Team:Shenzhen/Notebook/YAO.Channel

From 2012.igem.org

(Difference between revisions)
Line 27: Line 27:
<li>Apr. 18th - Apr.22th</li>  
<li>Apr. 18th - Apr.22th</li>  
<p>Events:</p>
<p>Events:</p>
-
<p>We find some papers to read to know something about transport systems</p>
+
<p>We found some papers related to transport systems for mitochondria to read. Several points we concerned for:  </p>
-
<p> - Problem to be solved:</p>
+
<p> - 1) All kinds of transport systems in the mitochondria of yeast；</p>
-
<p> - 1)kinds of transport systems in the mitochondria of yeast；</p>
+
<p> - 2) How the transport systems play their role in yeast</p>
-
<p> - 2)the way these systems transport proteins</p>
+
<p> - 3) Important proteins in the transport system</p>
-
<p> - 3)Important proteins in the transport system</p>
+
<p> - Several question remained to be answered: </p>
-
<p> - Important papers we read:</p>
+
<p> - 1) Weather the present situations of the transport systems allow us to do a good classification</p>
 +
<p> - 2) What’s the mechanism of assembling membrane proteins to the inner membrane.</p>
 +
<p> - 3) If we use chloroplast’s SRP system, how to assemble the related proteins?</p>
 +
<p> - 4) If we add new system in the outer membrane,how to let it work normally.</p>
 +
<p> - The papers we read:</p>
<p> - 1) How mitochondria import hydrophilic and hydrophobic proteins. Agnieszka Chacinska, Nikolaus Pfanner and Chris Meisinger.TRENDS in Cell Biology Vol.12 No.7 July 2002</p>
<p> - 1) How mitochondria import hydrophilic and hydrophobic proteins. Agnieszka Chacinska, Nikolaus Pfanner and Chris Meisinger.TRENDS in Cell Biology Vol.12 No.7 July 2002</p>
<p> - 2) Converting bacteria to organelles: evolution of mitochondrial protein Sorting. Johannes M. Herrmann. TRENDS in Microbiology Vol.11 No.2 February 2003</p>
<p> - 2) Converting bacteria to organelles: evolution of mitochondrial protein Sorting. Johannes M. Herrmann. TRENDS in Microbiology Vol.11 No.2 February 2003</p>
<p> - 3) Multiple pathways for sorting mitochondrial precursor proteins. Natalia Bolender 1,2, Albert Sickmann3, Richard Wagner 4, Chris Meisinger 1 & Nikolaus Pfanner 1+... EMBO reports (2008) 9, 42–49. doi:10.1038/sj.embor.7401126</p>
<p> - 3) Multiple pathways for sorting mitochondrial precursor proteins. Natalia Bolender 1,2, Albert Sickmann3, Richard Wagner 4, Chris Meisinger 1 & Nikolaus Pfanner 1+... EMBO reports (2008) 9, 42–49. doi:10.1038/sj.embor.7401126</p>
<p> - 4) Versatility of he mitochondrial protein import machinery. Nikolaus Pfanner and Andreas Geissler. NATURE REVIEWS  | MOLECULAR CELL BIOLOGY. VOLUME 2  | MAY 2001  | 339-349</p>
<p> - 4) Versatility of he mitochondrial protein import machinery. Nikolaus Pfanner and Andreas Geissler. NATURE REVIEWS  | MOLECULAR CELL BIOLOGY. VOLUME 2  | MAY 2001  | 339-349</p>
-
<p> - 5)Evolution of the Molecular Machines for Protein Import into Mitochondria , Pavel  Dolezal et al. Science 313,314 (2006);</p>
+
<p> - 5) Evolution of the Molecular Machines for Protein Import into Mitochondria, Pavel  Dolezal et al. Science 313,314 (2006);</p>
-
<p> - Something we are still unclear:</p>
+
-
<p> - 1)Weather the present situations of the transport systems allow us to do a good classification</p>
+
-
<p> - 2)What’s the mechanism of assembling membrane proteins to the inner membrane.</p>
+
-
<p> - 3)If we use chloroplast’s SRP system, how to assemble the related proteins?</p>
+
-
<p> - 4)If we add new system in the outer membrane,how to let it work normally.</p>
+
<p>Contributors:</p>
<p>Contributors:</p>
<p> - Qiwu XU, unguang XU, Haojun JIANG, Jie WANG, Qiong WU, Senwei TANG, Qinsi LIANG</p>   
<p> - Qiwu XU, unguang XU, Haojun JIANG, Jie WANG, Qiong WU, Senwei TANG, Qinsi LIANG</p>   
Line 49: Line 48:
<li>Apr. 27th</li>   
<li>Apr. 27th</li>   
<p>Events:</p>
<p>Events:</p>
-
<p> - We read some papers and share findings with others team members in our seminar.</p>
+
<p> - We read some papers and shared findings with others team members in our seminar: </p>
