Difference between revisions of "Team:Virginia/Attributions"

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                 <li><b>Colin Haws</b>: As our team captain, member of the Human Practices and Wetlab Committees, Julia helped organize our team, communicated with other iGEM teams, advisors, and experts through almost 100 emails, helped fill out safety forms, organized the recruitment for next year’s team, and was the primary point of contact with the iGEM organization overall. Also, Julia wrote the code of ethical conduct, worked on the blog for the iGEM engineering school website, and helped develop the resource hub. As part of the DNA subteam of the Wetlab committee, Julia helped design the DNA scaffold procedures and worked in the lab. </li>
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                 <li><b>Colin Haws</b>: As head of the modeling committee and member of the Wetlab committee, Colin focused on leading the modeling efforts to describe the efficiency of the MANIFOLD system. More specifically he worked on the promotor calculator and the reaction kinetics models. In Wetlab, Colin helped in the collection and assembly of BMC parts, both in the lab and virtually, and worked on the BMC procedures in the lab with Veronica.</li>
 
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                 <li><b>Julia Ball</b>: As our team captain, member of the Human Practices and Wetlab Committees, Julia helped organize our team, communicated with other iGEM teams, advisors, and experts through almost 100 emails, helped fill out safety forms, organized the recruitment for next year’s team, and was the primary point of contact with the iGEM organization overall. Also, Julia wrote the code of ethical conduct, worked on the blog for the iGEM engineering school website, and helped develop the resource hub. As part of the DNA subteam of the Wetlab committee, Julia helped design the DNA scaffold procedures and worked in the lab. </li>
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                 <li><b>Aparna Kola</b>: As co-head of the entrepreneurship committee and member of the Human Practices and Modeling Committee, Aparna worked on ____</li>
 
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          <div class="sectionTitle" id="Section 2">Section 2</div>
 
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              The invention consists of a protein shell comprising one or more proteins, one or more nucleic acid scaffolds of which there can be multiple copies, anabolic and/or catabolic enzymes specific to the desired biosynthesis pathway each containing a nucleic acid binding domain, recognition sequences for the utilized nucleic acid binding domains, nucleic acid spacers, and a linkage between the nucleic acid scaffolds and the protein shell. The protein shell (10) can take the form of any closed or open surface that comprises one or more repeating protein units (12). Examples of valid shells include bacterial microcompartments such as the Pdu, Eut, and carboxysome microcompartments, as well as modified,  but not necessarily closed, surfaces composed of mutated versions of these microcompartment shell proteins. The nucleic acid scaffolds (18) comprise multiple recognition sequences (22) and spacers (32) and can be made from any form of nucleic acid, including: deoxyribonucleic acid, ribonucleic acid, and synthetic nucleic acids such as xeno nucleic acids and peptide nucleic acids among others. These scaffolds are attached to the protein shell. The pathway enzymes are biological proteins whose exact sequences are dependent on the given use case of the invention, but which all contain a nucleic acid binding domain either internal to their structure, or at their N or C terminus.  
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                <li><b>Sophia Link</b>: As a member of the Wetlab and Wiki committees, Sophia worked on the design of the DNA scaffold and helped with the writeup and organization of Reverse transcriptase assembly Wetlab procedures. In addition, Sophia created most (if not all) of MANIFOLD’s graphics, including the one on our home page and the design of the flowcharts that can be seen on the experiments page. </li>
 
