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| | .offset-xl-11 { | | .offset-xl-11 { |
| | margin-left: 91.666667% | | margin-left: 91.666667% |
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| | + | .veggie td, |
| | + | .veggie th { |
| | + | padding: .75rem; |
| | + | vertical-align: top; |
| | + | border-top: 1px solid #F4F0DE; |
| | + | color: #F4F0DE; |
| | + | border-bottom: 1px solid #F4F0DE; |
| | + | z-index:100; |
| | + | } |
| | + | .veggie th { |
| | + | background-color: #2ecc71 !important; |
| | + | color: #232323 !important; |
| | + | z-index:100; |
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| | + | color: #adb3b7; |
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| | + | .veggie tbody+tbody { |
| | + | border-top: 2px solid #dee2e6; |
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| | .dropdown-menu { | | .dropdown-menu { |
| − | background-color: rgba(100, 100, 100, 1); | + | background-color: #232323; |
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| | <li id="ourStoryButton" class="nav-item mx-3"> | | <li id="ourStoryButton" class="nav-item mx-3"> |
| | <a class="nav-link" href="/Team:Tuebingen/Story" | | <a class="nav-link" href="/Team:Tuebingen/Story" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">OUR STORY</a> | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">OUR |
| | + | STORY</a> |
| | </li> | | </li> |
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| | <a class="dropdown-item" href="/Team:Tuebingen/Incretin" | | <a class="dropdown-item" href="/Team:Tuebingen/Incretin" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Incretin</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Incretin</a> |
| − | <a class="dropdown-item" href="/Team:Tuebingen/CPP" | + | <a class="dropdown-item" href="/Team:Tuebingen/Model" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Cell Penetrating Peptides</a> | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Model</a> |
| | + | <a class="dropdown-item" href="/Team:Tuebingen/Software" |
| | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Software</a> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Results" | | <a class="dropdown-item" href="/Team:Tuebingen/Results" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Results</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Results</a> |
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| | <a class="dropdown-item" href="/Team:Tuebingen/Notebook" | | <a class="dropdown-item" href="/Team:Tuebingen/Notebook" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Notebook</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Notebook</a> |
| − | <a class="dropdown-item" href="/Team:Tuebingen/Model"
| |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Model</a>
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| − | <a class="dropdown-item" href="/Team:Tuebingen/Software"
| |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Software</a>
| |
| | <a class="dropdown-item" href="/Team:Tuebingen/Outlook" | | <a class="dropdown-item" href="/Team:Tuebingen/Outlook" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Outlook</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Outlook</a> |
| | + | <a class="dropdown-item" href="/Team:Tuebingen/Entrepreneurship" |
| | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Entrepreneurship</a> |
| | </div> | | </div> |
| | </li> | | </li> |
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| | <div class="dropdown-menu"> | | <div class="dropdown-menu"> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Parts" | | <a class="dropdown-item" href="/Team:Tuebingen/Parts" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Parts Overview</a> | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Parts |
| | + | Overview</a> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Basic_Part" | | <a class="dropdown-item" href="/Team:Tuebingen/Basic_Part" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Basic Parts</a> | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Basic |
| | + | Parts</a> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Improved_Part" | | <a class="dropdown-item" href="/Team:Tuebingen/Improved_Part" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Improved Parts</a> | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Improved |
| | + | Parts</a> |
| | + | <a class="dropdown-item" href="/Team:Tuebingen/Characterized_Part" |
| | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Improved |
| | + | Parts</a> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Composite_Part" | | <a class="dropdown-item" href="/Team:Tuebingen/Composite_Part" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Composite Parts</a> | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Composite |
| | + | Parts</a> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Part_Collection" | | <a class="dropdown-item" href="/Team:Tuebingen/Part_Collection" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Part Collection</a> | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Part |
| | + | Collection</a> |
| | + | <a class="dropdown-item" href="/Team:Tuebingen/Downloads" |
| | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Downloads</a> |
| | </div> | | </div> |
| | </li> | | </li> |
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| | <a class="dropdown-item" href="/Team:Tuebingen/Collaborations" | | <a class="dropdown-item" href="/Team:Tuebingen/Collaborations" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Collaborations</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Collaborations</a> |
| − | <a class="dropdown-item" href="/Team:Tuebingen/Attributions"
| |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Attributions</a>
| |
| | <a class="dropdown-item" href="/Team:Tuebingen/Sponsors" | | <a class="dropdown-item" href="/Team:Tuebingen/Sponsors" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Sponsors</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Sponsors</a> |
