|
|
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| <div class="info"> | | <div class="info"> |
| <div class="title">Pyomancer: Novel Antibacterial Protein Complexes for MDR Infections</div> | | <div class="title">Pyomancer: Novel Antibacterial Protein Complexes for MDR Infections</div> |
− | <h5>Presented by: Team IIT Roorkee</h5>
| |
| <div class="text"> | | <div class="text"> |
| + | <h5>Presented by: Team IIT Roorkee</h5> |
| Our project is aimed at creating novel antibacterial protein complexes called | | Our project is aimed at creating novel antibacterial protein complexes called |
| Seekercins, designed to specifically bind and kill species of multidrug-resistant | | Seekercins, designed to specifically bind and kill species of multidrug-resistant |
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| Validation will be done experimentally, targeting the pathogen Acinetobacter baumannii, | | Validation will be done experimentally, targeting the pathogen Acinetobacter baumannii, |
| and production will be done in E. coli. | | and production will be done in E. coli. |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| Team: Sanjeevani Marcha, Muskaan Bhambri, Harkirat Singh Arora, Kushagra Rustagi, | | Team: Sanjeevani Marcha, Muskaan Bhambri, Harkirat Singh Arora, Kushagra Rustagi, |
| Pradum Kumar, Yash Aggrawal, Nitish Verma, Siddharth FItwe, Tishee Natani, | | Pradum Kumar, Yash Aggrawal, Nitish Verma, Siddharth FItwe, Tishee Natani, |
| Kartikey Kansal, Kanishk Sugotra, Lakshya Jain, Mihir Sachdeva. | | Kartikey Kansal, Kanishk Sugotra, Lakshya Jain, Mihir Sachdeva. |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| PI: Prof. Ranjana Pathania, Department of Biotechnology IITR. | | PI: Prof. Ranjana Pathania, Department of Biotechnology IITR. |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| Faculty Advisor: Prof. Naveen K. Navani, Department of Biotechnology IITR. | | Faculty Advisor: Prof. Naveen K. Navani, Department of Biotechnology IITR. |
| </div> | | </div> |
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| (VAPs) are one of the most severe comorbidities with ICU mortality rate of <b>45.6% | | (VAPs) are one of the most severe comorbidities with ICU mortality rate of <b>45.6% |
| to 60.9%</b>, reaching <b>84.3%</b> when caused by <b>XDR <i>A. baumannii</i></b>. | | to 60.9%</b>, reaching <b>84.3%</b> when caused by <b>XDR <i>A. baumannii</i></b>. |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| As a In our solution, we use pyocins, which are high molecular weight bactericidal | | As a In our solution, we use pyocins, which are high molecular weight bactericidal |
| protein complexes produced by <i>P. aeruginosa</i>. Pyocins attach to receptors on the | | protein complexes produced by <i>P. aeruginosa</i>. Pyocins attach to receptors on the |
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| have a high killing efficiency but a very narrow host spectrum, and are similar | | have a high killing efficiency but a very narrow host spectrum, and are similar |
| in structure to Myovirus bacteriophages. | | in structure to Myovirus bacteriophages. |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/2/21/T--IIT_Roorkee--Poster_images--poster-content--poster_intro1.png"/> | | <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/2/21/T--IIT_Roorkee--Poster_images--poster-content--poster_intro1.png"/> |
| </div> | | </div> |
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| <img src="https://static.igem.org/mediawiki/2020/9/9f/T--IIT_Roorkee--Poster_images--poster--Inspiration_and_Sol..png"/> | | <img src="https://static.igem.org/mediawiki/2020/9/9f/T--IIT_Roorkee--Poster_images--poster--Inspiration_and_Sol..png"/> |
| <div class="info"> | | <div class="info"> |
− | <div class="title">Inspiration</div> | + | <div class="title">Inspiration & Solution</div> |
| <div class="text"> | | <div class="text"> |
| + | <h3>Inspiration</h3> |
| Interviews with doctors and ICU specialists made us realise it clear the | | Interviews with doctors and ICU specialists made us realise it clear the |
| necessity for alternative treatments for drug resistant infections in the | | necessity for alternative treatments for drug resistant infections in the |
