Difference between revisions of "Team:BGIC China"

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This mechanism, along with the biosensors for target molecules, we can test the concentration of hormones, glucose, fatty acid or nitrates in plasma, urine or saliva. 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This provides solid proof that the system can sense a variety of types of molecules. Break down the finished plasmids into comprehensive components and submit them as BioBricks.\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003e1.2.2 Laboratory and clinical sample tests\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003eLaboratory sample and clinical sample tests: to test the effectiveness of the system on cell-free paper systems with these samples.\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003e1.2.3 To design, test and, if possible, manufacture test paper reader\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003eTo design, test and, if possible, manufacture test paper reader: To assemble a test paper reader according to existing blueprints and express the measurements via reporter proteins from single apertures.\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003e1.2.4 Pearl necklace-shaped test paper effectiveness assessment\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003ePearl necklace-shaped test paper effectiveness test. 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With the help of cell-free system, comprehensive limitations of biochemical reactions, for example, the fatality to the cell due to the toxicity of the product of metabolism and the prospect of the plasmid being controlled by the host due to negative feedback. A cell-free system has relatively higher operability, proved to be a better alternative for DNA transcription and expression. Plasmids assembled via synthetic biological methods can enable cells with the function of biosensors targeting at small molecules (e.g. glucose), hormones(e.g. oestrogen) and oxymethylene. Via adapting these biosensors into cell-free systems via which test papers are made, comprehensive medical detections can be done during everyday life, saving the efforts of comprehensive laboratory tasks. Compared with existing test-paper techniques (e.g. collaurum), the cell-free system has relatively lower manufactural costs while being able to detect molecules in relatively higher quantities. Its functions can be expanded and enhanced via sufficient and efficient application of BioBrick techniques. Based on the theoretical affirmation derived from the research of respectively Keith Pardee on paper-based synthetic gene networks and Alexis Courbet on detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates.\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003e1.3.2 Design\u003c/p\u003e\u003cp\u003e1.3.2.1 Plasmid Design\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003eThe genetic circuit is composed of two parts, the sensor device and the amplifier/output device. 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Output device: The output device consists of logic gate component loxp-stop-loxp(loxp fragmentterminator-loxp fragment) and reporter protein (LacZ/GFP/Luciferace,etc.) In the case of CRE expression’s absence, the terminator will stop transcription and translation, and thus preventing the downstream protein’s genetic fragments from being expressed; In the presence of CRE protein expression, the two loxp fragments will cut and reconstruct, resulting in the terminators 180 degree rotation about the plasmid, enabling the expression of downstream reporter genes. If the sensor’s component represses the expression of downstream CRE protein sequences in the presence of transcription factors, we can design the direction of the terminator’s rotation. This design enables analogue signal input’s continuous conversion into digital signal inputs. We have successfully achieved this function during a plasmid test in May using equivalent Boolean logic gate system. For further information, see fig. 4. V2- Output improvements Based on V1, we improved the output plasmid by increasing the number of terminators in the l-s-l region and adding longer CRE protein fragments. Due to the impossibility of ending all transcription\u003cbr\u003eexpressions in the plasmid, the terminator’s efficiency can never reach 100%, thus we increased the number of promoters to prevent the distraction of false positive results. The downstream CRE protein sequences will act as amplification device which can cause the rotation of more terminators in the output plasmid, the expression of reporter genes and therefore amplifying the signal via activating a smaller amount of downstream CRE protein expression in the output plasmid in the case of a low transcription factor concentration. V3- Sensor’s improvements To annihilate false positive results, initiate the cutting of output plasmid to prevent its expression via a new genetic editing system, NgAgo/gDNA when the transcription factor(target molecules) are repressing protein expression. NgAgo proteins can cut out a certain 24bp-fragment with the help of a single-strand guide DNA, sgDNA. (Reference. DNA-guided genome editing using the Natronobacterium gregoryi Argonaute by Mr. 韩春雨)\u003c/p\u003e\u003cp\u003e \u003c/p\u003e\u003cp\u003e1.3.2.2 The application of cell-free system\u003c/p\u003e\u003cp\u003e\u003cbr\u003eWe are using the two cell-free systems, S30 and S30T7 based on E.Coli lytic agents provided by Promega.Co. 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Designed Apps on phones that can initiate the ignition of the flashlight of mobile device was also considered as an alternative. Acknowledging the inactivation effect of cooling on cell-free system and cannot be quantified with certain colour samples although the designs above can provide accurate and articulate test results, an improved test-paper design with the mechanism of paper chromatography was accepted. Prepared cell-free system and plasmids were added and dried in precisely-carved slots. Add specific amount of samples to be tested to the sample region, letting the fluid containing target molecules to flow according to the capillarity mechanism.Each time it passes through a slot, a certain amount of target molecules bind with the plasmid, with the remaining molecules continuing its journey down to the next slot until reaching the completion of reaction. 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<h5> Styling your wiki </h5>
 
