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| | .h4, h4 { | | .h4, h4 { |
| | font-size: 1.5rem | | font-size: 1.5rem |
| − | }
| |
| − |
| |
| − | @media screen and (max-width: 500px){
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| − | h4{
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| − | font-size: 1.0rem;
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| − | }
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| | } | | } |
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| | .offset-xl-11 { | | .offset-xl-11 { |
| | margin-left: 91.666667% | | margin-left: 91.666667% |
| | + | } |
| | + | } |
| | + | |
| | + | .veggie { |
| | + | width: 100%; |
| | + | max-width: 100%; |
| | + | margin-bottom: 1rem; |
| | + | background-color: transparent; |
| | + | z-index:100; |
| | + | } |
| | + | .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; |
| | + | } |
| | + | .veggie caption { |
| | + | color: #adb3b7; |
| | + | z-index:100; |
| | + | } |
| | + | .veggie thead th { |
| | + | vertical-align: bottom; |
| | + | border-bottom: 2px solid #dee2e6; |
| | + | z-index:100; |
| | + | } |
| | + | .veggie tbody+tbody { |
| | + | border-top: 2px solid #dee2e6; |
| | + | z-index:100; |
| | + | } |
| | + | |
| | + | @media screen and (max-width: 800px) { |
| | + | .veggie { |
| | + | font-size: xx-small; |
| | + | z-index:100; |
| | } | | } |
| | } | | } |
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| | display: block; | | display: block; |
| | width: 100%; | | width: 100%; |
| − | overflow-x: auto; | + | overflow-x: break-words; |
| | -webkit-overflow-scrolling: touch; | | -webkit-overflow-scrolling: touch; |
| | -ms-overflow-style: -ms-autohiding-scrollbar | | -ms-overflow-style: -ms-autohiding-scrollbar |
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| | display: block; | | display: block; |
| | width: 100%; | | width: 100%; |
| − | overflow-x: auto; | + | overflow-x: break-words; |
| | -webkit-overflow-scrolling: touch; | | -webkit-overflow-scrolling: touch; |
| | -ms-overflow-style: -ms-autohiding-scrollbar | | -ms-overflow-style: -ms-autohiding-scrollbar |
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| | display: block; | | display: block; |
| | width: 100%; | | width: 100%; |
| − | overflow-x: auto; | + | overflow-x: break-words; |
| | -webkit-overflow-scrolling: touch; | | -webkit-overflow-scrolling: touch; |
| | -ms-overflow-style: -ms-autohiding-scrollbar | | -ms-overflow-style: -ms-autohiding-scrollbar |
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| | | | |
| | .bg-dark { | | .bg-dark { |
| − | background-color: #343a40 !important | + | background-color: #232323 !important |
| | } | | } |
| | | | |
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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>
| |
| − | <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/6/6a/T--Tuebingen--software-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) { |
| | .info h1 { | | .info h1 { |
| | margin-top: 15%; | | margin-top: 15%; |
| | + | } |
| | + | .header { |
| | + | height: 40vh; |
| | } | | } |
| | } | | } |
| | + | |
| | + | |
| | | | |
| | @media only screen and (max-width: 470px) { | | @media only screen and (max-width: 470px) { |
| | .info h1 { | | .info h1 { |
| − | margin-top: 20%; | + | margin-top: 10%; |
| | font-size: 1.9em; | | font-size: 1.9em; |
| | } | | } |
| | } | | } |
| − | @media only screen and (max-width: 345px) { | + | |
| | + | |
| | + | |
| | + | @media only screen and (max-width: 400px) { |
| | .info h1 { | | .info h1 { |
| − | margin-top: 24%; | + | margin-top: 20%; |
| | + | } |
| | + | .header { |
| | + | height: 27vh; |
| | } | | } |
| | } | | } |
| | | | |
| | + | @media only screen and (max-width: 350px) { |
| | + | .info h1 { |
| | + | margin-top: 25%; |
| | + | } |
| | + | } |
| | | | |
| | @keyframes grow { | | @keyframes grow { |
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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;">Software</h1> | + | <h1 style="font-family: 'Righteous', cursive; font-weight: normal; color:#2ecc71;">Experimenta</h1> |
| | </div> | | </div> |
| | </div> | | </div> |
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| | <div id="image-popups"> | | <div id="image-popups"> |
| | | | |
| − | <h2 style="font-family:'Righteous'; color:#2ecc71;">C3Pred - Cell-Penetrating Peptide Predictor</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> |
| − | Cell-penetrating peptides (CPPs) are short 4-30 amino acids long peptides, which possess the | + | The Experimenta Science Center (<a href="https://www.experimenta.science/" onclick='window.open("https://www.experimenta.science/","_self");'>Experimenta</a>) in Heilbronn, Baden-Wuerttemberg, |
| − | ability to transport different cargo over the cell membrane. These cargos include proteins, nanobodies, | + | Germany offers science at your fingertips on an area of around 25,000 square metres with around 275 |
| − | DNA molecules, and small molecule drugs. In recent years, numerous promising clinical and pre-clinical | + | interactive exhibits, four creative studios and nine laboratories, as well as an observatory and an |
| − | trials have been launched, with CPPs as a carrier for pharmacologically active small molecules. | + | extraordinary science dome with spectacular science shows. Additionally, last year, they set up the |
| | + | “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> |
| − | <p>
| |
| − | They can be classified into three general groups: cationic, amphipathic and hydrophobic CPPs.