| | + | <a class="dropdown-item" href="/Team:Tuebingen/Attributions" |
| | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Attributions</a> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Gallery" | | <a class="dropdown-item" href="/Team:Tuebingen/Gallery" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Gallery</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Gallery</a> |
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| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Overview</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Overview</a> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Public_Engagement" | | <a class="dropdown-item" href="/Team:Tuebingen/Public_Engagement" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Education & Public | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Education & Public Engagement</a> |
| − | Engagement</a>
| + | |
| | <a class="dropdown-item" href="/Team:Tuebingen/Experts" | | <a class="dropdown-item" href="/Team:Tuebingen/Experts" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Experts</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Experts</a> |
| − | <a class="dropdown-item" href="/Team:Tuebingen/Entrepreneurship"
| |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Entrepreneurship</a>
| |
| | <a class="dropdown-item" href="/Team:Tuebingen/SDG" | | <a class="dropdown-item" href="/Team:Tuebingen/SDG" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Sustainable Development | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Sustainable Development Goals</a> |
| − | Goals</a>
| + | |
| | <a class="dropdown-item" href="/Team:Tuebingen/Experimenta" | | <a class="dropdown-item" href="/Team:Tuebingen/Experimenta" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Experimenta Science | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Experimenta |
| − | Center</a> | + | Science Center</a> |
| | + | <a class="dropdown-item" href="/Team:Tuebingen/Survey" |
| | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Survey</a> |
| | </div> | | </div> |
| | </li> | | </li> |
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| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Integrated Human Practise</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Integrated Human Practise</a> |
| | <a class="dropdown-item" href="/Team:Tuebingen/Public_Engagement" | | <a class="dropdown-item" href="/Team:Tuebingen/Public_Engagement" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Education & Public | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Education & Public Engagement</a> |
| − | Engagement</a>
| + | |
| | <a class="dropdown-item" href="/Team:Tuebingen/Entrepreneurship" | | <a class="dropdown-item" href="/Team:Tuebingen/Entrepreneurship" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Supporting | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Supporting Entrepreneurship</a> |
| − | Entrepreneurship</a>
| + | |
| − | <a class="dropdown-item" href="/Team:Tuebingen/Measurement"
| + | |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Measurement</a>
| + | |
| | <a class="dropdown-item" href="/Team:Tuebingen/Model" | | <a class="dropdown-item" href="/Team:Tuebingen/Model" |
| | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Model</a> | | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">Model</a> |
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| | <li class="nav-item mx-3"> | | <li class="nav-item mx-3"> |
| | <a class="nav-link" href="https://igem.org/2019_Judging_Form?team=Tuebingen" target="_blank" | | <a class="nav-link" href="https://igem.org/2019_Judging_Form?team=Tuebingen" target="_blank" |
| − | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">JUDGING | + | style="font-family: 'Righteous', cursive; font-weight: normal; color: #2ecc71;">JUDGING FORM ⇗</a> |
| − | FORM ⇗</a>
| + | |
| | </li> | | </li> |
| | | | |
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| | -webkit-transform: translateZ(0) scale(1.0, 1.0); | | -webkit-transform: translateZ(0) scale(1.0, 1.0); |
| | transform: translateZ(0); | | transform: translateZ(0); |
| − | background: #1B2030 url(https://2019.igem.org/wiki/images/a/a0/T--Tuebingen--description-banner.jpg) center no-repeat; | + | background: #1B2030 url(https://2019.igem.org/wiki/images/5/50/T--Tuebingen--experimenta-banner.jpg) center no-repeat; |
| | background-size: 100%, 100%; | | background-size: 100%, 100%; |
| | animation: grow 30s linear 10ms infinite; | | animation: grow 30s linear 10ms infinite; |
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| | } | | } |
| | | | |
| − | .header {
| + | |
| − | height:40vh
| + | |
| − | }
| + | |
| | } | | } |
| | | | |
| − | @media only screen and (max-width: 600px) {
| + | |
| − | .header {
| + | |
| − | height:35vh
| + | |
| − | }
| + | |
| − | }
| + | |
| | | | |
| | @media only screen and (max-width: 560px) { | | @media only screen and (max-width: 560px) { |
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| | margin-top: 15%; | | margin-top: 15%; |
| | } | | } |
| − | }
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| − |
| |
| − | @media only screen and (max-width: 500px) {
| |
| | .header { | | .header { |
| − | height:30vh | + | height: 40vh; |
| | } | | } |
| | } | | } |
| | + | |
| | + | |
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| | @media only screen and (max-width: 470px) { | | @media only screen and (max-width: 470px) { |
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| | | | |
| − | @media only screen and (max-width: 450px) {
| + | |
| − | .header {
| + | |
| − | height:25vh
| + | |
| − | }
| + | |
| − | }
| + | |
| | | | |
| | @media only screen and (max-width: 400px) { | | @media only screen and (max-width: 400px) { |
| | .info h1 { | | .info h1 { |