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Project</a></li><li style="display:none;" data-reactid="31"><a class="s-font-body s-nav-item" href="#inkredible" data-reactid="32">1.1 What is it all about?</a></li><li style="display:none;" data-reactid="33"><a class="s-font-body s-nav-item" href="#specifications" data-reactid="34">1.2 Target</a></li><li style="display:none;" data-reactid="35"><a class="s-font-body s-nav-item" href="#label" data-reactid="36">1.3 Detailed description </a></li><li style="display:none;" data-reactid="37"><a class="s-font-body s-nav-item" href="#contact-us" data-reactid="38">1.4 Our results </a></li><li style="display:none;" data-reactid="39"><a class="s-font-body s-nav-item" href="#connect" data-reactid="40">1.5 Lab summary </a></li><li style="display:none;" data-reactid="41"><a class="s-font-body s-nav-item" data-reactid="42">1.6 Lab Journal </a></li><li style="display:none;" data-reactid="43"><a class="s-font-body s-nav-item" data-reactid="44">1.7 Intellectual Property </a></li><li data-reactid="45"><a class="s-font-body s-nav-item" data-reactid="46">2. Team</a></li><li style="display:none;" data-reactid="47"><a class="s-font-body s-nav-item" data-reactid="48">2.1 Meet the team</a></li><li style="display:none;" data-reactid="49"><a class="s-font-body s-nav-item" data-reactid="50">2.2 Team member intro </a></li><li style="display:none;" data-reactid="51"><a class="s-font-body s-nav-item" data-reactid="52">2.3 Group pic </a></li><li data-reactid="53"><a class="s-font-body s-nav-item" data-reactid="54">3. Human practice</a></li><li data-reactid="55"><a class="s-font-body s-nav-item" data-reactid="56">4. Safety</a></li><li style="display:none;" data-reactid="57"><a class="s-font-body s-nav-item" data-reactid="58">4.1 Laboratory safety assessment</a></li><li style="display:none;" data-reactid="59"><a class="s-font-body s-nav-item" data-reactid="60">4.2 Identified possible risks of our project</a></li><li data-reactid="61"><a class="s-font-body s-nav-item" data-reactid="62">5. Blog</a></li><li style="display:none;" data-reactid="63"><a class="s-font-body s-nav-item" data-reactid="64">博客</a></li></ul><br data-reactid="65"/><ul class="ib links" data-reactid="66"></ul></div><div class="button-container cta" data-reactid="67"><div class="button1 content" data-reactid="68"><div class="s-button s-component" data-reactid="69"><span data-reactid="70"><div class="s-component-content" data-reactid="71"><a class="s-action-button s-common-button s-font-body" href="#1" data-component="button" target="_self" data-reactid="72">TOP</a></div></span></div></div></div></div></div><div class="nav-cant-hide" data-reactid="73">This template doesn&#x27;t support hiding the navigation bar.</div></div><!-- react-empty: 74 --><ul class="slides s-page-1" data-reactid="75"><li class="slide" id="section-f_f4f55bd8-3b51-4909-8949-eb925bb027dc" data-reactid="76"><div class="waypoint" data-reactid="77"></div><a class="section-anchor" data-reactid="78"></a><div class="s-bg-image s-bg-light-text s-section s-title-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(//uploads.strikinglycdn.com/static/backgrounds/patterns/1.jpg);" data-reactid="79"><div class="container" data-reactid="80"><div class="columns sixteen" data-reactid="81"><div class="s-title-group " data-reactid="82"><div data-reactid="83"><div class="s-subtitle" data-reactid="84"><div class="s-component s-text" data-reactid="85"><h4 class="s-component-content s-font-heading" data-reactid="86"><p>iGEM Project of BGI College China</p></h4></div></div><div class="s-title " data-reactid="87"><div class="s-component s-text" data-reactid="88"><h1 class="s-component-content s-font-title" data-reactid="89"><p style="font-size: 80%;">Cell-Free system based test paper platform</p></h1></div></div></div></div></div></div></div></li><li class="slide" id="section-f_af65170e-e964-45f2-a2d9-9420e99a9e3b" data-reactid="90"><div class="waypoint" data-reactid="91"></div><a class="section-anchor" data-reactid="92"></a><div class="lazyload s-no-bg s-block-section s-section" data-reactid="93"><div class="container" data-reactid="94"><div class="columns sixteen" data-reactid="95"><div class="s-title-group " data-reactid="96"><div data-reactid="97"><div class="s-title " data-reactid="98"><div class="s-component s-text" data-reactid="99"><h2 class="s-component-content s-font-title" data-reactid="100"><p>1. Project</p></h2></div></div><div class="s-subtitle" data-reactid="101"><div class="s-component s-text" data-reactid="102"><h4 class="s-component-content s-font-heading" data-reactid="103"><p style="font-size: 80%;"><a href="#3">1.1 What is it all about?</a></p><p style="font-size: 80%;"><a href="#4">1.2 Target</a></p><p style="font-size: 80%;">1.2.1 Plasmids and standard parts registry</p><p style="font-size: 80%;">1.2.2 Laboratory and clinical sample tests</p><p style="font-size: 80%;">1.2.3 To design, test and, if possible, manufacture test paper reader</p><p style="font-size: 80%;">1.2.4 Pearl necklace-shaped test paper effectiveness assessment</p><p style="font-size: 80%;"><a href="#5">1.3 Detailed description</a></p><p style="font-size: 80%;">1.3.1 Abstract</p><p style="font-size: 80%;">1.3.2 Design</p><p style="font-size: 80%;">1.3.2.1 Plasmid Design</p><p style="font-size: 80%;">1.3.2.2 The application of cell-free system</p><p style="font-size: 80%;">1.3.2.3 Pearl necklace-shaped test paper design</p><p style="font-size: 80%;">1.3.3 Methods</p><p style="font-size: 80%;">1.3.3.1 The application of S30 T7 System</p><p style="font-size: 80%;">1.3.3.2 Fragment amplification and plasmid assembly</p><p style="font-size: 80%;">1.3.3.3 Creating Estradiol Receptor (E2R) and Progesterone Receptor (PR)</p><p style="font-size: 80%;">1.3.3.4 The testing of cell-free system reaction on a paper disc</p><p style="font-size: 80%;">1.3.4 Modelling</p><p style="font-size: 80%;"><a href="#6">1.4 Our results</a></p><p style="font-size: 80%;">1.4.1 BioBricks and part collections</p><p style="font-size: 80%;">1.4.2 Graphs plotted from amplification tests</p><p style="font-size: 80%;"><a href="#7">1.5 Lab summary</a></p><p style="font-size: 80%;"><a href="#8">1.6 Lab Journal</a></p><p style="font-size: 80%;"><a href="#9">1.7 Intellectual Property </a></p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="104"><div class="s-repeatable s-block s-component s-mh " data-reactid="105"></div></div></div></div></li><li class="slide" id="section-f_e8e055b9-1c4b-44e2-906e-3040c497c221" data-reactid="106"><div class="waypoint" data-reactid="107"></div><a class="section-anchor" data-reactid="108"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="109"><div class="container" data-reactid="110"><div class="columns sixteen" data-reactid="111"><div class="s-title-group " data-reactid="112"><div data-reactid="113"><div class="s-subtitle" data-reactid="114"><div class="s-component s-text" data-reactid="115"><h4 class="s-component-content s-font-heading" data-reactid="116"><p>1.1 What is it all about?</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="117"><div class="s-repeatable s-block s-component s-mh " data-reactid="118"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="119"><span data-reactid="120"><div data-reactid="121"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="122"><div class=" columns sixteen" data-reactid="123"><div class="s-component s-text" data-reactid="124"><div class="s-component-content s-font-body" data-reactid="125"><p>As the first team of BGI-college, we endeavour to apply the cell-free system to a semi-quantitative test paper system that can be observed by human eye (in a pearl necklace shape) which can estimate the concentration of target molecules in the sample within a certain range. This mechanism, along with the biosensors for target molecules, we can test the concentration of hormones, glucose, fatty acid or nitrates in plasma, urine or saliva. From these results the health status can be derived through comprehensive medical research&amp; investigations.</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="126"><span data-reactid="127"><div data-reactid="128"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="129"><div class=" columns sixteen" data-reactid="130"><div class="s-separator" data-reactid="131"><div class="s-separator-content" data-reactid="132"><div class="separator" data-reactid="133"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_e2881ddf-6687-4635-a688-c18104aad896" data-reactid="134"><div class="waypoint" data-reactid="135"></div><a class="section-anchor" data-reactid="136"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="137"><div class="container" data-reactid="138"><div class="columns sixteen" data-reactid="139"><div class="s-title-group " data-reactid="140"><div data-reactid="141"><div class="s-subtitle" data-reactid="142"><div class="s-component s-text" data-reactid="143"><h4 class="s-component-content s-font-heading" data-reactid="144"><p>1.2 Target</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="145"><div class="s-repeatable s-block s-component s-mh " data-reactid="146"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="147"><span data-reactid="148"><div data-reactid="149"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="150"><div class=" columns sixteen" data-reactid="151"><div class="s-component s-text" data-reactid="152"><div class="s-component-content s-font-body" data-reactid="153"><p>1.2.1 Plasmids and standard parts registry</p><p> </p><p>To design plasmid and standard parts registry and build up plasmids(E2 &amp;P) for comprehensive tests targeting at clinical samples (glucose/fatty acid or hormones in blood/urine/saliva). This provides solid proof that the system can sense a variety of types of molecules. Break down the finished plasmids into comprehensive components and submit them as BioBricks.</p><p> </p><p>1.2.2 Laboratory and clinical sample tests</p><p> </p><p>Laboratory sample and clinical sample tests: to test the effectiveness of the system on cell-free paper systems with these samples.</p><p> </p><p>1.2.3 To design, test and, if possible, manufacture test paper reader</p><p> </p><p>To design, test and, if possible, manufacture test paper reader: To assemble a test paper reader according to existing blueprints and express the measurements via reporter proteins from single apertures.</p><p> </p><p>1.2.4 Pearl necklace-shaped test paper effectiveness assessment</p><p> </p><p>Pearl necklace-shaped test paper effectiveness test. To test the operability of the pearl necklace-shaped test paper effectiveness and enhance it through modelling techniques.