Difference between revisions of "Team:York/Notebook"
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| + | <h1 style="-webkit-text-stroke: 2px black; color:#fff;">Notebook</h1> | ||
| + | <h1 style="-webkit-text-stroke: 2px black; color:#fff;">Tracking Our Progress</h1> | ||
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<h2 style="padding: 0px; margin-bottom: 0px;">Notebook</h2> | <h2 style="padding: 0px; margin-bottom: 0px;">Notebook</h2> | ||
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<!----------------------------- Week 1 --------------------------------------------> | <!----------------------------- Week 1 --------------------------------------------> | ||
<h3 id="week1">Week 1 (19 June - 25 June)</h3> | <h3 id="week1">Week 1 (19 June - 25 June)</h3> | ||
| Line 55: | Line 30: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | First week detailed experementation plan and lab supplies ordering. We have several candidates for a co-culture. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 64: | Line 39: | ||
<h4 class="media heading">Microscopy Division</h4> | <h4 class="media heading">Microscopy Division</h4> | ||
<p> | <p> | ||
| − | Had | + | Had the first meeting of the division. Discussed timeline and the components we have available. For now, we will order only camera. Figured out that Biology Labs do not have any lasers and optical benches. |
</p> | </p> | ||
</div> | </div> | ||
| Line 79: | Line 54: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | In the end of a last weeek, we decided to work with algae and bacteria. Biology Lab Safety talk for all team members. Prepared LB media for <i>E.coli</i> and pored it into plates. Freezig <i>E.coli</i> cells for an emergency. Checking plates for algae and liquid culture for transformation. Prepared for plasmid extraction via electrophoresis. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 101: | Line 76: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Digested and extracted pLM005. Prepared TAP media plates for algae. Performed colony PCR for ACA3. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 127: | Line 102: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Nanodroped and extracted PCR products. Re-streaked algae. Did cell counts through Optical Density and took pictures of Chlamydomonas. Currently we are devising growth experiments for algae and bacteria. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 154: | Line 129: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Obtaied bacteria growth curve in 96 well plate. Ethanol toxicity growth test should be run next week for <i>E.coli</i>. Some new plates were made. Performed Alkaline lysis, | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 177: | Line 152: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Growth tests are continuing. We are getting curve for bacteria. Repeating PCR using Polymerase Q5 for MEX1. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 207: | Line 182: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Started <i>E.coli</i> transformation. Designing growth test with 24 well plate for algae. 96 wels plate well's are too small for algae. Set-up co-culture with untransformed microorganisms. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 234: | Line 209: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Performed PCR for MEX1, again. Experimenting on our 'frankenstein' media for a co-culture. Co-culture testing in traditional media. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 257: | Line 232: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Obtained algae growth curve. Next is algae ethanol tolerance test. Still adjusting new media for co-culture. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 280: | Line 255: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Finally, we start transforming algae! In parallel, we run algae-bacteria depedence tests to find relationship between them. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 303: | Line 278: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | We have run initial transformation screening adn identified individual colonies containing assembled constructs. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 317: | Line 292: | ||
<br><br> | <br><br> | ||
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</li> | </li> | ||
</ul> | </ul> | ||
| Line 332: | Line 304: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Ordered BioBrick for <i>E.coli</i> that increases it's motility. Transformation did not proceed correctly. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 339: | Line 311: | ||
<h4 class="media heading">Microscopy Division</h4> | <h4 class="media heading">Microscopy Division</h4> | ||
<p> | <p> | ||
| − | We abandoned idea of using PDMS as a material for imaging chamber. | + | We abandoned idea of using PDMS as a material for imaging chamber. Aluminium case for our microscope is ready. We hope to get all parts by next week. |
</p> | </p> | ||
</div> | </div> | ||
| Line 355: | Line 327: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | It look like we will not be able to fix problem with algae transformation. It was ambitious task which was not possible to be done in such short period of time for us, but we still have the microscope. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 377: | Line 349: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Offered sacrifice sample of algae and bacteria to Microscopy Division. Analysing data from growth tests for algae and bacteria. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 384: | Line 356: | ||
<h4 class="media heading">Microscopy Division</h4> | <h4 class="media heading">Microscopy Division</h4> | ||
<p> | <p> | ||
| − | + | We have imaged <i>Chlamydomonas reinhardtii</i> and <i>E.coli</i> separately and together. We figured out that millichamber we have manufactured are too thick for your laser. Instead, we are using glass slide and coverslip. UI is completed. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 400: | Line 372: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Received BioBrick from iGEM HQ. We will transform <i>E.coli</i> to copmare motility of wild type and engineered organism. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 407: | Line 379: | ||
<h4 class="media heading">Microscopy Division</h4> | <h4 class="media heading">Microscopy Division</h4> | ||
<p> | <p> | ||
| − | + | We compared results from last week imaging and automated cell counter. It looks like our setup is working and we are able to calculate concetration of the microorganisms. We will do imaging of yeast and other bacteria and algae. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 423: | Line 395: | ||
<h4 class="media heading">Biology Division</h4> | <h4 class="media heading">Biology Division</h4> | ||
<p> | <p> | ||
| − | + | Transformed <i>E.coli</i>. If algae would be transformable so easily. | |
</p> | </p> | ||
<li class="media dry"> | <li class="media dry"> | ||
| Line 430: | Line 402: | ||
<h4 class="media heading">Microscopy Division</h4> | <h4 class="media heading">Microscopy Division</h4> | ||
<p> | <p> | ||
| − | + | Ran high motility bacteria on your DIHM. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 437: | Line 409: | ||
<br><br> | <br><br> | ||
| − | + | <!----------------------------- Week 17 --------------------------------------------> | |
| + | <h3 id="week16">Week 17 (9 October - 15 October)</h3> | ||
| + | <hr> | ||
| + | <ul class="media-list"> | ||
| + | <li class="media"> | ||
| + | <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" /> | ||
| + | <div class="media-body"> | ||
| + | <h4 class="media heading">Biology Division</h4> | ||
| + | <p> | ||
| + | Clenaing our lab space and helping to upload information to wiki. | ||
| + | </p> | ||
| + | <li class="media dry"> | ||
| + | <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" /> | ||
| + | <div class="media-body"> | ||
| + | <h4 class="media heading">Microscopy Division</h4> | ||
| + | <p> | ||
| + | Not much progress was done on laptop-microscope connection. | ||
| + | </p> | ||
| + | </div> | ||
| + | </li> | ||
| + | </ul> | ||
| + | <br><br> | ||
| + | |||
| + | <!----------------------------- Week 18 --------------------------------------------> | ||
| + | <h3 id="week18">Week 18 (16 October - 22 October)</h3> | ||
| + | <hr> | ||
| + | <ul class="media-list"> | ||
| + | <li class="media"> | ||
| + | <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" /> | ||
| + | <div class="media-body"> | ||
| + | <h4 class="media heading">Biology Division</h4> | ||
| + | <p> | ||
| + | Still clearing up the lab. | ||
| + | </p> | ||
| + | <li class="media dry"> | ||
| + | <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" /> | ||
| + | <div class="media-body"> | ||
| + | <h4 class="media heading">Microscopy Division</h4> | ||
| + | <p> | ||
| + | All content is being uploaded to wiki. | ||
| + | </p> | ||
| + | </div> | ||
| + | </li> | ||
| + | </ul> | ||
| + | <br><br> | ||
| + | |||
| + | <!----------------------------- Week 19 --------------------------------------------> | ||
| + | <h3 id="week19">Week 19 (23 October - 29 October)</h3> | ||
| + | <hr> | ||
| + | <ul class="media-list"> | ||
| + | <li class="media"> | ||
| + | <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" /> | ||
| + | <div class="media-body"> | ||
| + | <h4 class="media heading">Biology Division</h4> | ||
| + | <p> | ||
| + | Finished analysis of a growth curves and we are fully moved out of the lab. We will miss it. | ||
| + | </p> | ||
| + | <li class="media dry"> | ||
| + | <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" /> | ||
| + | <div class="media-body"> | ||
| + | <h4 class="media heading">Microscopy Division</h4> | ||
| + | <p> | ||
| + | Unfortunately, UI does not like computers other than were it was created. | ||
| + | </p> | ||
| + | </div> | ||
| + | </li> | ||
| + | </ul> | ||
| + | <br><br> | ||
| + | |||
| + | <!----------------------------- Week 19.5 --------------------------------------------> | ||
| + | <h3 id="week19.5">Week 19.5 (29 October - 1 November)</h3> | ||
| + | <hr> | ||
| + | <ul class="media-list"> | ||
| + | <li class="media"> | ||
| + | <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" /> | ||
| + | <div class="media-body"> | ||
| + | <h4 class="media heading">Biology Division</h4> | ||
| + | <p> | ||
| + | We are working on wiki, poster and presentation preparation. | ||
| + | </p> | ||
| + | <li class="media dry"> | ||
| + | <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" /> | ||
| + | <div class="media-body"> | ||
| + | <h4 class="media heading">Microscopy Division</h4> | ||
| + | <p> | ||
| + | Everybody is working hard on wiki and will do so until the deadline. | ||
| + | </p> | ||
| + | </div> | ||
| + | </li> | ||
| + | </ul> | ||
| + | <br><br> | ||
</div> | </div> | ||
</body> | </body> | ||
</html> | </html> | ||
{{:Team:York/Templates/Footer}} | {{:Team:York/Templates/Footer}} | ||
Latest revision as of 21:20, 31 October 2017
<!DOCTYPE html> <
Notebook
Week 1 (19 June - 25 June)
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Biology Division
First week detailed experementation plan and lab supplies ordering. We have several candidates for a co-culture.
-
Microscopy Division
Had the first meeting of the division. Discussed timeline and the components we have available. For now, we will order only camera. Figured out that Biology Labs do not have any lasers and optical benches.
Week 2 (26 June - 2 July)
-
Biology Division
In the end of a last weeek, we decided to work with algae and bacteria. Biology Lab Safety talk for all team members. Prepared LB media for E.coli and pored it into plates. Freezig E.coli cells for an emergency. Checking plates for algae and liquid culture for transformation. Prepared for plasmid extraction via electrophoresis.
Microscopy Division
We were given access to Physics Labs. It will be our home for the next weeks. We watched laser safety video and started taking pictures with freshly arrived Raspberry Pi V2 Camera. Made prototype of the DIHM. How easy was that?!
Week 3 (3 July - 9 July)
-
Biology Division
Digested and extracted pLM005. Prepared TAP media plates for algae. Performed colony PCR for ACA3.
Microscopy Division
Flower shape leaves pictures were obtained by shining laser on camera. Problem might be in IR filter on the lens of the camera. We ordered Raspberry Pi V2 NoIR camera which does not have IR filter. While waiting for a new camera, we were trying to make Rapsberry Pi to sent pictures automatically to desktop computer.
Week 4 (10 July - 16 July)
-
Biology Division
Nanodroped and extracted PCR products. Re-streaked algae. Did cell counts through Optical Density and took pictures of Chlamydomonas. Currently we are devising growth experiments for algae and bacteria.
Microscopy Division
Received NoIR camera. Leaves shape pattern solved. We were trying to observe diffraction from single slit experiment with a laser. Intensity of a laser was lowered with polarisation filter to avoid overexposure of camera. We used converging lens available in the lab to focus diffraction pattern on CMOS. Unfortunately, it was hard to setup to capture clear image. We are thinking to acquire lens with small focal distance to make setup as compact as possible.
Week 5 (17 July - 23 July)
-
Biology Division
Obtaied bacteria growth curve in 96 well plate. Ethanol toxicity growth test should be run next week for E.coli. Some new plates were made. Performed Alkaline lysis,
Microscopy Division
Removed lens from camera which was done easily. Now, light is shinning directly on CMOS. Still we have problems with alignment of laser, slits and camera. Moreover, single slit was too bright for naked CMOS. Now, we are using double slit experiment to observe interference in best tradition of Thomas Young.
Week 6 (24 July - 30 July)
-
Biology Division
Growth tests are continuing. We are getting curve for bacteria. Repeating PCR using Polymerase Q5 for MEX1.
Microscopy Division
After imaging double slit interference pattern we are moving to object imaging comperable with microorganisms size - microbeads. In parallel, we are translating software code for image reconstruction from LabVIEW to MATLAB. We received laser from TU Darmstadt team which is iterested in building DIHM, too.
Week 7 (31 July - 6 August)
-
Biology Division
Started E.coli transformation. Designing growth test with 24 well plate for algae. 96 wels plate well's are too small for algae. Set-up co-culture with untransformed microorganisms.
Microscopy Division
We were able to see single microbeads with our setup. Now, we have to be technical and measure precisely distances need for fully working DIHM. Also, we met with Dr Wilson to discuss our progress so far.
Week 8 (7 August - 13 August)
-
Biology Division
Performed PCR for MEX1, again. Experimenting on our 'frankenstein' media for a co-culture. Co-culture testing in traditional media.
Microscopy Division
Looks like we will have to make image analysis in Python for a beginning. We still see the noise on captured images.
Week 9 (14 August - 20 August)
-
Biology Division
Obtained algae growth curve. Next is algae ethanol tolerance test. Still adjusting new media for co-culture.
Microscopy Division
Last week we ordered a new laser and quality of the image changed drastically. Laser that we were using in the lab was inappropriate for Digital Holography as we have figured that out.
Week 10 (21 August - 27 August)
-
Biology Division
Finally, we start transforming algae! In parallel, we run algae-bacteria depedence tests to find relationship between them.
Microscopy Division
Image recostruction software is almost ready. We are thinking about the design of DIHM and seeking for inspiration around the campus. Teflon mold was made for us this week which we will use to cast PDMS.
Week 11 (28 August - 3 September)
-
Biology Division
We have run initial transformation screening adn identified individual colonies containing assembled constructs.
Microscopy Division
We find difficult to attach PDMS chamber to a glass slide. We met with plasma researcher in your university to discuss plasma bonding options. Whereas, UI for image capturing and analysis is rapidly developed.
Week 12 (4 September - 10 September)
-
Biology Division
Ordered BioBrick for E.coli that increases it's motility. Transformation did not proceed correctly.
Microscopy Division
We abandoned idea of using PDMS as a material for imaging chamber. Aluminium case for our microscope is ready. We hope to get all parts by next week.
Week 13 (11 September - 17 September)
-
Biology Division
It look like we will not be able to fix problem with algae transformation. It was ambitious task which was not possible to be done in such short period of time for us, but we still have the microscope.
Microscopy Division
Solution for imaging chamber was found by using acryl sheets and laser cutting. Desktop does not want to communicate with Raspberry Pi, but we will reconcile them.
Week 14 (18 September - 24 September)
-
Biology Division
Offered sacrifice sample of algae and bacteria to Microscopy Division. Analysing data from growth tests for algae and bacteria.
Microscopy Division
We have imaged Chlamydomonas reinhardtii and E.coli separately and together. We figured out that millichamber we have manufactured are too thick for your laser. Instead, we are using glass slide and coverslip. UI is completed.
Week 15 (25 September - 1 October)
-
Biology Division
Received BioBrick from iGEM HQ. We will transform E.coli to copmare motility of wild type and engineered organism.
Microscopy Division
We compared results from last week imaging and automated cell counter. It looks like our setup is working and we are able to calculate concetration of the microorganisms. We will do imaging of yeast and other bacteria and algae.
Week 16 (2 October - 8 October)
-
Biology Division
Transformed E.coli. If algae would be transformable so easily.
Microscopy Division
Ran high motility bacteria on your DIHM.
Week 17 (9 October - 15 October)
-
Biology Division
Clenaing our lab space and helping to upload information to wiki.
Microscopy Division
Not much progress was done on laptop-microscope connection.
Week 18 (16 October - 22 October)
-
Biology Division
Still clearing up the lab.
Microscopy Division
All content is being uploaded to wiki.
Week 19 (23 October - 29 October)
-
Biology Division
Finished analysis of a growth curves and we are fully moved out of the lab. We will miss it.
Microscopy Division
Unfortunately, UI does not like computers other than were it was created.
Week 19.5 (29 October - 1 November)
-
Biology Division
We are working on wiki, poster and presentation preparation.
Microscopy Division
Everybody is working hard on wiki and will do so until the deadline.