| − | margin-top: 15%; | + | margin-top: 20%; |
| | + | } |
| | + | .header { |
| | + | height: 27vh; |
| | } | | } |
| | } | | } |
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| | @media only screen and (max-width: 350px) { | | @media only screen and (max-width: 350px) { |
| | .info h1 { | | .info h1 { |
| − | margin-top: 18%; | + | margin-top: 25%; |
| | } | | } |
| | } | | } |
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| | <div class="header"> | | <div class="header"> |
| | <div class="info"> | | <div class="info"> |
| − | <h1 style="font-family: 'Righteous', cursive; font-weight: normal; color:#2ecc71;">Nissle</h1> | + | <h1 style="font-family: 'Righteous', cursive; font-weight: normal; color:#2ecc71;">Experimenta</h1> |
| | </div> | | </div> |
| | </div> | | </div> |
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| | | | |
| − | <div style="background-color: #232323; overflow-x: fragments; overflow-wrap: inherit"> | + | <div style="background-color: #232323; overflow-x: fragments; overflow-wrap: break-word"> |
| | | | |
| | <div class="glpContainer"> | | <div class="glpContainer"> |
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| | <div id="image-popups"> | | <div id="image-popups"> |
| | | | |
| − | <h2 style="font-family:'Righteous'; color:#2ecc71;">Introduction</h2> | + | <h2 style="font-family:'Righteous'; color:#2ecc71;">The Experimenta Science Center Heilbronn</h2> |
| | <div class="row"> | | <div class="row"> |
| | <div class="col-12"> | | <div class="col-12"> |
| | <p> | | <p> |
| − | Escherichia coli Nissle 1917 (EcN) is probably the most intensively investigated bacterial strain | + | The Experimenta Science Center (<a href="https://www.experimenta.science/" onclick='window.open("https://www.experimenta.science/","_self");'>Experimenta</a>) in Heilbronn, Baden-Wuerttemberg, |
| − | today[1]. Despite the fact that the EcN strain is widely used as a probiotic, a lot of questions | + | Germany offers science at your fingertips on an area of around 25,000 square metres with around 275 |
| − | remain. That is why we decided to dive deep into the characterization of EcN. Our goal was to find | + | interactive exhibits, four creative studios and nine laboratories, as well as an observatory and an |
| − | out more about EcN itself and to provide crucial information in order to include EcN as platform | + | extraordinary science dome with spectacular science shows. Additionally, last year, they set up the |
| − | organism for other iGEM Teams and researchers.
| + | “Schülerforschungszentrum” (SFZ), where young researchers are actively supported in their initial |
| | + | scientific work. It is directed at students from high schools in Heilbronn. Their general idea is to |
| | + | encourage students to develop their own projects while funding, lab space and supervision is granted. |
| | </p> | | </p> |
| | </div> | | </div> |
| | </div> | | </div> |
| | | | |
| − | <h2 style="font-family:'Righteous'; color:#2ecc71;">Growth Curves</h2> | + | <h2 style="font-family:'Righteous'; color:#2ecc71;">Our 4 Day Lab Course</h2> |
| | <div class="row"> | | <div class="row"> |
| | <div class="col-12"> | | <div class="col-12"> |
| − | <p> | + | <p>The course was held in a collaborative manner over a span of four days. Dr. Robert Friedrich, |
| − | The first step in the characterization of a bacterium are growth curves on different media and
| + | a biologist working for the SFZ, gave the general lab introduction and provided the overall lab |
| − | under different conditions. We chose to perform half of our experiments under aerobic and the | + | responsibility, while we were mainly responsible to teach the required theoretical background, |
| − | other half under anaerobic conditions. Under aerobic conditions, as a control we let EcN grow in | + | introduce bioinformatics data analysis (DNA-Seq) and finally project development. Additionally, |
| − | LB medium at 37°C and pH7. We changed the temperature to 25°C, 8°C, 4°C and 0°C, showing that | + | we were supporting Dr. Friedrich during the experiments and closely supervised the students.</p> |
| − | EcN growth is inhibited at 8°C, the temperature often used for cold shock. | + | </div> |
| − | </p>
| + | </div> |
| − | | + | <div class="row"> |
| − | <figure> | + | <div class="col-12"> |
| | + | <div class="row align-items-center"> |
| | + | <div class="col-12 col-md-6"> |
| | + | <figure> |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/b/b5/T--Tuebingen--pH7-diff-Temp-white.png" | + | href="https://2019.igem.org/wiki/images/e/e8/T--Tuebingen--Experimenta-Lab4.png" |
| | data-effect="mfp-zoom-out" | | data-effect="mfp-zoom-out" |
| | title="Some title"> | | title="Some title"> |
| − | <img src="https://2019.igem.org/wiki/images/b/b5/T--Tuebingen--pH7-diff-Temp-white.png" | + | <img src="https://2019.igem.org/wiki/images/e/e8/T--Tuebingen--Experimenta-Lab4.png" |
| | class="figure-img img-fluid rounded" | | class="figure-img img-fluid rounded" |
| − | alt="A generic square placeholder"></a> | + | alt="Placeholder"></a> |
| − | <figcaption style="font-size: small; color: #F4F0DE">Fig. 1: EcN growth in LB medium at pH7. All cultures were
| + | |
| − | inoculated with an overnight culture and grown for 120 minutes at 37°C. Next, temperature was
| + | |
| − | changed to 0°C, 4°C, 8°C and 25°C, while one control was kept at 37°C.
| + | |
| − | Shown are mean values of triplicates.</figcaption>
| + | |
| | </figure> | | </figure> |
| | | | |
| − | <p>
| + | </div> |
| − | Moreover, we evaluated the growth in the pH range from pH6 to pH1, since in our application EcN
| + | <div class="col-12 col-md-6 "> |
| − | will have to pass the acidity of the stomach. Here, at pH4 we discovered an interesting recovery
| + | <p>We conveyed the required theoretical background in a modern and interactive way, with the use of |
| − | of EcN growth after three hours.
