BerkiGEM2007 WikiPlaying2

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   <p><a href="https://2007.igem.org/Berkeley_UC">&lt;&lt;&lt; Return to UC Berkeley iGEM 2007 </a></p>
   <p><a href="https://2007.igem.org/Berkeley_UC">&lt;&lt;&lt; Return to UC Berkeley iGEM 2007 </a></p>
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   <p><a href="https://2007.igem.org/BerkiGEM2007Present3">&lt;&lt;Previous Section: Controller</a> | <a href="https://2007.igem.org/BerkiGEM2007Present2">Next Section: Freeze Drying&gt;&gt;</a></p>
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   <p><a href="https://2007.igem.org/BerkiGEM2007Present2">&lt;&lt;Previous Section: Freeze Drying</a> | <a href="https://2007.igem.org/Berkeley_Individual_Contributions">Next Section: Individual Contributions&gt;&gt;</a></p>
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<h1 align="center">Growth Control</h1>
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<h1 align="center">Human Practices</h1>
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<h2 align="center"><strong>Introduction</strong> </h2>
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<p align="justify">Human Practices examines the way synthetic biology might inform human security, health, and welfare through the new objects that synthetic biology brings into the world. It also observes the ways in which economic, political, and cultural forces may shape the development of  synthetic biology.</p>
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<p align="justify"> To prevent chance of infection or unwanted proliferation after hemoglobin production, we have engineered a genetic self-destruct  mechanism whereby when induced, the bacterial cell will express a genetic material-degrading toxin which kills the cell, but leaves it  physically intact. <br>
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<p align="justify">Growth control in our system is established by the incorporation of a plasmid that can be triggered to translate a toxin. The toxins are  endonucleases or RNAses that destroy the genetic material within a  bacteria and thus prevent the bacteria from replicating. Throughout the  summer, we worked on several different constructs of an inducible toxin and screened for the ones with the best phenotype. </p>
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<p align="center">&nbsp;</p>
<p align="center">&nbsp;</p>
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<h2 align="center"><strong>An Inducible Toxin</strong> </h2>
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<h2 align="center">Summer Work</h2>
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<p align="justify"> Using a PBAD promoter, we constructed several variations  of inducible toxins, including the colicin DNAse CeaB, endonucleases  BamHI and BglII, and RNAse barnase. Additionally, ribosome binding site  libraries were used in order to increase the likelihood of finding a  construct that would exhibit no growth after being induced with  arabinose, but normal growth when uninduced. </p>
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<p align="justify">I focused my investigation on the patentability of Bacto Blood where its parts are in an open source forum given that there are existing patents on oxygen-based therapeutics. If it were possible to patent Bacto Blood, how could my team obtain patent protection for their  product? Bacto Blood is patentable despite having its parts listed an open source forum. However, patentability of Bacto Blood may be complex. Two  questions that read on Bacto Blood’s patentability are: </p>
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<p align="justify">We screened libraries of potential hits with a Tecan growth assay, and in the end, the constructs that showed the desirable phenotype are the constructs shown below (I716408C and I716462). When uninduced, the cells show growth comparable to regular DH10B cells, but when induced,  the growth plateaus as the cells lose their ability to replicate due to RNA and DNA destruction.</p>
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<p align="justify">1. What aspects of Bacto Blood are patentable, the individual part(s), the part(s) as put together into the whole, or the  applications made possible by the part(s)? </p>
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<p align="center"><strong>I716408C:</strong><img src="https://static.igem.org/mediawiki/2007/3/3b/Berk-Figure-Barnase.png" alt="" name="" width="298" height="156" align="middle"></p>
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<p align="justify">2. What starts the timeline for patenting Bacto Blood: when the part is put on the registry or when the applications of the part is made public? </p>
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<p align="center"><strong>I716462:</strong><img src="https://static.igem.org/mediawiki/2007/3/38/Berk-Figure-BamHI.png" alt="" name="" width="299" height="125" align="middle"></p>
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<p align="justify">&nbsp;</p>
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<p align="justify">&nbsp;</p>
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<h2 align="center">Characterization of Growth Ability</h2>
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<p align="justify">Additional characterization of the systems include a titer experiment, where the cells were grown up in a cultures both with and without arabinose. The cultures were then diluted and plated such that the  number of colonies could be counted. It was shown that the cultures  induced with arabinose had significantly fewer colonies than those not  induced with arabinose, after taking into account the various  dilutions.</p>
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<p align="center"><img src="https://static.igem.org/mediawiki/2007/9/9c/Berk-KillSwitchTiterdata.jpg" alt="" name="" width="827" height="639" align="middle"></p>
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<p align="justify">&nbsp;</p>
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<h2 align="center">Phenotype of dead cells</h2>
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<p align="justify">Importantly, although the cells triggered with arabinose have lost their ability to reproduce, they do not lyse, because if the cells did  not remain intact, then they could not serve the purpose of transporting hemoglobin. Equally significant is the fact that the the  proteins within the cell are not degraded and still maintain their  function.</p>
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<p align="center"><img name="" src="https://static.igem.org/mediawiki/2007/b/b2/Berk-deadcellphenotype.jpg" width="482" height="186" alt=""></p>
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<p align="justify">This phenotype was confirmed by transforming an RFP expression plasmid into the cell and then taking microscopy pictures of the cells grown up  in cultures with and without arabinose. With microscopy, it is clear  that the cells are still capable of expressing the RFP protein even when their growth has been arrested.</p>