-
<p> - Things we have known:</p>
+
<p> - 1) More detail about how do proteins transporting membrane.And we find some 3D pictures that could clearly show this process.</p>
-
<p> - 1)More detail about how do proteins transporting membrane.And we find some 3D pictures that could clearly show this process.</p>
+
<p> - 2) Proteins that play important roles in this process.</p>
-
<p> - 2)Proteins that play important roles in this process.</p>
+
<p> - 3) The ways that these proteins assembled to membrane.</p>
-
<p> - 3)The ways that these proteins assembled to membrane.</p>
+
<p> - The papers we read:</p>
-
<p> - Our next step：</p>
+
<p> - 1) Versatility of he mitochondrial protein import machinery. Nikolaus Pfanner and Andreas Geissler. NATURE REVIEWS  | MOLECULAR CELL BIOLOGY. VOLUME 2  | MAY 2001  | 339-349</p>
-
<p> - Since we have acquainted entirely about the transport system about mitochondria.And our next step is to reform this system .</p>
+
<p> - 2) Functional cooperation and separation of translocators in protein import into mitochondria, the double-membrane bounded organelles. Toshiya Endo1,2,*, Hayashi Yamamoto1 and Masatoshi Esaki1, Journal of Cell Science 116, 3259-3267 © 2003 The Company of Biologists Ltd.doi:10.1242/jcs.00667</p>
-
<p> - Important papers we read:</p>
+
<p> - 3) ignal-anchored Proteins Follow a Unique Insertion Pathway into the Outer Membrane of Mitochondria*，Uwe Ahting‡§, Thomas Waizenegger‡, Walter Neupert, and Doron Rapaport，JBC Papers in Press, October 22, 2004, DOI 10.1074/jbc.M410905200</p>
-
<p> - 1)Versatility of he mitochondrial protein import machinery. Nikolaus Pfanner and Andreas Geissler. NATURE REVIEWS  | MOLECULAR CELL BIOLOGY. VOLUME 2  | MAY 2001  | 339-349</p>
+
<p> - 4) Assembling the mitochondrial outer membrane, Nikolaus Pfanner,2 November 2004;doi:10.1038/nsmb852</p>
-
<p> - 2)Functional cooperation and separation of translocators in protein import into mitochondria, the double-membrane bounded organelles. Toshiya Endo1,2,*, Hayashi Yamamoto1 and Masatoshi Esaki1, Journal of Cell Science 116, 3259-3267 © 2003 The Company of Biologists Ltd.doi:10.1242/jcs.00667</p>
+
-
<p> - 3)ignal-anchored Proteins Follow a Unique Insertion Pathway into the Outer Membrane of Mitochondria*，Uwe Ahting‡§, Thomas Waizenegger‡, Walter Neupert, and Doron Rapaport，JBC Papers in Press, October 22, 2004, DOI 10.1074/jbc.M410905200</p>
+
-
<p> - 4)Assembling the mitochondrial outer membrane, Nikolaus Pfanner,2 November 2004;doi:10.1038/nsmb852</p>
+
<p>Contributors:</p>
<p>Contributors:</p>
<p> - Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.</p>
<p> - Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.</p>
</ul>
</ul>
<ul>
<ul>
-
<li>May. 6th</li>
+
<li>May. 6th</li>  
<p>Events:</p>
<p>Events:</p>
-
<p> - We held a meeting to discuss how to reform the system .</p>
+
<p> - We held a meeting to discuss how to reform the system: </p>
-
<p> - Our conclusion:</p>
+
<p> - We can use the TOM complex  and TIM complex of chloroplast to replace these of mitochondria.But we haven't acknowledge enough information of chloroplast,so we have to read more papers about transport system of chloroplast.</p>
-
<p> - We can use the TOM complex  and TIM complex of chloroplast to replace these of mitochondria.But we baven’t acknowledge enough information of chloroplast,so we have to read more papers about transport system of chloroplase.</p>
+
<p>Contributors:</p>
<p>Contributors:</p>
<p> - Chengran Zhou,Luohao Xu,Denghui Liu,Yu Chen,Qinsi Liang, Kang KANG</p>
<p> - Chengran Zhou,Luohao Xu,Denghui Liu,Yu Chen,Qinsi Liang, Kang KANG</p>
Line 76: Line 71:
<li>May. 7th - May .21th</li>   
<li>May. 7th - May .21th</li>   
<p>Events:</p>
<p>Events:</p>
-
<p> - Read important papers:</p>
+
<p> - Read the papers related to transport system of chloroplast and searched for the approach for assembly the transport machine from chloroplast. the paper we read are as follows  :</p>
-