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                <li><b>Collin Marino</b>: </li>
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              <b>Fig 1.</b> Figure taken from iGEM Tainan 2019 for demo purposes. Notice how the figure is much longer than it is wide, and two images are coupled together to achive this. Try to do that as well so it looks good.
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              Additionally, protein linkers are usually present between this nucleic acid binding domain and the enzyme structure to prevent inhibition of enzyme activity. However the exact linker(s) used, if any, is(are) also dependent on the specific use case of the invention. These pathway enzymes are attached to the nucleic acid scaffolds via their nucleic acid binding domains. The nucleic acid recognition sequences (22) are unique or semi-unique sequences of nucleic acid monomers on the nucleic acid scaffolds to which the utilized nucleic acid binding domains have some degree of molecular complementarity. These nucleic recognition sequences comprise most of the scaffold and mark the locations to which the DNA binding domains of the pathway enzymes attach to the scaffolds. The nucleic acid spacers (32) are relatively short sequences of nucleic acid monomers that are also present on the nucleic acid scaffolds, between the recognition sequences. The linkage between the nucleic acid scaffolds (18) and protein shell (10) provides a means by which the nucleic acid scaffolds are bound to the protein shell through direct or multi-molecule complementarity. This linkage is found between the nucleic acid scaffolds and the protein shell. One example is through the addition of a nucleic acid binding domain (24) to one or more of the shell proteins forming a nucleic acid binding domain, shell protein fusion (14). Like the pathway enzymes, this nucleic acid binding-domain can be either internal to the shell protein structure or at its N or C terminus, where the exact placement depends on the shell protein being utilized. Alternatively, one or more intermediate proteins can be used to adhere the nucleic acid scaffolds to the shell, where the region of the protein interacting with the shell binds the shell via protein-protein complementarity (28) with a given shell protein, and the region of the protein interacting with the nucleic acid scaffold binds another recognition sequence on the nucleic acid scaffold through another nucleic acid binding domain (30). This forms a shell protein binding, nucleic acid domain fusion (26).<br/><br/><br/>
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                <li><b>Edward (Eddie) Micklovic</b>: As part of the Human Practices committee, Eddie spearheaded the Virginia iGEM podcast series “Mick and Mates”, filming and editing the videos and sound. In addition, Eddie helped work on the code of ethical conduct. </li>
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                <li><b>Dev Patel</b>: As head of the Human Practices Committee and member of the Wetlab, wiki, and modeling, Dev worked on writing the code of ethical conduct and most of the wiki write-up for the Human Practices committee. In modeling, Dev worked with Pietro to develop the NetLogo model to show substrate movement in BMCs. In addition, in Wetlab, Dev helped research collect and write the procedures for the Enzyme subteam, inputting those into Benchling, along with any sequences.</li>
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                <li><b>Jacob Polzin</b>: As head of the Wiki committee and member of the Modeling and Wetlab committees, Jacob ____</li>
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                <li><b>Apekchha Pradhan</b>: As a member of the Wetlab, Entrepreneurship, and Wiki committees, Apekchha was in charge of forming the sequences and parts for the 4Cl and STS enzymes in the resveratrol pathway. She worked with Peitro and Jacob in the lab, following the protocols for their enzyme sub-team. She also took part in helping build the wiki and got to be more familiar with web design and HTML/CSS. </li>
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                <li><b>Pietro Revelli</b>: As co-head of then Entrepreneurship Committee and member of the Wetlab and Modeling, Pietro worked on the market analysis of resveratrol, applied to countless grants and made the budget for the team. In addition, on the modeling team, Pietro worked on the Cobra Toolbox in Python and Matlab and was the one who pointed out the importance of the ACS and ACC in the resveratrol pathway. </li>
 
