Team:Hong Kong-CUHK/Laboratory/protocol

From 2011.igem.org

(Difference between revisions)
 
(17 intermediate revisions not shown)
Line 6: Line 6:
<div class="span-6 square">
<div class="span-6 square">
-
<a href="Team:HongKong-CUHK/Project"><img class="title-img" src="http://www.cse.cuhk.edu.hk/~zwang9/igem/img/lab.png" /></a>
+
<a href="#"><img class="title-img" src="http://www.cse.cuhk.edu.hk/~zwang9/igem/img/lab.png" /></a>
</div>
</div>
<div class="clear"></div>
<div class="clear"></div>
<div>
<div>
<ul class="nav-list" id="lab-list">
<ul class="nav-list" id="lab-list">
-
<li><a href="/Team:Hong_Kong-CUHK/Laboratory/safety">Safety</a></li>
+
<li><a href="/Team:Hong_Kong-CUHK/Notebook">Note Book</a></li>
-
<li><a href="/Team:Hong_Kong-CUHK/Notebook">log book</a></li>
+
<li><a class="selected"  href="/Team:Hong_Kong-CUHK/Laboratory/protocol">Protocol</a></li>
-
<li><a class="selected"  href="/Team:Hong_Kong-CUHK/Laboratory/protocol">protocol</a></li>
+
<li><a href="/Team:Hong_Kong-CUHK/Laboratory/collaboration" id="Collaboration">Collaboration</a></li>
<li><a href="/Team:Hong_Kong-CUHK/Laboratory/collaboration" id="Collaboration">Collaboration</a></li>
-
<li><a href="/Team:Hong_Kong-CUHK/Laboratory/biobricks" id="Biobricks">Biobricks construct</a></li>
+
<li><a href="/Team:Hong_Kong-CUHK/Laboratory/biobricks" id="Biobricks">Biobricks construction</a></li>
</ul>
</ul>
</div>
</div>
Line 23: Line 22:
<div class="span-17 last">
<div class="span-17 last">
-
<h3>Protocols Contents</h3>
+
<h2>Protocols Contents</h2><br/><br/>
<p>
<p>
1. Cloning
1. Cloning
Line 37: Line 36:
</p>
</p>
<p>
<p>
-
1.4Agarose Gel electrophoresis
+
1.4 Agarose Gel electrophoresis
</p>
</p>
<p>
<p>
Line 76: Line 75:
</p>
</p>
<p>
<p>
-
6. Measurement ofchloride concentration in bacterial lysate using fluorescent dye <em>N</em>-(ethoxycarbonylmethyl)-6-methoxyquinoliniumbromide (MQAE)
+
6. Measurement of chloride concentration in bacterial lysate using fluorescent dye <em>N</em>-(ethoxycarbonylmethyl)-6-methoxyquinoliniumbromide (MQAE)
</p>
</p>
<p>
<p>
-
7. Excitation ofbacteria to trigger the halorhopsin
+
7. Excitation of bacteria expressing halorhopsin
</p>
</p>
<p>
<p>
-
8. Controlledbacterial cell movement measurement
+
8. Measurment on controlled bacterial cell movement
</p>
</p>
<p>
<p>
Line 169: Line 168:
</p>
</p>
<p>
<p>
-
b) Primer solution (200 nM finalconcentration of each is recommended)  
+
b) Primer solution (200 nM final concentration of each is recommended)  
</p>
</p>
<p>
<p>
-
c) Template DNA solution (Total volume ofprimer and template solutions added can be 0.5-5 μl)
+
c) Template DNA solution (Total volume of primer and template solutions added can be 0.5-5 μl)
</p>
</p>
<p>
<p>
-
3. Mix contents of tubes and cover with mineral or silicone oil.Depending on the model of thermal cycler used, mineral or silicone oil may notbe necessary.  