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<p align="center"><img name="" src="https://static.igem.org/mediawiki/2007/4/4a/Berk-killswitchmicroscopy1.jpg" width="626" height="487" alt=""></p>
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<p align="center">&nbsp;</p>
<p align="center">&nbsp;</p>
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<p align="center"><img name="" src="https://static.igem.org/mediawiki/2007/9/90/Berk-killswitchmicroscopy2.jpg" width="626" height="476" alt=""></p>
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<h2 align="center">Novelty and Non Obvious</h2>
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<p align="center"><a href="https://2007.igem.org/Berkeley_UC">&lt;&lt;&lt; Return to UC Berkeley iGEM 2007 </a></p>
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<p align="justify">There are existing patents relating to different types of oxygen  therapeutics. These patents include PFC compunds’ as oxygen  therapeutics and methods to maximize the production yields of  hemoglobin using <em>Escherichia coli</em> expression systems. The application of Bacto Blood’s <em>E. coli</em> must be both novel and non-obvious over the prior art. The novelty and  nonobviousness of Bacto Blood relative to other oxygen therapeutics  lies in the expression of hemoglobin in an <em>E. coli</em> system that is genetically engineered to be safe <em>in vivo</em> human therapy. Bacto Blood is novel because the team created biological  parts that can be used to suppress the normal replication cycle of <em>E. coli</em> so that it does not cause sepsis in the human body. The “aseptic”  bacteria were then combined with other biological parts created by  different team members. The parts and the different devices generated  by the combinations of parts such as, (an oxygen carrier, a controller,  a self-destruct mechanism, and a freeze drying component) were  constructed and inserted into the “aseptic” <em>E. coli</em>.</p>
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<p align="center"><a href="https://2007.igem.org/BerkiGEM2007Present3">&lt;&lt;Previous Section: Controller</a> | <a href="https://2007.igem.org/BerkiGEM2007Present2">Next Section: Freeze Drying&gt;&gt;</a></p>
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<h2 align="center">Patent Application Timeline</h2>
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<p align="justify">The time line for the patent application would not start when the part  is listed in the registry. Instead, would begin when the application of  the part has been publicly disclosed. Patentability lies in the  combinations of parts that together provide a function. Parts alone may  not be patentable where they are not novel or where the innovation is  to small to be considered non-obvious.</p>
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<h2 align="center">Moving Forward</h2>
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<p align="justify">Patentability of Bacto Blood may depend on what aspects of the  invention are claimed in a patent application. The aspects of the  invention could include: </p>
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<p align="justify">1. Methods of using Bacto Blood </p>
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<p align="justify">2. Composition of Bacto Blood </p>
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<div align="justify">
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  <pre>      1. The system as a whole  </pre>
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  <pre>      2. Parts of the system or devices with in the <em>E. coli</em> chassis  </pre>
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<p align="justify">3. Methods of making Bacto Blood </p>
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<p align="justify">Each aspect be included as a claim or a set of claims in the application. Thus each aspect may be separately patentable. </p>
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<p align="center"><img name="" src="https://static.igem.org/mediawiki/2007/8/8c/Timeline.jpg" width="720" height="540" alt=""></p>
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<h2 align="center">Take Home Point</h2>
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<p align="justify">It is the sum of parts that become patentable when put together in an  applicable system. Parts can still be listed in a public registry as  means to disseminate knowledge. The parts may be well characterized.  The parts may not be made for just one specific use in one specific  system. The purpose of having well characterized and standardized parts  is that these parts can be used in many different systems. Different  systems may remain separately patentable despite haiving in common a  single part among their many parts. In some situations, a part that has  multiple applications may be separately patentable for each of its  methods of use.</p>
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<h2 align="center">Further Questions</h2>
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<p align="justify">1. Can we provide distinguishable definition of a part so that we  can distinguish between a device that is patentable and a part is not  patentable? </p>
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<div align="justify">
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  <pre>  a. Shows critical limitations of such expertise like patent lawyers.   </pre>
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<p align="justify">2. Given the challenge of integrating an open source approach with  current IP practices in Biotechnology, how might synthetic biology be a  driver for inventing new modes industrial practices and partnerships? </p>
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<p align="justify">3. How does one design research protocols that draw on both biological sciences and human practices? </p>
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<div align="justify">
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  <pre>**These three questions show the limitations to the technical answers provided above**  </pre>
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</div>
<p align="justify">&nbsp;</p>
<p align="justify">&nbsp;</p>
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<p align="center"><a href="https://2007.igem.org/Berkeley_UC">&lt;&lt;&lt; Return to UC Berkeley iGEM 2007 </a></p>
 +
<p align="center"><a href="https://2007.igem.org/BerkiGEM2007Present2">&lt;&lt;Previous Section: Freeze Drying</a> | <a href="https://2007.igem.org/Berkeley_Individual_Contributions">Next Section: Individual Contributions&gt;&gt;</a></p>
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Revision as of 22:56, 26 October 2007

