Team:Nagahama project

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<td width="162px" align="center" onMouseOver="this.bgColor='#FEE5AD'" onMouseOut="this.bgColor='#A1DBB2'" bgColor=#A1DBB2>  
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<a href="https://2014.igem.org/Team:Nagahama_parta" style="text-decoration:none;color:#1C140D">
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<a href="https://2014.igem.org/Team:Nagahama_Parts" style="text-decoration:none;color:#1C140D">
PARTS
PARTS
</a>
</a>
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<td width="162px" align="center" onMouseOver="this.bgColor='#FEE5AD'" onMouseOut="this.bgColor='#A1DBB2'" bgColor=#A1DBB2>   
<td width="162px" align="center" onMouseOver="this.bgColor='#FEE5AD'" onMouseOut="this.bgColor='#A1DBB2'" bgColor=#A1DBB2>   
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<a href="https://2014.igem.org/Team:Nagahama_H.P." style="text-decoration:none;color:#1C140D">
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<a href="https://2014.igem.org/Team:Nagahama_Policy_&_Practice" style="text-decoration:none;color:#1C140D">
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H.P.
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Policy & Practice
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<!-- navigation for project page-->
<!-- navigation for project page-->
 +
=Abstract=
 +
Cadmium is the heavy metal which is very harmful to a creature. The pollution of cadmium brings a serious problem for natural environments. It is very important to collect this efficiently. We tried to solve this problem with recombination ''Escherichia coli'' which our team made in this year.
 +
We decided to make two kinds of recombination ''Escherichia coli''. One traps cadmium on the outer membrane. It produces fusion protein with the heavy metal binding protein and outer membrane protein and it traps cadmium. Another collects other ''Escherichia coli''. It produces aspartic acid of positive chemotaxis factor to ''Escherichia coli''.
 +
Is it necessary to distribute it to two kinds of why? We suggest the following theory for this question.
 +
 +
<font size=3>"One ''E. coli'' has One function theory"</font>
 +
 +
There is the possibility that the following demerit occurs when I summarize two functions in one.The first is that the ability of the ''Escherichia coli'' situation decreases by producing multiple protein at a time.The second is that subsequent editing becomes difficult when we complete a  gene cassette once. The merit in case of one kind is next.
 +
At first it is that a function becomes very simple.We can make ''Escherichia coli'' which was specialized in it by a function becoming simple. The number of Escherichia coli just leads to the level of the function, analysis becomes easy.
=Our Project=
=Our Project=
-
We make various systems by interaction of cell-cell communication. We keep one function in one E.coli.  This means to make simple plasmid. The following is one example. We’d like to collect cadmium in water. Therefore we use two kinds of E.coli. One catches Cadmium. The other attracts all E.coli by using chemoattractant. Catches E.coli displays metallothionein a protein combines a heavy metal. Cadmium is a kind of heavy metal. The other synthesizes aspartic acid (Asp) one kind of chemoattractant. All E.coli gather in the E.coli synthesizes Asp. To use these E.coli, finally cadmium will be caught.
+
We make various systems by cell-cell communication. We keep one function in one ''E. coli''.  This means to make simple plasmid. The following is one example. We’d like to collect cadmium in water. Therefore we use two kinds of E.coli. One catches Cadmium. The other attracts all ''E.coli'' by using chemoattractant. Catches ''E.coli'' displays metallothionein a protein combines a heavy metal. Cadmium is a kind of heavy metal. The other synthesizes aspartic acid (Asp) one kind of chemoattractant. All E.coli gather in the ''E. coli'' synthesizes Asp. To use these E.coli, finally cadmium will be caught.
 +
 
 +
 
 +
[[File:One_or_two.png|700px|thumb|center|When we collect cadmium in the water, if use only catching ''E. coli''(Blue),they go away from cadmium. Because they have negative chemotaxisin contrast with cadmium. Consequently, they don't catch cadmium very much.[fig1-A] In constract, if we use two kind
 +
of recombinant ''Escherichia coli''(''E. coli'');gathering ''E. coli''(Red) and catching ''E. coli''(Blue), we can build the creature system which collects cadmium while sitting at cadmium by using two kinds of ''Escherichia coli''.[fig1-B]
 +
 
 +
 
 +
It is this theoretical merit that we can suggest two kinds of possibility that meeting condition and collection quantity of ''Escherichia coli'' are changed by changing the ratio of ''Escherichia coli'' in addition to cadmium solution.]]
 +
 
 +
 
 +
 
 +
[[File:AspA_last.png|700px|thumb|center|
 +
We constracted plasmid that synthesize aspartic acid in the presence of cadmium.
 +
Part's namber are BBa_K896008(promoter),(RBS),BBa_C0083(Protein coding sequences),(Double terminator).
 +
 
 +
BBa_K896008(zinTp) is a promoter inducing gene expression only in existence of cadmium.
 +
AspA mainly catalyzes the deamination of L-aspartic acid to produce fumarate and ammonium ion.
 +
As a result of having cultured it in the nutrient medium including the substrate, we confirmed synthesis of aspartic acid by thin layer chromatography.
 +
]]
 +
 