+
3. Mix contents of tubes and cover with mineral or silicone oil. Depending on the model of thermal cycler used, mineral or silicone oil may notbe necessary.  
</p>
</p>
<p>
<p>
Line 187: Line 186:
</p>
</p>
<p>
<p>
-
<em>*Thefollowing general procedures are suggested as guidelines for use of PCRSuperMix High Fidelity. Assembly of the reactions on ice from pre-chilledcomponents is recommended. Final reaction volumes described below areapproximately 50 μl. Reaction size may be altered to suit user preferences.</em>
+
<em>*Thefollowing general procedures are suggested as guidelines for use of PCRSuperMix High Fidelity. Assembly of the reactions on ice from pre-chilledcomponents is recommended. Final reaction volumes described below is areapproximately 50 μl. Reaction size may be altered to suit user preferences.</em>
</p>
</p>
<p>
<p>
Line 193: Line 192:
</p>
</p>
<p>
<p>
-
<em>**RecommendedCycling Program </em>
+
<em>**Recommended Cycling Program </em>
</p>
</p>
<p>
<p>
-
<em>1cycle of:&nbsp; 94°C for 30 seconds(Pre-amplification denaturation) </em>
+
<em>1 cycle of:&nbsp; 94°C for 30 seconds (Pre-amplification denaturation) </em>
</p>
</p>
<p>
<p>
-
<em>30–35cycles of: </em>
+
<em>30–35 cycles of: </em>
</p>
</p>
<p>
<p>
Line 211: Line 210:
</p>
</p>
<p>
<p>
-
<em>&nbsp;Use of 68°C during extension step of PCR isstrongly recommended for fragments &gt; 5 kb in length</em>
+
<em>&nbsp;Use of 68°C during extension step of PCR is strongly recommended for fragments &gt; 5 kb in length</em>
</p>
</p>
<p>
<p>
Line 229: Line 228:
</p>
</p>
<p>
<p>
-
37.6μl Insert/Vector +ddH<sub>2</sub>O<em><sub>*</sub></em>
+
37.6μl Insert/Vector + ddH<sub>2</sub>O<em><sub>*</sub></em>
</p>
</p>
<p>
<p>
-
5μl 10X Buffer3
+
5μl 10X NEB Buffer3
</p>
</p>
<p>
<p>
Line 277: Line 276:
</p>
</p>
<p>
<p>
-
1) Add5 volumes of Buffer PB to 1 volume of the PCR sample and mix. It is not &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;necessary to remove mineral oil orkerosene.
+
1) Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix. It is not &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;necessary to remove mineral oil or kerosene.
</p>
</p>
<p>
<p>
-
2) If pHindicator I has beein added to Buffer PB, check that the color of the mixtureis yellow. If the color of themixture is orange or violet, add 10 µl of 3 M sodium acetate, pH 5.0, and mix.The color of the mixture will turn to yellow.
+
2) If pH indicator I has been added to Buffer PB, check that the color of the mixture is yellow. If the color of the mixture is orange or violet, add 10 µl of 3 M sodium acetate (pH 5.0), and mix. The color of the mixture will turn to yellow.
</p>
</p>
<p>
<p>
Line 286: Line 285:
</p>
</p>
<p>
<p>
-
4) Tobind DNA, apply the sample to the QIAquick column and centrifuge for 30–60s.
+
4) To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60s.
</p>
</p>
<p>
<p>
Line 292: Line 291:
</p>
</p>
<p>
<p>
-
6) Towash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
+
6) To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
</p>
</p>
<p>
<p>
Line 301: Line 300:
</p>
</p>
<p>
<p>
-
9) Toelute DNA, add 50 μl Buffer EB (10 mM Tris·Cl, pH 8.5) or water (pH 7.0–8.5) tothe center of the QIAquick membrane and centrifuge the column for 1 min.Alternatively, for increased DNA concentration, add 30 μl elution buffer to thecenter of the QIAquick membrane, let the column stand for 1 min, and thencentrifuge.