| face of rapid AMR development. | | face of rapid AMR development. |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| Our key inspiration was TAU Israel’s 2019 iGEM Project, Pyo-Pyo. They | | Our key inspiration was TAU Israel’s 2019 iGEM Project, Pyo-Pyo. They |
| illustrated the similarity of pyocins and phages which led us to improve | | illustrated the similarity of pyocins and phages which led us to improve |
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| us to explore protein modelling, development of software and machine | | us to explore protein modelling, development of software and machine |
| learning tools. | | learning tools. |
− | </div>
| |
| | | |
− | <div class="title">Solution</div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| + | <h3>Solution</h3> |
| + | |
| Our solution is the development of ‘Seekercins’, novel antibacterial protein | | Our solution is the development of ‘Seekercins’, novel antibacterial protein |
| complexes by engineering of R-type pyocins to target specific drug resistant | | complexes by engineering of R-type pyocins to target specific drug resistant |
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| the Seekercins and perform antimicrobial assays against MDR <i>A. baumannii</i> | | the Seekercins and perform antimicrobial assays against MDR <i>A. baumannii</i> |
| strains and biochemical characterization. | | strains and biochemical characterization. |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/5/56/T--IIT_Roorkee--Poster_images--poster-content--poster_inspiration_solution_1.png"/> | | <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/5/56/T--IIT_Roorkee--Poster_images--poster-content--poster_inspiration_solution_1.png"/> |
| </div> | | </div> |
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| </li> | | </li> |
| </ol> | | </ol> |
| + | |
| + | <br/><br/> |
| | | |
− | </div>
| |
− | <div class="text">
| |
| After literature review of existing Acinetobacter baumannii phages, phage | | After literature review of existing Acinetobacter baumannii phages, phage |
| AP22 was selected as a suitable candidate for its large lytic spectrum. | | AP22 was selected as a suitable candidate for its large lytic spectrum. |
− | </div>
| |
| | | |
− | <div class="text">
| + | <br/><br/> |
| + | |
| Rational design of fusion tail fiber- | | Rational design of fusion tail fiber- |
− | </div>
| |
| | | |
− | <div class="text">
| + | <br/><br/> |
| + | |
| Analysis of key domains in AP22 tail fiber (Fig 4) revealed a conserved | | Analysis of key domains in AP22 tail fiber (Fig 4) revealed a conserved |
| lectin-fold similar to that of R2-pyocin tail fiber. C-terminal sequence | | lectin-fold similar to that of R2-pyocin tail fiber. C-terminal sequence |
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| specific bacteriophage AP22 tail fiber which naturally targets these | | specific bacteriophage AP22 tail fiber which naturally targets these |
| bacteria. Models of the fusion tail fiber were verified for integrity. | | bacteria. Models of the fusion tail fiber were verified for integrity. |
− | </div>
| |
| | | |
− | <div class="text">
| + | <br/><br/> |
| <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/5/58/T--IIT_Roorkee--Poster_images--poster-content--Poster_engineering1.png"/> | | <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/5/58/T--IIT_Roorkee--Poster_images--poster-content--Poster_engineering1.png"/> |
− | </div>
| |
| | | |
− | <div class="text">
| + | <br/><br/> |
| The gene responsible for the tail fiber from the wild-type pyocin gene | | The gene responsible for the tail fiber from the wild-type pyocin gene |
| cluster, PA0620 has been replaced by the fusion tail fiber. The gene | | cluster, PA0620 has been replaced by the fusion tail fiber. The gene |
| cluster and fusion tail fiber was synthesized by and received from IDT. | | cluster and fusion tail fiber was synthesized by and received from IDT. |
− | </div>
| |
| | | |
− | <div class="text">
| + | <br/><br/> |
| + | |
| <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/8/83/T--IIT_Roorkee--Poster_images--poster-content--poster_engineering2.png"/> | | <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/8/83/T--IIT_Roorkee--Poster_images--poster-content--poster_engineering2.png"/> |
− | </div>
| |
| | | |
− | <div class="text">
| + | <br/><br/> |
| + | |