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                    <li><b>Dr. Keith Kozminski</b>:__ </li>
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                    <li><b>Ms. Kathryn Christopher</b>: ___ </li>
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                  <li><b> Dr. Jason Papin </b>: Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.</li>
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                    <li><b>Dr. Cheryl Kerfeld</b>:We begin by cold-emailing Dr. Cheryl Kerfeld, a renowned researcher out of UCLA and Michigan State with a long history of experimenting with BMCs. Dr. Kerfeld agreed to talk about her cutting-edge BMC research, even explaining her current work on customizable BMC shells, and also gave feedback on our initial project ideas. She immediately took to our concepts, and she afforded us the endorsement of a researcher who's worked with BMCs for decades. She gave us multiple contacts for other top BMC researchers, as well as a better understanding of her field of work, all of which better helped us move forward.</li>
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                    <li><b>Professor Martin Warren</b>: We also reached out to Professor Martin Warren at the University of Kent in the UK after reading a paper of his. What began as a chance email became a continued dialogue about the initial paper of interest, as well as his pertinent work with BMCs. He also agreed to share a plasmid described in his paper, which provided us with the sequence, the ability to partially replicate his findings, and a much faster route to creating our final device. </li>
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                  <li><b>Dr. Laura Fontenas</b>: One protocol that no one on our team had previously performed is qPCR. This led to our advisor connecting us to Dr. Laura Fontenas, a research associate at UVA. She was happy to share her qPCR protocol, recommendations, steps for designing primers, and any other advice we may need during our lab work.</li>
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                  <li><b> Dr. Jason Papin </b>: Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.</li>
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                    <li><b>Dr. Keith Kozminski</b>:__ </li>
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                    <li><b>Ms. Kathryn Christopher</b>: ___ </li>
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                  <li><b> Dr. Jason Papin </b>: Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.</li>
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                    <li><b>Dr. Keith Kozminski</b>:__ </li>
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                    <li><b>Ms. Kathryn Christopher</b>: ___ </li>
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                  <li><b> Dr. Jason Papin </b>: Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.</li>
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                    <li><b>Dr. Keith Kozminski</b>:__ </li>
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                    <li><b>Ms. Kathryn Christopher</b>: ___ </li>
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                  <li><b> Dr. Jason Papin </b>: Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.</li>
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          <div class="sectionTitle" id="Section 7"> And a special thanks too... </div>
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                    <li><b>Ms. Kathryn Christopher</b>: ___ </li>
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                  <li><b> Dr. Jason Papin </b>: Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.</li>
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Revision as of 20:37, 24 October 2020