+
9) To elute DNA, add 50 μl Buffer EB (10 mM Tris·Cl, pH 8.5) or water (pH 7.0–8.5) to the center of the QIAquick membrane and centrifuge the column for 1 min. Alternatively, for increased DNA concentration, add 30 μl elution buffer to thecenter of the QIAquick membrane, let the column stand for 1 min, and then centrifuge.
</p>
</p>
<p>
<p>
-
10) Ifthe purified DNA is to be analyzed on a gel, add 1 volume of Loading Dye to
+
10) If the purified DNA is to be analyzed on a gel, add 1 volume of Loading Dye to
</p>
</p>
<p>
<p>
-
5volumes of purified DNA. Mix the solution by pipetting up and down before loadingthe gel.
+
5 volumes of purified DNA. Mix the solution by pipetting up and down before loading the gel.
</p>
</p>
<p>
<p>
-
IMPORTANT: Ensure that the elution buffer is dispensed directly onto theQIAquick
+
IMPORTANT: Ensure that the elution buffer is dispensed directly onto the QIAquick
</p>
</p>
<p>
<p>
-
membrane for complete elution of bound DNA. The average eluate volume is48 µl
+
membrane for complete elution of bound DNA. The average eluate volume is 48 µl
</p>
</p>
<p>
<p>
-
from 50 µlelution buffer volume, and 28 µl from 30 µl elution buffer.
+
from 50 µl elution buffer volume, and 28 µl from 30 µl elution buffer.
</p>
</p>
<p>
<p>
-
<em>*Protocol adopted fromQIAquick PCR purification kit protocol</em>
+
<em>*Protocol adopted from QIAquick PCR purification kit protocol</em>
</p>
</p>
<p>
<p>
Line 340: Line 339:
</p>
</p>
<p>
<p>
-
1) Dissolve 0.55g Agarose into 55ml 0.5X TBEbuffer.
+
1) Dissolve 0.55g Agarose into 55ml 0.5X TBE buffer.
</p>
</p>
<p>
<p>
-
2) Microwave for 1 minute.
+
2) Microwave (high power, 800W) for 1 minute.
</p>
</p>
<p>
<p>
Line 352: Line 351:
</p>
</p>
<p>
<p>
-
5)Pour the solution to tightened tank with gates and gel comb and allow it tosolidify.
+
5)Pour the solution to tightened tank with gates and gel comb and allow it to solidify.
</p>
</p>
<p>
<p>
Line 364: Line 363:
</p>
</p>
<p>
<p>
-
1)Orientthe gel with wells facing the black negative electrode. Check if the gel iscovered by TBE buffer in the tank. If not, add TBE buffer to cover it to about1mm.
+
1)Orient the gel with wells facing the black negative electrode. Check if the gel is covered by TBE buffer in the tank. If not, add TBE buffer to cover it to about 1mm.
</p>
</p>
<p>
<p>
-
2) Mix loadingdye and the insert/plasmid before adding to the wells. For example, if the DNAwe have got is 45μl, and the loading dye we have got is 10X, then add 5μl ofloading dye to the samples. Mixture should be in blue.
+
2) Mix loading dye and the insert/plasmid before adding to the wells. For example, if the DNA we have got is 45μl, and the loading dye we have got is 10X, then add 5μl of loading dye to the samples. Mixture should be in blue.
</p>
</p>
<p>
<p>
-
3)Torun gel, add all samples to the wells of gel. Then add 1kb DNA ladder to aseparate well. 1μl should be enough for detection under UV.
+
3)To run the gel, add all samples to the wells of gel. Then add 1kb DNA ladder to a separate well. 1μl should be enough for detection under UV.
</p>
</p>
<p>
<p>
-
4)Connectthe electrodes to the power supply with correct colour. Apply power supply with120V. Check if there are bubbles on the negative electrodes.