 +
 
 +
 
-
[[File:One_or_two.png|300px]]
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[[File:Ag43 device X.png|700px|thumb|center|
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<br>When collect cadmium in the water, if use only catching E.coli,they go away from cadmium. Because they have negative chemotaxisin contrast with cadmium. Consequently  they</br>
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We are constracting this plasmid now. Recombination Escherichia coli having this plasmid becomes the thing with the function to trap cadmium on outer membrane if construction of this plasmid is completed. It is fusion protein with metallothionine(MT);SmtA and adventitia protein;Ag43. The genetic origin of SmtA is Synechococcus PCC. 7942.
 +
]]
=Modeling=
=Modeling=
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[https://2014.igem.org/Team:UT-Tokyo UT-Tokyo].They readily compiled with our requests. Their model is ideal.We really appreciate their jobs We wish a friendly relationship with UT-Tokyo.Thank you so much!! The detail of their jobs are lists below!!
[https://2014.igem.org/Team:UT-Tokyo UT-Tokyo].They readily compiled with our requests. Their model is ideal.We really appreciate their jobs We wish a friendly relationship with UT-Tokyo.Thank you so much!! The detail of their jobs are lists below!!
<br>
<br>
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[[File:modeling-f1.png|thumb|Fig.1<br> means random walk of E.coli on swarming plate.The vertical axis means arbitrary unit.The horizontal axis means spatial axis.|none]]
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[[File:random_photo.png|700px|thumb|center|Fig.1<br> This is random walk of ''Escherichia coli'' on "swarming plate".The vertical axis means arbitrary unit.The horizontal axis means to spatial axis. We culture ''E.coli'' on "swarming plate". "swarming plate", a solid culture plate containing lower concentration of agar, on that plate,'' E. coli'' can swim.|none]]
<br>
<br>
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[[File:検証_正の走化性.png|thumb|Fig.2<br> means positive chemotaxis by E.coli.Assuming that distill aspartate center of swarming plate. E.coli gather to distilled point. |none]].
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[[File:result_photo_Asp.png|700px|thumb|center|Fig.2<br> This is positive chemotaxis by ''E.coli''.Assuming that spoted aspartic acid center of "swarming plate". '' E.coli'' has positivechemotaxis for aspartic acid. ''E.coli'' gather to spoted point.|none]].
<br>
<br>
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[[File:検証_負の走化性.png|thumb|Fig.3<br> means negativeChemotaxis by ''E.coli''.Assuming that distill cadmium center of swarming plate. ''E.coli'' run away from distilled point.|none]]
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[[File:result_photo_cadmium.png|700px|thumb|center|Fig.3<br> This is negativechemotaxis by ''E.coli''.Assuming that spoted cadmium center of "swarming plate". ''E.coli'' has negaitivechemotaxis for cadomium. ''E.coli'' run away from spoted point.|none]]
<br>
<br>
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[[File:リザルト.png|thumb|Fig.4<br> means our project. Assuming that distill cadmium (spatial axis 500). ''E.coli'' run away from distilled point (spatial axis 350~450 and 550~650). At that time ''E.coli''`s cadmium promoter is operate. Asparatate is produced by ''E.coli'|none]].
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[[File:last_result.png|700px|thumb|center|Fig.4<br> This model describes our project. Assuming cadmium was spotted on center of swarming plate (spatial axis 500). ''E.coli'' run away from spotted point (spatial axis 350~450 and 550~650). Then cadmium promoter of transgenic ''E.coli'' operates. So aspartase produced (spatial axis 350~450 and 550~650). |none]].
<br>
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[[File:東大集合写真.jpg|400px|thumb|Thank you very much!!|none]]
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[[File:members_photo.jpg|700px|thumb|center|Members of UT-Tokyo|none]]
=Method=
=Method=
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'''Bold text'''
 
==Medium==
==Medium==
-
===Trypton Broth===
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===Trypton broth===
Trypton                10g/L
Trypton                10g/L
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===Chemotaxis medium===
===Chemotaxis medium===
 +
 +
Potassium phosphate buffer (pH 7.0), 10⁻²M
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potassium EDTA, 10⁻⁴M
 +
 +
L-methionine 10⁻⁶M
===Synthesis medium===
===Synthesis medium===
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H₂O            1L
H₂O            1L
-
===M9 swarming Agar===
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===M9 swarming agar===
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20 % (v/v) 5×M9 salt
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M9 salt
1.25 % (v/v) glycerol
1.25 % (v/v) glycerol
-
0.3 % (v/v) agar
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0.3 % (w/v) agar
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0.1 % (v/v) 0.136M CaCl2 solution (after autoclave)
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0.1 % (w/v) CaCl₂ solution (after autoclave)
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0.1 % (v/v) 1M MgSo4 solution (after autoclave)
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0.1 % (w/v) MgSO₄ solution (after autoclave)
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0.03 % (w/v) 1mM thiamine (after autoclave)
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0.03 % (w/v) thiamine (after autoclave)
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stir until dissolved
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===5 × M9 stock solution===
-
===5×M9 stock solution===
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6.4 % (w/v) Na<SUB>2</SUB>HPO<SUB>4</SUB>
 +
 
