To be able to always get the necessary biobricks, we made an glycerol stock after every transformation. The glycerol stocks are stored at -80 degrees Celsius. If needed, they can retrieved from this storage to use for experiments.
\n'2
Transformation
July 27
Elise Grootscholten | Randall de Waard
b'
For further experiments there is isolated DNA needed of the biobricks J23100, K133071, K173003 and I134353. The DNA is isolated out of the bacteria with the help of a plasmid purifaction kit. After isolation this DNA can be used for digestion and ligation or other experiments. J23100 (from the glycerolstock): 325,59 ng/ul, K173003: 217,06 ng/ul, K133071: 186,79 ng/ul, I13453: 88,18 ng/ul
\n'3
Assessing Gas Production BioBricks in E.Coli
July 27
Rens Boeser
b'Connected the page uploader to the notebook generator'
01
Automation program
July 29
Rens Boeser
b'Created a program that uploads all updated pages'
02
Automatic uploader
July 29
Rens Boeser
b'Built a page builder that automatically adds the header and footer before uploading'
01
Page generator
July 31
Rens Boeser
b'Redone the google API handler for reusability and readability and made the google API handler generic'
02
Google Drive API
July 31
Rens Boeser
b'revamped the main program'
02
Automation program
July 31
Rens Boeser
b'Finished redoing the application for generating and uploading pages'
03
Automation program
August 1
Rens Boeser
b'Added month categorization to the page'
05
Notebook
August 2
Loraine Nelson | Elise Grootscholten | Paul Reusink
b'
For further experiments we needed isolated DNA. The DNA is isolated out of the bacteria with the help of a plasmid purifaction kit. After isolation this DNA can be used for digestion and ligation or other experiments.
\n'3
Transformation
August 9
Elise Grootscholten | Randall de Waard
b'
The biobricks J23100, K133071, K173003 and I134353 were sucessfully digested after the second time. After the digestions the biobricks K133071 and K173003 were dephosphorylated and ligated with the inserts J23100 and I13453. This was done in the original backbone of K133071 and K173003, and not another control backbone. To know if the biobricks were right ligated this was done by testing practically. See the experiments: Testing gas production.
\n'4
Assessing Gas Production BioBricks in E.Coli
August 10
Randall de Waard | Elise Grootscholten
b'
Testing different amounts of urea and sodiumpyruvate to know which concentrations the bacteria survive.
\n'1
Urea and sodium pyruvate test for resistance E.coli
August 10
Elise Grootscholten | Randall de Waard
b'
Transformations of the biobricks (K133071 + J23100), (K13071 + I1345), (K173003 + J23100) and (K173003 + I13453) in NEB10B\xc3\xa8ta. There was no grow except for the biobrick combination K133071 + J23100.
\n'5
Assessing Gas Production BioBricks in E.Coli
August 13
Elise Grootscholten | Randall de Waard
b"
A colony PCR is done for the NEB10B\xc3\xa8ta E.coli cells with expected the biobrick combination of K133071 with J23100. Nevertheless, on a gel the difference with and without promotor couldn't be seen. So there must be another way of proving the right biobricks are there.
\n"6
Assessing Gas Production BioBricks in E.Coli
August 13
Elise Grootscholten | Randall de Waard
b'The ligations and transformations of the biobricks K173003 + J23100, K173003 + I13453, and K133071 + I13453 has been performed again. There was a lot of grow on the agar plates. To know if the biobricks were right ligated this was done by testing practically. See the experiments: Testing gas production.\xe2\x80\x8b '
7
Assessing Gas Production BioBricks in E.Coli
August 13
Elise Grootscholten | Paul Reusink
b'
Making a set up for the gas production testing and testing it with NEB10B\xc3\xa8ta with the expected biobricks in it (K133071 + J23100) and a negative control.
\n'1
Testing gas production
August 16
Elise Grootscholten | Paul Reusink
b'
Making a set up for the gas production testing and testing it with NEB10B\xc3\xa8ta with the expected biobricks in it (K133071 + I13453), (K173003 + J23100), (K173003 + I13453) and a negative control.
\n'2
Testing gas production
August 23
Elise Grootscholten | Paul Reusink
b'
Gasproduction testing for the biobricks (K173003 + I13453), (K133071 + I13453) and negative controls (B0015 and K133071 without urea and arabinose).
\nK173003 + I13453 is tested with sodiumpyruvate and arabinose for gasproduction and K133071 + I13453 is tested with urea and arabinose for gasproduction.
\nThe negative control also produces a little bit gas.