+
4)Connect the electrodes to the power supply with correct colour. Set the power supply to 120V. Check if there are bubbles on the negative electrodes.
</p>
</p>
<p>
<p>
-
5) Allow it torun for about 20 - 30 mins. To avoid running the band off the gel, check theyellow band, which is the smallest fragments, should stay on the gel.
+
5) Allow it to run for about 40 - 60 mins. To avoid running the band off the gel, the yellow band (position of the smallest fragments) should stay on the gel.
</p>
</p>
<p>
<p>
Line 391: Line 390:
</p>
</p>
<p>
<p>
-
2. Weigh the gel slice in a 2 ml centrifuge tube. Add 3 volumes ofBuffer QG to  
+
2. Weigh the gel slice in a 2 ml centrifuge tube. Add 3 volumes of Buffer QG to  
</p>
</p>
<p>
<p>
Line 397: Line 396:
</p>
</p>
<p>
<p>
-
3. Incubate at 50°C until the gel slice has completely dissolved (around10&nbsp; min). Mix by vortexing the tube every2 mins during the incubation.
+
3. Incubate at 50°C until the gel slice has completely dissolved (around 10&nbsp; min). Mix by vortexing the tube every 2 mins during the incubation.
</p>
</p>
<p>
<p>
-
4. After the gel slice has dissolved completely, check that the color ofthe&nbsp; mixture is yellow. If the color ofthe mixture is orange or violet, add 5-10 μl of 3 M sodium acetate, pH 5.0, andmix until it turn to yellow.
+
4. After the gel slice has dissolved completely, check that the color of the&nbsp; mixture is yellow. If the color of the mixture is orange or violet, add 5-10 μl of 3 M sodium acetate (pH 5.0), and mix until it turns to yellow.
</p>
</p>
<p>
<p>
-
5. Add 1 gel volume of isopropanol to the sample and mix (for DNAfragments&nbsp; &lt;500 bp and &gt;4 kb).
+
5. Add 1 gel volume of isopropanol to the sample and mix (for DNA fragments&nbsp; &lt;500 bp and &gt;4 kb).
</p>
</p>
<p>
<p>
Line 409: Line 408:
</p>
</p>
<p>
<p>
-
7. To bind DNA, apply the sample to the QIAquick column, and centrifugefor 30 s. (The maximum volume of the column reservoir is 800 μl. For samplevolumes of more than 800 μl, simply load and spin again).
+
7. To bind DNA, apply the sample to the QIAquick column, and centrifuge for 30 s. (The maximum volume of the column reservoir is 800 μl. For sample volumes of more than 800 μl, simply load and spin again).
</p>
</p>
<p>
<p>
-
8. Discard flow-through and place QIAquick column back in the same&nbsp; collection tube. Collection tubes are re-usedto reduce plastic waste.
+
8. Discard flow-through and place QIAquick column back in the same&nbsp; collection tube. Collection tubes are re-used to reduce plastic waste.
</p>
</p>
<p>
<p>
Line 418: Line 417:
</p>
</p>
<p>
<p>
-
10. To wash, add 0.75 ml of Buffer PE to QIAquick column, stand for 2mins and centrifuge for 30 s.
+
10. To wash, add 0.75 ml of Buffer PE to QIAquick column, stand for 2 mins and centrifuge for 30 s.
</p>
</p>
<p>
<p>
-
11. Discard the flow-through and centrifuge the QIAquick column for anadditional 30 s and air-dry for 2 mins (This step can ensure all ethanol isremoved and the column is NOT over-dry)!
+
11. Discard the flow-through and centrifuge the QIAquick column for anadditional 30 s and air-dry for 2 mins (This step can ensure all ethanol is removed and the column is NOT over-dry)!
</p>
</p>
<p>
<p>
Line 433: Line 432:
</p>
</p>
<p>
<p>
-
membrane, wait2 mins and centrifuge the column for 2 mins at maximum speed.