<p> - 1)Svesnikova, N., Grimm, R., Soll, J. & Schleiff, E. Topologystudies of the chloroplast protein import channel Toc75.Biol. Chem. 381, 687–693 (2000).</p>
+
<p> - 1) Svesnikova, N., Grimm, R., Soll, J. & Schleiff, E. Topologystudies of the chloroplast protein import channel Toc75.Biol. Chem. 381, 687–693 (2000).</p>
-
<p> - 2)Functional cooperation and separation of translocators in protein import into mitochondria, the double-membrane bounded organelles. oshiya Endo1,2,*, Hayashi Yamamoto1 and Masatoshi Esaki1, Journal of Cell Science 116, 3259-3267 © 2003 The Company of Biologists Ltd.doi:10.1242/jcs.00667</p>
+
<p> - 2) Functional cooperation and separation of translocators in protein import into mitochondria, the double-membrane bounded organelles. oshiya Endo1,2,*, Hayashi Yamamoto1 and Masatoshi Esaki1, Journal of Cell Science 116, 3259-3267 © 2003 The Company of Biologists Ltd.doi:10.1242/jcs.00667</p>
<p>Contributors:</p>
<p>Contributors:</p>
<p> - Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.</p>
<p> - Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.</p>
Line 86: Line 81:
<p>Events:</p>
<p>Events:</p>
<p> - Seminar about how to reform transport system of mitochondria.</p>
<p> - Seminar about how to reform transport system of mitochondria.</p>
-
<p> - Important papers:</p>
+
<p> - We decided to employ Toc75, Toc34 and Tic proteins from Cyanidioschyzon Merolae to be our YAO. channel. Following are the papers we read:</p>
-
<p> - 1)Evolution of the Molecular Machines for Protein Import into Mitochondria , Pavel  Dolezal et al. Science 313,314 (2006);</p>
+
<p> - 1) Evolution of the Molecular Machines for Protein Import into Mitochondria , Pavel  Dolezal et al. Science 313,314 (2006);</p>
-
<p> - 2)Converting bacteria to organelles: evolution of mitochondrial protein Sorting. Johannes M. Herrmann. TRENDS in Microbiology Vol.11 No.2 February 2003</p>
+
<p> - 2) Converting bacteria to organelles: evolution of mitochondrial protein Sorting. Johannes M. Herrmann. TRENDS in Microbiology Vol.11 No.2 February 2003</p>
-
<p> - 3)Signal-anchored Proteins Follow a Unique Insertion Pathway into the Outer Membrane of Mitochondria*，Uwe Ahting‡§, Thomas Waizenegger‡, Walter Neupert, and Doron Rapaport¶，JBC Papers in Press, October 22, 2004, DOI 10.1074/jbc.M410905200</p>
+
<p> - 3) Signal-anchored Proteins Follow a Unique Insertion Pathway into the Outer Membrane of Mitochondria*，Uwe Ahting‡§, Thomas Waizenegger‡, Walter Neupert, and Doron Rapaport¶，JBC Papers in Press, October 22, 2004, DOI 10.1074/jbc.M410905200</p>
<p>Contributors:</p>
<p>Contributors:</p>
-
<p> - Kang Kang, Yu chen, Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.</p>
+
<p> - Kang Kang, Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.</p>
</ul>
</ul>
<ul>
<ul>
-
<li>Jun. 11th</li>  
+
<li>Jun. 1st</li>
<p>Events:</p>
<p>Events:</p>
-
<p> - Seminar about our experiment.</p>
+
<p> - Request Dr. Osami Misumi from Yamaguchi University the DNA and cells of Cyanidioschyzon Merolae</p>
-
<p> - We had a discussion about how to design our experiment.</p>
+
<p>Contributors:</p>
<p>Contributors:</p>
-
<p> - Qiwu Xu, Kang Kang, Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.</p>
+
<p> - Luohao XU</p>
</ul>
</ul>
<ul>
<ul>
-
<li>Jun. 15th - Jul. 20</li>
+
<li>Jun. 11th</li>  
-
<p>Events:</p>
+
-
<p> - Prepare for our experiment and read more papers about transport system.</p>
+
-
<p>Contributors:</p>
+
-
<p> - Qiwu Xu,Chengran Zhou</p>
+
-
</ul>
+
-
<ul>
+
-
<li>Jul. 20th - Aug. 20</li> 
+
-
<p>Events:</p>
+
-
<p> - Experiment with construction of signal peptide BioBricks.</p>
+
-
<p>Contributors:</p>
+
-
<p> - Qiwu Xu, Mingyu Gan.</p>
+
-
</ul>
+
-
<ul>
+
-
<li>Aug. 20th - Sep. 15th</li> 
+
-
<p>Events:</p>
+
-
<p> - YAO. Channel Biobricks,story, pictures preparation and presentation design.</p>
+
-
<p>Contributors:</p>
+
-
<p> - Yu CHEN, Kang KANG, Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.Mingyu Gan, Haosen Chen.</p>
+
-
</ul>
+
-
 