</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="154"><span data-reactid="155"><div data-reactid="156"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="157"><div class=" columns sixteen" data-reactid="158"><div class="s-separator" data-reactid="159"><div class="s-separator-content" data-reactid="160"><div class="separator" data-reactid="161"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_02f15f0e-2cff-4925-bb68-39aa47705391" data-reactid="162"><div class="waypoint" data-reactid="163"></div><a class="section-anchor" data-reactid="164"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="165"><div class="container" data-reactid="166"><div class="columns sixteen" data-reactid="167"><div class="s-title-group " data-reactid="168"><div data-reactid="169"><div class="s-subtitle" data-reactid="170"><div class="s-component s-text" data-reactid="171"><h4 class="s-component-content s-font-heading" data-reactid="172"><p>1.3 Detailed description</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="173"><div class="s-repeatable s-block s-component s-mh " data-reactid="174"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="175"><span data-reactid="176"><div data-reactid="177"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="178"><div class=" columns sixteen" data-reactid="179"><div class="s-component s-text" data-reactid="180"><div class="s-component-content s-font-body" data-reactid="181"><p>1.3.1 Abstract</p><p> </p><p>A cell-free system refers to the system of cell environment simulation which consists of cell extract and substrate; it enables DNA expression in vitro. With the help of cell-free system, comprehensive limitations of biochemical reactions, for example, the fatality to the cell due to the toxicity of the product of metabolism and the prospect of the plasmid being controlled by the host due to negative feedback. A cell-free system has relatively higher operability, proved to be a better alternative for DNA transcription and expression. Plasmids assembled via synthetic biological methods can enable cells with the function of biosensors targeting at small molecules (e.g. glucose), hormones(e.g. oestrogen) and oxymethylene. Via adapting these biosensors into cell-free systems via which test papers are made, comprehensive medical detections can be done during everyday life, saving the efforts of comprehensive laboratory tasks. Compared with existing test-paper techniques (e.g. collaurum), the cell-free system has relatively lower manufactural costs while being able to detect molecules in relatively higher quantities. Its functions can be expanded and enhanced via sufficient and efficient application of BioBrick techniques. Based on the theoretical affirmation derived from the research of respectively Keith Pardee on paper-based synthetic gene networks and Alexis Courbet on detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates.</p><p> </p><p>1.3.2 Design</p><p>1.3.2.1 Plasmid Design</p><p> </p><p>The genetic circuit is composed of two parts, the sensor device and the amplifier/output device. The design of plasmid had been through three phases (V1-V3) For plasmid composition, see Fig.3.</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="182"><span data-reactid="183"><div data-reactid="184"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="185"><div class=" columns sixteen" data-reactid="186"><div class="s-component s-image" data-reactid="187"><span data-reactid="188"><div class="s-component-content" data-reactid="189"><div data-reactid="190"><!-- react-text: 191 --> <!-- /react-text --><div class="s-ratio-box" style="max-width:1651px;max-height:1418px;" data-reactid="192"><div class="s-ratio-fill" style="padding-bottom:85.89%;" data-reactid="193"></div><div data-reactid="194"><img alt="" title="" data-description="" width="1651" height="1418" src="data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==" class="lazyload " data-src="//res.cloudinary.com/hrscywv4p/image/upload/c_limit,h_3000,w_1200,f_auto,q_90/v1/791914/%E5%B1%8F%E5%B9%95%E6%88%AA%E5%9B%BE_833_vvsned.png" data-sizes="auto" data-reactid="195"/><noscript data-reactid="196"><img alt="" title="" data-description="" width="1651" height="1418" src="//res.cloudinary.com/hrscywv4p/image/upload/c_limit,h_3000,w_1200,f_auto,q_90/v1/791914/%E5%B1%8F%E5%B9%95%E6%88%AA%E5%9B%BE_833_vvsned.png" class="" data-reactid="197"/></noscript></div></div><!-- react-text: 198 --> <!-- /react-text --></div></div></span></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="199"><span data-reactid="200"><div data-reactid="201"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="202"><div class=" columns sixteen" data-reactid="203"><div class="s-component s-text" data-reactid="204"><div class="s-component-content s-font-body" data-reactid="205"><p>fig.3 V-1 prototype design Sensor device: The sensor device consists of the promoter for the target molecule and CRE protein expression fragments. It can be activated with via the binding mechanism of small molecules and the promoter(acting as activators or enhancers) or repressed, vice versa, the expression of downstream CRE protein expression. Output device: The output device consists of logic gate component loxp-stop-loxp(loxp fragmentterminator-loxp fragment) and reporter protein (LacZ/GFP/Luciferace,etc.) In the case of CRE expression’s absence, the terminator will stop transcription and translation, and thus preventing the downstream protein’s genetic fragments from being expressed; In the presence of CRE protein expression, the two loxp fragments will cut and reconstruct, resulting in the terminators 180 degree rotation about the plasmid, enabling the expression of downstream reporter genes. If the sensor’s component represses the expression of downstream CRE protein sequences in the presence of transcription factors, we can design the direction of the terminator’s rotation. This design enables analogue signal input’s continuous conversion into digital signal inputs. We have successfully achieved this function during a plasmid test in May using equivalent Boolean logic gate system. For further information, see fig. 4. V2- Output improvements Based on V1, we improved the output plasmid by increasing the number of terminators in the l-s-l region and adding longer CRE protein fragments. Due to the impossibility of ending all transcription<br>expressions in the plasmid, the terminator’s efficiency can never reach 100%, thus we increased the number of promoters to prevent the distraction of false positive results. The downstream CRE protein sequences will act as amplification device which can cause the rotation of more terminators in the output plasmid, the expression of reporter genes and therefore amplifying the signal via activating a smaller amount of downstream CRE protein expression in the output plasmid in the case of a low transcription factor concentration. V3- Sensor’s improvements To annihilate false positive results, initiate the cutting of output plasmid to prevent its expression via a new genetic editing system, NgAgo/gDNA when the transcription factor(target molecules) are repressing protein expression. NgAgo proteins can cut out a certain 24bp-fragment with the help of a single-strand guide DNA, sgDNA. (Reference. DNA-guided genome editing using the Natronobacterium gregoryi Argonaute by Mr. 韩春雨)</p><p> </p><p>1.3.2.2 The application of cell-free system</p><p><br>We are using the two cell-free systems, S30 and S30T7 based on E.Coli lytic agents provided by Promega.Co. The S30T7 system had a higher transcription expression rate than S30 system as it contains the T7 polymerase, an RNA polymerase which targets at T7 promoters.</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="206"><span data-reactid="207"><div data-reactid="208"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="209"><div class=" columns sixteen" data-reactid="210"><div class="s-component s-image" data-reactid="211"><span data-reactid="212"><div class="s-component-content" data-reactid="213"><div data-reactid="214"><!-- react-text: 215 --> <!-- /react-text --><div class="s-ratio-box" style="max-width:2048px;max-height:700px;" data-reactid="216"><div class="s-ratio-fill" style="padding-bottom:34.18%;" data-reactid="217"></div><div data-reactid="218"><img alt="" title="" data-description="" width="2048" height="700" src="data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==" class="lazyload " data-src="//res.cloudinary.com/hrscywv4p/image/upload/c_limit,h_3000,w_1200,f_auto,q_90/v1/791914/%E5%B1%8F%E5%B9%95%E6%88%AA%E5%9B%BE_834_zy5g5i.png" data-sizes="auto" data-reactid="219"/><noscript data-reactid="220"><img alt="" title="" data-description="" width="2048" height="700" src="//res.cloudinary.com/hrscywv4p/image/upload/c_limit,h_3000,w_1200,f_auto,q_90/v1/791914/%E5%B1%8F%E5%B9%95%E6%88%AA%E5%9B%BE_834_zy5g5i.png" class="" data-reactid="221"/></noscript></div></div><!-- react-text: 222 --> <!-- /react-text --></div></div></span></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="223"><span data-reactid="224"><div data-reactid="225"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="226"><div class=" columns sixteen" data-reactid="227"><div class="s-component s-text" data-reactid="228"><div class="s-component-content s-font-body" data-reactid="229"><p>fig. 4</p><p> </p><p>1.3.2.3 Pearl necklace-shaped test paper design</p><p> </p><p>A concept of semi-quantitative test paper observable by human eye was adapted in previous discussions along with the following instructions: the test paper’s testing zone has a spherical shape, and the concentration of target molecules in the sample is detected by a specific detector containing light source and electronic sensor component. Designed Apps on phones that can initiate the ignition of the flashlight of mobile device was also considered as an alternative. Acknowledging the inactivation effect of cooling on cell-free system and cannot be quantified with certain colour samples although the designs above can provide accurate and articulate test results, an improved test-paper design with the mechanism of paper chromatography was accepted. Prepared cell-free system and plasmids were added and dried in precisely-carved slots. Add specific amount of samples to be tested to the sample region, letting the fluid containing target molecules to flow according to the capillarity mechanism.Each time it passes through a slot, a certain amount of target molecules bind with the plasmid, with the remaining molecules continuing its journey down to the next slot until reaching the completion of reaction. The suitable radius and size of guiding groove will be deduced via modelling, which will also adjust the amount of cell-free system and plasmid added to the paper, resulting in the eventual conversion of number of slots producing reporter proteins into concentration indices.