+
membrane, wait 2 mins and centrifuge the column for 2 mins at maximum speed.
</p>
</p>
<p>
<p>
Line 454: Line 453:
</p>
</p>
<p>
<p>
-
2μl 10X Ligationbuffer
+
2μl 10X ligation buffer
</p>
</p>
<p>
<p>
Line 472: Line 471:
</p>
</p>
<p>
<p>
-
Allow the reaction to be taken place at 16<sup>o</sup>C overnight, or 22<sup>o</sup>Cfor 1 hour.
+
Allow the reaction to be taken place at 16<sup>o</sup>C overnight, or 22<sup>o</sup>C for 1 hour.
</p>
</p>
<p>
<p>
Line 484: Line 483:
</p>
</p>
<p>
<p>
-
- Transformation ofE. coli (DH5α) with plasmid DNA
+
- Transformation of <i>E. coli</i> (<i>DH5α</i> or <i>BL21(DE)</i>) with plasmid DNA
</p>
</p>
<p>
<p>
Line 511: Line 510:
</p>
</p>
<p>
<p>
-
9) Spin down the remaining cells and discard large amountsupernatant (1ml), thenresuspend cells.
+
9) Spin down the remaining cells and discard large amount supernatant (1ml), then resuspend cells.
</p>
</p>
<p>
<p>
-
10) Incubate at 37<sup>o</sup>C overnightuntil colonies are obtained.
+
10) Incubate at 37<sup>o</sup>C overnight until colonies are obtained.
</p>
</p>
<p>
<p>
Line 532: Line 531:
</p>
</p>
<p>
<p>
-
2) Incubate at37<sup>o</sup>C for 12-16 hours with shaking at 250rpm.
+
2) Incubate at 37<sup>o</sup>C for 12-16 hours with shaking at 250rpm.
</p>
</p>
<p>
<p>
Line 538: Line 537:
</p>
</p>
<p>
<p>
-
<strong>Extractionof Plasmid DNA (Miniprep)</strong>
+
<strong>Extraction of Plasmid DNA (Miniprep)</strong>
</p>
</p>
<p>
<p>
Line 547: Line 546:
</p>
</p>
<p>
<p>
-
1. Resuspend pelleted bacterial cells in 250 µl Buffer P1 and transferto a micro-
+
1. Resuspend pelleted bacterial cells in 250 µl Buffer P1 and transfer to a micro-
</p>
</p>
<p>
<p>
Line 553: Line 552:
</p>
</p>
<p>
<p>
-
2. Add 250 µl Buffer P2 and mix thoroughly by inverting the tube 4–6times and incubate 2 min at room temperature. Do not vortex!  
+
2. Add 250 µl Buffer P2 and mix thoroughly by inverting the tube 4–6 times and incubate 2 min at room temperature. Do not vortex!  
</p>
</p>
<p>
<p>
-
3. Add 350 µl Buffer N3 and mix immediately and thoroughly by invertingthe tube
+
3. Add 350 µl Buffer N3 and mix immediately and thoroughly by inverting the tube
</p>
</p>
<p>
<p>
Line 562: Line 561:
</p>
</p>
<p>
<p>
-
4. Centrifuge for 10 min at 13,000 rpm in a table-top microcentrifuge. Acompact white pellet will form.
+
4. Centrifuge for 10 min at 13,000 rpm in a table-top microcentrifuge. A compact white pellet will form.
</p>
</p>
<p>
<p>
Line 571: Line 570:
</p>
</p>
<p>
<p>
-
7. Recommended: Wash the QIAprep spin column by adding 0.5 ml Buffer PBand
+
7. Recommended: wash the QIAprep spin column by adding 0.5 ml Buffer PB and
</p>
</p>
<p>
<p>
Line 577: Line 576:
</p>
</p>
<p>
<p>
-
8. Wash QIAprep spin column by adding 0.75 ml Buffer PE and centrifugingfor
+
8. Wash QIAprep spin column by adding 0.75 ml Buffer PE and centrifuging for
</p>
</p>
<p>
<p>
Line 583: Line 582:
</p>
</p>
<p>
<p>
-
9. Discard the flow-through, and centrifuge for an additional 1 min toremove residual
+
9. Discard the flow-through, and centrifuge for an additional 1 min to remove residual
</p>
</p>
<p>
<p>
Line 592: Line 591:
</p>
</p>
<p>
<p>
-
add 50 µl Buffer EB (10 mM Tris·Cl, pH 8.5) or water to the center ofeach QIAprep
+
add 50 µl Buffer EB (10 mM Tris·Cl, pH 8.5) or water to the center of each QIAprep
</p>
</p>
<p>
<p>
-
spin column, let stand for 1 min, and centrifuge for 1 min to elute theDNA.
+
spin column, let stand for 1 min, and centrifuge for 1 min to elute the DNA.
</p>
</p>
<strong><br clear="all" />
<strong><br clear="all" />
</strong>
</strong>
<p>
<p>
-
<strong><u>Electrodesfunctional test</u></strong>
+
<strong><u>Electrodes functional test</u></strong>
</p>
</p>
<p>
<p>
Line 608: Line 607:
- Protocol
- Protocol
</p>
</p>
-
<p>
+
<p> Put electrodes to 100 ml double distilled water, measure the voltage by multimeter between two electrodes until the reading becomes steady. Then, put electrodes to 100 ml, 0.4 M sodium chloride solution. Parallel connect a voltmeter and an ammeter (both are multimeter actually) between the two electrodes to measure voltage and current. Take the readings every minute.
-
1) Put electrodes to 100 ml doubledistilled water, measure the voltage by voltmeter between two electrodes untilthe reading achieve steady.
+
-
</p>
+
-
<p>
+
-
2) Put electrodes to 100 ml, 0.4 M sodiumchloride solution. Parallel connect a voltmeter and an ammeter to between twoelectrodes to measure voltage and current. Take the readings every 30 seconds.
+
-
</p>
+
-
<p>
+
-
3) When the voltage reading achieve steady,replace sodium chloride solution with double distilled water. While keep takingreadings every 30 seconds.
+
-
</p>
+
-
<p>
+
-
4) Putthe electrodes to fresh water. Keep taking the readings every 30 seconds untilthe voltage achieve steady.
+
</p>
</p>
<p>
<p>
-
5)Plot voltage vs. time and current vs. time. Calculate the power for every timepoint. Estimate the total electric work.
+
When the voltage reading achieve steady, replace sodium chloride solution with double distilled water. While keep taking readings every minute. Put the electrodes in fresh water again. Keep taking the readings every minute until the voltage achieve steady.Plot voltage vs. time and current vs. time. Calculate the power for every time point. Estimate the total electric work.
</p>
</p>
<p>
<p>
Line 636: Line 625:
</p>
</p>
<p>
<p>
-
1) Parallel connect the electrodes with avoltmeter and ammeter. Put two electrodes to 50 ml, O.D. 600 bacteria solutionand shut down all the light.  
+
The experiment was conducted within a Class 2 biosafety cabinet and under sterile condition. Before each experiment the electrodes (4 ply carbon cloth, 3x4 cm each) were rinsed twice by immersing in tap water for 1-2 minutes, then wrapped with aluminium foil and autoclaved at 121⁰C for 25 minutes. Other instruments such as multimeter were wiped thoroughly with 70% ethanol before the experiment starts. The electrodes were fixed at the wall of the beaker with maximum possible separation (~3 cm) and connected to a RIGOL DM3051 digital multimeter with unshielded cable. The background open-circuit potential was about -0.1 to +0.2 mV.</p>
-
</p>
+
 
-
<p>
+
<p>25 mL of e. coli bacterial suspension (see below) were poured into the 100mL beaker. We define the moment where pouring was completed as t=0. Potential reading was then taken every minute afterwards using automatic data logging function of the multimeter. The experiment was done at room temperature.</p>
-
2) Wait the voltage achieve steady, startrecord the voltage and current every 30 seconds, for totally 5 minutes.