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1.5 % (w/v) KH<SUB>2</SUB>PO<SUB>4</SUB>
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0.25 % (w/v) NaCl
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0.5 % (w/v) NH<SUB>4</SUB>Cl
==Aspartate synthesis==
==Aspartate synthesis==
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<br>
<br>
==SDS PAGE==
==SDS PAGE==
 +
・E. coli JM109 containing CdP-R.B.S-AspA-d.Ter (BBa_K1342001) or normal E. coli was precultured at 37 ℃ for 24 hr with shaking.
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 +
・The culture (OD600 0.6-1.0) was used for induction of protein expression by isopropylthio-β-D-galactoside 1mM and Cd2+ 100µM soln. 37℃、o hr, 0.5 hr, 2hr, 6 hr, 24hr.
 +
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・200 μl of the induced culture was centrifuge at 13,000 rpm for 1 min at 4 ℃.
 +
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・The supernatant was discarded and the pellet was stored at -20 ℃.
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・The stored pellet was resuspended in 1 x sample buffer (100 μL), followed by heating at 98 °C for 5 min.
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・The lysate was centrifuged at 13,000 rpm for 10 min. at 4℃.
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・The supernatant was collected into a new microcentrifuge tube.
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・20 μL of the supernatant was analyzed by SDS-PAGE.
 +
 +
==TLC assay==
<br>
<br>
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・Preculture E.coli holding a plasmid containing a target gene or nomal E.coli.
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 +
We analyzed L-aspartate by thin-layer chromatography (TLC). The equal volume of the supernatant of synthesis medium was added with 7 mg/mL 5-Dimethylamino naphthalene-1-sulfonyl Chloride (dissolved in acetone) and was incubated for more than 30 min at room temperature. Two microliters of the reactant was spotted on a TLC silica plate, and was developed in a mixture of ethyl acetate, pyridine, water, and acetic acid(162:21:11:6 v/v). It is observed by UV irradiation (365nm).
 +
 
 +
==Chemotaxis Assay==
 +
===Introduction===
 +
 
 +
Chemotaxis of ''E. coli'' against aspartic acis was assayed by two methods. One was "swarming assay", and the other was capillary assay. In "swarming assay", we have used "sawarming plate", a solid culture plate containing lower concentration of agar, on that plate,'' E. coli'' can swim. We have used capillary  containing aspartic acid. The capillary was set in chemotaxis medium containing motile ''E. coli''. The number of ''E. coli'' attracted to aspartic acid in capillary was determined  by colony formation on LB plate.
 +
 
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===Swarming Assay===
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We assayed chemotaxis of ''E. coli'' against cadmium and aspartic acid on soft agar, containing M9 synthetic medium, on that plate ''E. coli'' can swim.<br>
 +
 
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Protocol<br>
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1.''E. coli'' JM109 was cultured at 30℃ for 12 hours with shaking (50 rpm).
 +
 
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2. Aliquot of the culture was spotted on the center of agar plate.
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3. 10 mM L-aspartic acid (40 μl) or 100 mM cadmium chloride (4 μl) was spotted on 25 mm distant from the center of the agar plate.
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4. The plate was standed for 5 min at RT.
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5. The plate was incubated at 30℃.
 +
 
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===Capillary Assay===
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Object
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Assay the chemotaxis of ''E. coli'' against aspartic acid with capillary.
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Plotocol
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1. Preculture ''E. coli'' in tripton broth at 30 ℃ for 12  hr with shaking (50 rpm).
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2. Check the motility of ''E. coli'' by microscope (× 800).
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3. Dilute the ''E. coli'' culture (200 μL) with tripton broth (20 mL).
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4. Incubate at 30 ℃ with shaking (50 rpm) until log phase (OD600 = ~ 0.2).
 +
 
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5. Aliquote (500 μL) of the culture was centrifuged at 25℃ for 10 min at 3400 x G.
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6. Dicard the supernatant.
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7. Resuspend the pellets gently with wash medium (50 μL).
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8. Repeat 5~7 step.
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9. Resuspend the pellets gently with chemotaxis medium (500 μL).
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10. Check the motility of ''E. coli'' by microscope (× 800).
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11. Aliquote (100 μL) of ''E. coli'' suspended in chemotaxis medium was set into chamber apparatus.
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12. Prepare aspartic acid capillary and negative control capillary that contain 1 μL of chemotaxis medium with and without 10 mM aspartic acid, respectively.
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13. Both capillaries (asparate capillary and negative control capillary) were set into chamber apparatus.
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14. Incubate at 30 ℃ for 90 mim.
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15. The chemotaxis medium in capillary was collected in 100 μL of fresh chemotaxis medium.
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16. All chemotaxis medium containing attracted ''E. coli'' was plated on LB plate.
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17. Incubate at 37 ℃ for 12 hr.
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18. Count the number of colony.
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=Result & Discussion =
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===TLC Assay===
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[[File:TLC_20140929_.jpg|200px|thumb|Analysis of aspartic acid synthesized by <i>E. coli</i> JM109/[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1342001 BBa_K1342001] by thin-layer chromatography (TLC) Lane: 1, 2 no addition into culture (diluted 1:50 and 1:100 by synthesis medium, respectively) 3, additon of cadmium ion (250μM) 4, 5, 6 (diluted 1:50, 1:100 and 1:200 by synthesis medium, respectively)|left]]
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[[File:TLC_intensity_of_the_band.jpg|400px|thumb|center|
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fig.2
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・Measure OD600 0.6-1.0
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Estimation of aspartic acid content in spot
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Each intensity of spots indicating the content of aspartic acid, was estimated by Image J.
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.]]
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<br>
<br>
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・the expression of fusion protein by isopropylthio-β-D-galactoside (IPTG) and Cd2+ soln.
 