| |
| − | Each group of peptides has different physical-chemical properties and therefore differs in the internalization
| |
| − | mechanism. The pathways CPPs exploit to enter the cell can be divided into two larger groups, endocytic pathways,
| |
| − | and direct cell penetration. Since there are different, not fully understood mechanisms involved, simple models,
| |
| − | describing the relationship between sequence and function, are particularly challenging to generate. Hence,
| |
| − | the discovery of novel CPPs and activity optimization is mostly relying on large screening approaches.
| |
| − | </p>
| |
| − | <figure>
| |
| − | <a style="font-size: small"
| |
| − | href="https://2019.igem.org/wiki/images/2/23/T--Tuebingen--CPP-function-transparent.png"
| |
| − | data-effect="mfp-zoom-out"
| |
| − | title="Some title">
| |
| − | <img src="https://2019.igem.org/wiki/images/2/23/T--Tuebingen--CPP-function-transparent.png"
| |
| − | class="figure-img img-fluid rounded"
| |
| − | alt="A generic square placeholder"></a>
| |
| − |
| |
| − | </figure>
| |
| | </div> | | </div> |
| | </div> | | </div> |
| | | | |
| − | <h2 style="font-family:'Righteous'; color:#2ecc71;">Motivation</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, |
| − | As part of our project, we planned to utilize cell-penetrating peptides (CPPs) to allow a cargo,
| + | a biologist working for the SFZ, gave the general lab introduction and provided the overall lab |
| − | the Exendin-4 protein, to be transported across a eukaryotic cell-layer. A challenging part of
| + | responsibility, while we were mainly responsible to teach the required theoretical background, |
| − | our project design was to decide on a specific CPP out of the tremendous variety of different | + | introduce bioinformatics data analysis (DNA-Seq) and finally project development. Additionally, |
| − | transporting peptides. In October 2019, CPPsite 2.0, the largest database for CPPs, contained
| + | we were supporting Dr. Friedrich during the experiments and closely supervised the students.</p> |
| − | more than 1850 different peptide motifs, which are capable of delivering conjugates into cells. | + | |
| − | However, the CPPsite database only contains qualitative information about whether a peptide has
| + | |
| − | a cell-penetrating activity, but no quantitative information about how efficient cargo is | + | |
| − | transported across the cell membrane.
| + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | Therefore we decided to generate a predictive software tool, which allows assigning a transport | + | |
| − | efficiency score to CPPs. This allows making educated decisions on the design process.
| + | |
| − | </p>
| + | |
| | </div> | | </div> |
| | </div> | | </div> |
| − |
| |
| − | <h2 style="font-family:'Righteous';">Overview of our tool</h2>
| |
| | <div class="row"> | | <div class="row"> |
| | <div class="col-12"> | | <div class="col-12"> |
| − | <p> | + | <div class="row align-items-center"> |
| − | Our goal was to create an easy-to-use software tool, which allows scientists to make design
| + | <div class="col-12 col-md-6"> |
| − | choices for their system based on quantitative transport activity scores. We put a strong emphasis | + | <figure> |
| − | on good usability for different kinds of users. Firstly, we implemented an intuitive browser-based
| + | <a style="font-size: small" |
| − | graphical user interface for simple usability. Secondly, we also released our software tool as a
| + | href="https://2019.igem.org/wiki/images/e/e8/T--Tuebingen--Experimenta-Lab4.png" |
| − | Python package, which is easily installable for everyone using PIP, allowing other developers to
| + | data-effect="mfp-zoom-out" |
| − | incorporate our software tool into their scripts.