+
 
-
</p>
+
<p>To minimize the impact of external lighting on the experiments, most lights in the laboratory was turned off and the front glass of the biosafety cabinet was completely blocked by a polystyrene board after the bacterial suspension has been added. This is what we define as “dark condition” (<0.5 lux). The “light condition” was achieved by illuminating the beaker with a white LED (appox. 4160 lux at the beaker). The LED was a few centimeters above and aside from the beaker.</p>
-
<p>
+
 
-
3) Use light source directly illuminate onthe bacteria solution, take the reading every 30 seconds for totally 5 minutes.
+
-
</p>
+
-
<p>
+
-
4) Remove the light source and take thereading every 30 seconds, for totally 5 minutes.
+
-
</p>
+
-
<p>
+
-
5) Wait until the voltage become steady,start record the voltage and current every 30 seconds for totally 15 minutes.This step is for control.
+
-
</p>
+
-
<p>
+
-
6) Plot voltage vs. time and current vs.time for measurement and control respectively. Calculate the power and estimatetotal electric work.
+
-
</p>
+
<p>
<p>
&nbsp;
&nbsp;
</p>
</p>
<p>
<p>
-
<strong><u>Measuringvoltage vs. sodium chloride concentration relation of mixing entropy electrode</u></strong>
+
<strong><u>Measuring voltage vs. sodium chloride concentration relation of mixing entropy electrode</u></strong>
</p>
</p>
<p>
<p>
Line 665: Line 643:
- Protocol
- Protocol
</p>
</p>
-
<p>
+
<p>To start with, 0.6M stock sodium chloride solution was prepared by dissolving 5.310g of sodium chloride (Sigma Aldrich, Lot no: 090M01531V) in a small beaker and subsequently transferred into a 100 mL volumetric flask and made up to the graduation mark using deionized water. Other concentrations of sodium chloride solutiosn were prepared by mixing proper proportions of stock solution and deionized water in a 100 mL measuring cylinder.</p>
-
1) Put electrodes to double distilled waterand measure the voltage between to electrodes until the reading become steady.
+
 
-
</p>
+
<p>The sodium manganese electrode and the inert electrode, with the dimension of 3x4 cm each, were immersed in a random sequence into different concentrations of salt water, which was contained within a 100 mL beaker. The solution used each time was approximately 25 mL. Less than 1 cm of each electrode was immersed in the solution, but the entire electrode should be wet.</p>
-
<p>
+
 
-
2) Put electrodes to 100 ml 0.05 M sodiumchloride concentration and wait the reading achieve steady. Record the steadyvoltage.
+
<p>Three potential readings were taken after the potential reading became steady with a RIGOL DM3051 digital multimeter. This procedure is duplicated with another batch of stock solution to give 6 replicates at each concentration. It could take 30 minutes to a few hours for the potential to become steady, depending on the previous salinity that the electrode was exposed to. Sometimes the tendency for electrodes to repel or attract to each other can be observed. Thereby the electrodes must be fixed carefully to avoid undesirable short-circuit.</p>
-
</p>
+
 
-
<p>
+
-
3) Add sodium chloride powder to make thefinal concentration according to the table below. Record the steady voltage foreach concentration.