<br>
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・Transfer a sample a 200 µl in a microcentrifuge tube
 
<br>
<br>
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・Centrifuge at 13,000rpm for a minute at 4℃
 
<br>
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・Discard supernatant quantitative
 
<br>
<br>
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・Store pellet at -20 °C
 
<br>
<br>
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・Thaw pellet and resupend in Sample Buffer (100 µL 1xSample Buffer per samples)
 
<br>
<br>
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・Heat for 5 minutes at 98 °C
 
<br>
<br>
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・Centrifuge at 13,000rpm for 10 minutes at 4℃
 
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・Transfer supernatant to a new microcentrifuge tube
 
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・Analyze samples by SDS-PAGE.(Use 20 µL per samples)
 
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<br>
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==TLC assay==
 
<br>
<br>
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We analyzed L-aspartate by thin-layer chromatography (TLC). The same amount added Supernatant of synthesis medium to 7mg/mL 5-Dimethylamino naphthalene-1-sulfonyl Chloride (in Acetone) and incubated more than 30min. Two microliters of the sample was placed onto a TLC silica plate, and developed in a mixture of Ethyl acetate, pyridine, water, and acetic acid(162:21:11:6 V/V).
 
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==Chemotaxis Assay==
 
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===Introduction===
 
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Chemotaxis by  ''E.coli'' was assay by some methods. We assay the chemotaxis of ''E.coli'' against aspartate using two methods. One was swarming assay. We have used sawaming plate. swarming plate is medium that contained a low concentration by agar.'' E.coli'' can swim to aspartate on the swarming plate. The other was capillary assay. We have used capillary that including aspartate. We set capillary in chemotaxis medium including motile ''E.coli'' We have determined the number of ''E.coli'' attracted to capillary by colony formation on LB plate.
 
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===Swarmming Assay===
 
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===Capillary Assay===
 
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Object<br>
 
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To assay chemotaxis by ''E.coli'' against aspartarte using capillary.<br>
 
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Plotocol<br>
 
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1. Preculture ''E.coli'' with tripton broth at 30℃ 12 hr 50 rpm<br>
 
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2. Check motility under the microscope(×800).<br>
 
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3. Diluting the ''E.coli'' culture 100 times. (tripton broth:E.coli culture=20mL : 200μL)<br>
 
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4. Incubate 50rpm 30℃ until log phase (OD600 = ~ 0.2)<br>
 
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5. 500㎕ into micro tubes.<br>
 
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6. Centrifuge (25℃ 10min in 3400G)<br>
 
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7. Dicand the supernatant.<br>
 
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8. Add wash medium(50μL)<br>
 
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9. Resuspending pellets gently.<br>
 
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10. Do 5~9 step repeat.<br>
 
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11. Add chemotaxis medium(500μL)<br>
 
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12. Resuspending pellets gently.<br>
 
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13. Check motility under the microscope(×800).<br>
 
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14. ''E.coli'' chemotaxis medium into chamber apparatus.(100μL)<br>
 
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15. Prepare the positive and negative control capillary.(1μL of 10mM aspartate chemotaxis medium and chemotaxis medium into capillary)<br>
 
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16. Two capillary into chamber preparation.<br>
 
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17. 90mim 30℃ incubation.<br>
 
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18. Dilute the chemotaxis buffer in capillary`s liquid 100 times.<br>
 
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19. Prating to LBplate.<br>
 
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20. 37℃ 12h incubation.<br>
 
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21. Counting the colony.<br>
 
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=Result & Discussion =
 
-
===TLC Assay===
 
-
[[File:TLC_20140929_.jpg|200px|thumb|Analysis of aspartate from strain E.coli K-12/BBa_K1342001 by thin-layer chromatography (TLC) Lane: 1, not addition cadmium to previous culture of synthesis medium (diluted 1:50 by synthesis medium) 2, (diluted 1:100 by synthesis medium) 3, add cadmium (250μM) 4, (diluted 1:50 by synthesis medium) 5, (diluted 1:100 by synthesis medium) 6, (diluted 1:200 by synthesis medium)|none]]
 