| + | smart boards and current web tools. We focused on teaching the highly motivated students cutting-edge |
| − | </p> | + | research, while providing a theoretical foundation, preparing them for different biology competitions |
| | + | and eventually university.</p> |
| | + | </div> |
| | + | </div> |
| | + | </div> |
| | + | </div> |
| | | | |
| − | <figure> | + | <div class="row"> |
| | + | <div class="col-12"> |
| | + | <div class="row align-items-center"> |
| | + | <div class="col-12 col-md-6"> |
| | + | <figure> |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/c/cf/T--Tuebingen--37-diff-pH-white.png" | + | href="https://2019.igem.org/wiki/images/9/94/T--Tuebingen--Experimenta-Lab3.png" |
| | data-effect="mfp-zoom-out" | | data-effect="mfp-zoom-out" |
| | title="Some title"> | | title="Some title"> |
| − | <img src="https://2019.igem.org/wiki/images/c/cf/T--Tuebingen--37-diff-pH-white.png" | + | <img src="https://2019.igem.org/wiki/images/9/94/T--Tuebingen--Experimenta-Lab3.png" |
| | class="figure-img img-fluid rounded" | | class="figure-img img-fluid rounded" |
| − | alt="A generic square placeholder"></a> | + | alt="Placeholder"></a> |
| − | <figcaption style="font-size: small; color: #F4F0DE">Fig. 2: EcN growth curve in LB at 37°C under
| + | |
| − | different pH levels. Until 120min all cultures inoculated from one overnight culture grew at pH7.
| + | |
| − | Then, media was changed to the respective pH and cultures were grown for 3 hours. pH5 and pH6
| + | |
| − | grew as usual, pH1,2,3 did not grow at all, while pH4 started to grow after 3 hours. Thus,
| + | |
| − | media was changed again after 3 hours to pH7. pH6 and pH5 grew as usual, pH1,2,3 did not
| + | |
| − | recover. Cultures grown in pH4 recovered and grew as usual. Shown are values of one culture
| + | |
| − | for each pH.</figcaption>
| + | |
| | </figure> | | </figure> |
| | | | |
| − | <figure>
| + | </div> |
| | + | <div class="col-12 col-md-6 "> |
| | + | <figure> |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/b/b8/T--Tuebingen--pH4-3x-37-white.png" | + | href="https://2019.igem.org/wiki/images/6/69/T--Tuebingen--Experimenta-Lab5.png" |
| | data-effect="mfp-zoom-out" | | data-effect="mfp-zoom-out" |
| | title="Some title"> | | title="Some title"> |
| − | <img src="https://2019.igem.org/wiki/images/b/b8/T--Tuebingen--pH4-3x-37-white.png" | + | <img src="https://2019.igem.org/wiki/images/6/69/T--Tuebingen--Experimenta-Lab5.png" |
| | class="figure-img img-fluid rounded" | | class="figure-img img-fluid rounded" |
| − | alt="A generic square placeholder"></a> | + | alt="Placeholder"></a> |
| − | <figcaption style="font-size: small; color: #F4F0DE">Fig. 3: EcN growth in LB at 37°C with pH
| + | |
| − | changed from pH7 to pH4 after two hours of growth. After 150 minutes within pH4,
| + | |
| − | EcN started to grow comparable to pH7 cultures. Shown are the three cultures inoculated
| + | |
| − | from the same overnight culture of EcN.</figcaption>
| + | |
| | </figure> | | </figure> |
| | + | </div> |
| | + | </div> |
| | <p> | | <p> |
| − | To look into inflammatory stress, we subjected EcN to up to 100µM hydrogen peroxide [2] and showed | + | Please check out the material we prepared for the course - a script covering all the theoretical |
| − | that the growth is not substantially influenced by it. | + | background and a presentation: |
| | </p> | | </p> |
| − | <figure> | + | <ul style="color:#F4F0DE;"> |
| − | <a style="font-size: small"
| + | <li><a href="https://2019.igem.org/wiki/images/6/6c/T--Tuebingen--Experimenta_Labkurs_Skript.pdf" onclick='window.open("https://2019.igem.org/wiki/images/6/6c/T--Tuebingen--Experimenta_Labkurs_Skript.pdf","_self");'>Experimenta Labkurs</a></li> |
| − | href="https://2019.igem.org/wiki/images/b/bf/T--Tuebingen--H2O2-triplicates-white.png"
| + | <li><a href="https://2019.igem.org/wiki/images/1/10/T--Tuebingen--LabCoursePresentation.pdf" onclick='window.open("https://2019.igem.org/wiki/images/1/10/T--Tuebingen--LabCoursePresentation.pdf","_self");'>LabCourse Presentation</a>)</li> |
| − | data-effect="mfp-zoom-out"
| + | </ul> |
| − | title="Some title">
| + | |
| − | <img src="https://2019.igem.org/wiki/images/b/bf/T--Tuebingen--H2O2-triplicates-white.png"
| + | |
| − | class="figure-img img-fluid rounded"
| + | |
| − | alt="A generic square placeholder"></a>
| + | |
| − | <figcaption style="font-size: small; color: #F4F0DE">Fig. 4: EcN growth in different concentrations
| + | |
| − | of Hydrogen Peroxide, infused after two hours of growth at 37°C, pH7 in LB medium. 100µM Hydrogen
| + | |
| − | Peroxide with slightly inhibited growth. Shown are the means of triplicates for each concentration.</figcaption>
| + | |
| − | </figure>
| + | |
| | <p> | | <p> |
| − | Lastly, we performed dryfreezing and recovered EcN afterwards under control conditions [3][4][5], | + | Please see the schedule below. |
| − | showing that dryfreezing within skim milk protects the bacteria from substantial death.