3
Testing gas production
August 23
Elise Grootscholten | Paul Reusink
b'
Testing the gasproduction of the colonies 9 and 10 of biobricks (K173003 + J23100), colonies 5 and 7 of biobricks (K173003 + I13453) and colony 4 of biobricks (K133071 + I13453) with and without centrifuging the bacteria. There is also a negative control (J04450 pSB1K3) with Kanamycine. The negative contol started with a lot of gas inside the tube. We can not see wether there is produced more after a day or not. This have to be tested later.
\n'4
Testing gas production
August 23
Elise Grootscholten | Randall de Waard
b'
Minipreps are made of colonies 11 and 19 of biobrick combination K133071 + J23100. Results: 11. 270,57 ng/ul 19. 253,59 ng/ul.
\n'8
Assessing Gas Production BioBricks in E.Coli
August 27
Elise Grootscholten | Randall de Waard
b'
A miniprep of the biobrick K352002 is made. The concentration is 69,77 ng/ul.
\n'9
Assessing Gas Production BioBricks in E.Coli
August 27
Randall de Waard | Elise Grootscholten
b'
Testing different amounts of urea and sodiumpyruvate to know which concentrations the bacteria survive.
\n'2
Urea and sodium pyruvate test for resistance E.coli
August 28
None
b''
1
Chemo competent cells
August 30
Elise Grootscholten | Randall de Waard
b'
Digestions, gelelectrophoresis, dephosphorylations and ligations of different biobrick combinations. These biobrick combinations are 4 different promotors (J23100, I13453, K352002, K352003) with 4 different gasproduction biobricks (k173003, K173013, K133071, K133116). J23100 is about 1 kb to long. The rest seems likely to be right digested. The ligations will be transformed in NEB10b\xc3\xa8ta and digested again as control.
\n'10
Assessing Gas Production BioBricks in E.Coli
September 7
Elise Grootscholten | Randall de Waard
b'
Transformations of the biobrick combinations in NEB10b\xc3\xa8ta. The transformations are plated on kanamycine agar plates, because all the ligations were done in pSB1K3 (kanamycine resistence) backbone. Pink and with colonies appeared after incubation by 37 degrees Celcius for about 12h. The white colonies will be used for further experiments.
\n'11
Assessing Gas Production BioBricks in E.Coli
September 7
Elise Grootscholten | Randall de Waard
b'\n\t\n\t\t
\n\n
Plasmid DNA was isolated of 20 different colonies. The first time something went wrong. The second time we had good concentrations of isolated plasmid DNA. After this we will digest the DNA to see if the plasmids all have the required biobricks. The tube have a code from now on, see table 1.
\n
| Number | \n\t\t\tPromotor | \n\t\t\tGene | \n\t\t\tBackbone | \n\t\t
| A | \n\t\t\tK352002 (CooF) | \n\t\t\tK173013 | \n\t\t\tpSB1K3 | \n\t\t
| B | \n\t\t\tK352002 (CooF) | \n\t\t\tK133071 | \n\t\t\tpSB1K3 | \n\t\t
| C | \n\t\t\tK352002 (CooF) | \n\t\t\tK173003 | \n\t\t\tpSB1K3 | \n\t\t
| D | \n\t\t\tK352003 (CooM) | \n\t\t\tK133071 | \n\t\t\tpSB1K3 | \n\t\t
| E | \n\t\t\tK352003 (CooM) | \n\t\t\tK173003 | \n\t\t\tpSB1K3 | \n\t\t
| F | \n\t\t\tK352003 (CooM) | \n\t\t\tK173013 | \n\t\t\tpSB1K3 | \n\t\t
| H | \n\t\t\tI13453 | \n\t\t\tK173013 | \n\t\t\tpSB1K3 | \n\t\t
| I | \n\t\t\tI13453 | \n\t\t\tK173003 | \n\t\t\tpSB1K3 | \n\t\t
| J | \n\t\t\tII13453 | \n\t\t\tK133071 | \n\t\t\tpSB1K3 | \n\t\t
Table 1: list of biobricks of abbreviations
\n'12
Assessing Gas Production BioBricks in E.Coli
September 11
Elise Grootscholten | Randall de Waard
b'
The minipreps of experiment 12 are digested with the restriction enzymes: SmaI and ScaI. Only Sca and Sma are both incubated at 37 degrees Celcius. Sma has to be incubated at 25 degrees Celcius. This is done in experiment 15.
