Team:GeorgiaTech/Parts

From 2014.igem.org

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<h1 >WELCOME TO iGEM 2014! </h1>
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<p>Your team has been approved and you are ready to start the iGEM season!
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<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:GeorgiaTech/Parts&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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<h4 style="font: 18px 'Bitter' serif;">Jump to:</h4>
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    <a href="#May" style="font: 18px 'Bitter' serif; color: #B22222;">May</a>
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    <a href="#June" style="font: 18px 'Bitter' serif; color: #B22222;">June</a>
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    <a href="#July" style="font: 18px 'Bitter' serif; color: #B22222;">July</a>
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    <a href="#August" style="font: 18px 'Bitter' serif; color: #B22222;">August</a>
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    <a href="#September" style="font: 18px 'Bitter' serif; color: #B22222;">September</a>
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    <a href="#October" style="font: 18px 'Bitter' serif; color: #B22222;">October</a>
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<h1 id="Notebook">Notebook</h1>
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<h3 id="May">May</h3>
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<h2>Project Design</h2>
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<p>The month of May was largely focused on the selection and design of our Biobrick parts and devices. Two weeks were dedicated to the selection process for our team's 2014 iGEM project. Each acting team member identified a problem and proposed a solution via a genetically engineered organism; through discussion and popular vote, it was eventually determined that our team would work to express functional sMMO in E.coli for the purpose of methane remediation.</p>
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<p>At this time, the team also voted to continue characterization and expansion of the RBS insertion primers first designed by Georgia Tech's 2013 iGEM Team.</p>
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<p>May saw very little bench work besides training modules to develop wet lab skills and build our supply of biological resources.</p>
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<h3 id="June">June</h3>
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<h2>RBS and Promoter Primer Testing</h2>
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<p>Starting in June the team began testing of newly designed RBS insertion primers as well as newly designed promoter insertion primers based upon the same concept. Initial tests with these primers ultimately failed. It was deemed that the protocols and techniques developed by the team were not adequate enough for job. However, by the end of the month the team had achieved successes in inserting both a high and a low efficiency RBS site in front of the mCherry reporter gene in pSB1C3.</p>
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<h2>sMMO Project Planning</h2>
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<p>No bench work was performed on the sMMO project in the month of June, instead the time was spent meticulously designing our selected sMMO genes for DNA synthesis in order to ensure optimized expression in E. coli and an easy to manipulate gene in the lab. Additionally, the high cost of synthetic DNA drove our team to spend a great deal of time fundraising and obtaining discounts from molecular biology product suppliers.</p>
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<h3 id="July">July</h3>
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<!--Parts Submitted to the Registry  -->
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<h2>RBS and Promoter Primer Function Verification</h2>
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<tr><td > <h3> Parts Submitted to the Registry </h3></td>
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<p>Come July, refinement of the techniques and protocols used for RBS and promoter insertion finally came to fruition. Breaking the protocol into separate steps for RBS insertion and promoter insertion as well as a re-designing of the original promoter primers led to the verification of three new RBS primers and two new promoter primers. Although the strength of these PCR inserted sites had not yet been checked by flow cytometry, sequencing showed that the sequences had been inserted as predicted.</p>
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<h2>sMMO Gene Arrival</h2>
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<td > <h3>What information do I need to start putting my parts on the Registry? </h3></td>
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<p>The synthesized sMMO genes arrived during this month, and all efforts went towards inserting these genes into vectors (if they weren't already) and transforming E.coli with them for the purpose of creating safe frozen stocks.</p>
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An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will submit them to the <a href="http://partsregistry.org"> Registry of Standard Biological Parts</a>. The iGEM software provides an easy way to present the parts your team has created. The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. 
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<strong>Note that if you want to document a part you need to document it on the <a href="http://partsregistry.org Registry"> Registry</a>, not on your team wiki.</strong> Future teams and other users and are much more likely to find parts on the Registry than on your team wiki.
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<h3 id="August">August</h3>
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<h2>RBS and Promoter Relative Expression Analysis</h2>
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Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without a need to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.
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<p>Finally Flow cytometry characterization of the RBS and promoter primers was initiated. The cytometry provided information on the relative expression rates of combinations of various strength RBS and promoters. This knowledge aided in our selection of primers to use with the individual sMMO genes.</p> <p>It was noted that the value of these primers would be more tangible if they were also compared to an mCherry reporter with an RBS and promoter site synthesized through more traditional 3A assembly or ordered digestion and ligation.</p>
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</p>
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<h2>Generation of New Biobrick Parts</h2>
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<p>sMMO genes were inserted into Biobrick format over the month of August in vector pSB1C3.</p>
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<h3 id="September">September</h3>
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<h3>When should you put parts into the Registry?</h3>
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As soon as possible! We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better recall you will have of all details surrounding your parts. Remember you don't need to send us the DNA to create an entry for a part on the Registry. However, you must send us the sample/DNA before the Jamboree. Only parts for which you have sent us samples/DNA are eligible for awards and medal requirements.
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The information needed to initially create a part on the Registry is:
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. Check out part <a href="http://parts.igem.org/Part:BBa_K404003">BBa_K404003</a> for an excellent example of a highly characterized part.
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You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry"> Add a Part to the Registry</a> link.
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<tr><td colspan="3" > <h3> Parts Table</h3></td></tr>
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Any parts your team has created will appear in this table below:</td></tr>
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<groupparts>iGEM013 GeorgiaTech</groupparts>
 