| + | |
| | </p> | | </p> |
| | + | </div> |
| | + | </div> |
| | | | |
| | + | <div class="row"> |
| | + | <div class="col-12"> |
| | <figure> | | <figure> |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/9/90/T--Tuebingen--Dryfreeze-white.png" | + | href="https://2019.igem.org/wiki/images/f/f1/T--Tuebingen--table_test.png" |
| | data-effect="mfp-zoom-out" | | data-effect="mfp-zoom-out" |
| | title="Some title"> | | title="Some title"> |
| − | <img src="https://2019.igem.org/wiki/images/9/90/T--Tuebingen--Dryfreeze-white.png" | + | <img src="https://2019.igem.org/wiki/images/f/f1/T--Tuebingen--table_test.png" |
| | class="figure-img img-fluid rounded" | | class="figure-img img-fluid rounded" |
| − | alt="A generic square placeholder"></a> | + | alt="Placeholder"></a> |
| − | <figcaption style="font-size: small; color: #F4F0DE">Fig. 5: EcN growth of cultures previously
| + | |
| − | subjected to a dryfreeze protocol. Shown are the mean values of triplicates of cultures
| + | |
| − | grown at 37°C, pH7 in LB grown for recovery.</figcaption>
| + | |
| | </figure> | | </figure> |
| − | <p>
| + | </div> |
| − | Anaerobic conditions were used to characterize EcN growth under the circumstances provided in
| + | </div> |
| − | the human intestines. Thus, as a control we compared EcN growth in LB medium versus mGAM medium
| + | |
| − | under anaerobic conditions, showing that mGAM, a medium designed for anaerobic application,
| + | <div class="row"> |
| − | is in fact a more suitable medium. Then, we subjected the bacteria to metformin treatment,
| + | <div class="col-12"> |
| − | since it is one of the most common treatments of diabetes and is known to accumulate to 720 µM
| + | <p>Due to the interactive design of the course, we also discussed the experiments with the students |
| − | to 7,2 mM within the intestines due to low bioavailability. [6][7]. We showed that EcN growth
| + | and tried to summarize what we did on the blackboard:</p> |
| − | is not substantially influenced by 1,3 mM of metformin into mGAM medium. Moreover, we tested for
| + | |
| − | EcN’s resistance against cholic acid, since it is commonly secreted into the ileum. Here, we
| + | <div class="row align-items-center"> |
| − | added 0.25 mM of cholic acid to mGAM medium, considering that the concentration of free bile
| + | <div class="col-12 col-md-6"> |
| − | salts may rise to 0.25 to 1 mM of total bile salts in the Ileum, with cholic acid only being | + | <figure> |
| − | one component [8][9]. Our results suggest that EcN growth is not greatly influenced by cholic acid.
| + | |
| − | </p> | + | |
| − | <figure>
| + | |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/b/b2/T--Tuebingen--anaerobic-all-4x-white.png" | + | href="https://2019.igem.org/wiki/images/b/be/T--Tuebingen--Experimenta-Lab1.png" |
| | data-effect="mfp-zoom-out" | | data-effect="mfp-zoom-out" |
| | title="Some title"> | | title="Some title"> |
| − | <img src="https://2019.igem.org/wiki/images/b/b2/T--Tuebingen--anaerobic-all-4x-white.png" | + | <img src="https://2019.igem.org/wiki/images/b/be/T--Tuebingen--Experimenta-Lab1.png" |
| | class="figure-img img-fluid rounded" | | class="figure-img img-fluid rounded" |
| − | alt="A generic square placeholder"></a> | + | alt="Placeholder"></a> |
| − | <figcaption style="font-size: small; color: #F4F0DE">Fig. 6: EcN growth under four anaerobic
| + | |
| − | conditions compared to EcN aerobic growth. Shown are the mean values of four samples
| + | |
| − | inoculated with the same overnight culture. Experiments were conducted at 37°C and pH7.