-
<br><br>
 
===SDS PAGE===
===SDS PAGE===
 +
[[File:PAGE1.jpg|500px|thumb|Analyzed aspartase by ''E. coli'' JM109 and ''E. coli'' JM109/[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1342001 BBa_K1342001] by SDS-PAGE ,37℃ for 0,6 hr
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Lane:1,10 Protein Marker(Precision Plus Protein Standards (BIO-RAD))
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Lane:2,3 ''E. coli'' JM109
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Lane:4,5 ''E. coli'' JM109/BBa_K1342001
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Lane:6,7 ''E. coli'' JM109/BBa_K1342001 (Additon of cadmium ion 100μM)
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Lane:8,9 ''E. coli'' JM109/BBa_K1342001 (Additon of cadmium ion 100μM and IPTG 1mM)
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respectively.
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OD600=0.74 CdCl2 100μM/IPTG 1mM
 +
AspA has 1482bp. It is about 54kDa.|left]]
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<br>
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Aspartase synthesize was not detect by CBB stain.
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[[File:PAGE2.jpg]]
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===Swarming Assay===
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1. marker 2. 0hr 3. 0.5hr 4. 2hr 5. 6hr 6. 24hr 7. Marker
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-
marker:Precision Plus Protein Standards (BIO-RAD)
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 +
[[File:Asp_swamming.png|10000px|thumb|Fig.1 ''E. coli'' swarming to aspartic acid <br> L: aspartic acid (10 mM, 40 μl) R: ddH<SUB>2</SUB>O (40 μl)<br>Incubation: 108 hours <br> temperature: 30 ℃ <br>''E. coli'' cultured was spotted on the center of agar plate, and chemotaxis was spotted on 25 mm distant from the center.<br><br>             
 +
The swarming circle of aspartic acid (L) was larger than that of ddH<SUB>2</SUB>O (R), and the swarming area around aspartate acid (L) was more larger than that of ddH<SUB>2</SUB>O (R), suggesting that E. coli swarming to aspartate acid.<br>
 +
This experiment indicate that ''E. coli'' may have positive chemotaxis for aspartic acid.
 +
|left]]
-
OD600=0.74
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[[File:Cd_swamming.png|8000px|thumb|Fig.2 ''E. coli'' swarming to cadmium <br> L: cadmium(100 mM, 4 μl) R: ddH<SUB>2</SUB>O (40 μl)<br>Incubation: 110 hours <br> temperature: 30 ℃ <br> ''E. coli'' cultured was spotted on the center of agar plate, and chemotaxis was spotted on 25 mm distant from the center. <br><br>
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CdCl2 100μM/IPTG 1mM
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The swarming circle of cadmium (L) was smaller than that of ddH<SUB>2</SUB>O (R), and the swarming area around cadmium (L) was more smaller than that of ddH<SUB>2</SUB>O (R), suggesting that ''E.'' ''coli'' hate cadmium.<br>This experiment indicate that ''E. coli'' may have negative chemotaxis for cadmium.
 +
|none]]
 +
===Capillary Assay===
-
[[File:PAGE3-1.jpg]] <br>
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Result
-
[[File:PAGE4.jpg]]
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-
===Swarming Assay===
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[[File:result_photo_1.png|400px|thumb|Fig.1 Left : Aspartic acid, Right : control<br>There were 13 colonies on Asp plate. One other plate has 1326 colonies.|none]]
-
===Capillary Assay===
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Discussion
-
This assay didn`t check chemotaxis by ''E.coli''. We did eleven assays. But all results weren`t authenticity.
+
At this method. We didn't assay aspartic acid cehmotaxis of ''E.coli''. We did eleven assays.In this assay, ''E.coli'' formation will appear on aspartic acid plate more than conrol plate. But at result of Fig.1,'' E.coli'' colonies appeared control plate more than aspartic acid plate. And all result were not authenticity.
-
 
+
There are some problems. One is heat of bacteria spreader. At plating moments. I may burn  'E.coli'' to death. Next is diameter of capillary. I made capillary by myself.
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[[File:Asp_(2).jpg|300px|thumb|Fig.1-A was result that plating Asp contained capillary. There were 50 colonies.|left]]
+
There were various sizes of capillary. I used their capillary. So colonies formation were ununiformity. Last is the number of times of assays. In our source journal (Reference No.7), they assayed more then us.
-
[[File:Control_(2).jpg|250px|thumb|Fig.1-B was result that plating control contained capillary. There were 22 colonies.|center]]
+
=Future work=
=Future work=
 +
We performed a project to collect cadmium using chemotaxis of Escherichia coli this year. But the second plasmid is still building it. We want to perform an experiment such as fig.1-B with two kinds of Escherichia coli as soon as construction is completed. In addition, the chemotactic instruction and control that we used have the applied nature to other projects very much. We want to create the new project using chemotaxis of Escherichia coli.
=Reference=
=Reference=
 +
 +
[1][http://www.ncbi.nlm.nih.gov/pubmed/12480884 Ferianc, P, et al, Regulation of yodA encoding a novel cadmium-induced protein in Escherichia coli, Microbiology, vol.148, 3801–3811, (2002)]<br>
 +
[2][https://2012.igem.org/Team:Goettingen/Notebook/Results iGEM Goettingen, Homing Coli, https://2012.igem.org/Team:Goettingen/Notebook/Results, (2012)]<br>
 +
[3][http://www.ccbi.cam.ac.uk/iGEM2006/index.php/Protocols#Autoclaving_stock_solutions_or_glassware_.28sterilisation.29  iGEM University Of Cambridge, Making swimming Agar, http://www.ccbi.cam.ac.uk/iGEM2006/index.php/Protocols#Autoclaving_stock_solutions_or_glassware_.28sterilisation.29, (2006)]<br>
 +
[4][https://2011.igem.org/Team:UT-Tokyo/Data/Method iGEM UT-Tokyo, L-aspartate chemotaxis assay, https://2011.igem.org/Team:UT-Tokyo/Data/Method, (2011)]<br>
 +
[5][http://ecocyc.org/ Keseler et al, EcoCyc, http://ecocyc.org/, (2013)]<br>
 +
[6][http://www.ncbi.nlm.nih.gov/pubmed/17650676 Chmiel, A, Selection and activation of Escherichia coli strains for L-aspartic acid biosynthesis, Polish J. Microbiol, Vol.56, 71-76, (2007)]<br>
 +
[7][http://www.ncbi.nlm.nih.gov/pubmed/4632978 ADLER, J, A method for measuring chemotaxis and use of the method to determine optimum conditions for chemotaxis by Escherichia coli, Polish J. General Microbiol, Vol.74, 77-91, (1973)]<br>
 +
[8][http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ Sternberg, C, et al, New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria, Polish J. Microbiol, Vol.64, 2240–2246, (1998)]<br>
 +
[9][https://2010.igem.org/Team:UPO-Sevilla/Project/Assays iGEM UPO-Sevilla, Bacterial crowding, https://2010.igem.org/Team:UPO-Sevilla/Project/Assays, (2010)]