</p><p> </p><p>1.3.3 Methods</p><p>1.3.3.1 The application of S30 T7 System</p><p> </p><p>(Blank)</p><p> </p><p>1.3.3.2 Fragment amplification and plasmid assembly</p><p> </p><p>(Blank)</p><p> </p><p>1.3.3.3 Creating Estradiol Receptor (E2R) and Progesterone Receptor (PR)</p><p> </p><p>(Blank)</p><p> </p><p>1.3.3.4 The testing of cell-free system reaction on a paper disc</p><p> </p><p>(Blank)</p><p> </p><p>1.3.4 Modelling</p><p> </p><p>(Blank)</p><p> </p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="230"><span data-reactid="231"><div data-reactid="232"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="233"><div class=" columns sixteen" data-reactid="234"><div class="s-separator" data-reactid="235"><div class="s-separator-content" data-reactid="236"><div class="separator" data-reactid="237"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_62682e60-a935-4c0a-8574-655d9d852ef9" data-reactid="238"><div class="waypoint" data-reactid="239"></div><a class="section-anchor" data-reactid="240"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="241"><div class="container" data-reactid="242"><div class="columns sixteen" data-reactid="243"><div class="s-title-group " data-reactid="244"><div data-reactid="245"><div class="s-subtitle" data-reactid="246"><div class="s-component s-text" data-reactid="247"><h4 class="s-component-content s-font-heading" data-reactid="248"><p>1.4 Our results </p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="249"><div class="s-repeatable s-block s-component s-mh " data-reactid="250"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="251"><span data-reactid="252"><div data-reactid="253"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="254"><div class=" columns sixteen" data-reactid="255"><div class="s-component s-text" data-reactid="256"><div class="s-component-content s-font-body" data-reactid="257"><p>1.4.1 BioBricks and part collections</p><p> </p><p>(Blank)</p><p> </p><p>1.4.2 Graphs plotted from amplification tests</p><p> </p><p>(Blank)</p><p> </p><p> </p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="258"><span data-reactid="259"><div data-reactid="260"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="261"><div class=" columns sixteen" data-reactid="262"><div class="s-separator" data-reactid="263"><div class="s-separator-content" data-reactid="264"><div class="separator" data-reactid="265"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_ffdeee76-9bf3-483a-b433-e1fb24f28975" data-reactid="266"><div class="waypoint" data-reactid="267"></div><a class="section-anchor" data-reactid="268"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="269"><div class="container" data-reactid="270"><div class="columns sixteen" data-reactid="271"><div class="s-title-group " data-reactid="272"><div data-reactid="273"><div class="s-subtitle" data-reactid="274"><div class="s-component s-text" data-reactid="275"><h4 class="s-component-content s-font-heading" data-reactid="276"><p>1.5 Lab summary </p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="277"><div class="s-repeatable s-block s-component s-mh " data-reactid="278"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="279"><span data-reactid="280"><div data-reactid="281"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="282"><div class=" columns sixteen" data-reactid="283"><div class="s-component s-text" data-reactid="284"><div class="s-component-content s-font-body" data-reactid="285"><p>(Blank)</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="286"><span data-reactid="287"><div data-reactid="288"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="289"><div class=" columns sixteen" data-reactid="290"><div class="s-separator" data-reactid="291"><div class="s-separator-content" data-reactid="292"><div class="separator" data-reactid="293"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_164e0d20-8b85-477f-9ec7-8159128c8a90" data-reactid="294"><div class="waypoint" data-reactid="295"></div><a class="section-anchor" data-reactid="296"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="297"><div class="container" data-reactid="298"><div class="columns sixteen" data-reactid="299"><div class="s-title-group " data-reactid="300"><div data-reactid="301"><div class="s-subtitle" data-reactid="302"><div class="s-component s-text" data-reactid="303"><h4 class="s-component-content s-font-heading" data-reactid="304"><p>1.6 Lab Journal </p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="305"><div class="s-repeatable s-block s-component s-mh " data-reactid="306"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="307"><span data-reactid="308"><div data-reactid="309"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="310"><div class=" columns sixteen" data-reactid="311"><div class="s-component s-text" data-reactid="312"><div class="s-component-content s-font-body" data-reactid="313"><p>(Blank)</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="314"><span data-reactid="315"><div data-reactid="316"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="317"><div class=" columns sixteen" data-reactid="318"><div class="s-separator" data-reactid="319"><div class="s-separator-content" data-reactid="320"><div class="separator" data-reactid="321"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_7681efda-5f52-46c5-9143-9ff61605321f" data-reactid="322"><div class="waypoint" data-reactid="323"></div><a class="section-anchor" data-reactid="324"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="325"><div class="container" data-reactid="326"><div class="columns sixteen" data-reactid="327"><div class="s-title-group " data-reactid="328"><div data-reactid="329"><div class="s-subtitle" data-reactid="330"><div class="s-component s-text" data-reactid="331"><h4 class="s-component-content s-font-heading" data-reactid="332"><p>1.7 Intellectual Property </p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="333"><div class="s-repeatable s-block s-component s-mh " data-reactid="334"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="335"><span data-reactid="336"><div data-reactid="337"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="338"><div class=" columns sixteen" data-reactid="339"><div class="s-component s-text" data-reactid="340"><div class="s-component-content s-font-body" data-reactid="341"><p>(Blank)</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="342"><span data-reactid="343"><div data-reactid="344"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="345"><div class=" columns sixteen" data-reactid="346"><div class="s-separator" data-reactid="347"><div class="s-separator-content" data-reactid="348"><div class="separator" data-reactid="349"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_2b5c6fea-d812-496c-9508-e8f21c7ff016" data-reactid="350"><div class="waypoint" data-reactid="351"></div><a class="section-anchor" data-reactid="352"></a><div class="lazyload s-no-bg s-block-section s-section" data-reactid="353"><div class="container" data-reactid="354"><div class="columns sixteen" data-reactid="355"><div class="s-title-group " data-reactid="356"><div data-reactid="357"><div class="s-title " data-reactid="358"><div class="s-component s-text" data-reactid="359"><h2 class="s-component-content s-font-title" data-reactid="360"><p>2. Team</p></h2></div></div><div class="s-subtitle" data-reactid="361"><div class="s-component s-text" data-reactid="362"><h4 class="s-component-content s-font-heading" data-reactid="363"><p style="font-size: 80%;"><a href="#11">2.1 Meet the team</a></p><p style="font-size: 80%;"><a href="#12">2.2 Team member intro </a></p><p style="font-size: 80%;"><a href="#13">2.3 Group pic </a></p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="364"><div class="s-repeatable s-block s-component s-mh " data-reactid="365"></div></div></div></div></li><li class="slide" id="section-f_724ce88b-8a10-41dd-86ea-178e504ca3a4" data-reactid="366"><div class="waypoint" data-reactid="367"></div><a class="section-anchor" data-reactid="368"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="369"><div class="container" data-reactid="370"><div class="columns sixteen" data-reactid="371"><div class="s-title-group " data-reactid="372"><div data-reactid="373"><div class="s-subtitle" data-reactid="374"><div class="s-component s-text" data-reactid="375"><h4 class="s-component-content s-font-heading" data-reactid="376"><p>2.1 Meet the team</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="377"><div class="s-repeatable s-block s-component s-mh " data-reactid="378"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="379"><span data-reactid="380"><div data-reactid="381"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="382"><div class=" columns sixteen" data-reactid="383"><div class="s-component s-text" data-reactid="384"><div class="s-component-content s-font-body" data-reactid="385"><p>(Blank)</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="386"><span data-reactid="387"><div data-reactid="388"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="389"><div class=" columns sixteen" data-reactid="390"><div class="s-separator" data-reactid="391"><div class="s-separator-content" data-reactid="392"><div class="separator" data-reactid="393"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_9bc62bfe-fe53-4694-aa06-c1293b1c70f8" data-reactid="394"><div class="waypoint" data-reactid="395"></div><a class="section-anchor" data-reactid="396"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="397"><div class="container" data-reactid="398"><div class="columns sixteen" data-reactid="399"><div class="s-title-group " data-reactid="400"><div data-reactid="401"><div class="s-subtitle" data-reactid="402"><div class="s-component s-text" data-reactid="403"><h4 class="s-component-content s-font-heading" data-reactid="404"><p>2.2 Team member intro </p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="405"><div class="s-repeatable s-block s-component s-mh " data-reactid="406"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="407"><span data-reactid="408"><div data-reactid="409"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="410"><div class=" columns sixteen" data-reactid="411"><div class="s-component s-text" data-reactid="412"><div class="s-component-content s-font-body" data-reactid="413"><p>(Blank)</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="414"><span data-reactid="415"><div data-reactid="416"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="417"><div class=" columns sixteen" data-reactid="418"><div class="s-separator" data-reactid="419"><div class="s-separator-content" data-reactid="420"><div class="separator" data-reactid="421"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_4c421b73-e237-4779-8ee5-04709d302be9" data-reactid="422"><div class="waypoint" data-reactid="423"></div><a class="section-anchor" data-reactid="424"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="425"><div class="container" data-reactid="426"><div class="columns sixteen" data-reactid="427"><div class="s-title-group " data-reactid="428"><div data-reactid="429"><div class="s-subtitle" data-reactid="430"><div class="s-component s-text" data-reactid="431"><h4 class="s-component-content s-font-heading" data-reactid="432"><p>2.3 Group pic </p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="433"><div class="s-repeatable s-block s-component s-mh " data-reactid="434"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="435"><span data-reactid="436"><div data-reactid="437"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="438"><div class=" columns sixteen" data-reactid="439"><div class="s-component s-text" data-reactid="440"><div class="s-component-content s-font-body" data-reactid="441"><p>(Blank)</p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="442"><span data-reactid="443"><div data-reactid="444"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="445"><div class=" columns sixteen" data-reactid="446"><div class="s-separator" data-reactid="447"><div class="s-separator-content" data-reactid="448"><div class="separator" data-reactid="449"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_4e622fe2-969f-4d8f-a449-ebca10a8d7be" data-reactid="450"><div class="waypoint" data-reactid="451"></div><a class="section-anchor" data-reactid="452"></a><div class="lazyload s-no-bg s-block-section s-section" data-reactid="453"><div class="container" data-reactid="454"><div class="columns sixteen" data-reactid="455"><div class="s-title-group " data-reactid="456"><div data-reactid="457"><div class="s-title " data-reactid="458"><div