| + | title="Some title"> |
| − | </p>
| + | <img src="https://2019.igem.org/wiki/images/e/e8/T--Tuebingen--Experimenta-Lab4.png" |
| − | <p>
| + | class="figure-img img-fluid rounded" |
| − | Short peptide sequences can be submitted to the program by either using a sequence string in
| + | alt="Placeholder"></a> |
| − | FASTA-format, an Uniprot ID or an iGEM Registry ID of coding DNA sequences. Our tool computes
| + | </figure> |
| − | a transport efficiency score for each sequence, which is automatically interpreted for the user
| + | |
| − | by comparing it to well-characterized CPPs.
| + | |
| − | </p> | + | |
| | | | |
| | + | </div> |
| | + | <div class="col-12 col-md-6 "> |
| | + | <p>We conveyed the required theoretical background in a modern and interactive way, with the use of |
| | + | smart boards and current web tools. We focused on teaching the highly motivated students cutting-edge |
| | + | research, while providing a theoretical foundation, preparing them for different biology competitions |
| | + | and eventually university.</p> |
| | + | </div> |
| | </div> | | </div> |
| | </div> | | </div> |
| | + | </div> |
| | | | |
| − |
| |
| − | <h2 style="font-family:'Righteous';">Installation and usage of our tool</h2>
| |
| | <div class="row"> | | <div class="row"> |
| | <div class="col-12"> | | <div class="col-12"> |
| − | <p>Our tool can be used on Linux, Windows and Mac OS. Please follow the installation instruction LINK.</p> | + | <div class="row align-items-center"> |
| − | <p>When starting our tool, the landing page allows navigating to the three running modes (from protein sequence,
| + | <div class="col-12 col-md-6"> |
| − | Uniprot Accession number & iGEM Registry ID). Additional information about the running modes can | + | <figure> |
| − | be displayed by clicking on “more info”.</p>
| + | <a style="font-size: small" |
| − | </div>
| + | href="https://2019.igem.org/wiki/images/9/94/T--Tuebingen--Experimenta-Lab3.png" |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Prediction using a sequence string</h4>
| + | data-effect="mfp-zoom-out" |
| − | <div class="col-12">
| + | title="Some title"> |
| | + | <img src="https://2019.igem.org/wiki/images/9/94/T--Tuebingen--Experimenta-Lab3.png" |
| | + | class="figure-img img-fluid rounded" |
| | + | alt="Placeholder"></a> |
| | + | </figure> |
| | + | |
| | + | </div> |
| | + | <div class="col-12 col-md-6 "> |
| | + | <figure> |
| | + | <a style="font-size: small" |
| | + | href="https://2019.igem.org/wiki/images/6/69/T--Tuebingen--Experimenta-Lab5.png" |
| | + | data-effect="mfp-zoom-out" |
| | + | title="Some title"> |
| | + | <img src="https://2019.igem.org/wiki/images/6/69/T--Tuebingen--Experimenta-Lab5.png" |
| | + | class="figure-img img-fluid rounded" |
| | + | alt="Placeholder"></a> |
| | + | </figure> |
| | + | </div> |
| | + | </div> |
| | <p> | | <p> |
| − | To predict the transport effectivity of a FASTA-formatted amino acid string, please make sure | + | Please check out the material we prepared for the course - a script covering all the theoretical |
| − | that the sequence does only contain letters corresponding to the genetic code of the 20 standard
| + | background and a presentation: |
| − | amino acids. Moreover, please make sure that the submitted sequence is not longer than 50 residues. | + | |
| | </p> | | </p> |
| − | </div>
| + | <ul style="color:#F4F0DE;"> |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Using a Uniprot Accession number</h4>
| + | <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> |
| − | <div class="col-12">
| + | <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> |
| | + | </ul> |
| | <p> | | <p> |
| − | Since Uniprot is one of the largest publicly accessible resources for proteins, our tool allows | + | Please see the schedule below. |
| − | using the Uniprot Accession number as input, which consists of 6-10 characters (e.g. Q86FU0).
