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| <!--Write the text explaining this section --> | | <!--Write the text explaining this section --> |
| <div class="text"> | | <div class="text"> |
− | <p>Presented by Team Paris Bettencourt 2020</p> | + | <p>By Team Paris Bettencourt 2020</p> |
| <br /> | | <br /> |
| <p><b>Amandine Maire<sup>1</sup>, Anu Susan Kurian<sup>1</sup>, Chetan Kumar | | <p><b>Amandine Maire<sup>1</sup>, Anu Susan Kurian<sup>1</sup>, Chetan Kumar |
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| <br /> | | <br /> |
| <br /> | | <br /> |
− | <p class="padding-left">Public health was one of our primary concerns that awakened with the advent of lockdown. The question of what impact could the lockdown have on our health led us to examine the skin microbiome. | + | <p class="padding-left">Public health was one of our primary concerns during the lockdown. We were intrigued by the question of the impact that the lockdown could have on our health. This led us to examine the skin microbiome. |
| + | |
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| </p> | | </p> |
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| <div class="subsection two_thirds"> | | <div class="subsection two_thirds"> |
− | <p class="padding-right">Through our experience and the advice gathered from health experts, we decided to study the skin microbiome. The impact of sanitary measures, in particular frequent washing, on the skin microbiome, which has proven to be crucial for populations with eczema symptoms, legitimated our approach. This discussion drew our interest for dysbiosis induced pathologies and possible treatments involving synthetic biology. | + | <p class="padding-right">Through our experience and the advice gathered from health experts, we decided to study the human skin microbiome. The impact of sanitary measures on the skin microbiome, in particular frequent washing of hands and other surfaces of the body, which has proven to be crucial for populations with eczema symptoms, legitimated our approach. This discussion drew our interest for dysbiosis induced pathologies and possible treatments involving synthetic biology. |
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| </p> | | </p> |
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| <br /> | | <br /> |
| <br /> | | <br /> |
− | <p class="padding-left">While lockdown posed a threat to the development of social interactions, we wanted to connect people through science by putting Open and Citizen Science at the core of our 2020 iGEM project. | + | <p class="padding-left">While lockdown posed a threat to social interactions, we wanted to connect people through science by putting Open and Citizen Science at the core of our 2020 iGEM project. |
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| </p> | | </p> |
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| <!--Write the text explaining this section --> | | <!--Write the text explaining this section --> |
| <div class="text"> | | <div class="text"> |
− | <p>Quaranskin, a combination of Quarantine and skin, is a project that brings together all the components to collect and analyse skin microbiome samples, collected from participants across Europe. Within this study, we aimed to investigate the impact of behavioural factors such as hygiene, exercise, and social interaction, on the composition of the human skin microbiome. | + | <p>Quaranskin, a word derived by the combination of Quarantine and Skin, is a project that brings together all the components to collect and analyze the skin microbiome samples collected from participants across Europe. Within this study, we aimed to investigate the impact of behavioral factors such as hygiene, exercise, and social interaction, on the composition of the human skin microbiome. |
| </p> | | </p> |
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| </p> | | </p> |
| <p><b>Participants enrollment</b></p> | | <p><b>Participants enrollment</b></p> |
− | <p>To be involved in the study each participant has to fill in a participation form and sign a consent form. Afterwards, they are asked to create an account on a platform called Open Humans in order to retrieve an ID code used to ensure their anonymity. | + | <p>Each participant has to fill a participation form and sign a consent form to be part of the study. After signing up to participate in the study, they are asked to create an account on a platform called Open Humans. Open Humans is a community-based platform that enables personal data collections across data streams, giving individuals more personal data access and control of sharing authorizations, and enabling academic research as well as patient-led projects. |
| </p> | | </p> |
− | <p>A link is sent to them allowing them to create a account on the OpenHumans platform in | + | <p>Participants are sent a link allowing them to create an account on the Open Humans platform that will generate an eight digit unique ID for each of them. This unique ID helps preserve anonymity of the participants in the study. |
− | order to furnish them an ID code which we use to keep anonymity
| + | |
| </p> | | </p> |
| <p><b>Participants action</b></p> | | <p><b>Participants action</b></p> |
− | <p>Once officially enrolled in the study, the participant is shipped a kit containing all the tools needed to sample their skin microbiome from 4 body sites. In parallel, the participant is asked to answer an online questionnaire with questions covering 4 main topics: personal characteristic (age, sexe, nationality...), hygiene habits, level of confinement and potential skin disorders. | + | <p>Once officially enrolled in the study, each participant is shipped a kit containing all the tools needed to sample their skin microbiome from 4 body sites. In parallel, the participants are asked to answer an online questionnaire with questions covering 4 main topics: personal characteristic (age, sex, nationality, etc.), hygiene habits, level of confinement and potential skin disorders. |
| </p> | | </p> |
| <p><b>Microbiome sequencing</b></p> | | <p><b>Microbiome sequencing</b></p> |
− | <p>Samples are then sent to a sequencing company, Genewiz. Bacterial DNA extraction is performed from the samples, before amplification of the V3-V4 regions of the 16S RNA gene, and sequencing of the amplicons. | + | <p>Samples are then sent to a sequencing company (Genewiz). Bacterial DNA extraction is performed from the samples, before amplification of the V3-V4 regions of the 16S RNA gene, and sequencing of the amplicons. |
| </p> | | </p> |
| <p><b>Statistical analysis</b></p> | | <p><b>Statistical analysis</b></p> |
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| <!--Write the text explaining this section --> | | <!--Write the text explaining this section --> |
| <div class="text"> | | <div class="text"> |
− | <p><b class="heading">Ethical consideration</b></p> | + | <p><b class="heading">Ethical considerations</b></p> |
− | <p>As Quaranskin is a collection of data extracted from human derived samples (skin | + | <p>As Quaranskin is a collection of data extracted from human derived samples and contains personal information, our research depends on the legal procedures related to research involving human being. This leads to particular care to respect people’s privacy and data protection. |
− | microbiome) and personal information (answer to the questionnaire), it’s important to
| + | |
− | learn about the ethical rules that govern research involving human being in Europe in
| + | |
− | order to respect the protection of the participants in our study.
| + | |
| </p> | | </p> |
− | <p>In France, Research Involving Human Being (RIPH) has to be approved and framed by the | + | <p>In France, Research Involving Human Being (RIPH) has to be approved and framed by the Committees for the Protection of Persons (CPP). |
− | Committees for the Protection of Persons (CPP).
| + | |
| </p> | | </p> |
− | <p>We have submitted to the ethics committee a complete file presenting our study in detail. | + | <p>We have submitted to the ethics committee a complete file presenting our study in detail. This file consisted mainly of a research protocol plus an information leaflet for the participants. Even though we already recruited participants and set up all the logistic aspects of the study, we are still waiting for their feedback to collect and analyse the samples. |
− | This file consisted mainly of a research protocol and all the information documents for
| + | |
− | the study participants. Even though we already recruit participant and set up all the
| + | |
− | logistic aspect of the study, we are still waiting for their approval to collect and
| + | |
− | analyse samples.
| + | |
| </p> | | </p> |
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| <p><b class="heading">Contribution to the scientific community</b></p> | | <p><b class="heading">Contribution to the scientific community</b></p> |
| <ol> | | <ol> |
− | <li>Increase the knowledge we have about the microbiome and more precisely about the | + | <li>Increase knowledge on the skin microbiome, more specifically the environmental factors that influence it |
− | external factors that can impact it.
| + | |
| </li> | | </li> |
− | <li>Create an open database of skin microbiome from people in the context of a pandemic. | + | <li>Create a skin microbiome open database in the special context of a pandemic with living restrictions |
| </li> | | </li> |
− | <li>Develop Science@Home by providing pipeline and protocols useful for future | + | <li>Develop Science@Home by providing reproducible pipeline and protocols which can be used in future studies |
− | microbiome studies based on citizen science
| + | |
| </li> | | </li> |
− | <li>Instruct participants about their microbiome by sending them back their microbiome | + | <li>Instruct participants about their skin microbiome by sending them back their skin microbiome profile after analysis |
− | profile after analysis.
| + | |
| </li> | | </li> |
| </ol> | | </ol> |
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| <div class="text"> | | <div class="text"> |
− | <p>Biological engineering allowed us to develop solutions for our objectives.</p>
| + | |
| <p><b class="heading">Purpose</b></p> | | <p><b class="heading">Purpose</b></p> |
| <p>We aim to sense and modulate population dynamics of the skin microbiome in order to help | | <p>We aim to sense and modulate population dynamics of the skin microbiome in order to help |
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| class="logo"> | | class="logo"> |
| </div> | | </div> |
− | <p>EpiFlex aims to make the bacterium a chassis for synthetic biology. | + | <p>EpiFlex aims to make the <i>Staphylococcus epidermidis</i> bacterium a chassis for synthetic biology. |
| </p> | | </p> |
| | | |
| <p><b class="heading">MoClo Toolkit</b></p> | | <p><b class="heading">MoClo Toolkit</b></p> |
− | <p>The MoClo is a modular cloning method based on Golden Gate assembly. EpiFlex is a Moclo | + | <p>MoClo is a modular cloning method based on Golden Gate assembly. EpiFlex is a Moclo |
| toolkit developed with parts that function specifically in S.epidermidis. | | toolkit developed with parts that function specifically in S.epidermidis. |
| </p> | | </p> |
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| <div class="text"> | | <div class="text"> |
− | <p>EpiGlow is the proof of concept of our EpiFlex toolkit. We choose to express mCherry | + | <p>EpiGlow is the proof of concept of our EpiFlex toolkit. We chose to express mCherry |
| in <i>S. epidermidis</i> to demonstrate that our parts are functional. | | in <i>S. epidermidis</i> to demonstrate that our parts are functional. |
| </p> | | </p> |
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| <ul> | | <ul> |
− | <li>We explored optimised electroporation protocols1 by testing different voltages and a | + | <li>We explored and optimized electroporation protocols<sup>1</sup> by testing different voltages and a |
− | newer heat shock/ electroporation combination2, to see which protocol would yield | + | newer heat shock/ electroporation combination<sup>2</sup>, to see which protocol would yield |
| more transformants. | | more transformants. |
| </li> | | </li> |
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| <p><b class="heading">Results</b></p> | | <p><b class="heading">Results</b></p> |
| <ul> | | <ul> |
− | <li>Using our EpiFlex system we were able to successfully build a construct that | + | <li>Using our EpiFlex system, we were able to successfully build a construct that |
| expressed mCherry in <i>S. epidermidis</i> | | expressed mCherry in <i>S. epidermidis</i> |
| </li> | | </li> |
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| <ul> | | <ul> |
− | <li>In our optimisation of the electroporation of <i>S. epidermidis</i>, we found that a | + | <li>In our optimization of the electroporation of <i>S. epidermidis</i>, we found that a |
| voltage of 2.5kV yielded the greatest transformation efficiency. We achieve around 3 | | voltage of 2.5kV yielded the greatest transformation efficiency. We achieve around 3 |
| - 7 transformants per plate using this protocol. | | - 7 transformants per plate using this protocol. |
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| temperatures as low as 33°C (hands, feet, nose), up to 40°C (severe conditions). | | temperatures as low as 33°C (hands, feet, nose), up to 40°C (severe conditions). |
| </p> | | </p> |
− | <p>For each temperature, the growth was measured in TSB for 15 h via optical density. | + | <p>At each temperature, the growth was measured in TSB for 15 hours via optical density measurements. |
| </p> | | </p> |
| <p><b>2. Acidity</b></p> | | <p><b>2. Acidity</b></p> |
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| genital area) depending on the region of the body it is covering. | | genital area) depending on the region of the body it is covering. |
| </p> | | </p> |
− | <p>We tested pH range from pH3 to pH10. The measurement has been done in the same way as for | + | <p>We tested in pH range from pH3 to pH10. The measurement has been done in the same way as for |
| the Temperature tests. | | the Temperature tests. |
| </p> | | </p> |
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| <p>With respect to the skin, there can be variations in salinity caused mainly by sweat and | | <p>With respect to the skin, there can be variations in salinity caused mainly by sweat and |
| sebaceous glands. The evaporation of water from the release of heat enables the salts to | | sebaceous glands. The evaporation of water from the release of heat enables the salts to |
− | remain present on the skin. | + | remain on the skin. |
| </p> | | </p> |
− | <p>We made vary the salinity of the media from 0.5% to 5.5% of NaCl. Again, the measurements | + | <p>We varied the salinity of the media from 0.5% to 5.5% of NaCl. Again, the measurements |
− | have been done over 15h of growth in TSB. | + | have been done over 15 hours of growth in TSB. |
| </p> | | </p> |
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| 37°C which is the normal human body temperature. | | 37°C which is the normal human body temperature. |
| </li> | | </li> |
− | <li><i>S. epidermidis</i> thrive better in the neutral and basic pH conditions. | + | <li><i>S. epidermidis</i> thrives better in the neutral and basic pH conditions. |
| </li> | | </li> |
| <li><i>S. epidermidis</i> is halo tolerant and it grows best in media with about 0.5 | | <li><i>S. epidermidis</i> is halo tolerant and it grows best in media with about 0.5 |
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| <div class="info"> | | <div class="info"> |
| <!--Write the title of the section --> | | <!--Write the title of the section --> |
− | <div class="title"> Future Work (EpiFlex and EpiGrow)</div> | + | <div class="title"> Future Work - EpiFlex and EpiGlow</div> |
| <!--Write the text explaining this section --> | | <!--Write the text explaining this section --> |
| <div class="text"> | | <div class="text"> |
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| </b></p> | | </b></p> |
| <ul> | | <ul> |
− | <li>Improve transformation efficiency form electroporation | + | <li>Improve transformation efficiency from electroporation |
| </li> | | </li> |
| <li>Build more constructs using the EpiFlex toolkit to characterize all the parts | | <li>Build more constructs using the EpiFlex toolkit to characterize all the parts |
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| </b></p> | | </b></p> |
| <ul> | | <ul> |
− | <li>Using EpiFlex to build a genetic circuit aiming to control population dynamic in the | + | <li>Using EpiFlex to build a genetic circuit aiming to control population dynamics in the |
| skin microbiome. | | skin microbiome. |
| </li> | | </li> |
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| <div class="info"> | | <div class="info"> |
| <!--Write the title of the section --> | | <!--Write the title of the section --> |
− | <div class="title">Future Work (EpiGrow)</div> | + | <div class="title">Future Work - EpiGrow</div> |
| <!--Write the text explaining this section --> | | <!--Write the text explaining this section --> |
| <div class="text"> | | <div class="text"> |
| <p><b class="heading">EpiGrow</b></p> | | <p><b class="heading">EpiGrow</b></p> |
| <ul> | | <ul> |
− | <li>We would like to investigate the difference of growth kinetic between <i>S. epidermidis</i> | + | <li>We would like to investigate the difference of growth kinetics between <i>S. epidermidis</i> |
| grown in 2D and in 3D media. | | grown in 2D and in 3D media. |
| </li> | | </li> |
− | <li>To do so, we decided to build an artificial skin model and develop a method to | + | <li>We decided to build an artificial skin model of the human palm to develop a method to |
| measure growth on 2D media while having comparable data with growth in 3D media. | | measure growth on 2D media while having comparable data with growth in 3D media. |
− |
| |
| </li> | | </li> |
| </ul> | | </ul> |