Untitled Document

<<< Return to UC Berkeley iGEM 2007

<<Previous Section: Freeze Drying | Next Section: Individual Contributions>>

Human Practices

Human Practices examines the way synthetic biology might inform human security, health, and welfare through the new objects that synthetic biology brings into the world. It also observes the ways in which economic, political, and cultural forces may shape the development of synthetic biology.

 

Summer Work

I focused my investigation on the patentability of Bacto Blood where its parts are in an open source forum given that there are existing patents on oxygen-based therapeutics. If it were possible to patent Bacto Blood, how could my team obtain patent protection for their product? Bacto Blood is patentable despite having its parts listed an open source forum. However, patentability of Bacto Blood may be complex. Two questions that read on Bacto Blood’s patentability are:

1. What aspects of Bacto Blood are patentable, the individual part(s), the part(s) as put together into the whole, or the applications made possible by the part(s)?

2. What starts the timeline for patenting Bacto Blood: when the part is put on the registry or when the applications of the part is made public?

 

Novelty and Non Obvious

There are existing patents relating to different types of oxygen therapeutics. These patents include PFC compunds’ as oxygen therapeutics and methods to maximize the production yields of hemoglobin using Escherichia coli expression systems. The application of Bacto Blood’s E. coli must be both novel and non-obvious over the prior art. The novelty and nonobviousness of Bacto Blood relative to other oxygen therapeutics lies in the expression of hemoglobin in an E. coli system that is genetically engineered to be safe in vivo human therapy. Bacto Blood is novel because the team created biological parts that can be used to suppress the normal replication cycle of E. coli so that it does not cause sepsis in the human body. The “aseptic” bacteria were then combined with other biological parts created by different team members. The parts and the different devices generated by the combinations of parts such as, (an oxygen carrier, a controller, a self-destruct mechanism, and a freeze drying component) were constructed and inserted into the “aseptic” E. coli.

Patent Application Timeline

The time line for the patent application would not start when the part is listed in the registry. Instead, would begin when the application of the part has been publicly disclosed. Patentability lies in the combinations of parts that together provide a function. Parts alone may not be patentable where they are not novel or where the innovation is to small to be considered non-obvious.

Moving Forward

Patentability of Bacto Blood may depend on what aspects of the invention are claimed in a patent application. The aspects of the invention could include:

1. Methods of using Bacto Blood

2. Composition of Bacto Blood

      1.	The system as a whole  
      2.	Parts of the system or devices with in the E. coli chassis  

3. Methods of making Bacto Blood

Each aspect be included as a claim or a set of claims in the application. Thus each aspect may be separately patentable.

Take Home Point

It is the sum of parts that become patentable when put together in an applicable system. Parts can still be listed in a public registry as means to disseminate knowledge. The parts may be well characterized. The parts may not be made for just one specific use in one specific system. The purpose of having well characterized and standardized parts is that these parts can be used in many different systems. Different systems may remain separately patentable despite haiving in common a single part among their many parts. In some situations, a part that has multiple applications may be separately patentable for each of its methods of use.

Further Questions

1. Can we provide distinguishable definition of a part so that we can distinguish between a device that is patentable and a part is not patentable?

   a.	Shows critical limitations of such expertise like patent lawyers.   

2. Given the challenge of integrating an open source approach with current IP practices in Biotechnology, how might synthetic biology be a driver for inventing new modes industrial practices and partnerships?

3. How does one design research protocols that draw on both biological sciences and human practices?

**These three questions show the limitations to the technical answers provided above**  

 

<<< Return to UC Berkeley iGEM 2007

<<Previous Section: Freeze Drying | Next Section: Individual Contributions>>