+

Revision as of 04:24, 23 September 2012




Journal
  • Apr. 18th - Apr.22th

    • Events:

    We found some papers related to transport systems for mitochondria to read. Several points we concerned for:

    - 1) All kinds of transport systems in the mitochondria of yeast；

    - 2) How the transport systems play their role in yeast

    - 3) Important proteins in the transport system

    - Several question remained to be answered:

    - 1) Weather the present situations of the transport systems allow us to do a good classification

    - 2) What’s the mechanism of assembling membrane proteins to the inner membrane.

    - 3) If we use chloroplast’s SRP system, how to assemble the related proteins?

    - 4) If we add new system in the outer membrane,how to let it work normally.

    - The papers we read:

    - 1) How mitochondria import hydrophilic and hydrophobic proteins. Agnieszka Chacinska, Nikolaus Pfanner and Chris Meisinger.TRENDS in Cell Biology Vol.12 No.7 July 2002

    - 2) Converting bacteria to organelles: evolution of mitochondrial protein Sorting. Johannes M. Herrmann. TRENDS in Microbiology Vol.11 No.2 February 2003

    - 3) Multiple pathways for sorting mitochondrial precursor proteins. Natalia Bolender 1,2, Albert Sickmann3, Richard Wagner 4, Chris Meisinger 1 & Nikolaus Pfanner 1+... EMBO reports (2008) 9, 42–49. doi:10.1038/sj.embor.7401126

    - 4) Versatility of he mitochondrial protein import machinery. Nikolaus Pfanner and Andreas Geissler. NATURE REVIEWS | MOLECULAR CELL BIOLOGY. VOLUME 2 | MAY 2001 | 339-349

    - 5) Evolution of the Molecular Machines for Protein Import into Mitochondria, Pavel Dolezal et al. Science 313,314 (2006);

    Contributors:

    - Qiwu XU, unguang XU, Haojun JIANG, Jie WANG, Qiong WU, Senwei TANG, Qinsi LIANG

  • Apr. 27th

    • Events:

    - We read some papers and shared findings with others team members in our seminar:

    - 1) More detail about how do proteins transporting membrane.And we find some 3D pictures that could clearly show this process.

