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<div class="fixed-header-container"> | <div class="fixed-header-container"> | ||
− | + | <section class="fixed-image-header"> | |
− | + | <img src="https://static.igem.org/mediawiki/2019/8/81/T--Humboldt_Berlin--Notebook_Header.jpeg" alt="notebook" /> | |
− | + | </section> | |
− | + | <h1 class="page-headline description">Notebook</h1> | |
− | + | </div> | |
− | + | <div class="full-height fixed-header-content notebook"> | |
− | + | <div class="width-limit padding-container" style="margin: 50px 0;"> | |
− | + | <img src="https://static.igem.org/mediawiki/2019/e/e3/T--Humboldt_Berlin--notebook_final.png" alt="our stuffed calendar"/></br> | |
− | + | </div> | |
+ | <section class="width-limit"> | ||
+ | <div class="category-container"> | ||
+ | <h3>Select category</h3> | ||
<div class="category" data-category="synthesis"> | <div class="category" data-category="synthesis"> | ||
<img src="https://static.igem.org/mediawiki/2019/6/6f/T--Humboldt_Berlin--label_notebook_synthesis.png" alt="Synthesis: Parts and Vectors" /> | <img src="https://static.igem.org/mediawiki/2019/6/6f/T--Humboldt_Berlin--label_notebook_synthesis.png" alt="Synthesis: Parts and Vectors" /> | ||
Line 105: | Line 108: | ||
</div> | </div> | ||
<div class="category" data-category="chlamy"> | <div class="category" data-category="chlamy"> | ||
− | <img src="https://static.igem.org/mediawiki/2019/a/ac/T--Humboldt_Berlin--label_notebook_chlamy.png" alt="c. reinhardtii cultivation and transformations" /> | + | <img src="https://static.igem.org/mediawiki/2019/a/ac/T--Humboldt_Berlin--label_notebook_chlamy.png" alt="c. reinhardtii cultivation and transformations"/> |
</div> | </div> | ||
− | <div class="category" data-category="bioreaktor"> | + | <!--<div class="category" data-category="bioreaktor"> |
<img src="https://static.igem.org/mediawiki/2019/6/66/T--Humboldt_Berlin--label_notebook_bioreaktor.png" alt="bioreaktor" /> | <img src="https://static.igem.org/mediawiki/2019/6/66/T--Humboldt_Berlin--label_notebook_bioreaktor.png" alt="bioreaktor" /> | ||
− | </div> | + | </div>--> |
</div> | </div> | ||
<div class="timeline"> | <div class="timeline"> | ||
Line 117: | Line 120: | ||
- Research on PETase degradation <br> | - Research on PETase degradation <br> | ||
- Planning construction design for Golden Gate cloning using 10 different fusion sites according to Patron <br> | - Planning construction design for Golden Gate cloning using 10 different fusion sites according to Patron <br> | ||
− | - Designing Primers for C. reinhardtii specified promotor PsaD containing BpiI recognition site with MoClo fusion sites and fusion sites compatible for L0 backbone. Primers containing mutation to delete BpiI site (Primer 5,6,11-13)." | + | - Designing Primers for <i>C. reinhardtii</i> specified promotor PsaD containing BpiI recognition site with MoClo fusion sites and fusion sites compatible for L0 backbone. Primers containing mutation to delete BpiI site (Primer 5,6,11-13)." |
data-date="10/08 - 10/14" | data-date="10/08 - 10/14" | ||
data-category="synthesis"> | data-category="synthesis"> | ||
Line 123: | Line 126: | ||
</div> | </div> | ||
<div class="timeline-dot" | <div class="timeline-dot" | ||
− | data-text="- Research on C. reinhardtii cultivation <br> | + | data-text="- Research on <i>C. reinhardtii</i> cultivation <br> |
<h2>YFP</h2> | <h2>YFP</h2> | ||
- Designing Primers for YFP with B5-B5 fusion sites taken from AG Hegemann plasmid p135 (Primer 7+8)" | - Designing Primers for YFP with B5-B5 fusion sites taken from AG Hegemann plasmid p135 (Primer 7+8)" | ||
Line 210: | Line 213: | ||
- overnight cultures of DH10B with L0-PsaD A1/A3 and L0-PsaD A1/B1 | - overnight cultures of DH10B with L0-PsaD A1/A3 and L0-PsaD A1/B1 | ||
<div style='text-indent:20px;'>- plasmid prep of ON-culture</div> | <div style='text-indent:20px;'>- plasmid prep of ON-culture</div> | ||
