Team:Korea U Seoul/Notebook/Aug

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              <h4><p id="title">Notebook : August</p></h4>
 +
    <dt>
 +
<b> A. August, 1, 2012 </b>
 +
</dt>
 +
            <p style="padding-left:30px;">We have discussed about how to dectect and kill 'Xanthomonas oryzae’</p>
 +
            <br>
 +
            <dd>
 +
<b> 1) Idea development </b>
 +
                <br>
 +
               
 +
                <b>&nbsp;&nbsp;Haerim Song</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;raxR/H is target for raxSTAB.
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sulfur plays an important role in activity of AX21; it won’t work without sulfur
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;overexpression of raxST(sulfur attachment to AX21), RaxR/Q(transformation of PAPS into ATP) is possible in E.coli
 +
</p>               
 +
               
 +
                <b>&nbsp;&nbsp;Advisor’s advice</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  test any promoter which binds to raxR/H
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  is it possible for Xanthomonas to produce AX21 without plant receptor?
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  (Professor’s comment) we can run a test using E/coli which has plant receptor
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Method for detecting AX21 production?
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  (Professor’s comment) use mass spectrometry or put florescence after ax21 gene then cut with restriction enzyme
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Jihoon Jung </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Find A
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Kyeongwoo Jang’s opinion </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;find system which utilizes logic gate in natural world
 +
</p>
 +
         
 +
                <br>
 +
               
 +
                <b> 2) Next meeting </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1) research rax operon
 +
</p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;How to detect Ax21 : HyunKee Kim
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Research raxR/H paper : Byeongnam Min
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Research Xanthomonas : Jeongmin
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Activity of the substance only with raxR/H:  Haerim Song
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2) team
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Logic gate: Jihoon Jung, Kyeongwoo Jang
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Science camp presentation:  Haerim Song
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Wiki update: Byeongnam Min, Kyeongwoo Jang, Sanghoon Han
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Notebook translation: HyunKee Kim
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Study Modeling: Sanghoon Han, Byeongnam Min
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Design team: Jeongmin Lee, Kyeongjin Kim, Jihyong Nam, Haerim Song
 +
                </p>
 +
           
 +
            <br><br><br>
 +
            </dd>
 +
                <dt>
 +
<b> B. August 8, 2012 </b>
 +
</dt>
 +
            <br>
 +
            <p style="padding-left:30px;">We have discussed about how to dectect and kill 'Xanthomonas oryzae.’ Solidifying the idea and circuit</p>
 +
            <dd>
 +
<b> 1) Idea development </b>           
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  raxR, raxH can be detected using His tag; however, experiments using cloning technique don’t use this.
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  No indication of functional opetation only with raxR, raxH
 +
                </p>
 +
 
 +
                <b>&nbsp;&nbsp;Haerim Song</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  raxH without transmembrane segment was autophosphorylation, but no raxR transphosphrylation.
 +
                </p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  raxH H222 and RaxR D51 is responsible for phosphorylation.
 +
                </p>
 +
               
 +
                <b>&nbsp;&nbsp;Lab team</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  acquisition of PCEL, raxRH promoter, mRFP using PCR
 +
                </p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  cloning is expected to be held this week
 +
                </p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  raxR/H is constitutive, so use other promoter
 +
                </p>
 +
               
 +
                <br>
 +
                <b> 2) Team placement and H.W </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;logic gate: find A: Sanghoon Han, Jihoon Jung, Kyeongwoo Jang
 +
</p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ax21 production: Wonwook Lee, JungMin, Kyeongjin, Haerim Song, Byeongnam Min, Hyunkee Kim
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Brochure: Jeongmin Lee, Kyeongjin Kim, Jihyong Nam,  Haerim Song
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Science camp presentation:  Haerim Song
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Wiki update: Nam, Byeongnam Min, Kyeongwoo Jang, Sanghoon Han
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Notebook translation: HyunKee Kim
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Study Modeling: Sanghoon Han, Byeongnam Min
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Design team: Jeongmin Lee, Kyeongjin Kim, Jihyong Nam,  Haerim Song
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;CCP: Sanghoon Han
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;KAIST Contact; Byeongnam Min
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Team attire: Jihoon Jung
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;upload at least one copy of design to the homepage (mandatory)
 +
                </p>
 +
            </dd>
 +
           
 +
            <br><br><br>
 +
           
 +
            <dt>
 +
<b> C. August 15, 2012 </b>
 +
</dt>
 +
            <br>
 +
            <p style="padding-left:30px;">We have discussed about how to dectect and kill 'Xanthomonas oryzae.’ Solidifying the idea and circuit</p>
 +
            <dd>
 +
<b> Idea development </b>
 +
                <br>
 +
                <b>&nbsp;&nbsp;Kyeongwoo Jang: logic gate biosensing</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  researched logic gate used by organism to detect certain chemical
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  British Columbia University already did similar project; it was about concentration dependent color changing bacteria.
 +
                </p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Logic gate using single step is more efficient than using several input and output steps
 +
                </p>
 +
               