| + | |
| − | LB aerobic growth as a control. Other samples are LB anaerobic growth, mGAM anaerobic
| + | |
| − | growth, as well as mGAM medium supplemented with either 1.3 mM Metformin or 0.25mM Cholic
| + | |
| − | Acid. Samples for RNA sequencing were taken after 270 minutes for all anaerobic conditions,
| + | |
| − | since the increase of pressure within the flasks indicated a change of metabolism of EcN to
| + | |
| − | fermentation processes. Aerobic LB growth samples were taken at OD600=1.0.</figcaption>
| + | |
| | </figure> | | </figure> |
| − | <p>
| |
| − | Finally, we tested EcN interaction with other bacteria by adding bacterial supernatant to our
| |
| − | medium. The supernatant was sterilized and provided by Dr. Lisa Maier. We chose Bacteroides
| |
| − | thetaiotaomicron, Prevotella copri and Ruminococcus gnavus since they are commonly found within
| |
| − | the human microbiome [10]. Bifidobacterium adolescentis was chosen due to its probiotic nature
| |
| − | and Clostridium difficile supernatant was used, since it is often found in the microbiome of people
| |
| − | with chronic inflammation [10][11]. The results suggest that EcN grows under all additions,
| |
| − | however was initially inhibited in its growth by the addition of Bacteroides spp., thus we used
| |
| − | these samples for RNA-seq.
| |
| − | </p>
| |
| | | | |
| − | <figure>
| + | </div> |
| | + | <div class="col-12 col-md-6 "> |
| | + | <figure> |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/7/74/T--Tuebingen--bacterial-SN-white.png" | + | href="https://2019.igem.org/wiki/images/d/df/T--Tuebingen--Experimenta-Lab2.png" |
| | data-effect="mfp-zoom-out" | | data-effect="mfp-zoom-out" |
| | title="Some title"> | | title="Some title"> |
| − | <img src="https://2019.igem.org/wiki/images/7/74/T--Tuebingen--bacterial-SN-white.png" | + | <img src="https://2019.igem.org/wiki/images/d/df/T--Tuebingen--Experimenta-Lab2.png" |
| | class="figure-img img-fluid rounded" | | class="figure-img img-fluid rounded" |
| − | alt="A generic square placeholder"></a> | + | alt="Placeholder"></a> |
| − | <figcaption style="font-size: small; color: #F4F0DE">Fig. 7: EcN growth in mGAM medium under
| + | |
| − | anaerobic conditions at 37°C, pH 7 supplemented with either 50% supernatant of different
| + | |
| − | species or 50% of water as a control for depleted nutrients. All cultures were inoculated
| + | |
| − | with the same overnight culture of EcN. Bacteroides spp. with strongest change in growth
| + | |
| − | within the first 200 min of the experiment. Shown are mean values of four samples each.
| + | |
| − | Bacteroides samples were taken for RNA sequencing after 225 minutes.</figcaption>
| + | |
| | </figure> | | </figure> |
| | + | </div> |
| | + | </div> |
| | </div> | | </div> |
| | </div> | | </div> |
| | | | |
| − | <h2 style="font-family:'Righteous';">RNASeq</h2>
| |
| | <div class="row"> | | <div class="row"> |
| | <div class="col-12"> | | <div class="col-12"> |
| | + | <p>The students were also very interested in iGEM and our work. Hence, we not only introduced iGEM |
| | + | and our project to them, but also let them critically evaluate our project. They were also given |
| | + | the chance to conduct PCRs related to our project and could therefore gain insights into the upcoming |
| | + | challenges when starting a new project or experiment where not everything has been optimised for |
| | + | easy functionality. Many students were interested in the iGEM competition itself and in the process |
| | + | of finding a project and making it feasible. Therefore, we also invested into giving valuable input |
| | + | and advice on starting a project and encouraged the students to participate in iGEM or similar projects |
| | + | themselves. Several questions and concerns relating the functionality of our probiotic under different |
| | + | conditions, such as patients taking medications or antibiotics were also raised by the students. These |
| | + | fruitful discussions, as well as our exchange with several experts, contributed to the final design |
| | + | of our RNA-Seq experiment providing valuable input and different aspects to be considered |
| | + | [<a href="https://2019.igem.org/Team:Tuebingen/Experts" onclick='window.open("https://2019.igem.org/Team:Tuebingen/Experts","_self");'>Experts</a>, <a href="https://2019.igem.org/Team:Tuebingen/Nissle" onclick='window.open("https://2019.igem.org/Team:Tuebingen/Nissle","_self");'>Nissle</a>].</p> |
| | + | |
| | <p> | | <p> |
| − | The transcriptome describes the set of whole RNA molecules in a population of cells and is subject | + | Due to the high interest of the students and the positive feedback from the Experimenta itself, |
| − | to continuous changes. Understanding the complete transcriptome, the expressed genes, post-transcriptional
| + | we discussed the possibility of creating an iGEM high school team in Heilbronn in 2020. |
| − | modifications, single-nucleotide polymorphisms (SNPs) and additional properties of interest is | + | The Experimenta is highly interested in participating in iGEM 2020 with motivated students and |
| − | imperative towards understanding genetic cause, disease and possible treatment strategies. | + | will provide the required laboratories, supervision and funding. Our team will still be serving |
| − | The inherent complexity of the transcriptome requires precise and scaling analysis techniques. RNA sequencing (RNA-seq),
| + | as advisors for the planned iGEM high school team next year. Furthermore, a new student lab course |
| − | also known as whole transcriptome shotgun sequencing (WTSS), is most commonly used for this purpose, | + | on CRISPR/Cas will be introduced at the Experimenta on the grounds of the theoretical background, |
| − | today. It uses next-generation sequencing (NGS) to detect and quantify RNA in biological samples. | + | input and inspiration iGEM Tuebingen conveyed. |
| − | The generated RNA-Seq read data is then analyzed according to a sample RNA-Seq work-flow as shown below.