class="s-component s-text" data-reactid="459"><h2 class="s-component-content s-font-title" data-reactid="460"><p>3. Human practice</p></h2></div></div><div class="s-subtitle" data-reactid="461"><div class="s-component s-text" data-reactid="462"><h4 class="s-component-content s-font-heading" data-reactid="463"><p>3.1Sponsorship&amp; Attribution</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="464"><div class="s-repeatable s-block s-component s-mh " data-reactid="465"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="466"><span data-reactid="467"><div data-reactid="468"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="469"><div class=" columns sixteen" data-reactid="470"><div class="s-component s-text" data-reactid="471"><div class="s-component-content s-font-body" data-reactid="472"><p>(Blank)</p></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_f8941d76-dd7b-46bd-bff8-eb3625a0ec1c" data-reactid="473"><div class="waypoint" data-reactid="474"></div><a class="section-anchor" data-reactid="475"></a><div class="lazyload s-no-bg s-block-section s-section" data-reactid="476"><div class="container" data-reactid="477"><div class="columns sixteen" data-reactid="478"><div class="s-title-group " data-reactid="479"><div data-reactid="480"><div class="s-title " data-reactid="481"><div class="s-component s-text" data-reactid="482"><h2 class="s-component-content s-font-title" data-reactid="483"><p>4. Safety</p></h2></div></div><div class="s-subtitle" data-reactid="484"><div class="s-component s-text" data-reactid="485"><h4 class="s-component-content s-font-heading" data-reactid="486"><p style="font-size: 80%;"><a href="#16">4.1 Laboratory safety assessment</a></p><p style="font-size: 80%;">4.1.2 Materials used</p><p style="font-size: 80%;">4.1.3 Protection</p><p style="font-size: 80%;">4.1.4 Disposal</p><p style="font-size: 80%;"><a href="#17">4.2 Identified possible risks of our project</a></p><p style="font-size: 80%;">4.2.1 Risks to the safety and health of team members, or other people working in the lab</p><p style="font-size: 80%;">4.2.2 Risks to the safety and health of the general public (if any biological materials escaped from our lab)</p><p style="font-size: 80%;">4.2.3 Risks to the environment (from waste disposal, or from materials escaping from our lab)<br>4.2.4 Risks to security through malicious misuse by individuals, groups, or countries</p><p style="font-size: 80%;">4.2.5 What new risks might arise from our project's growth?</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="487"><div class="s-repeatable s-block s-component s-mh " data-reactid="488"></div></div></div></div></li><li class="slide" id="section-f_aa116216-5f93-4a06-8510-a3a8d66910b8" data-reactid="489"><div class="waypoint" data-reactid="490"></div><a class="section-anchor" data-reactid="491"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="492"><div class="container" data-reactid="493"><div class="columns sixteen" data-reactid="494"><div class="s-title-group " data-reactid="495"><div data-reactid="496"><div class="s-subtitle" data-reactid="497"><div class="s-component s-text" data-reactid="498"><h4 class="s-component-content s-font-heading" data-reactid="499"><p>4.1 Laboratory safety assessment</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="500"><div class="s-repeatable s-block s-component s-mh " data-reactid="501"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="502"><span data-reactid="503"><div data-reactid="504"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="505"><div class=" columns sixteen" data-reactid="506"><div class="s-component s-text" data-reactid="507"><div class="s-component-content s-font-body" data-reactid="508"><p>4.1.1 Materials used</p><p> </p><p>(Blank)</p><p> </p><p>4.1.2 Protection</p><p> </p><p>(Blank)</p><p> </p><p>4.1.3 Disposal</p><p> </p><p>(Blank)</p><p> </p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="509"><span data-reactid="510"><div data-reactid="511"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="512"><div class=" columns sixteen" data-reactid="513"><div class="s-separator" data-reactid="514"><div class="s-separator-content" data-reactid="515"><div class="separator" data-reactid="516"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_dd9ebd6d-a000-472b-bc80-6d88b2c1b02e" data-reactid="517"><div class="waypoint" data-reactid="518"></div><a class="section-anchor" data-reactid="519"></a><div class="lazyload s-bg-image s-bg-light-text s-block-section s-section" style="background-repeat:repeat;background-size:auto;background-color:transparent;background-position:50% 50%;background-image:url(data:image/gif;base64,R0lGODlhAQABAAAAACH5BAEKAAEALAAAAAABAAEAAAICTAEAOw==);" data-bg="//uploads.strikinglycdn.com/static/backgrounds/pastel-solids/33.jpg" data-reactid="520"><div class="container" data-reactid="521"><div class="columns sixteen" data-reactid="522"><div class="s-title-group " data-reactid="523"><div data-reactid="524"><div class="s-subtitle" data-reactid="525"><div class="s-component s-text" data-reactid="526"><h4 class="s-component-content s-font-heading" data-reactid="527"><p>4.2 Identified possible risks of our project</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="528"><div class="s-repeatable s-block s-component s-mh " data-reactid="529"><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="530"><span data-reactid="531"><div data-reactid="532"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="533"><div class=" columns sixteen" data-reactid="534"><div class="s-component s-text" data-reactid="535"><div class="s-component-content s-font-body" data-reactid="536"><p>4.2.1 Risks to the safety and health of team members, or other people working in the lab</p><p> </p><p>(Blank)</p><p> </p><p>4.2.2 Risks to the safety and health of the general public (if any biological materials escaped from our lab) </p><p> </p><p>(Blank)</p><p> </p><p>4.2.3 Risks to the environment (from waste disposal, or from materials escaping from our lab)</p><p> </p><p>(Blank)</p><p><br>4.2.4 Risks to security through malicious misuse by individuals, groups, or countries</p><p> </p><p>(Blank)</p><p> </p><p>4.2.5 What new risks might arise from our project's growth?</p><p> </p><p>(Blank)</p><p> </p></div></div></div></div></div></span></div><div class="s-block-item s-repeatable-item s-block-sortable-item " data-reactid="537"><span data-reactid="538"><div data-reactid="539"><div class="s-block-item-inner clearfix" style="position:relative;" data-reactid="540"><div class=" columns sixteen" data-reactid="541"><div class="s-separator" data-reactid="542"><div class="s-separator-content" data-reactid="543"><div class="separator" data-reactid="544"></div></div></div></div></div></div></span></div></div></div></div></div></li><li class="slide" id="section-f_d39f9726-5fc7-4410-b0b0-401e5384d250" data-reactid="545"><div class="waypoint" data-reactid="546"></div><a class="section-anchor" data-reactid="547"></a><div class="lazyload s-no-bg s-block-section s-section" data-reactid="548"><div class="container" data-reactid="549"><div class="columns sixteen" data-reactid="550"><div class="s-title-group " data-reactid="551"><div data-reactid="552"><div class="s-title " data-reactid="553"><div class="s-component s-text" data-reactid="554"><h2 class="s-component-content s-font-title" data-reactid="555"><p>5. Blog</p></h2></div></div><div class="s-subtitle" data-reactid="556"><div class="s-component s-text" data-reactid="557"><h4 class="s-component-content s-font-heading" data-reactid="558"><p>Feel free to subscribe our blog!</p></h4></div></div></div></div></div><div class="alignment-container " data-reactid="559"><div class="s-repeatable s-block s-component s-mh " data-reactid="560"></div></div></div></div></li><li class="slide" id="section-f_152a36d5-4f8a-493b-b1a2-1ed21c61d6b3" data-reactid="561"><div class="waypoint" data-reactid="562"></div><a class="section-anchor" data-reactid="563"></a><div class="lazyload s-no-bg s-blog-section s-section" data-reactid="564"><div class="container" data-reactid="565"><div class="columns sixteen" data-reactid="566"><!-- react-empty: 567 --><div class="s-component s-async-wrapper" data-reactid="568"><div class="s-loading" data-reactid="569"></div><div class="waypoint" data-reactid="570"></div></div></div></div></div><div class="waypoint" data-reactid="571"></div></li></ul><!-- react-empty: 572 --><div id="strikingly-tooltip-container" data-reactid="573"> </div><div class="s-footer-section s-section " data-reactid="574"><div class="container s-layout-vertical" data-reactid="575"><div class="columns row sixteen" data-reactid="576"><div class="" data-reactid="577"><div class="s-component s-async-wrapper" data-reactid="578"><div class="s-loading" data-reactid="579"></div><div class="waypoint" data-reactid="580"></div></div></div><div class="s-footer-text" data-reactid="581"><div class="s-component s-text" data-reactid="582"><div class="s-component-content s-font-body" data-reactid="583"><p>iGEM BGI College© 2016</p></div></div></div></div></div></div><!-- react-empty: 584 --><div class="s-floated-components" data-reactid="585"><div class="ecommerce-buy-dialog s-edit-modal extend" id="ecommerce-buy-dialog" data-reactid="586"><div class="s-async-wrapper s-component" data-reactid="587"><div class="s-loading" data-reactid="588"></div></div></div><div id="s-ecommerce-shopping-cart-wrapper" class="s-ecommerce-shopping-cart-wrapper" data-reactid="589"></div></div></div></div> <div id='fb-root'></div> <div id='app-script-root'></div> <div id='app-view-root'></div> <script id='blog-collection-tmpl' type='text/html'> <div class='s-blog-col-head'></div> <div class='s-blog-col-body'> {{ _.each(blogPosts, function(blog) { }} <div class='s-blog-entry'> <div class='s-blog-entry-inner'> {{ if ($S && $S.conf && $S.conf.preview_mode) { }} <a class='s-blog-overlay-link' href='{{=blog.publicUrl}}'>&nbsp;</a> {{ } else { }} <a class='s-blog-overlay-link' href='{{=blog.relativeUrl}}'>&nbsp;</a> {{ } }} {{ if (blog.iconUrl) { }} <div class='s-blog-entry-left'> {{ if (UrlHelper.imageHasContent(blog.iconUrl)) { }} <div class='s-blog-avatar' style='background-image:url({{=blog.iconUrl}});'></div> {{ } else { }} <div class='s-blog-default-avatar'> <div class='entypo-bookmark'></div> </div> {{ } }} </div> {{ } }} <div class='s-blog-entry-right'> <div class='s-blog-details'> <div class='s-blog-details-head s-blog-row'> <div class='s-blog-title s-font-heading'> {{=blog.title}} </div> <div class='s-blog-date'> {{=blog.publishedAt}} </div> </div> {{ if (blogSettings.previewLayout == 1) { }} <div class='s-blog-details-blurb s-blog-row'> {{=blog.blurb}} </div> {{ } }} </div> </div> </div> </div> {{ }) }} {{ if (blogPosts.length == 0) { }} <div class='s-blog-entry'> <div class='s-common-status no-posts-error'> There are no blog posts. </div> </div> {{ } }} </div> {{ if (blogPosts.length > 0) { }} <div class='s-blog-col-foot'> <a class='s-blog-link s-blog-next-link' href='javascript:void(0);'> &laquo; Newer </a> &nbsp; <ul class='s-blog-pagination' style='display:none;'> <li> <a class='s-blog-link s-blog-pagination-page' href='javascript:void(0);'></a> </li> </ul> &nbsp; <a class='s-blog-link s-blog-prev-link' href='javascript:void(0);'> Older &raquo; </a> </div> {{ } }} </script> <script src="//ajax.googleapis.com/ajax/libs/jquery/1.10.0/jquery.min.js"></script> <script>
 