 +
                <b>&nbsp;&nbsp;Sanghoon Han: finding ‘a’ chemical</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  DSF(diffusible signaling factor)
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Haerim Song: bacterial leaf blight</b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  had presentation about iGEM during ‘Lifescience camp’
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  in order to prevent bacterial leaf blight, chemical-pesticide was given. However, it was proven to be ineffective.
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Bacterial leaf blight resistant plant was developed but, later sub-population eliminated effect of ‘gene R.’
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Wonwook Lee: sponsor </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  LG lifescience, Celltrion, Rural development administration, cosmogenetech: yet positive reply, he will continue to contact.
 +
</p>
 +
               
 +
                <b>&nbsp;&nbsp;Sanghoon Han </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Small Protein-Mediated Quorum Sensing in a Gram- Negative Bacterium (PMID : 22174954) To elucidate this function, we previously isolated and characterized eight genes required for Ax21 activity (rax genes). raxA, raxB and raxC encode components of a predicted type I secretion system (TOSS). Ax21requires this RaxABC TOSS for activity and secretion [3,4]. The RaxB protein carries two highly conserved N terminal proteolytic subdomains characteristic of transporters in Gram-positive bacteria that cleave N-terminal peptides prior to substrate secretion [4]. These data, together with the presence of a predicted N-terminal signal sequence in Ax21, suggest that Ax21 is cleaved by the RaxB transporter prior to secretion. raxST, raxP and raxQ encode enzymes involved in sulfation
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  This indicates AX21 is synthesized without a plant
 +
</p>         
 +
 
 +
                <br>
 +
             
 +
                <b> 2) Design </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Benchmark : http://www.linocoms.co.kr/index.htm
 +
</p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;need to use ‘Flash’ program
 +
                </p>
 +
               
 +
                <br>
 +
             
 +
                <b> 3) CCP: report due on 24th (logic gate and DIY) </b>
 +
            </dd>
 +
 
 +
            <dt>
 +
<b> C. August 22, 2012 </b>
 +
</dt>
 +
            <br>
 +
            <p style="padding-left:30px;">We discussed about our wiki page design, content, uniform design, and part allocation.</p>
 +
            <dd>
 +
<b> 1) iGEM participation fee </b>
 +
                <br>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Regional Jamboree registration : 275 USD
 +
</p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Airfare : 40~50 KRW
 +
                </p>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  Hotel reservation : iGEM will propose several hotels in a discount charge
 +
                </p>         
 +
 
 +
                <br>
 +
             
 +
                <b> 2) assigned part </b>
 +
                <p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sanghoon Han : CCP report, video making, researching logic gate background & design, modeling, Note-book, protocol production
 +
</p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Jihoon Jung : CCP report, video making, uniform order(later)
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Kyeongwoo Jang: CCP report , video making, logic gate background & design
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Jeongmin Lee: Xanthomonas Abstract & background
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hyunkee Kim : Xanthomonas Abstract & background, Note-book, Safety question
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Haerim Song: mainframe design, poster design(later)
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Byeongnam Min: modeling
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Jihyong Nam: protocol
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Kyeongjin Kim: get sponsor
 +
                </p>
 +
                <p>
 +
                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Wonwook Lee : get sponsor
 +
                </p>
 +
               
 +
                <br>
 +
             
 +
                <b> 3) Please update your info in English by next Wednesday </b>
 +
            </dd>
     </div>
     </div>
   </div>
   </div>

Revision as of 09:03, 26 September 2012

Notebook : August

A. August, 1, 2012

We have discussed about how to dectect and kill 'Xanthomonas oryzae’


1) Idea development
  Haerim Song

     raxR/H is target for raxSTAB.

     Sulfur plays an important role in activity of AX21; it won’t work without sulfur

     overexpression of raxST(sulfur attachment to AX21), RaxR/Q(transformation of PAPS into ATP) is possible in E.coli

  Advisor’s advice

      test any promoter which binds to raxR/H

      is it possible for Xanthomonas to produce AX21 without plant receptor?

      (Professor’s comment) we can run a test using E/coli which has plant receptor

      Method for detecting AX21 production?

      (Professor’s comment) use mass spectrometry or put florescence after ax21 gene then cut with restriction enzyme

  Jihoon Jung

     Find A

  Kyeongwoo Jang’s opinion

     find system which utilizes logic gate in natural world


2) Next meeting

     (1) research rax operon

      How to detect Ax21 : HyunKee Kim

      Research raxR/H paper : Byeongnam Min

      Research Xanthomonas : Jeongmin

      Activity of the substance only with raxR/H: Haerim Song

     (2) team

      Logic gate: Jihoon Jung, Kyeongwoo Jang

      Science camp presentation: Haerim Song

      Wiki update: Byeongnam Min, Kyeongwoo Jang, Sanghoon Han

      Notebook translation: HyunKee Kim

      Study Modeling: Sanghoon Han, Byeongnam Min

      Design team: Jeongmin Lee, Kyeongjin Kim, Jihyong Nam, Haerim Song




B. August 8, 2012

We have discussed about how to dectect and kill 'Xanthomonas oryzae.’ Solidifying the idea and circuit

1) Idea development

      raxR, raxH can be detected using His tag; however, experiments using cloning technique don’t use this.

      No indication of functional opetation only with raxR, raxH

  Haerim Song

      raxH without transmembrane segment was autophosphorylation, but no raxR transphosphrylation.

      raxH H222 and RaxR D51 is responsible for phosphorylation.

  Lab team

      acquisition of PCEL, raxRH promoter, mRFP using PCR

      cloning is expected to be held this week

      raxR/H is constitutive, so use other promoter


2) Team placement and H.W

     logic gate: find A: Sanghoon Han, Jihoon Jung, Kyeongwoo Jang

     Ax21 production: Wonwook Lee, JungMin, Kyeongjin, Haerim Song, Byeongnam Min, Hyunkee Kim

     Brochure: Jeongmin Lee, Kyeongjin Kim, Jihyong Nam, Haerim Song

     Science camp presentation: Haerim Song

     Wiki update: Nam, Byeongnam Min, Kyeongwoo Jang, Sanghoon Han

     Notebook translation: HyunKee Kim

     Study Modeling: Sanghoon Han, Byeongnam Min

     Design team: Jeongmin Lee, Kyeongjin Kim, Jihyong Nam, Haerim Song

     CCP: Sanghoon Han

     KAIST Contact; Byeongnam Min

     Team attire: Jihoon Jung

     upload at least one copy of design to the homepage (mandatory)




C. August 15, 2012

We have discussed about how to dectect and kill 'Xanthomonas oryzae.’ Solidifying the idea and circuit

Idea development
  Kyeongwoo Jang: logic gate biosensing

      researched logic gate used by organism to detect certain chemical

      British Columbia University already did similar project; it was about concentration dependent color changing bacteria.

      Logic gate using single step is more efficient than using several input and output steps

  Sanghoon Han: finding ‘a’ chemical

      DSF(diffusible signaling factor)

  Haerim Song: bacterial leaf blight

      had presentation about iGEM during ‘Lifescience camp’

      in order to prevent bacterial leaf blight, chemical-pesticide was given. However, it was proven to be ineffective.

      Bacterial leaf blight resistant plant was developed but, later sub-population eliminated effect of ‘gene R.’

  Wonwook Lee: sponsor

      LG lifescience, Celltrion, Rural development administration, cosmogenetech: yet positive reply, he will continue to contact.

  Sanghoon Han

      Small Protein-Mediated Quorum Sensing in a Gram- Negative Bacterium (PMID : 22174954) To elucidate this function, we previously isolated and characterized eight genes required for Ax21 activity (rax genes). raxA, raxB and raxC encode components of a predicted type I secretion system (TOSS). Ax21requires this RaxABC TOSS for activity and secretion [3,4]. The RaxB protein carries two highly conserved N terminal proteolytic subdomains characteristic of transporters in Gram-positive bacteria that cleave N-terminal peptides prior to substrate secretion [4]. These data, together with the presence of a predicted N-terminal signal sequence in Ax21, suggest that Ax21 is cleaved by the RaxB transporter prior to secretion. raxST, raxP and raxQ encode enzymes involved in sulfation

      This indicates AX21 is synthesized without a plant


2) Design

     Benchmark : http://www.linocoms.co.kr/index.htm

     need to use ‘Flash’ program


3) CCP: report due on 24th (logic gate and DIY)
C. August 22, 2012

We discussed about our wiki page design, content, uniform design, and part allocation.

1) iGEM participation fee

      Regional Jamboree registration : 275 USD

      Airfare : 40~50 KRW

      Hotel reservation : iGEM will propose several hotels in a discount charge


2) assigned part

     Sanghoon Han : CCP report, video making, researching logic gate background & design, modeling, Note-book, protocol production

     Jihoon Jung : CCP report, video making, uniform order(later)

     Kyeongwoo Jang: CCP report , video making, logic gate background & design

     Jeongmin Lee: Xanthomonas Abstract & background

     Hyunkee Kim : Xanthomonas Abstract & background, Note-book, Safety question

     Haerim Song: mainframe design, poster design(later)

     Byeongnam Min: modeling

     Jihyong Nam: protocol

     Kyeongjin Kim: get sponsor

     Wonwook Lee : get sponsor


3) Please update your info in English by next Wednesday

Retrieved from "http://2012.igem.org/Team:Korea_U_Seoul/Notebook/Aug"