Manifold

HOME
Main Abstract Problem Solution
PROJECT
Inspiration Description Design Experiments Results Modeling Device Notebook Safety
PARTS
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OUTREACH
Human Practices Public Engagement Collaborations Meet Ups
TEAM
Members Attributions Gallery
AWARDS
Awards Medals
RESOURCES
Papers Nucleic Acids Protocols Software
Index:
Attributions
Team
  • Julia Ball: As our team captain, member of the Human Practices and Wetlab Committees, Julia helped organize our team, communicated with other iGEM teams, advisors, and experts through almost 100 emails, helped fill out safety forms, organized the recruitment for next year’s team, and was the primary point of contact with the iGEM organization overall. Also, Julia wrote the code of ethical conduct, worked on the blog for the iGEM engineering school website, and helped develop the resource hub. As part of the DNA subteam of the Wetlab committee, Julia helped design the DNA scaffold procedures and worked in the lab.
  • Veronica Gutierrez: As a member of the Wetlab, Wiki, and Entrepreneurship committees, Veronica helped research and write procedures regarding the construction of the BMC, aided in the overall structure and organization of the wiki and helped collect details on current or pending patents. In the lab, Veronica worked with Colin Haws to go through the different procedures pertaining to BMC formation and analyze the results.
  • Colin Haws: As head of the modeling committee and member of the Wetlab committee, Colin focused on leading the modeling efforts to describe the efficiency of the MANIFOLD system. More specifically he worked on the promotor calculator and the reaction kinetics models. In Wetlab, Colin helped in the collection and assembly of BMC parts, both in the lab and virtually, and worked on the BMC procedures in the lab with Veronica.
  • Aparna Kola: As co-head of the entrepreneurship committee and member of the Human Practices and Modeling Committee, Aparna worked on ____
  • Sophia Link: As a member of the Wetlab and Wiki committees, Sophia worked on the design of the DNA scaffold and helped with the writeup and organization of Reverse transcriptase assembly Wetlab procedures. In addition, Sophia created most (if not all) of MANIFOLD’s graphics, including the one on our home page and the design of the flowcharts that can be seen on the experiments page.
  • Collin Marino:
  • Edward (Eddie) Micklovic: As part of the Human Practices committee, Eddie spearheaded the Virginia iGEM podcast series “Mick and Mates”, filming and editing the videos and sound. In addition, Eddie helped work on the code of ethical conduct.
  • Dev Patel: As head of the Human Practices Committee and member of the Wetlab, wiki, and modeling, Dev worked on writing the code of ethical conduct and most of the wiki write-up for the Human Practices committee. In modeling, Dev worked with Pietro to develop the NetLogo model to show substrate movement in BMCs. In addition, in Wetlab, Dev helped research collect and write the procedures for the Enzyme subteam, inputting those into Benchling, along with any sequences.
  • Jacob Polzin: As head of the Wiki committee and member of the Modeling and Wetlab committees, Jacob ____
  • Apekchha Pradhan: As a member of the Wetlab, Entrepreneurship, and Wiki committees, Apekchha was in charge of forming the sequences and parts for the 4Cl and STS enzymes in the resveratrol pathway. She worked with Peitro and Jacob in the lab, following the protocols for their enzyme sub-team. She also took part in helping build the wiki and got to be more familiar with web design and HTML/CSS.
  • Pietro Revelli: As co-head of then Entrepreneurship Committee and member of the Wetlab and Modeling, Pietro worked on the market analysis of resveratrol, applied to countless grants and made the budget for the team. In addition, on the modeling team, Pietro worked on the Cobra Toolbox in Python and Matlab and was the one who pointed out the importance of the ACS and ACC in the resveratrol pathway.
    • Advisors
  • Dr. Keith Kozminski:__
  • Ms. Kathryn Christopher: ___
  • Dr. Jason Papin : Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.
    • Wetlab Advising and Support
  • Dr. Cheryl Kerfeld:We begin by cold-emailing Dr. Cheryl Kerfeld, a renowned researcher out of UCLA and Michigan State with a long history of experimenting with BMCs. Dr. Kerfeld agreed to talk about her cutting-edge BMC research, even explaining her current work on customizable BMC shells, and also gave feedback on our initial project ideas. She immediately took to our concepts, and she afforded us the endorsement of a researcher who's worked with BMCs for decades. She gave us multiple contacts for other top BMC researchers, as well as a better understanding of her field of work, all of which better helped us move forward.
  • Professor Martin Warren: We also reached out to Professor Martin Warren at the University of Kent in the UK after reading a paper of his. What began as a chance email became a continued dialogue about the initial paper of interest, as well as his pertinent work with BMCs. He also agreed to share a plasmid described in his paper, which provided us with the sequence, the ability to partially replicate his findings, and a much faster route to creating our final device.
  • Dr. Laura Fontenas: One protocol that no one on our team had previously performed is qPCR. This led to our advisor connecting us to Dr. Laura Fontenas, a research associate at UVA. She was happy to share her qPCR protocol, recommendations, steps for designing primers, and any other advice we may need during our lab work.
    • Human Practices Advising and Support
  • Dr. Jason Papin : Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.
    • Modeling Advising and Support
  • Dr. Keith Kozminski:__
  • Ms. Kathryn Christopher: ___
  • Dr. Jason Papin : Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.
    • Wiki Advising and Support
  • Dr. Keith Kozminski:__
  • Ms. Kathryn Christopher: ___
  • Dr. Jason Papin : Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.
    • Entrepreneurship, Legal and/or Business Advising and Support
  • Dr. Keith Kozminski:__
  • Ms. Kathryn Christopher: ___
  • Dr. Jason Papin : Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.
    • And a special thanks too...
  • Dr. Keith Kozminski:__
  • Ms. Kathryn Christopher: ___
  • Dr. Jason Papin : Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.
    • FOLLOW US: