Difference between revisions of "Team:UCSF/Description"

"<p class='headerProjectSub'>BASIC CIRCUIT</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Induction: Doxycycline</b></br></br><img style='float:right;margin-right:0px;margin-top:-80px' src='https://static.igem.org/mediawiki/2015/b/bf/UCSF_Basic_Circuit_Diagram_Part_1-01.png' alt='Circuit Part 1' height='210' width='350'><b>Activate cell through the use of an induction factor and inducible promoters.</b></br></br><b style='color:#368E8C'>Design:</b> Doxcycline binds with rtTA produced by a constitutive promoter.</br><b style='color:#368E8C'>Purpose:</b> Something here about why we do this.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p></br>");

"<p class='headerProjectSub'>BASIC CIRCUIT</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Induction: Doxycycline</b></br></br><img style='float:right;margin-right:0px;margin-top:-80px' src='https://static.igem.org/mediawiki/2015/b/bf/UCSF_Basic_Circuit_Diagram_Part_1-01.png' alt='Circuit Part 1' height='210' width='350'><b>Activate cell through the use of an induction factor and inducible promoters.</b></br></br><b style='color:#368E8C'>Design:</b> Doxcycline binds with rtTA produced by a constitutive promoter.</br><b style='color:#368E8C'>Purpose:</b> Something here about why we do this.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p></br>");

"<p class='headerProjectSub'>BASIC CIRCUIT</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Individual Response: GFP</b></br></br><img style='float:right;margin-right:0px;margin-top:-80px' src='https://static.igem.org/mediawiki/2015/2/27/UCSF_Basic_Circuit_Diagram_Part_2-01.png' alt='Circuit Part 2' height='210' width='350'><b>Cells produce GFP in response to doxcycline.</b></br></br><b style='color:#368E8C'>Design:</b> pTET inducible promoter drives production of GFP.</br><b style='color:#368E8C'>Purpose:</b> Something here about why we do this.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p></br>");

"<p class='headerProjectSub'>BASIC CIRCUIT</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Communication Signal: mFα</b></br></br><img style='float:right;margin-right:0px;margin-top:-80px' src='https://static.igem.org/mediawiki/2015/a/aa/UCSF_Basic_Circuit_Diagram_Part_3-01.png' alt='Circuit Part 3' height='210' width='350'><b>Cells produce mFα in response to doxcycline.</b></br></br><b style='color:#368E8C'>Design:</b> pTET inducible promoter drives production of mFα.</br><b style='color:#368E8C'>Purpose:</b> Something here about why we do this.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p></br>");

"<p class='headerProjectSub'>BASIC CIRCUIT</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Community Response: RFP</b></br></br><img style='float:right;margin-right:0px;margin-top:-80px' src='https://static.igem.org/mediawiki/2015/b/b7/UCSF_Basic_Circuit_Diagram_Part_5-01.png' alt='Circuit Part 3' height='210' width='350'><b>Cells produce RFP and LexADBD in response to mFα.</b></br></br><b style='color:#368E8C'>Design:</b> pAga inducible promoter drives production of RFP and LexADBD.</br><b style='color:#368E8C'>Purpose:</b> Something here about why we do this.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p></br>");

"<p class='headerProjectSub'>BASIC CIRCUIT</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Feedback: Increased Activation</b></br></br><img style='float:right;margin-right:0px;margin-top:-80px' src='https://static.igem.org/mediawiki/2015/4/45/UCSF_Basic_Circuit_Diagram_Part_6-01.png' alt='Circuit Part 3' height='210' width='350'><b>Cells produce RFP and LexADBD in response to mFα.</b></br></br><b style='color:#368E8C'>Design:</b> LexAOps inducible promoter drives production of feedback gene.</br><b style='color:#368E8C'>Purpose:</b> Something here about why we do this.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p></br>");

"<p class='headerProjectSub'>CAN YOU SENSE ME NOW?</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Positive Feedback</b></br></br><img style='float:right;margin-right:100px;margin-top:0px' src='https://static.igem.org/mediawiki/2015/9/9d/UCSF_Increased_Secretion.png' alt='Increased Secretion' height='250' width='250'><b>Increased Secretion: Generating more alpha factor signal to increase communication range and amplify local concentrations.</b></br></br><b style='color:#368E8C'>Design:</b> LexA transcription factor inducible promoter driving production of mFα.</br><b style='color:#368E8C'>Purpose:</b> Activated cells will up-regulate mFα, which will produce and secrete more alpha factor signal to the community. This will generate a positive feedback loop that will amplify both communication range and local concentrations of signal, essentially generating local communities of activated cells. We believe that this motif is essential for community decision making because increased secretion will allow cells to “talk” to individuals farther away in the community. However, through diffusion mechanisms, alpha factor will create a concentration gradient, allowing local cells to sense the community signal more strongly.</br><b style='color:#368E8C'>Inspiration:</b> T Cells, through sensing and secreting the community signal IL2, will up-regulate secretion of IL2 and “talk” to neighboring T Cells better.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><img style='float:right;margin-right:100px;margin-top:0px' src='https://static.igem.org/mediawiki/2015/8/8c/UCSF_Increased_Receptor.png' alt='Increased Receptor' height='250' width='250'><b>Increased Reception: Production of more alpha factor receptor to sense more alpha factor and polarize communities.</b></br></br><b style='color:#368E8C'>Design:</b> LexA transcription factor inducible promoter driving production of Ste2.</br><b style='color:#368E8C'>Purpose:</b> Activated cells will up-regulate Ste2, an integral ligand receptor of alpha factor in the mating pathway. This will allow cells to sense more alpha factor, producing a selfish feedback loop and amplifying the gap between “ON” and “OFF” states. Due to proximity of signal and receptor, cells with high Ste2 expression will engage in asocial behavior, and sense signal produced themselves. This selfish feedback will sharpen concentration gradients and create stronger local concentrations of alpha factor.</br><b style='color:#368E8C'>Inspiration:</b> Similar to the positive feedback of IL2 secretion in T Cells, sensing IL2 will up-regulate the production of IL2 receptor. This allows cells to “listen” to their neighbors better.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p>");