| + | |
| − | Information about the accession numbers can be found on the <a href="https://www.uniprot.org/help/accession_numbers" onclick='window.open("https://www.uniprot.org/help/accession_numbers","_self");'>Uniprot Website</a>.
| + | |
| | </p> | | </p> |
| | </div> | | </div> |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Prediction using an iGEM Registry ID</h4>
| + | </div> |
| | + | |
| | + | <div class="row"> |
| | <div class="col-12"> | | <div class="col-12"> |
| − | <p> | + | <figure> |
| − | Prediction on sequences in the iGEM registry can only be made on parts tagged in the subcategory | + | <a style="font-size: small" |
| − | “coding sequence”, otherwise the submitted identifier is rejected for the prediction.
| + | href="https://2019.igem.org/wiki/images/f/f1/T--Tuebingen--table_test.png" |
| − | The DNA sequences are automatically translated into protein sequences.
| + | data-effect="mfp-zoom-out" |
| − | </p> | + | title="Some title"> |
| | + | <img src="https://2019.igem.org/wiki/images/f/f1/T--Tuebingen--table_test.png" |
| | + | class="figure-img img-fluid rounded" |
| | + | alt="Placeholder"></a> |
| | + | </figure> |
| | </div> | | </div> |
| | </div> | | </div> |
| − |
| |
| − | <h2 style="font-family:'Righteous'; color:#2ecc71;">Implementation</h2>
| |
| − |
| |
| | | | |
| | <div class="row"> | | <div class="row"> |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Input</h4>
| |
| | <div class="col-12"> | | <div class="col-12"> |
| − | <p> | + | <p>Due to the interactive design of the course, we also discussed the experiments with the students |
| − | C3Pred accepts three possible input formats for protein data:
| + | and tried to summarize what we did on the blackboard:</p> |
| − | </p>
| + | |
| − | <ul style="color: #2ecc71">
| + | <div class="row align-items-center"> |
| − | <li>FASTA-formatted sequences</li>
| + | <div class="col-12 col-md-6"> |
| − | <li>UniProtKB Accession Number</li>
| + | <figure> |
| − | <li>iGEM Part ID</li>
| + | |
| − | </ul>
| + | |
| − | <p>
| + | |
| − | C3Pred automatically fetches and parses the information about the given identifiers using the
| + | |
| − | UniProt website REST API or using the iGEM Registry API, respectively. For this function, an internet connection is required.
| + | |
| − | </p>
| + | |
| − | </div>
| + | |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Input requirements</h4>
| + | |
| − | <div class="col-12">
| + | |
| − | <p>
| + | |
| − | All proteins submitted to the tool must fulfill certain criteria, such that a transport
| + | |
| − | efficiency score can be computed. CPPs usually have a length between 4-30 amino acids,
| + | |
| − | thus only protein sequences with a length in this range are accepted as input. Moreover,
| + | |
| − | only the 20 standard amino acids are allowed. Our tool provides an additional option,
| + | |
| − | which also allows non-standard encodings (e.g. B encoding for asparagine/aspartate or S for | + | |
| − | selenocysteine). Since information about those amino acids is not backed up by the training data,
| + | |
| − | results produced for those peptides must be interpreted with caution.
| + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | For iGEM Part IDs further requirements need to be fulfilled, such that a prediction can be made.
| + | |
| − | C3Pred only accepts parts defined as coding sequences. If the sequence is coding, our tool
| + | |
| − | automatically translates it into a protein sequence, beginning the translation from the start
| + | |
| − | codon. If there is no start codon present, the sequence is translated from the first frame onwards.
| + | |
| − | </p> | + | |
| − | </div>
| + | |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Output</h4>
| + | |
| − | <div class="col-12">
| + | |
| − | <p>
| + | |
| − | For each peptide, a transport efficiency score is computed. For peptides without a carrier
| + | |
| − | property, the score is close to zero. For extremely active peptides, the score is close to ten.
| + | |
| − | The values computed for different peptides can be directly compared. Since the output is a
| + | |
| − | dimensionless numerical value, a straightforward classification into no/low/medium/high
| + | |
| − | activity is provided for the user to facilitate the interpretation process.