    - 2) Proteins that play important roles in this process.

    - 3) The ways that these proteins assembled to membrane.

    - The papers we read:

    - 1) Versatility of he mitochondrial protein import machinery. Nikolaus Pfanner and Andreas Geissler. NATURE REVIEWS | MOLECULAR CELL BIOLOGY. VOLUME 2 | MAY 2001 | 339-349

    - 2) Functional cooperation and separation of translocators in protein import into mitochondria, the double-membrane bounded organelles. Toshiya Endo1,2,*, Hayashi Yamamoto1 and Masatoshi Esaki1, Journal of Cell Science 116, 3259-3267 © 2003 The Company of Biologists Ltd.doi:10.1242/jcs.00667

    - 3) ignal-anchored Proteins Follow a Unique Insertion Pathway into the Outer Membrane of Mitochondria*，Uwe Ahting‡§, Thomas Waizenegger‡, Walter Neupert, and Doron Rapaport，JBC Papers in Press, October 22, 2004, DOI 10.1074/jbc.M410905200

    - 4) Assembling the mitochondrial outer membrane, Nikolaus Pfanner,2 November 2004;doi:10.1038/nsmb852

    Contributors:

    - Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.

  • May. 6th

    • Events:

    - We held a meeting to discuss how to reform the system:

    - We can use the TOM complex and TIM complex of chloroplast to replace these of mitochondria.But we haven't acknowledge enough information of chloroplast,so we have to read more papers about transport system of chloroplast.

    Contributors:

    - Chengran Zhou,Luohao Xu,Denghui Liu,Yu Chen,Qinsi Liang, Kang KANG

  • May. 7th - May .21th

    • Events:

    - Read the papers related to transport system of chloroplast and searched for the approach for assembly the transport machine from chloroplast. the paper we read are as follows  :

    - 1) Svesnikova, N., Grimm, R., Soll, J. & Schleiff, E. Topologystudies of the chloroplast protein import channel Toc75.Biol. Chem. 381, 687–693 (2000).

    - 2) Functional cooperation and separation of translocators in protein import into mitochondria, the double-membrane bounded organelles. oshiya Endo1,2,*, Hayashi Yamamoto1 and Masatoshi Esaki1, Journal of Cell Science 116, 3259-3267 © 2003 The Company of Biologists Ltd.doi:10.1242/jcs.00667

    Contributors:

    - Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.

  • May. 31th

    • Events:

    - Seminar about how to reform transport system of mitochondria.

    - We decided to employ Toc75, Toc34 and Tic proteins from Cyanidioschyzon Merolae to be our YAO. channel. Following are the papers we read:

    - 1) Evolution of the Molecular Machines for Protein Import into Mitochondria , Pavel Dolezal et al. Science 313,314 (2006);

    - 2) Converting bacteria to organelles: evolution of mitochondrial protein Sorting. Johannes M. Herrmann. TRENDS in Microbiology Vol.11 No.2 February 2003

    - 3) Signal-anchored Proteins Follow a Unique Insertion Pathway into the Outer Membrane of Mitochondria*，Uwe Ahting‡§, Thomas Waizenegger‡, Walter Neupert, and Doron Rapaport¶，JBC Papers in Press, October 22, 2004, DOI 10.1074/jbc.M410905200

    Contributors:

    - Kang Kang, Denghui Liu, Luohao Xu, Chengran Zhou, Qinsi Liang.

  • Jun. 1st

    • Events:

    - Request Dr. Osami Misumi from Yamaguchi University the DNA and cells of Cyanidioschyzon Merolae

    Contributors:

    - Luohao XU

  • Jun. 11th


    • </div>

    Context 2

    </div>


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