− | <div style='text-indent:20px;'>- Nano- | + | <div style='text-indent:20px;'>- Nano-Drop concentration</div> |
- sequencing result: positive sequencing result of 1 clone each" | - sequencing result: positive sequencing result of 1 clone each" | ||
data-date="11/26 - 12/02" | data-date="11/26 - 12/02" | ||
Line 330: | Line 333: | ||
February | February | ||
</div> | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>His-Tag</h2> | ||
+ | - Corrected sequencing results of L0-6xHis-Tag B5-B5 | ||
+ | <h2>B2 Linker for Level 1 plasmid</h2> | ||
+ | - Designing DNA Oligos as a Linker module containing B2 fusion sites ('Primer' 72/73)" | ||
+ | data-category="synthesis" | ||
+ | data-date="02/04 - 02/10"> | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>Paromomycin</h2> | ||
+ | - Designing primers for aphVIII with B3-B4 fusion sites taken from AG Hegemann plasmid p114 (Primer 75+76) | ||
+ | <h2>Hygromycin</h2> | ||
+ | - Designing primers for aphVII with B3-B4 fusion sites taken from AG Hegemann plasmid p360 (Primer 77+78) | ||
+ | <h2>B2 Linker for Level 1 plasmid</h2> | ||
+ | - Oligo Annealing of B2 Linker using Primers 72/73" | ||
+ | data-category="synthesis" | ||
+ | data-date="02/11 - 02/17"> | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<div class='two-columns'><div> | ||
+ | <h2>Paromomycin</h2> | ||
+ | - <b>02/18</b> Doing a PCR with primers 75+76 and p114; PCR-clean up<br> | ||
+ | - <b>02/20</b> Golden Gate Restriction/Ligation of Paromomycin PCR Product (Paro B3-B4) with L0-RFP plasmid using <i>Bpi</i>I<br> | ||
+ | - <b>02/22</b> Heatshock Transformation of L0-Paro B3-B4 into heat-competent <i>E.coli</i> DH10B<br> | ||
+ | - Colony PCR | ||
+ | <h2>Hygromycin</h2> | ||
+ | - <b>02/18</b> Doing a PCR with primers 77+78 and p360 → Failed<br> | ||
+ | - <b>02/19</b> Repeating PCR with primers 77+78 and p360 → Failed<br> | ||
+ | - Optimization of annealing temperature to 62°C → we got the wanted product<br> | ||
+ | - <b>02/21</b> Golden Gate Restriction/Ligation of Hygromycin PCR Product (Hyg B3-B4) with L0-RFP plasmid using <i>Bpi</i>I<br> | ||
+ | - <b>02/22</b> Heatshock Transformation of L0-Hyg B3-B4 into heat-competent <i>E.coli</i> DH10B<br> | ||
+ | - Colony PCR with white colonies → Failed | ||
+ | </div> | ||
+ | <div> | ||
+ | <h2>Amp/Ori part for level 1 plasmid</h2> | ||
+ | - PCR to amplify Amp/Ori from pICH47732 backbone using primers 56/57<br> | ||
+ | - restriction of Amp/Ori with <i>Xba</i>I and BamHI | ||
+ | <h2>L1a,b,c-RFP part for level 1 plasmid</h2> | ||
+ | - PCR to amplify RFP from L0-RFP backbone using different primers to get 3 different L1 overhang versions<br> | ||
+ | -- L1a-RFP: Primer 58,59<br> | ||
+ | -- L1b-RFP: Primer: 60, 61<br> | ||
+ | -- L1c-RFP: Primer: 62, 63<br> | ||
+ | - Digestion of different PCR products using <i>Spe</i>I & <i>BamH</i>I | ||
+ | <h2>L1 Plasmids</h2> | ||
+ | - Ligation of Amp/Ori with<br> | ||
+ | -- 1) L1a-RFP<br> | ||
+ | -- 2) L1b-RFP<br> | ||
+ | -- 3) L1c-RFP using T4 ligase<br> | ||
+ | - Heat-shock Transformation into competent DH10B cells Result: not succesful | ||
+ | </div></div>" | ||
+ | data-category="synthesis" | ||
+ | data-date="02/18 - 02/24" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/b/be/T--Humboldt_Berlin--notebook_s_0218_1.png"> | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<div class='two-columns'><div> | ||
+ | <h2>Paromomycin</h2> | ||
+ | - Preparation of 3 overnight cultures of clones 1, 2, 3 (colony PCR 22.02.) <br> | ||
+ | - Plasmid prep the next day<br> | ||
+ | - Sending plasmids for sequencing <br> | ||
+ | - Corrected sequencing results of L0-Paro B3-B4 | ||
+ | <h2>Hygromycin</h2> | ||
+ | - <b>03/26</b> Second try of doing a colony PCR → worked out<br> | ||
+ | - Preparation of 3 overnight cultures K4,7,9<br> | ||