| + | |
| − | Moreover, a range of activity values of frequently used CPPs in the literature is also
| + | |
| − | provided in the GUI for direct comparison.
| + | |
| − | </p>
| + | |
| − | </div>
| + | |
| − | <figure>
| + | |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/d/d6/T--Tuebingen--Workflow-transparent.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/d/d6/T--Tuebingen--Workflow-transparent.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> |
| | + | </figure> |
| | | | |
| | + | </div> |
| | + | <div class="col-12 col-md-6 "> |
| | + | <figure> |
| | + | <a style="font-size: small" |
| | + | href="https://2019.igem.org/wiki/images/d/df/T--Tuebingen--Experimenta-Lab2.png" |
| | + | data-effect="mfp-zoom-out" |
| | + | title="Some title"> |
| | + | <img src="https://2019.igem.org/wiki/images/d/df/T--Tuebingen--Experimenta-Lab2.png" |
| | + | class="figure-img img-fluid rounded" |
| | + | alt="Placeholder"></a> |
| | </figure> | | </figure> |
| | + | </div> |
| | + | </div> |
| | + | </div> |
| | </div> | | </div> |
| − | <h2 style="font-family:'Righteous'; color:#2ecc71;">Core Algorithm</h2>
| + | |
| | <div class="row"> | | <div class="row"> |
| | <div class="col-12"> | | <div class="col-12"> |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">XGBoost</h4>
| + | <p>The students were also very interested in iGEM and our work. Hence, we not only introduced iGEM |
| − | <p>The algorithm, C3PRed uses to compute transport activity scores for peptides, is the gradient | + | and our project to them, but also let them critically evaluate our project. They were also given |
| − | boosted trees implementation of the XGBoost library. Gradient boosted trees are a commonly used | + | the chance to conduct PCRs related to our project and could therefore gain insights into the upcoming |
| − | algorithm for supervised machine learning problems. Key advantages are their inherently fast | + | challenges when starting a new project or experiment where not everything has been optimised for |
| − | training speed and high accuracy for problems, which cannot be solved using deep learning techniques, | + | easy functionality. Many students were interested in the iGEM competition itself and in the process |
| − | due to too little data. The key idea of the gradient boosted trees algorithm is to map a set of input | + | of finding a project and making it feasible. Therefore, we also invested into giving valuable input |
| − | features onto a single numerical value. In our case, the input is the encoded protein sequence | + | and advice on starting a project and encouraged the students to participate in iGEM or similar projects |
| − | and the predicted numerical value is the activity scores. For this purpose, numerous decision | + | themselves. Several questions and concerns relating the functionality of our probiotic under different |
| − | trees are generated which are iteratively added to the model, such that with each addition the model improves.</p> | + | conditions, such as patients taking medications or antibiotics were also raised by the students. These |
| − | </div>
| + | fruitful discussions, as well as our exchange with several experts, contributed to the final design |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Data</h4>
| + | of our RNA-Seq experiment providing valuable input and different aspects to be considered |
| − | <div class="col-12">
| + | [<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> |
| − | To train our model we used the publically available dataset by Ramaker et. al, consisting of | + | Due to the high interest of the students and the positive feedback from the Experimenta itself, |
| − | transport efficiency values for 474 short peptide motifs. In their experiments, short peptides | + | we discussed the possibility of creating an iGEM high school team in Heilbronn in 2020. |
| − | were coupled with a fluorophore and the transport over the membrane was then measured using | + | The Experimenta is highly interested in participating in iGEM 2020 with motivated students and |
| − | fluorescence as a read-out. The transport efficiency data for each peptide were log2-transformed | + | will provide the required laboratories, supervision and funding. Our team will still be serving |
| − | to facilitate the fitting process. | + | as advisors for the planned iGEM high school team next year. Furthermore, a new student lab course |
| | + | on CRISPR/Cas will be introduced at the Experimenta on the grounds of the theoretical background, |
| | + | input and inspiration iGEM Tuebingen conveyed. |
| | </p> | | </p> |
| − | </div>
| |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Encoding</h4>
| |
| − | <div class="col-12">
| |
| − | <p>
| |
| − | To encode the peptides for the machine learning step, we chose an extended version of the
| |
| − | BLOMAP encoding. BLOMAP is a machine-learning oriented representation of amino acids.