| As a chassis we chose to produce them in <i>Escherichia coli</i>, | | As a chassis we chose to produce them in <i>Escherichia coli</i>, |
| specifically strain BL21(DE3).As an expression vector, we chose | | specifically strain BL21(DE3).As an expression vector, we chose |
| pET-28 a from Novagen which contains a T7 promoter and lac | | pET-28 a from Novagen which contains a T7 promoter and lac |
| operator, allowing IPTG-controllableinduced protein expression. | | operator, allowing IPTG-controllableinduced protein expression. |
− | </div>
| |
| | | |
− | <div class="text">
| + | <br/><br/> |
| + | |
| <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/6/63/T--IIT_Roorkee--Poster_images--poster-content--poster_engineering3.png"/> | | <img class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/6/63/T--IIT_Roorkee--Poster_images--poster-content--poster_engineering3.png"/> |
− | </div>
| + | |
| + | <br/><br/> |
| | | |
| </div> | | </div> |
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| We modeled our protein using all the three bioinformatics-based modeling techniques. | | We modeled our protein using all the three bioinformatics-based modeling techniques. |
| 11 models obtained through these methods were compared and the best one was chosen. | | 11 models obtained through these methods were compared and the best one was chosen. |
− | </div>
| + | |
− |
| + | <br/><br/> |
− | <div class="text">
| + | |
| <div class="row"> | | <div class="row"> |
| <div class="section quarter"> | | <div class="section quarter"> |
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| <div class="text"> | | <div class="text"> |
| <b>BASIC PARTS:</b> | | <b>BASIC PARTS:</b> |
− | </div>
| + | |
− | <div class="text">
| + | <br/> |
| + | |
| We have introduced two new basic Parts to the iGEM registry as a contribution for us ebay future iGEM teams. | | We have introduced two new basic Parts to the iGEM registry as a contribution for us ebay future iGEM teams. |
− | </div>
| + | |
− | <div class="text">
| + | <br/> |
| + | |
| <img alt="" src="https://static.igem.org/mediawiki/2020/c/c7/T--IIT_Roorkee--Poster_images--poster-content--poster_Parts_1.png"/> | | <img alt="" src="https://static.igem.org/mediawiki/2020/c/c7/T--IIT_Roorkee--Poster_images--poster-content--poster_Parts_1.png"/> |
− | </div>
| + | |
− | <div class="text">
| + | <br/> |
| + | |
| <p> | | <p> |
| <b>Part: BBa_K3564001 :</b>Gene cluster encoding for R-type pyocin with the tail fiber gene deleted | | <b>Part: BBa_K3564001 :</b>Gene cluster encoding for R-type pyocin with the tail fiber gene deleted |
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| <b>Part: BBa_K3564002 :</b>Fusion tail fiber of R pyocin tail fiber and Acinetobacter phage AP22 tail fiber | | <b>Part: BBa_K3564002 :</b>Fusion tail fiber of R pyocin tail fiber and Acinetobacter phage AP22 tail fiber |
| </p> | | </p> |
− | </div> | + | |
− | <div class="text">
| + | <br/> |
| + | |
| <b>BASIC PARTS:</b> | | <b>BASIC PARTS:</b> |
− | </div>
| + | |
− | <div class="text">
| + | <br/> |
| + | |
| <img alt="" src="https://static.igem.org/mediawiki/2020/3/32/T--IIT_Roorkee--Poster_images--poster-content--Poster_Parts_2.png"/> | | <img alt="" src="https://static.igem.org/mediawiki/2020/3/32/T--IIT_Roorkee--Poster_images--poster-content--Poster_Parts_2.png"/> |
− | </div> | + | |
− | <div class="text">
| + | <br/> |
| + | |
| Part:BBa_K3564102 : Composite of BBa_K3564001 and BBa_K3564002 that expresses a Seekercin, i.e. a pyocin targeted to specifically Bind and kill Acinetobacter baumannii | | Part:BBa_K3564102 : Composite of BBa_K3564001 and BBa_K3564002 that expresses a Seekercin, i.e. a pyocin targeted to specifically Bind and kill Acinetobacter baumannii |
| <br/> | | <br/> |
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| <div class="info"> | | <div class="info"> |
| <div class="title">Integrated Human Practices</div> | | <div class="title">Integrated Human Practices</div> |
| + | <div class="text"> |
| <div class="row"> | | <div class="row"> |
| <div class="section third"> | | <div class="section third"> |
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| </ul> | | </ul> |
| </div> | | </div> |
| + | </div> |
| </div> | | </div> |
| </div> | | </div> |
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| <div class="text"> | | <div class="text"> |