+ | - <b>03/27</b> plasmid prep + sending them in for sequencing<br> | ||
+ | - <b>03/28</b> Corrected sequencing results of L0-Hyg B3-B4 | ||
+ | </div> | ||
+ | <div> | ||
+ | <h2>L1a,b,c - RFP</h2> | ||
+ | - mistake: it was noticed that primer to amplify 3 different RFP versions were designed wrong → buffer bases were missing, so that the restriction enzymes did not attach to the DNA <br> | ||
+ | - designing and ordering new primers containing buffer bases (primer 84-89) | ||
+ | </div></div>" | ||
+ | data-date="02/25 - 03/03" | ||
+ | data-category="synthesis" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/b/bf/T--Humboldt_Berlin--notebook_s_0225_1.png"> | ||
+ | March | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>L1a,c,b, -RFP</h2> | ||
+ | - new PCR to amplify different RFP versions" | ||
+ | data-category="synthesis" | ||
+ | data-date="03/11 - 03/17"> | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<h2>YFP</h2> | ||
+ | - Primer design for a new YFP B4-B4 contruct (Primer 111 + 27)" | ||
+ | data-category="synthesis" | ||
+ | data-date="05/13 - 05/19"> | ||
+ | May | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<h2>YFP</h2> | ||
+ | - PCR of YFP B4-B4; size: 749 bp <br> | ||
+ | - Ligation YFP B4-B4 with L0-RFP" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/f/f7/T--Humboldt_Berlin--notebook_s_0527.png" | ||
+ | data-category="synthesis" | ||
+ | data-date="05/27 - 06/02"> | ||
+ | June | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>YFP</h2> | ||
+ | - Transformation L0-YFP B4-B4 into <i>E. coli </i><br> | ||
+ | - Colony PCR YFP-B4-B4 in <i>E. coli</i>" | ||
+ | data-category="synthesis" | ||
+ | data-date="06/03 - 06/09"> | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>YFP</h2> | ||
+ | - sequencing result of YFP B4-B4 clone 2 was positive" | ||
+ | data-category="synthesis" | ||
+ | data-date="06/17 - 06/23"> | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<h2>B2 Linker</h2> | ||
+ | - creating new primers" | ||
+ | data-category="synthesis" | ||
+ | data-date="07/01 - 07/07"> | ||
+ | July | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>B2 Linker</h2> | ||
+ | - Oligo Annealing B2 Linker<br> | ||
+ | - succesfull" | ||
+ | data-category="synthesis" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/e/e8/T--Humboldt_Berlin--notebook_s_0708.png" | ||
+ | data-date="06/17 - 06/23"> | ||
+ | </div> | ||
+ | |||
+ | |||
<!-- human practice --> | <!-- human practice --> | ||
− | <div class="timeline- | + | <div class="timeline-month" |
− | data-text=" | + | data-text="<h2>Green Week Berlin/ Microplastic presentation of BfR</h2> |
− | + | - participants: Fabienne, Andrej" | |
− | - | + | data-date="January 2019" |
− | data-date=" | + | data-image="https://static.igem.org/mediawiki/2019/4/45/T--Humboldt_Berlin--notebook_h_Jan19.jpeg" |
data-category="human-practice"> | data-category="human-practice"> | ||
+ | January 2019 | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<h2>TV report about “Chlamylicious”</h2> | ||
+ | - participants: Fabienne, Juli, Andrej, Dimitri" | ||
+ | data-date="May 2019" | ||
+ | data-category="human-practice" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/2/24/T--Humboldt_Berlin--notebook_h_May19.png"> | ||
+ | May | ||
</div> | </div> | ||
<div class="timeline-dot" | <div class="timeline-dot" | ||
− | data-text=" | + | data-text="<h2>2 week study at MPI Göttingen</h2> |
− | + | - participant: Darius" | |
− | - | + | |
− | + | ||
data-category="human-practice" | data-category="human-practice" | ||
− | data-date=" | + | data-date="May 2019"> |
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>Upcycling Project at the family event of Humboldt University with the collaboration of Satch backpacks</h2> | ||
+ | - participants: Sophia, Luise, Fabienne" | ||
+ | data-category="human-practice" | ||