Latest revision as of 02:07, 18 October 2014


Contents

Abstract

Cadmium is the heavy metal which is very harmful to a creature. The pollution of cadmium brings a serious problem for natural environments. It is very important to collect this efficiently. We tried to solve this problem with recombination Escherichia coli which our team made in this year. We decided to make two kinds of recombination Escherichia coli. One traps cadmium on the outer membrane. It produces fusion protein with the heavy metal binding protein and outer membrane protein and it traps cadmium. Another collects other Escherichia coli. It produces aspartic acid of positive chemotaxis factor to Escherichia coli.

Is it necessary to distribute it to two kinds of why? We suggest the following theory for this question.

"One E. coli has One function theory"

There is the possibility that the following demerit occurs when I summarize two functions in one.The first is that the ability of the Escherichia coli situation decreases by producing multiple protein at a time.The second is that subsequent editing becomes difficult when we complete a gene cassette once. The merit in case of one kind is next. At first it is that a function becomes very simple.We can make Escherichia coli which was specialized in it by a function becoming simple. The number of Escherichia coli just leads to the level of the function, analysis becomes easy.


Our Project

We make various systems by cell-cell communication. We keep one function in one E. coli. This means to make simple plasmid. The following is one example. We’d like to collect cadmium in water. Therefore we use two kinds of E.coli. One catches Cadmium. The other attracts all E.coli by using chemoattractant. Catches E.coli displays metallothionein a protein combines a heavy metal. Cadmium is a kind of heavy metal. The other synthesizes aspartic acid (Asp) one kind of chemoattractant. All E.coli gather in the E. coli synthesizes Asp. To use these E.coli, finally cadmium will be caught.


When we collect cadmium in the water, if use only catching E. coli(Blue),they go away from cadmium. Because they have negative chemotaxisin contrast with cadmium. Consequently, they don't catch cadmium very much.[fig1-A] In constract, if we use two kind of recombinant Escherichia coli(E. coli);gathering E. coli(Red) and catching E. coli(Blue), we can build the creature system which collects cadmium while sitting at cadmium by using two kinds of Escherichia coli.[fig1-B] It is this theoretical merit that we can suggest two kinds of possibility that meeting condition and collection quantity of Escherichia coli are changed by changing the ratio of Escherichia coli in addition to cadmium solution.


We constracted plasmid that synthesize aspartic acid in the presence of cadmium. Part's namber are BBa_K896008(promoter),(RBS),BBa_C0083(Protein coding sequences),(Double terminator). BBa_K896008(zinTp) is a promoter inducing gene expression only in existence of cadmium. AspA mainly catalyzes the deamination of L-aspartic acid to produce fumarate and ammonium ion. As a result of having cultured it in the nutrient medium including the substrate, we confirmed synthesis of aspartic acid by thin layer chromatography.



We are constracting this plasmid now. Recombination Escherichia coli having this plasmid becomes the thing with the function to trap cadmium on outer membrane if construction of this plasmid is completed. It is fusion protein with metallothionine(MT);SmtA and adventitia protein;Ag43. The genetic origin of SmtA is Synechococcus PCC. 7942.

Modeling

We consigned modeling of our project to UT-Tokyo.They readily compiled with our requests. Their model is ideal.We really appreciate their jobs We wish a friendly relationship with UT-Tokyo.Thank you so much!! The detail of their jobs are lists below!!

Fig.1
This is random walk of Escherichia coli on "swarming plate".The vertical axis means arbitrary unit.The horizontal axis means to spatial axis. We culture E.coli on "swarming plate". "swarming plate", a solid culture plate containing lower concentration of agar, on that plate, E. coli can swim.


Fig.2
This is positive chemotaxis by E.coli.Assuming that spoted aspartic acid center of "swarming plate". E.coli has positivechemotaxis for aspartic acid. E.coli gather to spoted point.
.


Fig.3
This is negativechemotaxis by E.coli.Assuming that spoted cadmium center of "swarming plate". E.coli has negaitivechemotaxis for cadomium. E.coli run away from spoted point.


Fig.4
This model describes our project. Assuming cadmium was spotted on center of swarming plate (spatial axis 500). E.coli run away from spotted point (spatial axis 350~450 and 550~650). Then cadmium promoter of transgenic E.coli operates. So aspartase produced (spatial axis 350~450 and 550~650).
.