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  window.jQuery || document.write('<script src="//assets.strikingly.com/assets/jquery-922e33319d5ae7b73ff04ad1a35eb620.js"><\/script>');
 
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</script> <script src="//assets.strikingly.com/assets/i18n-7084be07962957b7b916254184af5fb0.js"></script> <script src="//assets.strikingly.com/assets/v4/page-site-bundle-a171ac15aa4ba1bc145551a36eada726.js"></script> </body> </html> <!-- Powered by Strikingly.com 4 (1898) Jun 22, 2016 at 23:40-->
 
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<div class="column half_size" >
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<h5> Editing your wiki </h5>
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<p>On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world! </p>
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<p> <a href="https://2016.igem.org/wiki/index.php?title=Team:Example&action=edit"> Click here to edit this page! </a></p>
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</div>
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<div class="column half_size" >
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<h5>Tips</h5>
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<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
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<ul>
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<li>State your accomplishments! Tell people what you have achieved from the start. </li>
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<li>Be clear about what you are doing and how you plan to do this.</li>
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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
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<li>Make sure information is easy to find; nothing should be more than 3 clicks away. </li>
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<li>Avoid using very small fonts and low contrast colors; information should be easy to read. </li>
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<li>Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the <a href="https://2016.igem.org/Calendar">iGEM 2016 calendar</a> </li>
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<li>Have lots of fun! </li>
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</ul>
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</div>
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<div class="column half_size" >
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<h5>Inspiration</h5>
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<p> You can also view other team wikis for inspiration! Here are some examples:</p>
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<ul>
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<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
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<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
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<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
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<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
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<li> <a href="https://2014.igem.org/Team:SCU-China"> 2014 SCU-China </a></li>
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</ul>
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</div>
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<h5> Uploading pictures and files </h5>
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<p> You can upload your pictures and files to the iGEM 2016 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name. <br />
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When you upload, set the "Destination Filename" to <code>Team:YourOfficialTeamName/NameOfFile.jpg</code>. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)</p>
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<div class="button_click"  onClick=" parent.location= 'https://2016.igem.org/Special:Upload '"> 
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UPLOAD FILES
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Revision as of 06:41, 23 June 2016

