Difference between revisions of "Team:WHU-China/Description"

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                     <li><a href="https://2015.igem.org/Team:WHU-China/Description?num=1">Overview</a></li>

                     <li><a href="javascript:return false;">Results</a></li>

                     <li><a href="https://2015.igem.org/Team:WHU-China/Basic_Parts">Basis Parts</a></li>

                    <li><a href="javascript:return false;">Favorite Parts</a></li>

             <h2>Description</h2>

                 <span>A signal filter that simplifies complex vibration is vital in information processing [1]. This summer, we aim to build one and explore its application in biocomputing and oral health care. Light inputs are achieved by our light-sensing protein and then further processed by a negative feedback circuit [2]. <a href="https://2015.igem.org/Team:WHU-China/Description?num=3">The criticality detector</a> generates pulse output when the input’s vibration exceeds predefined threshold. For biocomputing, the detector is equipped with a <a href="https://2015.igem.org/Team:WHU-China/Description?num=6">binary system</a> to store information in a “living register”. For oral health care, the detector is used to control the dosage of a powerful drug ^[3] in <a href="https://2015.igem.org/Team:WHU-China/Description?num=8">the dosage control system</a> .</span>

                 <h2>Details</h2>

                <span>Criticality detection system, which we intend to construct, combines biosensor with signal converter. The work pattern is that the system receives the specific input signal and then generates pulse output when the input’s vibration exceeds predefined threshold. </span>

                <img src="https://static.igem.org/mediawiki/2015/2/2a/WHU-China_Fig1.png" height="400" />

                <span style="margin-top:410px">Fig.1 The schematic diagram indicating the relationship between input and output.</span>

            <h2>Description</h2>

                <div class="member">

                        <span>The detection of threshold is achieved with the help of a red-light-sensing part and a specially designed negative feedback circuit. A fusion protein called Cph8 senses red light and activates three OmpC promoters when red light intensity in the environment drops below a threshold. An output (GFP) keeps being generated until it is inhibited by the negative feedback circuit we built (see Fig.2). A relatively long feedback circuit was designed to generate pulse of good intensity and modularity.

</span>

                        <span>Considering the system construction and work pattern, our criticality detection system can function as a pulse generator, a signal filter and so on. In our case, the module is proved to have potential application in biocomputer development and health care.</span>

                        <span>Our system can be used as a signal filter in the biocomputer development. Combin-ing criticality detection system with pairs of integrase and excisionase, we set up a binary counting system composed of some two-state latch modules that switch between states "0" and "1".</span>

                        <span>Working as a pulse generator in dental caries prevention, the system release a suita-ble amount of antimicrobial peptides by adjusting the length and intensity of the pulse and maintain the population of oral flora at a satisfactory level.</span>

                        <img src="https://static.igem.org/mediawiki/2015/7/7c/WHU-China_Fig2.png" height="400"/>

                        <span style="margin-top:410px">Fig.2 The schematic diagram showing how the criticality detector works.</span>

         <h2>Criticality Detector</h2>

             <span>The design of our criticality detector came occasionally from a paper about edge detection (A Synthetic Genetic Edge Detection Program.Jeffrey J. Tabor etc. j.cell.2009.04.048 ). Their gene circuit detects edge by recognizing the diffusion near the boundary of an object. Essentially speaking, they use a limitation of diffusion and the spatial distribution it causes to mark the edge. Inspired by their work, we design the negative feedback circuit to create a delay to mark the threshold.</span>

                <span>Therefore, the criticality detector could be divided into two parts: a series of protein for light-sensing and a negative feedback for pulse generating. </span>

                 <img src="https://static.igem.org/mediawiki/2015/2/22/WHU-China_CD1.png" height="400">

                 <span style="margin-top:410px">Fig.1</span>

         <h2>Criticality Detector</h2>

                 <img src="https://static.igem.org/mediawiki/2015/a/a0/WHU-China_CD2.png" height="300">

                 <span style="margin-top:310px">Fig.2 Negative feedback circuit.</span>

                <span style="margin-top:20px">First two OmpC promoters receive input signals and generate taRNA and output signal. The taRNA will change the structure of an artificial riboregulator and expose the RBS to make CI protein express. The CI protein will inhibit the expression of the output.</span>

            <span style="margin-top:20px">The OmpC promoters receive the signal. The output and taRNA are generated. Because taRNA used to unlock riboregulator and CI protein haven’t accumulated to the predefined level, the output is maintained for a while.</span>

         <h2>Criticality Detector</h2>

             <img src="https://static.igem.org/mediawiki/2015/f/f0/WHU-China_CD4.png" height="300">

                 <span style="margin-top:310px">Fig.4 The work pattern of the negative circuit after reaching the threshold for a while.</span>

            <span style="margin-top:20px">Remaining below the threshold for a while, taRNAs accumulate and unlock crloops to express CI proteins. When CI protein binds to its binding site, the output is blocked.</span>

             <h1>Binary System</h1>

<h2>Binary System</h2>

             <h1>Dosage control system</h1>

<span>Antimicrobial peptides are recently regarded as a promising choice to kill microbes due to their strong microbicidal effects and their unlikeliness of triggering resistance in microorganisms. Since there are also various kinds of probiotics living in our mouth besides oral pathogens, and since antimicrobial peptides have effect on general kinds of microorganisms, it’s more wise to modify the antimicrobial peptide into a targeted one by adding a S.mutans targeted sequence on the N-terminal, so that only S.mutans can be killed. Thus we design two fused peptides, CAP-glyglygly-Bac8c and CAP-glyglygly-APP2, to targetedly inhibit the growth of S.mutans in oral cavity, where CAP is an optimized peptide that can specifically bind to the comD receptor on the surface of S.mutans, while Bac8c and APP2 are two kinds of peptides that assume strong bactericidal effect in acidic environment.  

<span>We first fuse CAP and Bac8c(or APP2) with linker “-glyglygly-” to construct targeted antimicrobial peptides. Then in order to prove their function, we express them in Pet28a with the induction of IPTG, and observe their bactericidal effect on E.coli and S.mutans to see if they have targeted effect. And finally we add criticality detector circuit on the upstream of antimicrobial peptide expression gene to control its expression, and use acid sensitive promoter AsR as the input signal sensor of criticality detector to complete the whole system. </span>