| Team iGEM IIT Roorkee understands the importance of working in the team and for the team. We truly realize the impact of collaborative work projects on any social, technical, or cultural issue. With the same inspiration, we collaborated with competing iGEM teams to help spread their as well as our cause to aware, acknowledge, and educate the population worldwide. We reached out to huge masses and successfully increased the awareness quotient of people to an impressive 35 - 40% extent. | | Team iGEM IIT Roorkee understands the importance of working in the team and for the team. We truly realize the impact of collaborative work projects on any social, technical, or cultural issue. With the same inspiration, we collaborated with competing iGEM teams to help spread their as well as our cause to aware, acknowledge, and educate the population worldwide. We reached out to huge masses and successfully increased the awareness quotient of people to an impressive 35 - 40% extent. |
− | </div>
| + | <div class="sponsor-images" style="display: flex; flex-flow: wrap;"> |
− | <div class="sponsor-images" style="display: flex; flex-flow: wrap;">
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/3/3e/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab1.PNG"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/3/3e/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab1.PNG"/>
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/1/18/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab2.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/1/18/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab2.png"/>
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/5/56/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab3.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/5/56/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab3.png"/>
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/2/24/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab4.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/2/24/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab4.png"/>
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/c/c5/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab5.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/c/c5/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab5.png"/>
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/2/21/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab6.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/2/21/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab6.png"/>
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/f/fc/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab7.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/f/fc/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab7.png"/>
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/4/42/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab8.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/4/42/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab8.png"/>
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/0/0a/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab9.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/0/0a/T--IIT_Roorkee--Poster_images--poster-content--Poster_Collab9.png"/>
| + | </div> |
| </div> | | </div> |
| </div> | | </div> |
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| OBSERVE. UNDERSTAND. ACT. SUSTAIN. | | OBSERVE. UNDERSTAND. ACT. SUSTAIN. |
| </b> | | </b> |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| Establishing peace and prosperity requires efforts from not one but every human being on the planet. With this achieved, we can eradicate all other issues prevalent globally, like poverty, poor health, hunger, inequality, poor usage of resources, deteriorating climatic conditions, injustice, and so on. To create an impact and eradicate the above-said problems, the United Nations (UN) came up with 17 focused SDGs to be achieved by 2030. So playing our part, we have contributed to three of such goals (as mentioned below) through our project Pyomancer. | | Establishing peace and prosperity requires efforts from not one but every human being on the planet. With this achieved, we can eradicate all other issues prevalent globally, like poverty, poor health, hunger, inequality, poor usage of resources, deteriorating climatic conditions, injustice, and so on. To create an impact and eradicate the above-said problems, the United Nations (UN) came up with 17 focused SDGs to be achieved by 2030. So playing our part, we have contributed to three of such goals (as mentioned below) through our project Pyomancer. |