+ | data-date="May 2019" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/f/fa/T--Humboldt_Berlin--notebook_h_May19_2.png"> | ||
</div> | </div> | ||
<div class="timeline-month" | <div class="timeline-month" | ||
− | data-text="<h2> | + | data-text="<h2>Long Night of The Sciences Berlin</h2> |
− | - | + | - participants: Juli, Darius, Luise, Paul, Johannes, Andrej, Ale, Patrick, Marc, Elena, Dimitri, Sandra, Fabienne, Saskia" |
− | + | data-date="June 2019" | |
− | + | ||
− | + | ||
− | + | ||
− | data-date=" | + | |
data-category="human-practice" | data-category="human-practice" | ||
− | data-image="https://static.igem.org/mediawiki/2019/ | + | data-image="https://static.igem.org/mediawiki/2019/8/8b/T--Humboldt_Berlin--notebook_h_Jun19.png"> |
− | November | + | June |
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<h2>Visit at MINT Microalgae Engineering</h2> | ||
+ | - participants: Paul, Darius, Dimitri, Andrej" | ||
+ | data-date="July 2019" | ||
+ | data-category="human-practice" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/6/69/T--Humboldt_Berlin--notebook_h_Jul19_1.png"> | ||
+ | July | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>Visit and presentation at ResearchGate Berlin</h2> | ||
+ | - participants: Juli, Darius, Andrej, Paul" | ||
+ | data-category="human-practice" | ||
+ | data-date="July 2019" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/2/2b/T--Humboldt_Berlin--notebook_h_Jul19_2.png"> | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>Visit and project presentation at MERCK</h2> | ||
+ | - participants: Andrej, Dimitri, Darius, Sophia, Saskia, Juli" | ||
+ | data-category="human-practice" | ||
+ | data-date="July 2019" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/5/5a/T--Humboldt_Berlin--notebook_h_Jul19_4.png"> | ||
+ | </div> | ||
+ | <div class="timeline-dot" | ||
+ | data-text="<h2>Visit at algae farm</h2> | ||
+ | - participants: Andrej, Dimitri, Darius, Fabienne, Johannes, Luise, Paul, Simon" | ||
+ | data-category="human-practice" | ||
+ | data-date="July 2019" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/b/b2/T--Humboldt_Berlin--notebook_h_Jul_5.jpeg"> | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<h2>Panel discussion about genetic editing</h2> | ||
+ | - participants: Luise, Sophia, Fabienne" | ||
+ | data-date="October 2019" | ||
+ | data-category="human-practice" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/5/5e/T--Humboldt_Berlin--notebook_h_oct19_3.png"> | ||
+ | October | ||
+ | </div> | ||
+ | |||
+ | <!-- reinhardtii cultivation and transformations (chlamy) --> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<h2>Cultivation of <i>C. reinhardtii</i> in the lab started, introductions to sterile working conditions</h2> | ||
+ | - participants: Alexander Bergmüller, Simon Kelterborn" | ||
+ | data-date="November 2018" | ||
+ | data-category="chlamy"> | ||
+ | November 2018 | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="<h2>First toxicity-tests on algal growth (strain CC-125) of ethylene glycol at concentrations between 0,005-5 % yields no results</h2> | ||
+ | - participants: Alexander Bergmüller" | ||
+ | data-date="November 2018 - December 2018" | ||
+ | data-category="chlamy"> | ||
+ | December | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="- Toxicity-tests: Inhibition of algal growth (strains CC-125 and CC-3403) by ethylene glycol at a concentration between 6-7 % was shown<br> | ||
+ | - Terephthalic acid shown not to inhibit algal growth<br><br> | ||
+ | - participants: Alexander Bergmüller, Sophia Schiebler Darius Rauch, Paul Herrmann" | ||
+ | data-date="January 2019" | ||
+ | data-category="chlamy"> | ||
+ | January | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="- First Toxicity-tests in a multicultivator, which measures algal growth under different conditions: Inhibition of C. reinhardtii by ethylene glycol at a concentration of 6 % was confirmed<br> | ||