| |
| − | It is based on a transformed BLOSUM substitution matrix. The encoding is extended by
| |
| − | numerical values by physicochemical properties of each the amino acids, including flexibility, weight, isoelectric point, hydrophobicity, polarity, and area.
| |
| − | Each peptide is represented as the set of all possible sliding windows of the size of 14 residues. Shorter peptides are padded at the N- and C-terminus.
| |
| − | An advantage of such an encoding is that after the training steps, it is possible to analyze the final prediction tool for the most influential features. This allows a better understanding of the transport mechanism and the general characteristics of CPPs.
| |
| − | An issue with this encoding is that modified amino acids that are not among the 20 standard ones cannot be represented properly.
| |
| − | </p>
| |
| − | </div>
| |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Training</h4>
| |
| − | <div class="col-12">
| |
| − | <p>
| |
| − | For each sliding window of a peptide, an activity score is computed. The total activity of the peptide is determined by the mean of all activity values of all sliding windows.
| |
| − | Our CPP transport activity prediction model was fitted to optimize Pearson's correlation coefficient of the predicted values against the experimentally derived ones. To find good hyperparameters of the gradient boosted trees algorithm, a random search was performed.
| |
| − | The evaluation of the performance of our predictor was performed using a 10-fold cross-validation.
| |
| − | </p>
| |
| − | <h5 style="font-family: 'Righteous'; color: #2ecc71;">Hyperparameters List</h5>
| |
| − | <ul style="color: #2ecc71">
| |
| − | <li>window_size = 14</li>
| |
| − | <li>n_estimators = 600</li>
| |
| − | <li>learning_rate = 0.4</li>
| |
| − | <li>max_depth = 5</li>
| |
| − | <li>subsample = 0.6</li>
| |
| − | <li>gamma = 3</li>
| |
| − | <li>min_child_weight = 0.75</li>
| |
| − | <li>colsample_bytree = 0.8</li>
| |
| − | </ul>
| |
| | </div> | | </div> |
| | </div> | | </div> |
| | | | |
| − | <h2 style="font-family:'Righteous';">Performance</h2> | + | <h3 style="font-family:'Righteous'; color:#2ecc71;">Panel Discussion - „Biohacking – genetic experiments done at home“</h3> |
| | <div class="row"> | | <div class="row"> |
| | <div class="col-12"> | | <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> | | <p> |
| − | Predicted activity values of the 10-fold cross-validation are plotted against the experimentally | + | In collaboration with Dr. Robert Friedrich, we designed a discussion around the status of current |
| − | derived ones. Each point represents a peptide. If the predictions would be perfectly accurate, | + | research on CRISPR / Cas, the effectiveness of the method and its limitations, the prospects of |
| − | all points would be on the diagonal. | + | 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> | | </p> |
| − | <p> | + | |
| − | Pearson correlation: 0.804<br>
| + | <div class="row align-items-center"> |
| − | Euclidean distance: 27.795
| + | <div class="col-12 col-md-6"> |
| − | </p>
| + | <figure> |
| − | <figure>
| + | |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/f/f6/T--Tuebingen--predicted-values-scatter.png_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/f/f6/T--Tuebingen--predicted-values-scatter.png_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"></a> | + | alt="Placeholder"></a> |
| | </figure> | | </figure> |
| − | <p>
| + | |
| − | The importance of each feature of the BLOMAP encoding is shown in this visualization. The higher
| + | </div> |
| − | the values, the greater is the importance of the feature on the results of the prediction.
| + | <div class="col-12 col-md-6 "> |
| − | The feature isoelectric point is the most important one, which indicates that charged amino acids
| + | <figure> |
| − | play the most important role in high activity values.