Members of UT-Tokyo

Method

Medium

Trypton broth

Trypton 10g/L

NaCl 10g/L

H2O 1L

Wash medium

Potassium phosphate buffer (pH 7.0), 10⁻²M

MgSO₄, 10⁻³M

potassium ethylenediaminetetraacetate (EDTA), 10⁻⁴M

Chemotaxis medium

Potassium phosphate buffer (pH 7.0), 10⁻²M

potassium EDTA, 10⁻⁴M

L-methionine 10⁻⁶M

Synthesis medium

Sodium hydrogen fumarate 46g/L

Ammonium chloride 17.8g/L

Magnesium sulfate 7 hydrate 0.25g/L

H₂O 1L

Ph8.5with sodium hydrogen

LB medium

Tryptone 10g/L

Yeast extract 5g/L

NaCl 10g/L

(agar 15g/L)

H₂O 1L

2×YT medium

Tripton 16g/L

Yeast extract 10g/L

NaCl 5g/L

(agar 15g/L)

H₂O 1L

M9 swarming agar

M9 salt

1.25 % (v/v) glycerol

0.3 % (w/v) agar

0.1 % (w/v) CaCl₂ solution (after autoclave)

0.1 % (w/v) MgSO₄ solution (after autoclave)

0.03 % (w/v) thiamine (after autoclave)

5 × M9 stock solution

6.4 % (w/v) Na2HPO4

1.5 % (w/v) KH2PO4

0.25 % (w/v) NaCl

0.5 % (w/v) NH4Cl

Aspartate synthesis

E.coli K12 transformed with CdP-R.B.S-AspA-d.Ter (BBa_K1342001) previous cultured with cadmium in LB medium (250μM) in 37℃ for 12hr at 120rpm. Adjust Cell mass (OD1.0) and therefor centrifuged 4000rpm for 20 min. Cell pellets ware activated in synthesis medium in 37℃ for 2hr at 120rpm/min.

SDS PAGE

・E. coli JM109 containing CdP-R.B.S-AspA-d.Ter (BBa_K1342001) or normal E. coli was precultured at 37 ℃ for 24 hr with shaking.

・The culture (OD600 0.6-1.0) was used for induction of protein expression by isopropylthio-β-D-galactoside 1mM and Cd2+ 100µM soln. 37℃、o hr, 0.5 hr, 2hr, 6 hr, 24hr.

・200 μl of the induced culture was centrifuge at 13,000 rpm for 1 min at 4 ℃.

・The supernatant was discarded and the pellet was stored at -20 ℃.

・The stored pellet was resuspended in 1 x sample buffer (100 μL), followed by heating at 98 °C for 5 min.

・The lysate was centrifuged at 13,000 rpm for 10 min. at 4℃.

・The supernatant was collected into a new microcentrifuge tube.

・20 μL of the supernatant was analyzed by SDS-PAGE.

TLC assay


We analyzed L-aspartate by thin-layer chromatography (TLC). The equal volume of the supernatant of synthesis medium was added with 7 mg/mL 5-Dimethylamino naphthalene-1-sulfonyl Chloride (dissolved in acetone) and was incubated for more than 30 min at room temperature. Two microliters of the reactant was spotted on a TLC silica plate, and was developed in a mixture of ethyl acetate, pyridine, water, and acetic acid(162:21:11:6 v/v). It is observed by UV irradiation (365nm).

Chemotaxis Assay

Introduction

Chemotaxis of E. coli against aspartic acis was assayed by two methods. One was "swarming assay", and the other was capillary assay. In "swarming assay", we have used "sawarming plate", a solid culture plate containing lower concentration of agar, on that plate, E. coli can swim. We have used capillary containing aspartic acid. The capillary was set in chemotaxis medium containing motile E. coli. The number of E. coli attracted to aspartic acid in capillary was determined by colony formation on LB plate.

Swarming Assay

We assayed chemotaxis of E. coli against cadmium and aspartic acid on soft agar, containing M9 synthetic medium, on that plate E. coli can swim.

Protocol

1.E. coli JM109 was cultured at 30℃ for 12 hours with shaking (50 rpm).

2. Aliquot of the culture was spotted on the center of agar plate.

3. 10 mM L-aspartic acid (40 μl) or 100 mM cadmium chloride (4 μl) was spotted on 25 mm distant from the center of the agar plate.

4. The plate was standed for 5 min at RT.

5. The plate was incubated at 30℃.

Capillary Assay

Object

Assay the chemotaxis of E. coli against aspartic acid with capillary.

Plotocol

1. Preculture E. coli in tripton broth at 30 ℃ for 12 hr with shaking (50 rpm).

2. Check the motility of E. coli by microscope (× 800).

3. Dilute the E. coli culture (200 μL) with tripton broth (20 mL).

4. Incubate at 30 ℃ with shaking (50 rpm) until log phase (OD600 = ~ 0.2).

5. Aliquote (500 μL) of the culture was centrifuged at 25℃ for 10 min at 3400 x G.

6. Dicard the supernatant.

7. Resuspend the pellets gently with wash medium (50 μL).

8. Repeat 5~7 step.

9. Resuspend the pellets gently with chemotaxis medium (500 μL).

10. Check the motility of E. coli by microscope (× 800).

11. Aliquote (100 μL) of E. coli suspended in chemotaxis medium was set into chamber apparatus.

12. Prepare aspartic acid capillary and negative control capillary that contain 1 μL of chemotaxis medium with and without 10 mM aspartic acid, respectively.

13. Both capillaries (asparate capillary and negative control capillary) were set into chamber apparatus.

14. Incubate at 30 ℃ for 90 mim.

15. The chemotaxis medium in capillary was collected in 100 μL of fresh chemotaxis medium.

16. All chemotaxis medium containing attracted E. coli was plated on LB plate.

17. Incubate at 37 ℃ for 12 hr.

18. Count the number of colony.

Result & Discussion

TLC Assay

Analysis of aspartic acid synthesized by E. coli JM109/[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1342001 BBa_K1342001] by thin-layer chromatography (TLC) Lane: 1, 2 no addition into culture (diluted 1:50 and 1:100 by synthesis medium, respectively) 3, additon of cadmium ion (250μM) 4, 5, 6 (diluted 1:50, 1:100 and 1:200 by synthesis medium, respectively)
fig.2
Estimation of aspartic acid content in spot Each intensity of spots indicating the content of aspartic acid, was estimated by Image J. .