− | </div>
| + | <div class="sponsor-images" style="text-align: center;"> |
− | <div class="text sponsor-images" style="text-align: center;">
| + | <div class="section third"> |
− | <div class="section third">
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/0/0d/T--IIT_Roorkee--Poster_images--poster-content--SDG1.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/0/0d/T--IIT_Roorkee--Poster_images--poster-content--SDG1.png"/>
| + | <ul class="wiki-ul"> |
− | <ul class="wiki-ul">
| + | <li class="wiki-li"> |
− | <li class="wiki-li">
| + | Providing a revolutionized treatment for HAIs |
− | Providing a revolutionized treatment for HAIs
| + | </li> |
− | </li>
| + | <li class="wiki-li"> |
− | <li class="wiki-li">
| + | Running Awareness program on Social Media |
− | Running Awareness program on Social Media
| + | </li> |
− | </li>
| + | </ul> |
− | </ul>
| + | </div> |
− | </div>
| + | <div class="section third"> |
− | <div class="section third">
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/c/c8/T--IIT_Roorkee--Poster_images--poster-content--SDG2.jpg"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/c/c8/T--IIT_Roorkee--Poster_images--poster-content--SDG2.jpg"/>
| + | <ul class="wiki-ul"> |
− | <ul class="wiki-ul">
| + | <li class="wiki-li"> |
− | <li class="wiki-li">
| + | Educating children, young adults, and the general public about AMR, Synthetic Biology, and Technology |
− | Educating children, young adults, and the general public about AMR, Synthetic Biology, and Technology
| + | </li> |
− | </li>
| + | </ul> |
− | </ul>
| + | </div> |
− | </div>
| + | <div class="section third"> |
− | <div class="section third">
| + | <img alt="" src="https://static.igem.org/mediawiki/2020/c/c7/T--IIT_Roorkee--Poster_images--poster-content--SDG3.png"/> |
− | <img alt="" src="https://static.igem.org/mediawiki/2020/c/c7/T--IIT_Roorkee--Poster_images--poster-content--SDG3.png"/>
| + | <ul class="wiki-ul"> |
− | <ul class="wiki-ul">
| + | <li class="wiki-li"> |
− | <li class="wiki-li">
| + | Collaborations with fellow iGEM teams and college groups |
− | Collaborations with fellow iGEM teams and college groups
| + | </li> |
− | </li>
| + | <li class="wiki-li"> |
− | <li class="wiki-li">
| + | Initiated and participated in iGEM x SDGs Projects |
− | Initiated and participated in iGEM x SDGs Projects
| + | </li> |
− | </li>
| + | </ul> |
− | </ul>
| + | </div> |
| </div> | | </div> |
| </div> | | </div> |
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| <img alt="" src="https://static.igem.org/mediawiki/2020/6/64/T--IIT_Roorkee--Poster_images--poster-content--Poster_SC_PE_4.png"/> | | <img alt="" src="https://static.igem.org/mediawiki/2020/6/64/T--IIT_Roorkee--Poster_images--poster-content--Poster_SC_PE_4.png"/> |
| </div> | | </div> |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| <b>Webinars</b> | | <b>Webinars</b> |
| <br/> | | <br/> |
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| Detection of Antibiotic Resistant Genes (DARG) | | Detection of Antibiotic Resistant Genes (DARG) |
| </b></p> | | </b></p> |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/a/af/T--IIT_Roorkee--Poster_images--poster-content--poster_ML_1.png"/> | | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/a/af/T--IIT_Roorkee--Poster_images--poster-content--poster_ML_1.png"/> |
| <br/> | | <br/> |
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| TailScout | | TailScout |
| </b></p> | | </b></p> |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| We have developed a web application <b>TailScout</b> which generates secondary structure of the Engineered pyocin by taking the name of the target bacterium from the user as Input. We have used the JPred REST API and Clustal Omega REST API on the Django REST framework for the processes. | | We have developed a web application <b>TailScout</b> which generates secondary structure of the Engineered pyocin by taking the name of the target bacterium from the user as Input. We have used the JPred REST API and Clustal Omega REST API on the Django REST framework for the processes. |