| + | |
| | </p> | | </p> |
| − | <figure> | + | </div> |
| | + | </div> |
| | + | |
| | + | <h3 style="font-family:'Righteous'; color:#2ecc71;">Panel Discussion - „Biohacking – genetic experiments done at home“</h3> |
| | + | <div class="row"> |
| | + | <div class="col-12"> |
| | + | <p>In addition to the lab course, we also decided to host a panel discussion at the Experimenta. |
| | + | At the beginning of the <a href="https://2019.igem.org/wiki/images/2/24/T--Tuebingen--panelDiscussion.pdf" onclick='window.open("https://2019.igem.org/wiki/images/2/24/T--Tuebingen--panelDiscussion.pdf","_self");'>panel discussion</a>, we gave a talk about on the CRISPR / Cas method itself. |
| | + | We also included an overview of our ongoing project and the iGEM competition in general.</p> |
| | + | |
| | + | <p> |
| | + | In collaboration with Dr. Robert Friedrich, we designed a discussion around the status of current |
| | + | research on CRISPR / Cas, the effectiveness of the method and its limitations, the prospects of |
| | + | future CRISPR / Cas developments, the availability and legality of so-called Do-It-Yourself CRISPR / |
| | + | Cas Kits and the ethical implications on society. The panel consisted out of Prof. Dr. Christoph |
| | + | Thyssen (<a href="www.bio.uni-kl.de/organisation/mitarbeiter/s-u/thyssen-christoph/" onclick='window.open("www.bio.uni-kl.de/organisation/mitarbeiter/s-u/thyssen-christoph/","_self");'>Christoph Thyssen</a>), an expert for subject |
| | + | didactics in biology and two of our team members - Marietheres Evers and Famke Baeuerle. |
| | + | </p> |
| | + | |
| | + | <div class="row align-items-center"> |
| | + | <div class="col-12 col-md-6"> |
| | + | <figure> |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/7/7f/T--Tuebingen--RNA-Seq-transparent.png" | + | href="https://2019.igem.org/wiki/images/5/54/T--Tuebingen--Biohacking_05.jpg" |
| | data-effect="mfp-zoom-out" | | data-effect="mfp-zoom-out" |
| | title="Some title"> | | title="Some title"> |
| − | <img src="https://2019.igem.org/wiki/images/7/7f/T--Tuebingen--RNA-Seq-transparent.png" | + | <img src="https://2019.igem.org/wiki/images/5/54/T--Tuebingen--Biohacking_05.jpg" |
| | class="figure-img img-fluid rounded" | | class="figure-img img-fluid rounded" |
| − | alt="A generic square placeholder image with rounded corners in a figure."></a> | + | alt="Placeholder"></a> |
| | </figure> | | </figure> |
| − | <p>
| |
| − | We set ourselves the goal of understanding the transcriptomic changes that E.coli Nissle undergoes
| |
| − | under various stress conditions to gain a deeper insight into its responses. Understanding the
| |
| − | stress responses of E.coli Nissle could lead to the development of more stress robust strains,
| |
| − | which not only our project would benefit from, but also scientists working on probiotic drugs in general.
| |
| − | </p>
| |
| − | <p>
| |
| − | We divided our experimental design into two parts. We not only wanted to investigate the effect
| |
| − | of environmental stress on E.coli Nissle under aerobic conditions, but were also specifically
| |
| − | interested in anaerobic conditions. Hence, our experimental design looks as follows:
| |
| − | </p>
| |
| − | <p>
| |
| − | The respective temperature, pH values and doses were determined by growth curves, shown above.
| |
| − | To get the most out of RNA-Seq applied to stress factors, it is important to find the cutoff
| |
| − | values, where E.coli Nissle is put under stress the most, but still survives.
| |
| − | </p>
| |
| − | <p>
| |
| − | Sequencing and library preparation was conducted on two sites. All aerobic samples were prepared
| |
| − | and sequenced at the NGS Competence Center Tübingen (NCCT), whereas all anaerobic samples were
| |
| − | prepared and sequenced at the European Molecular Biology Laboratory (EMBL) in Heidelberg.
| |
| − | For more details please visit our <a href="https://2019.igem.org/Team:Tuebingen/Notebook" onclick='window.open("https://2019.igem.org/Team:Tuebingen/Notebook","_self");'>Notebook</a>
| |
| − | and <a href="https://2019.igem.org/Team:Tuebingen/Attributions" onclick='window.open("https://2019.igem.org/Team:Tuebingen/Attributions","_self");'>Attributions</a>.