SDS PAGE

Analyzed aspartase by E. coli JM109 and E. coli JM109/[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1342001 BBa_K1342001] by SDS-PAGE ,37℃ for 0,6 hr Lane:1,10 Protein Marker(Precision Plus Protein Standards (BIO-RAD)) Lane:2,3 E. coli JM109 Lane:4,5 E. coli JM109/BBa_K1342001 Lane:6,7 E. coli JM109/BBa_K1342001 (Additon of cadmium ion 100μM) Lane:8,9 E. coli JM109/BBa_K1342001 (Additon of cadmium ion 100μM and IPTG 1mM) respectively. OD600=0.74 CdCl2 100μM/IPTG 1mM AspA has 1482bp. It is about 54kDa.



Aspartase synthesize was not detect by CBB stain.























Swarming Assay

Fig.1 E. coli swarming to aspartic acid
L: aspartic acid (10 mM, 40 μl) R: ddH2O (40 μl)
Incubation: 108 hours
temperature: 30 ℃
E. coli cultured was spotted on the center of agar plate, and chemotaxis was spotted on 25 mm distant from the center.

The swarming circle of aspartic acid (L) was larger than that of ddH2O (R), and the swarming area around aspartate acid (L) was more larger than that of ddH2O (R), suggesting that E. coli swarming to aspartate acid.
This experiment indicate that E. coli may have positive chemotaxis for aspartic acid.
Fig.2 E. coli swarming to cadmium
L: cadmium(100 mM, 4 μl) R: ddH2O (40 μl)
Incubation: 110 hours
temperature: 30 ℃
E. coli cultured was spotted on the center of agar plate, and chemotaxis was spotted on 25 mm distant from the center.

The swarming circle of cadmium (L) was smaller than that of ddH2O (R), and the swarming area around cadmium (L) was more smaller than that of ddH2O (R), suggesting that E. coli hate cadmium.
This experiment indicate that E. coli may have negative chemotaxis for cadmium.

Capillary Assay

Result

Fig.1 Left : Aspartic acid, Right : control
There were 13 colonies on Asp plate. One other plate has 1326 colonies.

Discussion

At this method. We didn't assay aspartic acid cehmotaxis of E.coli. We did eleven assays.In this assay, E.coli formation will appear on aspartic acid plate more than conrol plate. But at result of Fig.1, E.coli colonies appeared control plate more than aspartic acid plate. And all result were not authenticity. There are some problems. One is heat of bacteria spreader. At plating moments. I may burn 'E.coli to death. Next is diameter of capillary. I made capillary by myself. There were various sizes of capillary. I used their capillary. So colonies formation were ununiformity. Last is the number of times of assays. In our source journal (Reference No.7), they assayed more then us.

Future work

We performed a project to collect cadmium using chemotaxis of Escherichia coli this year. But the second plasmid is still building it. We want to perform an experiment such as fig.1-B with two kinds of Escherichia coli as soon as construction is completed. In addition, the chemotactic instruction and control that we used have the applied nature to other projects very much. We want to create the new project using chemotaxis of Escherichia coli.

Reference

[1][http://www.ncbi.nlm.nih.gov/pubmed/12480884 Ferianc, P, et al, Regulation of yodA encoding a novel cadmium-induced protein in Escherichia coli, Microbiology, vol.148, 3801–3811, (2002)]
[2]iGEM Goettingen, Homing Coli, https://2012.igem.org/Team:Goettingen/Notebook/Results, (2012)
[3][http://www.ccbi.cam.ac.uk/iGEM2006/index.php/Protocols#Autoclaving_stock_solutions_or_glassware_.28sterilisation.29 iGEM University Of Cambridge, Making swimming Agar, http://www.ccbi.cam.ac.uk/iGEM2006/index.php/Protocols#Autoclaving_stock_solutions_or_glassware_.28sterilisation.29, (2006)]
[4]iGEM UT-Tokyo, L-aspartate chemotaxis assay, https://2011.igem.org/Team:UT-Tokyo/Data/Method, (2011)
[5][http://ecocyc.org/ Keseler et al, EcoCyc, http://ecocyc.org/, (2013)]
[6][http://www.ncbi.nlm.nih.gov/pubmed/17650676 Chmiel, A, Selection and activation of Escherichia coli strains for L-aspartic acid biosynthesis, Polish J. Microbiol, Vol.56, 71-76, (2007)]
[7][http://www.ncbi.nlm.nih.gov/pubmed/4632978 ADLER, J, A method for measuring chemotaxis and use of the method to determine optimum conditions for chemotaxis by Escherichia coli, Polish J. General Microbiol, Vol.74, 77-91, (1973)]
[8][http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ Sternberg, C, et al, New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria, Polish J. Microbiol, Vol.64, 2240–2246, (1998)]
[9]iGEM UPO-Sevilla, Bacterial crowding, https://2010.igem.org/Team:UPO-Sevilla/Project/Assays, (2010)