document.getElementById("tab1").innerHTML = '<h2>Assembly Plan</h2><img class="schedule" src="https://static.igem.org/mediawiki/2014/6/6e/Uppsala2014_TheYensystem.png"</img><h2> Communication using quorum sensing</h2><p>Quorum sensing (QS) is the communication tool of bacteria. It is usually done through secretion and detection of small signal molecules or proteins. Depending on the bacterial density, these molecules can trigger a change of behaviour, i.e. invoke a function only when there are enough bacteria present in that one area. Quorum sensing can control several things, from biofilm formation to bioluminescence. The most commonly known and most explored QS system is the Lux system, which was originally isolated from Vibrio fischeri, where it controls the production of luciferase, an enzyme that aids in the production of a yellow light.</p><h2> Using the pathogens own quorum sensing system to detect and track its source</h2><p>When we decided that we wanted to fight pathogens it became obvious that we needed a way to detect and track them. After doing some research, we decided that this could be  done by hijacking the pathogen’s own quorum sensing. Naturally, the first thought that came to our minds was to use the Lux system from V. fischeri. However, this had been done before in 2008 by Heidelberg and it also did not provide the specificity that we wanted for our system. We decided to dig deeper and see if we could find a more unique quorum sensing system. Among some potential candidates was Yersinia enterocolitica, which uses a quorum sensing system called the Yen system.</p><h2>The Yen system </h2><p>As it turns out Y. enterocolitica has a homologous quorum sensing system to the famous Lux system, the Yen system. From this system we chose to steal two parts. A recognition region called the yenbox fused together with a promoter and an activator, YenR, that can recognise and interact with the yenbox. When YenR binds to the yenbox it induces the expression level of the promoter fused to the yenbox. Later, in the presence of Y. enterocolitica, its signaling molecules, 3-oxo-hexanoyl homoserine lactone (OHHL), will start flowing into our system, interacting with YenR. When binding occurs between OHHL and YenR, YenR will lose its active shape and thereby its ability to interact with the yenbox. The induction will then be lost and the expression level will return to its base level. [1]<br></br>By BioBricking and characterizing this system, we wish to make it possible to get a Y. enterocolitica density triggered response. Our goal with this system is to control our two other systems, the Targeting and the Killing system.</p><h3>System Design</h3><p>While stealing the yenbox together with the wild type promoter fused with it, we had no idea about the strength of the wild type promoter or if it would even work at all. Because of this, we created an alternative version where we replaced the wild type promoter with a standardised one (J23113). In the wild type version there is an overlap between the wild type promoter and the yenbox. Hence, we mimicked the same while creating our customized version where we had an overlap between the promoter and the yenbox. Since the strength of the promoter would correspond to the leakage in our system, we wanted to have a weak promoter to minimize the leakage. We chose the constitutive promoter J23113 (BBa_J23113) from the Anderson library. Unfortunately, the promoter J23113 did not begin with the same two bases as the end of the yenbox. We were left with the option of either changing the two bases in the yenbox sequence or changing the two bases in the sequence of the promoter J23113. In the article by Ching-Sung Tsai and Stephen C. Winanas [1] they discovered that the binding between the activator YenR and the recognition region of the yenbox is not dependent on the entire sequence of the yenbox. Depending on which part of the yenbox is changed or replaced, YenR binds to the yenbox with different strengths. However, it still interacts with the yenbox and induces the strength of the promoter. Based on this fact, together with the knowledge that the Anderson promoters are very sequence dependent, we chose to change two bases in the sequence of the yenbox.<br><br>We also stole the coding sequence [2] of the activator YenR, from Y. enterocolitica, which we codon optimized for E. coli using a web tool [3] and synthesized it together with the RBS B0034 (BBa_B0034). Since we always want production of the activator YenR, it was coupled to three different constitutive promoters from the Anderson promoter library with three different strengths.</p>;