| + | |
| − | </p>
| + | |
| − | <figure>
| + | |
| | <a style="font-size: small" | | <a style="font-size: small" |
| − | href="https://2019.igem.org/wiki/images/b/bc/T--Tuebingen--feature-importance_transparent.png" | + | href="https://2019.igem.org/wiki/images/4/4d/T--Tuebingen--Biohacking_10.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/b/bc/T--Tuebingen--feature-importance_transparent.png" | + | <img src="https://2019.igem.org/wiki/images/4/4d/T--Tuebingen--Biohacking_10.jpg" |
| | class="figure-img img-fluid rounded" | | class="figure-img img-fluid rounded" |
| − | alt="A generic square placeholder"></a> | + | alt="Placeholder"></a> |
| | </figure> | | </figure> |
| | + | </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, |
| | + | many participants were eager to talk about scenarios they have heard about. |
| | + | </p> |
| | </div> | | </div> |
| | + | </div> |
| | | | |
| − | <h2 style="font-family:'Righteous';">Results</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"> |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Validation against experimental data</h4>
| |
| | <div class="col-12"> | | <div class="col-12"> |
| − | <p> | + | <p>During the collaboration with the Experimenta Heilbronn, we sat together with Dr. Robert Friedrich |
| − | We used the data obtained from the experimental work of previous iGEM teams to validate the
| + | and Norbert Hommrichhausen to discuss the foundation of an iGEM high school team at the Experimenta |
| − | results of our prediction tool. In the past years, numerous teams have worked with CPPs. Some
| + | Heilbronn. The Experimenta is highly interested in starting a team in Heilbronn and the motivated |
| − | of them conducted experiments to compare the transport efficiency of the peptides, which again | + | and interested students encouraged us to team up and further pursue this plan. Plans for an iGEM |
| − | indicates the potential usefulness of our tool to other teams. | + | high school team 2020 were made, in which the Experimenta Heilbronn will be the main partner |
| − | </p>
| + | providing lab space, supervision and funding. The role of the iGEM Team Tuebingen is that of |
| − | <p>
| + | experienced advisors, who can assist in questions concerning the iGEM competition itself, the |
| − | The ATOMS Turkiye team of 2013 compared the efficiency of the two CPPs <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202006" onclick='window.open("http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202006","_self");'>TAT</a>
| + | workflow of an iGEM year, as well as deliver expert knowledge and guidance in the laboratory or |
| − | and <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202009" onclick='window.open("http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202009","_self");'>MPG</a>
| + | in questions concerning bioinformatics, design and human practices. Both the Experimenta and the |
| − | to transport an apoptosis-inducing protein into different cell lines. Their
| + | iGEM Team Tuebingen aim at establishing a long-term collaboration in the scope of iGEM.</p> |
| − | findings of TAT fusion protein being better transported into the cell than the MPG fusion protein, | + | |
| − | are in accordance with our predicted values. | + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | Predicted activity values (higher is better):<br>TAT - 5.522<br>MPG - 5.099
| + | |
| − | </p>
| + | |
| − | <p><a href="http://parts.igem.org/Part:BBa_K1202009" onclick='window.open("http://parts.igem.org/Part:BBa_K1202009","_self");'>Their results summary</a></p>
| + | |
| − | <p>
| + | |
| − | The iGEM Team DLUT-China of 2018 conducted a similar comparative experiment for multiple CPPs.
| + | |
| − | They compared R8, <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202006" onclick='window.open("http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202006","_self");'>TAT</a>, | + | |
| − | <a href="http://parts.igem.org/Part:BBa_K2752011" onclick='window.open("http://parts.igem.org/Part:BBa_K2752011","_self");'>Pep-1 and cyclic heptapeptide DNP</a>.<br> | + | |
| − | Predicted activity values (higher is better):<br>R8: 5.714<br>TAT - 5.522<br>Pep-1 : 5.496<br>cyclic heptapeptide DNP: 2.943 | + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | Their results for R8, TAT and Pep-1 are in accordance with our predictions. R8 was the most transported
| + | |
| − | peptides in their experiments and also scored best in our prediction.
| + | |
| − | However, our tool predicts a bad score for the cyclic heptapeptide DNP, which shows high transport efficiency in their | + | |
| − | experiment. This can be explained by the fact that our tool was trained only with linear protein sequences containing the standard 20 amino acids. Special peptides like this, probably cannot be predicted by our tool correctly.
| + | |
| − | </p>
| + | |
| − | <p><a href="http://2018.igem.org/Team:DLUT_China/Results#A4.3" onclick='window.open("http://2018.igem.org/Team:DLUT_China/Results#A4.3","_self");'>Their results summary</a></p>
| + | |
| | | | |
| − |
| |
| − | </div>
| |
| − | </div>
| |
| − | <h2 style="font-family:'Righteous';">How our software influenced our project</h2>
| |
| − | <div class="row">
| |
| − | <h4 style="font-family:'Righteous'; color: #2ecc71;">Validation against experimental data</h4>
| |
| − | <div class="col-12">
| |
| | <p> | | <p> |
| − | We used the results of C3Pred to analyze CPPs to decide on a suitable CPP for our project. | + | Next to the foundation of a high school iGEM team, the Experimenta will also introduce new lab |
| − | We analyzed a series of CPP which were already present in the iGEM Registry and additional | + | courses for school classes, one of them being a CRISPR/Cas course. The theoretical background, |
| − | peptides which were frequently referred to in the literature. | + | first steps and foundation of this course arose from the collaboration with iGEM Tuebingen this year. |
| | + | A more detailed outline and implementation of the course will be part of another collaboration |
| | + | between the Experimenta and iGEM Tuebingen. |
| | </p> | | </p> |
| − | <p>
| |
| − | <a href="http://parts.igem.org/Part:BBa_K2660000" onclick='window.open("http://parts.igem.org/Part:BBa_K2660000","_self");'>Penetratin : 7.258914470672607</a><br>
| |
| − | <a href="http://parts.igem.org/Part:BBa_K380005" onclick='window.open("http://parts.igem.org/Part:BBa_K380005","_self");'>Tp10 : 6.653654098510742</a><br>
| |
| − | <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202006" onclick='window.open("http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202006","_self");'>TAT: 5.522</a>
| |
| − | </p>
| |
| − | <p>
| |
| − | Since Penetratin showed the highest scores compared to the other parts available in the iGEM Registry,
| |
| − | we decided to select this specific CPP as the carrier for the Exendin-4 protein of our project.
| |
| − | </p>
| |
| − | <p>
| |
| − | Moreover, we computed an elevated transport activity for the CPP fusion protein
| |
| − | <a href="http://parts.igem.org/Part:BBa_K3096016" onclick='window.open("http://parts.igem.org/Part:BBa_K3096016","_self");'>TAT-LK15</a>
| |
| − | , which has been reported to enhance the properties of TAT.
| |
| − | </p>
| |
| − | <p>
| |
| − | <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202006" onclick='window.open("http://parts.igem.org/wiki/index.php?title=Part:BBa_K1202006","_self");'>TAT : 5.522</a><br>
| |
| − | <a href="http://parts.igem.org/Part:BBa_K3096016" onclick='window.open("http://parts.igem.org/Part:BBa_K3096016","_self");'>TAT-LK15 : 7.838017463684082</a>
| |
| − | </p>
| |
| − | </div>
| |
| | </div> | | </div> |
| − | | + | </div> |
| | </div> | | </div> |
| − |
| |
| − | <div id="glpreferences" class="row">
| |
| − | <h3 style="font-family:'Righteous'; color: #2ecc71;">References</h3>
| |
| − | <div class="col-12" style="font-size: x-small; overflow-wrap: break-word;">
| |
| − | <ol>
| |
| − | <li style="color: #F4F0DE"><a href=https://www.nature.com/articles/s41467-018-04874-6>https://www.nature.com/articles/s41467-018-04874-6</a></li>
| |
| − | <li id="ref_2" style="color: #F4F0DE"><a href="https://www.nature.com/articles/s41598-018-30790-2">https://www.nature.com/articles/s41598-018-30790-2</a></li>
| |
| − | <li id="ref_3" style="color: #F4F0DE"><a href="https://www.doi.org/10.1016/j.tips.2017.01.003">https://www.doi.org/10.1016/j.tips.2017.01.003</a></li>
| |
| − | <li id="ref_4" style="color: #F4F0DE"><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324683/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324683/</a></li>
| |
| − | <li id="ref_5" style="color: #F4F0DE"><a href="http://dx.doi.org/10.1145/2939672.2939785">http://dx.doi.org/10.1145/2939672.2939785</a></li>
| |
| − | <li id="ref_6" style="color: #F4F0DE"><a href="https://doi.org/10.1142/9781860947322_0014">https://doi.org/10.1142/9781860947322_0014</a></li>
| |
| − | <li id="ref_7" style="color: #F4F0DE"><a href="https://doi.org/10.1080/10717544.2018.1458921">https://doi.org/10.1080/10717544.2018.1458921</a></li>
| |
| − | </ol>
| |
| − | </div>
| |
| − | </div>
| |
| | </main> | | </main> |
| | </div> | | </div> |