Team:Bielefeld-Germany/Labjournal/week11

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==Week 11 (07/09 - 07/15/12)==
 
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===Monday July 9th===
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* '''Team Student Academy:''' This week the Student Academy took place. Today we held a presentation about the background of our experiments and answered all the questions the pupils had. Furthermore two of us participated at the an unconstrained meeting between the instructors and the pupils in the evening.
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* '''Team Site Directed Mutagenesis:''' Council with Katharina Thiedig, who did the Site Directed Mutagenesis for the last years iGEM-Team-Bielefeld, about how to use the “QuikChange Primer Design”-program and the SDM-protocol
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===Tuesday July 10th===
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* '''Team Site Directed Mutagenesis:''' Generated primer-sequences with Agilent Technologies “QuikChange Primer Design” for bpul, xccl, ecol and tthl.
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* '''Team Cellulose Binding Domain:''' Searched NCBI for Cellulose, Chitin & Keratin binding motifs in accessible organisms; found two Chitin-binding-domains in Bacillus halodurans
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* '''Team Student Academy:''' The experiments were performed by one half of the pupils in groups of 2-3. Afterwards we held a presentation about the iGEM competition, the project of the last two teams from Bielefeld and about our project. In the evening we had a barbecue with the pupils and the iGEM team with a lot of interesting discussions.
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* '''Team Fungal Laccases:'''
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* We got the sequences for five different fungal laccases from the requested plasmids from [https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week10#Monday_July_2nd Monday 2nd] and they wanted to send us plasmids which contain the cDNA sequences of five different laccases from ''Trametes versicolor'' and ''Pycnoporus cinnabarinus''.
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/Starting"><strong>Prologue</strong></a></li>
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                <li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week1"><strong>Week 1</strong></a></li>
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                <li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week2"><strong>Week 2</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week3"><strong>Week 3</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week4"><strong>Week 4</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week5"><strong>Week 5</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week6"><strong>Week 6</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week7"><strong>Week 7</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week8"><strong>Week 8</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week9"><strong>Week 9</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week10"><strong>Week 10</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week11"><strong>Week 11</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week12"><strong>Week 12</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week13"><strong>Week 13</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week14"><strong>Week 14</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week15"><strong>Week 15</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week16"><strong>Week 16</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week17"><strong>Week 17</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week18"><strong>Week 18</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week19"><strong>Week 19</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week20"><strong>Week 20</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week21"><strong>Week 21</strong></a></li>
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<li><a href="https://2012.igem.org/Team:Bielefeld-Germany/Labjournal/week22"><strong>Week 22</strong></a></li>
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:* Tv5 from ''Trametes versicolor''
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:* Tv10 from ''Trametes versicolor''
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:* Tv13 from ''Trametes versicolor''
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:* Tv20 from ''Trametes versicolor''
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:* Pc35 from ''Pycnoporus cinnabarinus''
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* We designed primer pairs with prefix and suffix overhanging ends for cloning in pSB1C3 and a primer pair for cloning in shuttle vector.
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* The first primer pairs were designed with standard prefix and suffix sequence and 20 bases complementary to the start and end of the ORF sequences.
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==Week 11 (07/09 - 07/15/12)==
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* Additional primer pairs were designed with ''Aar''I restriction site and Kozak consensus sequence before the first 20 bases from the start of the ORF (forward primers). The reverse primers were designed with the last 20 bases of the laccase genes and a terminator overhanging end and a ''Aar''I restriction site.
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===Wednesday July 11th===
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* '''Team Cellulose Binding Domain:''' Looked up the sequence of Clostridium cellulovorans cellulose binding protein gene (cbp A) http://www.ncbi.nlm.nih.gov/nuccore/M73817 made a Clonemanagerfile and protein-BLASTed the sequence to find out the domain of the Cellulose-Binding-Domain: 103bp-378bp
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* '''Team Student Academy:''' The experiments were performed by the second half of the pupils and the groups from yesterday analyzed their plates.
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* '''Team Bacterial Laccases:''' We made glycerin cultures of the finished biobricks.
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===Thursday July 12th===
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===Friday July 13th===
 
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* '''Team Student Academy:''' The groups from Wednesday analyzed their plates. Together with the pupils we made a final analysis of the results, discussed about all problems and questions and helped with the preparation of a presentation, they had to hold in front of all instructors and participants.
 
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* '''Team Bacterial Laccases''': We got new ''Streptomyces'' DNA from or supervisor C. Rueckert. He did an alignment with our ''S. griseus'' and ''S. lavendulae'' sequences against a local database for Streptomyces and identified ''S. rosechromogenes'', ''S. tuebingen'' and ''S.goettingen''. Those laccase genes showed simularity to our laccase genes. Since he had isolated chromosomal DNA we were able to work with them. We set the PCR with the three ''Streptomyces''. On this PCR ''S. tuebingen'' DNA could be amplified, but it wasn't specific for that what we expected. No products could be amplified on the other two.
 
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===Saturday July 14th===
 
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===Sunday July 15th===
 
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Sunday
 
{{Team:Bielefeld/Sponsoren}}
{{Team:Bielefeld/Sponsoren}}

Latest revision as of 21:21, 25 September 2012


Week 11 (07/09 - 07/15/12)

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Fifteen students from different fields of study from the Bielefeld University aspired to complete a project called TOXIC COMPOUNDS IN NATURAL WATER - A CASE FOR LACCASE. In his Wiki we document our achievements and our approach.

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