Difference between revisions of "Team:TU Dresden/Project/Description"

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<h1>Meetings</h1>
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<h1>Description</h1>
  
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<h2>Weekly meetings</h2>
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<h2>Introduction</h2>
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<p style="line-height:1.8">Since the 20<sup>th</sup> of February we had weekly meetings on Monday with everybody from the team including the supervisors. In these meetings we discussed the progress of each person's work, the tasks for the upcoming week and also the results. Since not everyone was following what everyone was doing, the meetings were a good opportunity to catch up and discuss all together. </p>
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<p style="line-height:1.8">Our project is called <b>SPACE-P</b> (Structural Phage Assisted Continuous Evolution of Proteins) and is part of the Synthetic Biology field. It focuses on accelerating the process of developing protein binding partners, which is required in pharmaceutical research as well as biotechnology and many other fields of science. Thus far phage display is the most commonly used method for the discovery of protein binding partners. In this method a large library of potential binding partners is created where the strongest candidates are selected for further affinity testing. This process is very time consuming, cost intensive, requires human intervention steps, and is limited to the size of the given library. Our platform will make it possible to start with a single molecule, transform it by mutation and selection pressure to improve the binding affinity towards a target protein. This method is not only easy to implement, utilizing simple organisms and devices, but also significantly faster and cheaper than currently used tools. </p>
  
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<h2>Background</h2>
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<h3>PACE</h3>
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<p style="line-height:1.8">During the development of our project we had four meetings with the group leaders of the Biotechnology Center of the TU Dresden (BIOTEC). These meetings take place the first Monday of every month. The first one we attended focused on the idea we wanted to realize. The leaders helped us to think about difficulties we could face and gave valuable impulses. In the second one we presented our finance plan and they confirmed their support for an iGEM team. The third and fourth meeting were used to present the progress of our project as well as to check the finances. To sum up, we got input from diverse groups in the BIOTEC concerning both technical issues and ways to fund our group. This helped us to illuminate the project idea from numerous points of view.Phage assisted continuous evolution or PACE, is a system designed for the continuous, directed evolution of biomolecules. The principle is that E. coli flow through a lagoon in which M13 are present and viable.  Important to note is that the flow rate of the E.Coli is adjusted so that it is faster than their doubling time but not of that of the M13.  Another important aspect of this setup is the deletion of gene P3 on M13, which is necessary for infection and proliferation. Instead the gene P3 of the M13 is encoded on the E. coli plasmid, under the control of an upstream activating sequence (UAS). To undergo further infection cycles, the initial infectious generation of transgenic phage must activate the UAS by binding their activating domain (AD) to the binding domain (BD). This requires favorable protein-protein interactions between an X provided by the M13 and Y provided by the UAS of the E.Coli. As a result, and some additional help from a mutagenesis plasmid, M13 evolves this interaction between X and Yin order to stay in the lagoon. A stronger interaction creates a selection advantage and will be favored over a weaker interaction.</p>
  
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<h2>Group leader meetings</h2>
 
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<p style="line-height:1.8">During the development of our project we had four meetings with the group leaders of the Biotechnology Center of the TU Dresden (BIOTEC). These meetings take place the first Monday of every month. The first one we attended focused on the idea we wanted to realize. The leaders helped us to think about difficulties we could face and gave valuable impulses. In the second one we presented our finance plan and they confirmed their support for an iGEM team. The third and fourth meeting were used to present the progress of our project as well as to check the finances. To sum up, we got input from diverse groups in the BIOTEC concerning both technical issues and ways to fund our group. This helped us to illuminate the project idea from numerous points of view.</p>
 
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<h2>Meetings with iGEM veterans</h2>
 
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<p style="line-height:1.8"> A very special opportunity for us was to meet Robert Braun, Prof. Thomas Mascher and his PhD student Julia Bartels: three iGEM veterans from the TU Bielefeld and the LMU Munic, respectively. As soon as they heard that there was an iGEM team in Dresden for the first time since many years, they contacted us and we met with them. They did not only inform us about their experiences, their work and the competition, but they gave us valuable information to fit the iGEM requirements and standards. The meetings led us to reorganize the project and make it more realistic for the competition. After these discussions we could renew our courage and we could contact them any time we needed help and advice. </p>
 
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<h2>Meetings with companies</h2>
 
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<p style="line-height:1.8"> In order to sponsors and economical support from the scientific community in Dresden, we had to send several (hundreds) of  e-mails and meet representatives of companies. One of the companies we met twice was Biosaxoy, located in the same building as the BIOTEC. In these meetings we explained our project and goals to the representatives and we got valuable feedback from them on how to improve our project and make it more attractive to other companies. Since it was not possible for them to directly support us, they gave us several contacts from other companies and sectors.</p>
 
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<h2>Bonding Firmenkontaktmesse</h2>
 
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<p style="line-height:1.8"> On the 28<sup>th</sup> and 29<sup>th</sup> the <a href="http://dresden.firmenkontaktmesse.de/">bonding Firmenkontaktmesse</a> took place in Dresden. In this fair several companies from different fields present career opportunities and information about themselves. Two different members of the group attended the fair on both days: Bo and Bastian were there during the first day, and Marvin and Ashwin on the second. Our team members tried to approach the representatives of the companies and ask for their advice and support, but the success was quite limited.</p>
 
  
 
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Revision as of 10:47, 26 August 2015


Description

Introduction

Our project is called SPACE-P (Structural Phage Assisted Continuous Evolution of Proteins) and is part of the Synthetic Biology field. It focuses on accelerating the process of developing protein binding partners, which is required in pharmaceutical research as well as biotechnology and many other fields of science. Thus far phage display is the most commonly used method for the discovery of protein binding partners. In this method a large library of potential binding partners is created where the strongest candidates are selected for further affinity testing. This process is very time consuming, cost intensive, requires human intervention steps, and is limited to the size of the given library. Our platform will make it possible to start with a single molecule, transform it by mutation and selection pressure to improve the binding affinity towards a target protein. This method is not only easy to implement, utilizing simple organisms and devices, but also significantly faster and cheaper than currently used tools.

Background

PACE

During the development of our project we had four meetings with the group leaders of the Biotechnology Center of the TU Dresden (BIOTEC). These meetings take place the first Monday of every month. The first one we attended focused on the idea we wanted to realize. The leaders helped us to think about difficulties we could face and gave valuable impulses. In the second one we presented our finance plan and they confirmed their support for an iGEM team. The third and fourth meeting were used to present the progress of our project as well as to check the finances. To sum up, we got input from diverse groups in the BIOTEC concerning both technical issues and ways to fund our group. This helped us to illuminate the project idea from numerous points of view.Phage assisted continuous evolution or PACE, is a system designed for the continuous, directed evolution of biomolecules. The principle is that E. coli flow through a lagoon in which M13 are present and viable. Important to note is that the flow rate of the E.Coli is adjusted so that it is faster than their doubling time but not of that of the M13. Another important aspect of this setup is the deletion of gene P3 on M13, which is necessary for infection and proliferation. Instead the gene P3 of the M13 is encoded on the E. coli plasmid, under the control of an upstream activating sequence (UAS). To undergo further infection cycles, the initial infectious generation of transgenic phage must activate the UAS by binding their activating domain (AD) to the binding domain (BD). This requires favorable protein-protein interactions between an X provided by the M13 and Y provided by the UAS of the E.Coli. As a result, and some additional help from a mutagenesis plasmid, M13 evolves this interaction between X and Yin order to stay in the lagoon. A stronger interaction creates a selection advantage and will be favored over a weaker interaction.