+ | - Cultivation of strain CC-125 in high salt medium shows inhibited growth <br><br> | ||
+ | - participants: Paul Herrmann, Andrej Andjelic" | ||
+ | data-date="May 2019" | ||
+ | data-category="chlamy"> | ||
+ | May | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="- started the transformations of L1-constructs into Chlamy<br> | ||
+ | - checked the functionality of our paromomycin and hygromycin selection cassettes<br> | ||
+ | - Cultivation tests of strain SAG 11-32b in high salt medium with added PET in concentrations of 10-800 mg/L. Wastewater contains 250 mg/L PET before treatment. <br><br> | ||
+ | - participants: Simon Kelterborn, Darius Rauch, Dimitri Schumacher, Elena Rätsch, Juliana Rojas Pión, Paul Herrmann" | ||
+ | data-date="June 2019" | ||
+ | data-image="https://static.igem.org/mediawiki/2019/4/40/T--Humboldt_Berlin--HSM_PET.jpeg" | ||
+ | data-category="chlamy"> | ||
+ | June | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="- First Chlamy transformations are discarded, since they were contaminated<br> | ||
+ | - Transformation of further L1-constructs<br> | ||
+ | - constructs containing YFP: colony-PCR showed integration of the plasmid into Chlamy’s genome, but no fluorescence could be measured by the plate reader <br> | ||
+ | - PETase-YFP-containing constructs displayed fluorescence visible under the confocal microscopy<br><br> | ||
+ | - participants: Darius Rauch, Dimitri Schumacher, Elena Rätsch, Juliana Rojas Pión, Paul Herrmann" | ||
+ | data-date="July 2019" | ||
+ | data-category="chlamy"> | ||
+ | July | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="- Started with the construction of our own bioreactor. Conceptualization of the functionalities and necessary features had before been experimentally determined during our multicultivation tests<br>" | ||
+ | data-date="August 2019" | ||
+ | data-category="chlamy"> | ||
+ | August | ||
+ | </div> | ||
+ | <div class="timeline-month" | ||
+ | data-text="- Wiring and programming the sensors and LEDs on the DIY-bioreactor<br> | ||
+ | - laser-cutting of the shell and cultivation compartment of our bioreactor" | ||
+ | data-date="September 2019" | ||
+ | data-category="chlamy"> | ||
+ | September | ||
</div> | </div> | ||
</div> | </div> | ||
Line 446: | Line 690: | ||
function setFixedElements() { | function setFixedElements() { | ||
− | + | var timelineOffset = document.querySelector('.timeline').getBoundingClientRect().top; | |
+ | |||
+ | if (timelineOffset < 150) { | ||
infobox.classList.add('fixed') | infobox.classList.add('fixed') | ||
} else { | } else { | ||
Line 487: | Line 733: | ||
const activeElements = document.querySelectorAll('.active-timeline-el'); | const activeElements = document.querySelectorAll('.active-timeline-el'); | ||
− | + | var lastActive = activeElements[activeElements.length - 1]; | |
+ | if (lastActive === undefined) { | ||
+ | lastActive = document.querySelectorAll('.timeline > div.visible')[0]; | ||
+ | } | ||
if (lastActive !== undefined) { | if (lastActive !== undefined) { |
Latest revision as of 21:47, 21 October 2019
![notebook](https://static.igem.org/mediawiki/2019/8/81/T--Humboldt_Berlin--Notebook_Header.jpeg)
Notebook
![our stuffed calendar](https://static.igem.org/mediawiki/2019/e/e3/T--Humboldt_Berlin--notebook_final.png)
Select category
![Synthesis: Parts and Vectors](https://static.igem.org/mediawiki/2019/6/6f/T--Humboldt_Berlin--label_notebook_synthesis.png)
![human practice](https://static.igem.org/mediawiki/2019/e/e6/T--Humboldt_Berlin--label_notebook_human_practise.png)
![c. reinhardtii cultivation and transformations](https://static.igem.org/mediawiki/2019/a/ac/T--Humboldt_Berlin--label_notebook_chlamy.png)
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