\n'13
Assessing Gas Production BioBricks in E.Coli
September 11
Elise Grootscholten | Randall de Waard
b'
Digestions have been done of the biobrickcombinations K352002 +K133116 + pSB1K3 and K352003 + K133116 + pSB1K3 with restriction-enzymes ScaI and SmaI
\n'15
Assessing Gas Production BioBricks in E.Coli
September 13
Elise Grootscholten | Randall de Waard
b'
All the digestions of experiment 13 have digested again with SmaI for an our at 25 degrees Celcius. Because earlier the digestions have been put immediately bt 37 degrees Celcius. It looks like H1, J1 and D2 include the right biobricks.
\n'16
Assessing Gas Production BioBricks in E.Coli
September 14
Elise Grootscholten | Randall de Waard
b'
Minipreps of the biobrick combinations: K352002+K133116+pSB1K3 (1) and K352003+K133116+pSB1K3 (2) are done. The DNA concentration is for 1:189,3 ng/\xc2\xb5l and for 2: 355,3 ng/\xc2\xb5l.
\n'14
Assessing Gas Production BioBricks in E.Coli
September 17
Elise Grootscholten | Paul Reusink
b"
Different strains of E.coli are tested as negative control. Those strains were: NEB10B\xc3\xa8ta, BL21 (DE3), BL21, HB101, DH5alpha and JM109. NEB10B\xc3\xa8ta produced the most gas. BL21, HB101 and JM101 produced none/almost none gas. Because BL21 isn't a K12 strain we can not use that one. That is why we will test further gasproduction in HB101 and JM109. And maybe those will be our final E.coli strains.
\n"5
Testing gas production
September 17
Elise Grootscholten | Randall de Waard
b'32 minipreps have been performed. A lot of them have a low concentration nucleic acid and/or have a high 260/280 and 260/230 rate. Therefore those will be done again.'
17
Assessing Gas Production BioBricks in E.Coli
September 20
Elise Grootscholten | Randall de Waard
b'
Making overnight cultures of the numbers: A1, A4, A5, A6, B1, B5, B6 C1, C2, C3, C4, C5, C6, E1, E2, E5, E6, F4, F5 with Kanamycin. These biobrick combinations can be found in experiment 12. Also the first digestions with XbaI, Eco0109I, HindIII and SspI-HF have been done.
\n'19
Assessing Gas Production BioBricks in E.Coli
September 26
Elise Grootscholten | Randall de Waard
b'
Minipreps have been made of the numbers: A1, A4, A5, A6, B1, B5, B6 C1, C2, C3, C4, C5, C6, E1, E2, E5, E6, F4, F5.
\n'20
Assessing Gas Production BioBricks in E.Coli
September 27
Elise Grootscholten | Randall de Waard
b"
From 27-09 until 04-10 more than 200 digestions and 17 gelelectrophoresis have been performed. This was done as a control for our composite parts. We digested with XbaI, Eco01019 and SspI-HF/HindIII. Every restriction-enzyme has an unique place to cut in our constructs. With this we could test if the promoter, backbone and gas production gene was present. However, the digestions didn't show us very good results. After this we started with PCR.
\n"21
Assessing Gas Production BioBricks in E.Coli
September 27
Elise Grootscholten | Randall de Waard
b''
22
Assessing Gas Production BioBricks in E.Coli
October 5
Randall de Waard | Elise Grootscholten
b''
1
PCR
October 7
Elise Grootscholten | Randall de Waard
b'
Digestions with EcoRI-HF and PstI are done for the biobrick numbers A2, B1, B5, B6, D1, E1, E3, I1, J1, J1.2, CooA (8) and pSB1C3. This is done because now the Kanamycin backbone can be replaced for the Chloramphenicol backbone. This is done by dephosphorylation and ligation.
\n'25
Assessing Gas Production BioBricks in E.Coli
October 8
Elise Grootscholten | Randall de Waard
b''
23
Assessing Gas Production BioBricks in E.Coli
October 11
Elise Grootscholten | Randall de Waard
b''
24
Assessing Gas Production BioBricks in E.Coli
October 11
Elise Grootscholten | Randall de Waard
b''
26
Assessing Gas Production BioBricks in E.Coli
October 11
Elise Grootscholten | Paul Reusink
b'\n\t\n\t\t
\n\n
Overnight cultures made of the following strains with the right plasmid:
\n\n| Number | \n\t\t\tHB101 | \n\t\t\tJM109 | \n\t\t
| J1 | \n\t\t\t1x | \n\t\t\t1x | \n\t\t
| I1 | \n\t\t\t3x | \n\t\t\t3x | \n\t\t
| D1 | \n\t\t\t2x | \n\t\t\t2x | \n\t\t
| B1 | \n\t\t\t1x | \n\t\t\t1x | \n\t\t
| B6 | \n\t\t\t1x | \n\t\t\t1x | \n\t\t
Table 1: Overnight culture scheme.
\n'6