Revision as of 16:25, 3 October 2014

Notebook

May

Project Design

The month of May was largely focused on the selection and design of our Biobrick parts and devices. Two weeks were dedicated to the selection process for our team's 2014 iGEM project. Each acting team member identified a problem and proposed a solution via a genetically engineered organism; through discussion and popular vote, it was eventually determined that our team would work to express functional sMMO in E.coli for the purpose of methane remediation.

At this time, the team also voted to continue characterization and expansion of the RBS insertion primers first designed by Georgia Tech's 2013 iGEM Team.

May saw very little bench work besides training modules to develop wet lab skills and build our supply of biological resources.

June

RBS and Promoter Primer Testing

Starting in June the team began testing of newly designed RBS insertion primers as well as newly designed promoter insertion primers based upon the same concept. Initial tests with these primers ultimately failed. It was deemed that the protocols and techniques developed by the team were not adequate enough for job. However, by the end of the month the team had achieved successes in inserting both a high and a low efficiency RBS site in front of the mCherry reporter gene in pSB1C3.

sMMO Project Planning

No bench work was performed on the sMMO project in the month of June, instead the time was spent meticulously designing our selected sMMO genes for DNA synthesis in order to ensure optimized expression in E. coli and an easy to manipulate gene in the lab. Additionally, the high cost of synthetic DNA drove our team to spend a great deal of time fundraising and obtaining discounts from molecular biology product suppliers.

July

RBS and Promoter Primer Function Verification

Come July, refinement of the techniques and protocols used for RBS and promoter insertion finally came to fruition. Breaking the protocol into separate steps for RBS insertion and promoter insertion as well as a re-designing of the original promoter primers led to the verification of three new RBS primers and two new promoter primers. Although the strength of these PCR inserted sites had not yet been checked by flow cytometry, sequencing showed that the sequences had been inserted as predicted.

sMMO Gene Arrival

The synthesized sMMO genes arrived during this month, and all efforts went towards inserting these genes into vectors (if they weren't already) and transforming E.coli with them for the purpose of creating safe frozen stocks.

August

RBS and Promoter Relative Expression Analysis

Finally Flow cytometry characterization of the RBS and promoter primers was initiated. The cytometry provided information on the relative expression rates of combinations of various strength RBS and promoters. This knowledge aided in our selection of primers to use with the individual sMMO genes.

It was noted that the value of these primers would be more tangible if they were also compared to an mCherry reporter with an RBS and promoter site synthesized through more traditional 3A assembly or ordered digestion and ligation.

Generation of New Biobrick Parts

sMMO genes were inserted into Biobrick format over the month of August in vector pSB1C3.

September

October

Retrieved from "http://2014.igem.org/Team:GeorgiaTech/Parts"