− | </div>
| + | <br/><br/> |
− | <div class="text">
| + | |
| <b> | | <b> |
| Classifying broadly it is a three step process: | | Classifying broadly it is a three step process: |
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| <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/d/db/T--IIT_Roorkee--Poster_images--poster-content--poster_implementation_1.jpg"/> | | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/d/db/T--IIT_Roorkee--Poster_images--poster-content--poster_implementation_1.jpg"/> |
| </div> | | </div> |
− | <div class="text"> | + | <div class=""> |
| Surfactant consists of 80-85 % phospholipids, 5-10 % neutral lipids, and 8-10 % protein, with 5-6 % of the four specific proteins of surfactant. Broadly, the formulation has the following structure: | | Surfactant consists of 80-85 % phospholipids, 5-10 % neutral lipids, and 8-10 % protein, with 5-6 % of the four specific proteins of surfactant. Broadly, the formulation has the following structure: |
| </div> | | </div> |
− | <div class="text"> | + | <br/><br/> |
| + | <div class=""> |
| <div class="table-responsive"> | | <div class="table-responsive"> |
| <table class="table table-hover table-bordered"> | | <table class="table table-hover table-bordered"> |
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| </div> | | </div> |
| </div> | | </div> |
− | <div class="text"> | + | <br/><br/> |
| + | <div class=""> |
| By instilling a particular microvolume of liquid into the upper airways and moving the plug by programmed air ventilation into the desired region of the lung, the aqueous liquid containing soluble drugs can be delivered into targeted branches of the lung airway and deposited onto the lung epithelium . | | By instilling a particular microvolume of liquid into the upper airways and moving the plug by programmed air ventilation into the desired region of the lung, the aqueous liquid containing soluble drugs can be delivered into targeted branches of the lung airway and deposited onto the lung epithelium . |
| </div> | | </div> |
− | <div class="text"> | + | <br/><br/> |
| + | <div class=""> |
| <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/8/84/T--IIT_Roorkee--Poster_images--poster-content--poster_implementation_2.jpg"/> | | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/8/84/T--IIT_Roorkee--Poster_images--poster-content--poster_implementation_2.jpg"/> |
| </div> | | </div> |
− | <div class="text"> | + | <br/><br/> |
| + | <div class=""> |
| We researched and decided on delivery of pyocins through nebulizers however, in India there is a disproportionately large problem with VAPs in the Newborn Intensive Care Units. | | We researched and decided on delivery of pyocins through nebulizers however, in India there is a disproportionately large problem with VAPs in the Newborn Intensive Care Units. |
| <br/> | | <br/> |
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| <div class="info"> | | <div class="info"> |
| <div class="title">Results</div> | | <div class="title">Results</div> |
− | <h3 class="wiki-h wiki-h3">
| |
− | Wet Lab
| |
− | </h3>
| |
| <div class="text"> | | <div class="text"> |
− | Initial experiments were performed in March but had to be aborted due to the pandemic and closing of our institute. We have laid out contingency plans for multiple scenarios based on the expected results of our wet lab experiments. | + | <h3 class="wiki-h wiki-h3"> |
− | </div>
| + | Wet Lab |
− | <br/><br/>
| + | </h3> |
− | <h3 class="wiki-h wiki-h3">
| + | <br/><br/> |
− | Dry Lab
| + | Initial experiments were performed in March but had to be aborted due to the pandemic and closing of our institute. We have laid out contingency plans for multiple scenarios based on the expected results of our wet lab experiments. |
− | </h3>
| + | <br/><br/> |
− | <div class="text">
| + | <h3 class="wiki-h wiki-h3"> |
− | <div class="row">
| + | Dry Lab |
− | <div class="section quarter">
| + | </h3> |
− | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/3/3f/T--IIT_Roorkee--Poster_images--poster-content--poster_results1.jpg"/>
| + | <br/><br/> |
| + | <div class="row"> |
| + | <div class="section quarter"> |
| + | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/3/3f/T--IIT_Roorkee--Poster_images--poster-content--poster_results1.jpg"/> |
| + | </div> |
| + | <div class="section three_quarters"> |
| + | <b> |
| + | Root Mean Square Deviation |
| + | </b> |
| + | <br/> |
| + | Calculated and compared the RMSD of each fusion-protein model with: |
| + | <ul class="wiki-ul"> |
| + | <li class="wiki-li"> |
| + | The R2-NTF tail fibre protein |
| + | </li> |
| + | <li class="wiki-li"> |
| + | The AP-22 bacteriophage tail fibre protein |
| + | </li> |
| + | </ul> |
| + | </div> |
| </div> | | </div> |
− | <div class="section three_quarters"> | + | <div class="row"> |
− | <b> | + | <div class="section quarter"> |
− | Root Mean Square Deviation | + | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/f/f7/T--IIT_Roorkee--Poster_images--poster-content--poster_results2.jpg"/> |
− | </b> | + | </div> |
− | <br/> | + | <div class="section three_quarters"> |
− | Calculated and compared the RMSD of each fusion-protein model with:
| + | <b> |
− | <ul class="wiki-ul">
| + | Ramachandran Plot |
− | <li class="wiki-li">
| + | </b> |
− | The R2-NTF tail fibre protein
| + | <br/> |
− | </li>
| + | <ul class="wiki-ul"> |
− | <li class="wiki-li">
| + | <li class="wiki-li"> |
− | The AP-22 bacteriophage tail fibre protein | + | Gives information about the energetically allowed and disallowed regions in the protein |
− | </li> | + | </li> |
− | </ul> | + | <li class="wiki-li"> |
| + | Prepared and compared plots for 6 models |
| + | </li> |
| + | </ul> |
| + | <br/><br/> |
| + | </div> |
| </div> | | </div> |
− | </div>
| + | <br/><br/> |
− | <div class="row">
| + | <br/> |
− | <div class="section quarter"> | + | <br/><br/> |
− | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/f/f7/T--IIT_Roorkee--Poster_images--poster-content--poster_results2.jpg"/>
| + | <div class="table-responsive"> |
− | </div>
| + | <table class="table table-hover table-bordered"> |
− | <div class="section three_quarters">
| + | <thead class="thead-dark"> |
− | <b>
| + | <tr> |
− | Ramachandran Plot
| + | <th scope="col"> |
− | </b>
| + | Model/Data |
− | <br/>
| + | </th> |
− | <ul class="wiki-ul">
| + | <th scope="col"> |
− | <li class="wiki-li">
| + | RMSD with lower part (4mtm) |
− | Gives information about the energetically allowed and disallowed regions in the protein
| + | </th> |
− | </li>
| + | <th scope="col"> |
− | <li class="wiki-li">
| + | RMSD with upper part (6cu2) |
− | Prepared and compared plots for 6 models
| + | </th> |
− | </li>
| + | <th scope="col"> |
− | </ul>
| + | Residues in disallowed regions |
− | <br/><br/>
| + | </th> |
− | </div> | + | <th scope="col"> |
− | </div>
| + | Residues in favoured regions |
− | </div>
| + | </th> |
− | <br/>
| + | </tr> |
− | <div class="text">
| + | </thead> |
− | <div class="table-responsive">
| + | <tbody> |
− | <table class="table table-hover table-bordered">
| + | <tr> |
− | <thead class="thead-dark">
| + | <td> |
− | <tr>
| + | |
− | <th scope="col">
| + | |
− | Model/Data
| + | |
− | </th>
| + | |
− | <th scope="col">
| + | |
− | RMSD with lower part (4mtm)
| + | |
− | </th>
| + | |
− | <th scope="col">
| + | |
− | RMSD with upper part (6cu2)
| + | |
− | </th>
| + | |
− | <th scope="col">
| + | |
− | Residues in disallowed regions
| + | |
− | </th>
| + | |
− | <th scope="col">
| + | |
− | Residues in favoured regions
| + | |
− | </th>
| + | |
− | </tr>
| + | |
− | </thead>
| + | |
− | <tbody>
| + | |
− | <tr>
| + | |
− | <td>
| + | |
| | | |
− | Ab-initio Model 1
| + | Ab-initio Model 1 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0.435
| + | 0.435 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 2.648
| + | 2.648 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0%
| + | 0% |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 89.2%
| + | 89.2% |
− | </td>
| + | </td> |
− | </tr>
| + | </tr> |
− |
| + | |
− | <tr>
| + | <tr> |
− | <td>
| + | <td> |
| | | |
− | Ab-initio Model 2
| + | Ab-initio Model 2 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0.419
| + | 0.419 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 6.264
| + | 6.264 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0%
| + | 0% |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 87.8%
| + | 87.8% |
− | </td>
| + | </td> |
− | </tr>
| + | </tr> |
− |
| + | |
− | <tr>
| + | <tr> |
− | <td>
| + | <td> |
| | | |
− | Ab-initio Model 3
| + | Ab-initio Model 3 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0.375
| + | 0.375 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 2.335
| + | 2.335 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0%
| + | 0% |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 86.1%
| + | 86.1% |
− | </td>
| + | </td> |
− | </tr>
| + | </tr> |
− |
| + | |
− | <tr>
| + | <tr> |
− | <td>
| + | <td> |
| | | |
− | Ab-initio Model 4
| + | Ab-initio Model 4 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0.475
| + | 0.475 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 4.024
| + | 4.024 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0.2%
| + | 0.2% |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 86%
| + | 86% |
− | </td>
| + | </td> |
− | </tr>
| + | </tr> |
− |
| + | |
− | <tr>
| + | <tr> |
− | <td>
| + | <td> |
| | | |
− | Ab-initio Model 5
| + | Ab-initio Model 5 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
− | 0.427
| + | 0.427 |
| | | |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 4.631
| + | 4.631 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
− | 0
| + | 0 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
− | 89.4%
| + | 89.4% |
− | </td>
| + | </td> |
− | </tr>
| + | </tr> |
− |
| + | |
− | <tr>
| + | <tr> |
− | <td>
| + | <td> |
| | | |
− | Swiss Model
| + | Swiss Model |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 4.666
| + | 4.666 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 1.527
| + | 1.527 |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 0.3%
| + | 0.3% |
− | </td>
| + | </td> |
− | <td>
| + | <td> |
| | | |
− | 88.1%
| + | 88.1% |
− | </td>
| + | </td> |
− | </tr>
| + | </tr> |
− |
| + | |
− | </tbody>
| + | </tbody> |
− | </table>
| + | </table> |
− | </div>
| + | </div> |
− | </div>
| + | <br/><br/> |
| | | |
− | <div class="text">
| + | |
− | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/c/cc/T--IIT_Roorkee--Poster_images--poster-content--poster_results3.png"/>
| + | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/c/cc/T--IIT_Roorkee--Poster_images--poster-content--poster_results3.png"/> |
− | </div>
| + | <br/><br/><br/> |
− | <br/>
| + | |
| | | |
− | <div class="text">
| + | <b> |
− | <b>
| + | Best Model → Ab-initio Model 1 |
− | Best Model → Ab-initio Model 1
| + | |
| | | |
− | </b>
| + | </b> |
− | <ul class="wiki-ul">
| + | <ul class="wiki-ul"> |
− | <li class="wiki-li">
| + | <li class="wiki-li"> |
− | After choosing the best model, we performed energy minimization for it to ensure the most stable state
| + | After choosing the best model, we performed energy minimization for it to ensure the most stable state |
− | </li>
| + | </li> |
− | <li class="wiki-li">
| + | <li class="wiki-li"> |
− | We used YASARA Energy Minimization Toolkit for this
| + | We used YASARA Energy Minimization Toolkit for this |
− | </li>
| + | </li> |
− | </ul>
| + | </ul> |
− | </div>
| + | <br/><br/> |
| + | <br/> |
| | | |
− | <br/>
| + | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/b/b2/T--IIT_Roorkee--Poster_images--poster-content--poster_results4.png"/> |
− | | + | <br/> |
− | <div class="text">
| + | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/6/6c/T--IIT_Roorkee--Poster_images--poster-content--poster_results5.png"/> |
− | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/b/b2/T--IIT_Roorkee--Poster_images--poster-content--poster_results4.png"/>
| + | |
− | </div>
| + | |
− | <br/>
| + | |
− | <div class="text">
| + | |
− | <img alt="" class="poster-content-image poster-content-image-full" src="https://static.igem.org/mediawiki/2020/6/6c/T--IIT_Roorkee--Poster_images--poster-content--poster_results5.png"/>
| + | |
| </div> | | </div> |
| </div> | | </div> |
Line 949: |
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| <div class="text"> | | <div class="text"> |
| References: | | References: |
− | </div>
| + | <br/><br/><br/> |
− | <br/>
| + | |
− | <div class="text">
| + | |
| <ol class="wiki-ol"> | | <ol class="wiki-ol"> |
| <li class="wiki-li"> | | <li class="wiki-li"> |
Line 1,011: |
Line 1,004: |
| </li> | | </li> |
| </ol> | | </ol> |
− | </div>
| + | <br/> |
− | <br/>
| + | <br/><br/> |
− | <div class="text">
| + | |
| Acknowledgements: | | Acknowledgements: |
| <h4> | | <h4> |
Line 1,066: |
Line 1,058: |
| | | |
| | | |
− | </div></body></html> | + | </div></div></body></html> |