"<p class='headerProjectSub'>RAISING THE BAR1</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Signal Degradation</b></br></br><img style='float:right;margin-right:100px;margin-top:0px' src='https://static.igem.org/mediawiki/2015/d/da/UCSF_Signal_Degradation_2.png' alt='Signal Degradation' height='250' width='250'><b>Using an alpha factor protease to set a threshold for cellular activation.</b></br></br><b style='color:#368E8C'>Design:</b> pTEF1 constitutive promoter (and mutants) driving production of Bar1.</br><b style='color:#368E8C'>Purpose:</b> We have engineered constitutive expression of Bar1, an endogenous alpha factor protease, with varying activity levels. Degradation of mFα signal will sharpen concentration gradients and “raise the bar” for cells to sense the community and activate a RFP community response. This will set of threshold for cells to activate and thus increase the gap between “ON” and “OFF” cells.</br><b style='color:#368E8C'>Inspiration:</b> The immune system has a subset of T-Regulatory Cells that will sponge up the IL2 signal secreted by T Cells. This prevents all cells from proliferating and attacking, and selects for the cells best suited for the response. T-Regulatory Cells have been shown to be essential in preventing autoimmune diseases.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p>");

"<p class='headerProjectSub'>CELLULAR HOTSPOTS</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Feedback: Activated Clustering</b></br></br><img style='float:right;margin-right:100px;margin-top:0px' src='https://static.igem.org/mediawiki/2015/e/e7/UCSF_Activated_Clustering.png' alt='Clustering' height='250' width='423'><b>Maintaining activated cells in local clusters to strengthen communication.</b></br></br><b style='color:#368E8C'>Design:</b> LexA transcription factor inducible promoter driving production of Aga-Mgfp5.</br><b style='color:#368E8C'>Purpose:</b> Repurposing parts from UCSF 2011, we are using modified surface display proteins in yeast to induce cell adhesion through gene specific heterodimers. Particularly, we are utilizing a yeast surface display system using a fusion protein with a cell wall anchoring protein (Aga1 and Aga2) and a bioadhesive endogenously found in mussels (Mgfp5). In closer proximity, cells should be able to communicate with their local community more efficiently. This will essentially polarize cellular communities into their local clusters.</br><b style='color:#368E8C'>Inspiration:</b> We know from natural systems that distance between individuals in a community is a crucial factor in how well they communicate with one another. T Cells, after being activated by an antigen, will be maintained in lymph nodes by a protein, CD69. This spatial retention of activated cells will allow them to talk better to one another since they are all within a small range of communication.</br>This motif is also found in quorum sensing V. fischeri, who sense and secrete a species specific autoinducer that allows individuals to measure population size. These organisms are found in the light organs of the Hawaiian Bobtail Squid, and, when in an enclosed space with a high cell density, are able to communicate together their decision to bioluminesce. This is due to the limited diffusion of the signaling molecule, and thus, more effective communication.</br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p>");

"<p class='headerProjectSub'>INTRODUCTION</p><div class='headerBreakSub' style='width:100%'></div></br><p class='content1'><b style='color:#368E8C;font-size:1.5em'>Inspiration</b></br></br>We drew inspiration for this sense and secrete signaling motif by its ubiquity in natural systems. By sensing a self-generated signal, cells participate in social and asocial behaviors that allow them to communicate decisions effectively with their neighbors. This process is generally stochastic, due to the random local concentration makeups and molecular proximities of cells and signals. However, sense and secrete signaling motifs allow for powerful mechanisms to alter community phenotypes. Cellular populations use this signaling molecule to create robust decisions for the whole population through: convergence, divergence, cell differentiation, or other community responses.</br></br>Sense and secrete circuits are found in most bacterial communities through species specific quorum sensing. V. fischeri, aquatic bacteria that bioluminesce at certain cell densities, sense and secrete an autoinducer to keep a census of their population. Low signal concentrations are correlated with low cell density and high signal concentrations are correlated with high cell density. However, when confined to a small area, these signal concentrations are dramatically amplified and the bacteria activate a signaling cascade to bioluminesce. This is an example of cellular populations averaging out the variation of the individual through communication.</br></br>The adaptive immune system is comprised of T Cells with varied responses to a specific antigen. When a T Cell senses an antigen, it initiates a signaling cascade in which a signaling cytokine, IL2, is secreted and a receptor for IL2 is produced. After communicating to neighboring T Cells with IL2, the T Cell population coordinates its efforts to proliferate only the cells best suited to fight off the antigen. Thus, we see varied individual responses leading way to divergent community responses in T Cell populations after communication.</br></br>Community decision making can also be found in bacterial communities, such as B. subtilis. These cellular populations are made of genetically identical cells that utilize extracellular signals to differentiate into phenotypically different cells that play specific roles in the survival of the community. B. subtilis utilizes a sense-and-secrete motif, similar to quorum sensing autoinducers, that couple with local environmental factors to assign “jobs” to individual cells in the community, and thus different molecular makeups. By communicating with members of their community, B. subtilis communities are able to amplify individual responses to differentiate cells into multiple distinct cell fates.</br></br><b style='color:#368E8C'>References:</b></br><span style='font-size:1em'>Insert references here</span></br></p>");