<!DOCTYPE html>   iGEM BGI College                                 
  • iGEM Project of BGI College China

    Cell-Free system based test paper platform

  • 1. Project

    1.1 What is it all about?

    1.2 Target

    1.2.1 Plasmids and standard parts registry

    1.2.2 Laboratory and clinical sample tests

    1.2.3 To design, test and, if possible, manufacture test paper reader

    1.2.4 Pearl necklace-shaped test paper effectiveness assessment

    1.3 Detailed description

    1.3.1 Abstract

    1.3.2 Design

    1.3.2.1 Plasmid Design

    1.3.2.2 The application of cell-free system

    1.3.2.3 Pearl necklace-shaped test paper design

    1.3.3 Methods

    1.3.3.1 The application of S30 T7 System

    1.3.3.2 Fragment amplification and plasmid assembly

    1.3.3.3 Creating Estradiol Receptor (E2R) and Progesterone Receptor (PR)

    1.3.3.4 The testing of cell-free system reaction on a paper disc

    1.3.4 Modelling

    1.4 Our results

    1.4.1 BioBricks and part collections

    1.4.2 Graphs plotted from amplification tests

    1.5 Lab summary

    1.6 Lab Journal

    1.7 Intellectual Property

  • 1.1 What is it all about?

    As the first team of BGI-college, we endeavour to apply the cell-free system to a semi-quantitative test paper system that can be observed by human eye (in a pearl necklace shape) which can estimate the concentration of target molecules in the sample within a certain range. This mechanism, along with the biosensors for target molecules, we can test the concentration of hormones, glucose, fatty acid or nitrates in plasma, urine or saliva. From these results the health status can be derived through comprehensive medical research& investigations.

  • 1.2 Target

    1.2.1 Plasmids and standard parts registry

    To design plasmid and standard parts registry and build up plasmids(E2 &P) for comprehensive tests targeting at clinical samples (glucose/fatty acid or hormones in blood/urine/saliva). This provides solid proof that the system can sense a variety of types of molecules. Break down the finished plasmids into comprehensive components and submit them as BioBricks.

    1.2.2 Laboratory and clinical sample tests

    Laboratory sample and clinical sample tests: to test the effectiveness of the system on cell-free paper systems with these samples.

    1.2.3 To design, test and, if possible, manufacture test paper reader

    To design, test and, if possible, manufacture test paper reader: To assemble a test paper reader according to existing blueprints and express the measurements via reporter proteins from single apertures.