| |
| − | </p>
| |
| | | | |
| | + | </div> |
| | + | <div class="col-12 col-md-6 "> |
| | + | <figure> |
| | + | <a style="font-size: small" |
| | + | href="https://2019.igem.org/wiki/images/4/4d/T--Tuebingen--Biohacking_10.jpg" |
| | + | data-effect="mfp-zoom-out" |
| | + | title="Some title"> |
| | + | <img src="https://2019.igem.org/wiki/images/4/4d/T--Tuebingen--Biohacking_10.jpg" |
| | + | class="figure-img img-fluid rounded" |
| | + | alt="Placeholder"></a> |
| | + | </figure> |
| | + | </div> |
| | </div> | | </div> |
| − | </div>
| + | <p> |
| − | | + | A lot of questions were asked during the <a href="https://2019.igem.org/wiki/images/1/13/T--Tuebingen--Panel_discussion_allg.pdf" onclick='window.open("https://2019.igem.org/wiki/images/1/13/T--Tuebingen--Panel_discussion_allg.pdf","_self");'>panel discussion</a> and the presentation. We discussed |
| − | | + | the ethical implications of the CRISPR / Cas Method with the audience. Surprisingly, |
| − | <h2 style="font-family:'Righteous';">Data Analysis</h2>
| + | many participants were eager to talk about scenarios they have heard about. |
| − | <div class="row">
| + | </p> |
| − | <div class="col-12">
| + | |
| − | <p>Quality Control Differential Expression Analysis
| + | |
| − | Pathway Analysis</p> | + | |
| | </div> | | </div> |
| | </div> | | </div> |
| | | | |
| − | <h2 style="font-family:'Righteous'; color:#2ecc71;">Metabolic Model</h2> | + | <h3 style="font-family:'Righteous'; color:#2ecc71;">Outlook - Advisors of the Experimenta iGEM team 2020 & New student lab course</h3> |
| − | | + | |
| − | | + | |
| | <div class="row"> | | <div class="row"> |
| | <div class="col-12"> | | <div class="col-12"> |
| − | <p>Insert here</p> | + | <p>During the collaboration with the Experimenta Heilbronn, we sat together with Dr. Robert Friedrich |
| − | </div>
| + | and Norbert Hommrichhausen to discuss the foundation of an iGEM high school team at the Experimenta |
| − | </div>
| + | Heilbronn. The Experimenta is highly interested in starting a team in Heilbronn and the motivated |
| | + | and interested students encouraged us to team up and further pursue this plan. Plans for an iGEM |
| | + | high school team 2020 were made, in which the Experimenta Heilbronn will be the main partner |
| | + | providing lab space, supervision and funding. The role of the iGEM Team Tuebingen is that of |
| | + | experienced advisors, who can assist in questions concerning the iGEM competition itself, the |
| | + | workflow of an iGEM year, as well as deliver expert knowledge and guidance in the laboratory or |
| | + | in questions concerning bioinformatics, design and human practices. Both the Experimenta and the |
| | + | iGEM Team Tuebingen aim at establishing a long-term collaboration in the scope of iGEM.</p> |
| | | | |
| − | </div>
| + | <p> |
| − | | + | Next to the foundation of a high school iGEM team, the Experimenta will also introduce new lab |
| − | <div id="glpreferences" class="row">
| + | courses for school classes, one of them being a CRISPR/Cas course. The theoretical background, |
| − | <h3 style="font-family:'Righteous'; color: #2ecc71;">References</h3>
| + | first steps and foundation of this course arose from the collaboration with iGEM Tuebingen this year. |
| − | <div class="col-12" style="font-size: x-small; overflow-wrap: break-word;">
| + | A more detailed outline and implementation of the course will be part of another collaboration |
| − | <ol> | + | between the Experimenta and iGEM Tuebingen. |
| − | <li style="color: #F4F0DE"><a href=https://doi.org/10.1093/femsle/fnw212> Ulrich Sonnenborn, Escherichia coli strain Nissle 1917—from bench to bedside and back: history of a special Escherichia coli strain with probiotic properties, FEMS Microbiology Letters, Volume 363, Issue 19, October 2016, fnw212,</a></li> | + | </p> |
| − | <li id="ref_2" style="color: #F4F0DE">Sana Ben Othman and Tomio Yabe. Use of Hydrogen Peroxide and Peroxl Radicals to induce Oxidative Stress in Neuronal Cells. Reviews in Agricultural Science, 3:40-45, 2015. Doi: 10.7831/ras.3.40</li> | + | |
| − | <li id="ref_3" style="color: #F4F0DE;">P. Capela, T.K.C. Hay, N.P. Shah. Effect of cryoprotectants, prebiotics and microencapsulation on survival of probiotic organisms in yoghurt and freeze-dried yoghurt. Food Research International. Volume 39, Issue 2, 2006, Pages 203-211, ISSN 0963-9969, https://doi.org/10.1016/j.foodres.2005.07.007.</li>
| + | |
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