    1.2.4 Pearl necklace-shaped test paper effectiveness assessment

    Pearl necklace-shaped test paper effectiveness test. To test the operability of the pearl necklace-shaped test paper effectiveness and enhance it through modelling techniques.

  • 1.3 Detailed description

    1.3.1 Abstract

    A cell-free system refers to the system of cell environment simulation which consists of cell extract and substrate; it enables DNA expression in vitro. With the help of cell-free system, comprehensive limitations of biochemical reactions, for example, the fatality to the cell due to the toxicity of the product of metabolism and the prospect of the plasmid being controlled by the host due to negative feedback. A cell-free system has relatively higher operability, proved to be a better alternative for DNA transcription and expression. Plasmids assembled via synthetic biological methods can enable cells with the function of biosensors targeting at small molecules (e.g. glucose), hormones(e.g. oestrogen) and oxymethylene. Via adapting these biosensors into cell-free systems via which test papers are made, comprehensive medical detections can be done during everyday life, saving the efforts of comprehensive laboratory tasks. Compared with existing test-paper techniques (e.g. collaurum), the cell-free system has relatively lower manufactural costs while being able to detect molecules in relatively higher quantities. Its functions can be expanded and enhanced via sufficient and efficient application of BioBrick techniques. Based on the theoretical affirmation derived from the research of respectively Keith Pardee on paper-based synthetic gene networks and Alexis Courbet on detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates.

    1.3.2 Design

    1.3.2.1 Plasmid Design

    The genetic circuit is composed of two parts, the sensor device and the amplifier/output device. The design of plasmid had been through three phases (V1-V3) For plasmid composition, see Fig.3.

    fig.3 V-1 prototype design Sensor device: The sensor device consists of the promoter for the target molecule and CRE protein expression fragments. It can be activated with via the binding mechanism of small molecules and the promoter(acting as activators or enhancers) or repressed, vice versa, the expression of downstream CRE protein expression. Output device: The output device consists of logic gate component loxp-stop-loxp(loxp fragmentterminator-loxp fragment) and reporter protein (LacZ/GFP/Luciferace,etc.) In the case of CRE expression’s absence, the terminator will stop transcription and translation, and thus preventing the downstream protein’s genetic fragments from being expressed; In the presence of CRE protein expression, the two loxp fragments will cut and reconstruct, resulting in the terminators 180 degree rotation about the plasmid, enabling the expression of downstream reporter genes. If the sensor’s component represses the expression of downstream CRE protein sequences in the presence of transcription factors, we can design the direction of the terminator’s rotation. This design enables analogue signal input’s continuous conversion into digital signal inputs. We have successfully achieved this function during a plasmid test in May using equivalent Boolean logic gate system. For further information, see fig. 4. V2- Output improvements Based on V1, we improved the output plasmid by increasing the number of terminators in the l-s-l region and adding longer CRE protein fragments. Due to the impossibility of ending all transcription
    expressions in the plasmid, the terminator’s efficiency can never reach 100%, thus we increased the number of promoters to prevent the distraction of false positive results. The downstream CRE protein sequences will act as amplification device which can cause the rotation of more terminators in the output plasmid, the expression of reporter genes and therefore amplifying the signal via activating a smaller amount of downstream CRE protein expression in the output plasmid in the case of a low transcription factor concentration. V3- Sensor’s improvements To annihilate false positive results, initiate the cutting of output plasmid to prevent its expression via a new genetic editing system, NgAgo/gDNA when the transcription factor(target molecules) are repressing protein expression. NgAgo proteins can cut out a certain 24bp-fragment with the help of a single-strand guide DNA, sgDNA. (Reference. DNA-guided genome editing using the Natronobacterium gregoryi Argonaute by Mr. 韩春雨)

    1.3.2.2 The application of cell-free system


    We are using the two cell-free systems, S30 and S30T7 based on E.Coli lytic agents provided by Promega.Co. The S30T7 system had a higher transcription expression rate than S30 system as it contains the T7 polymerase, an RNA polymerase which targets at T7 promoters.

    fig. 4

    1.3.2.3 Pearl necklace-shaped test paper design

    A concept of semi-quantitative test paper observable by human eye was adapted in previous discussions along with the following instructions: the test paper’s testing zone has a spherical shape, and the concentration of target molecules in the sample is detected by a specific detector containing light source and electronic sensor component. Designed Apps on phones that can initiate the ignition of the flashlight of mobile device was also considered as an alternative. Acknowledging the inactivation effect of cooling on cell-free system and cannot be quantified with certain colour samples although the designs above can provide accurate and articulate test results, an improved test-paper design with the mechanism of paper chromatography was accepted. Prepared cell-free system and plasmids were added and dried in precisely-carved slots. Add specific amount of samples to be tested to the sample region, letting the fluid containing target molecules to flow according to the capillarity mechanism.Each time it passes through a slot, a certain amount of target molecules bind with the plasmid, with the remaining molecules continuing its journey down to the next slot until reaching the completion of reaction. The suitable radius and size of guiding groove will be deduced via modelling, which will also adjust the amount of cell-free system and plasmid added to the paper, resulting in the eventual conversion of number of slots producing reporter proteins into concentration indices.

    1.3.3 Methods

    1.3.3.1 The application of S30 T7 System

    (Blank)

    1.3.3.2 Fragment amplification and plasmid assembly

    (Blank)

    1.3.3.3 Creating Estradiol Receptor (E2R) and Progesterone Receptor (PR)

    (Blank)

    1.3.3.4 The testing of cell-free system reaction on a paper disc

    (Blank)

    1.3.4 Modelling

    (Blank)

  • 1.4 Our results

    1.4.1 BioBricks and part collections

    (Blank)

    1.4.2 Graphs plotted from amplification tests

    (Blank)

  • 1.5 Lab summary

    (Blank)

  • 1.6 Lab Journal

    (Blank)

  • 1.7 Intellectual Property

    (Blank)

  • 2.1 Meet the team

    (Blank)

  • 2.2 Team member intro

    (Blank)

  • 2.3 Group pic

    (Blank)

  • 3. Human practice

    3.1Sponsorship& Attribution

    (Blank)

  • 4. Safety

    4.1 Laboratory safety assessment

    4.1.2 Materials used

    4.1.3 Protection

    4.1.4 Disposal

    4.2 Identified possible risks of our project

    4.2.1 Risks to the safety and health of team members, or other people working in the lab

    4.2.2 Risks to the safety and health of the general public (if any biological materials escaped from our lab)

    4.2.3 Risks to the environment (from waste disposal, or from materials escaping from our lab)
    4.2.4 Risks to security through malicious misuse by individuals, groups, or countries

    4.2.5 What new risks might arise from our project's growth?

  • 4.1 Laboratory safety assessment

    4.1.1 Materials used

    (Blank)

    4.1.2 Protection

    (Blank)

    4.1.3 Disposal

    (Blank)

  • 4.2 Identified possible risks of our project

    4.2.1 Risks to the safety and health of team members, or other people working in the lab

    (Blank)

    4.2.2 Risks to the safety and health of the general public (if any biological materials escaped from our lab)

    (Blank)

    4.2.3 Risks to the environment (from waste disposal, or from materials escaping from our lab)

    (Blank)


    4.2.4 Risks to security through malicious misuse by individuals, groups, or countries

    (Blank)

    4.2.5 What new risks might arise from our project's growth?

    (Blank)

  • 5. Blog

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