+
-
</p>
+
-
<table border="1" cellpadding="0" cellspacing="0">
+
-
<tbody>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
Final concentration  (M)
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
Total volume (ml)
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
Weight of total  sodium chloride (g)
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
Weight of added  sodium chloride (g)
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.10
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.58
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.15
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.88
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.20
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
1.17
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.25
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
1.46
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.30
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
1.75
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.35
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
2.05
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.40
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
2.34
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.45
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
2.63
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.50
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
2.92
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.55
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
3.21
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
<tr> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
0.60
+
-
</p>
+
-
</td> 
+
-
<td valign="top">
+
-
<p align="center">
+
-
100
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
3.51
+
-
</p>
+
-
</td> 
+
-
<td valign="bottom">
+
-
<p align="center">
+
-
0.29
+
-
</p>
+
-
</td>
+
-
</tr>
+
-
</tbody>
+
-
</table>
+
-
<p>
+
-
&nbsp;
+
-
</p>
+
-
<p>
+
-
4) Put the electrode in double distilledwater until the reading become steady to wash away sodium chloride. Repeat thisstep for 2 times. Then take the reading for concentration 0 M.
+
-
</p>
+
-
<p>
+
-
5) Repeat the whole process for two moretimes.<a name="_GoBack"></a>
+
-
</p>
+
<p>
<p>
&nbsp;
&nbsp;
Line 958: Line 656:
</p>
</p>
<p>
<p>
-
<strong>Preparation of growth medium (500mlLB (Luria Broth), 500ml 1M NaCl LB and 500ml 1M KCl LB)</strong>
+
<strong>Preparation of growth medium (500ml LB (Luria Broth), 500ml 1M NaCl LB and 500ml 1M KCl LB)</strong>
</p>
</p>
<p>
<p>
Line 967: Line 665:
</p>
</p>
<p>
<p>
-
1) Weigh 12.5gLB powder and add the powder into a 500ml bottle.
+
1) Weigh 12.5g LB powder and add the powder into a 500ml bottle.
</p>
</p>
<p>
<p>
Line 976: Line 674:
</p>
</p>
<p>
<p>
-
4) 29.22g NaCland 37.25g KCl is added respectively to prepare 500ml 1M NaCl LB and 500ml 1MKCl LB.
+
4) 29.22g NaCl and 37.25g KCl is added respectively to prepare 500ml 1M NaCl LB and 500ml 1M KCl LB.
</p>
</p>
<p>
<p>
Line 1,000: Line 698:
</p>
</p>
<p>
<p>
-
4) Pick a single colony from plate spread with DH5α transformedwith pET27b HR and add it into the falcon.
+
4) Pick a single colony from plate spread with <i>DH5α</i> transformed with pET27b HR and add it into the falcon.
</p>
</p>
<p>
<p>
Line 1,241: Line 939:
</p>
</p>
<p>
<p>
-
2) Add 2ul IPTG(only applicable to those with IPTG,otherwise go to step 3).
+
2) Add 2ul IPTG (only applicable to those with IPTG, otherwise go to step 3).
</p>
</p>
<p>
<p>
-
3) Add 40ul of DH5α transformedwith pET27b HR start culture into each tube.
+
3) Add 40ul of <i>DH5α</i> transformed with pET27b HR start culture into each tube.
</p>
</p>
<p>
<p>
-
4) Use a test tube rack to hold all the tubes andput the rack inside the incubator at 37℃. andshaking 200rpm(?).
+
4) Use a test tube rack to hold all the tubes and put the rack inside the incubator at 37℃. and shaking 200 rpm(?).
</p>
</p>
<p>
<p>
Line 1,265: Line 963:
</p>
</p>
<p>
<p>
-
3) Pipette up and down to mix the solution by P1000pipette.
+
3) Pipette up and down to mix the solution by P1000 pipette.
</p>
</p>
<p>
<p>
Line 1,286: Line 984:
</p>
</p>
<p>
<p>
-
3) Measure the OD600 and calculate the relativeamount of bacteria needed and add into the conical flasks (usually 1%inoculums).
+
3) Measure the OD600 and calculate the relative amount of bacteria needed and add into the conical flasks (usually 1% inoculums).
</p>
</p>
<p>
<p>
Line 1,313: Line 1,011:
</p>
</p>
<p>
<p>
-
3) Lyse the cells by mixing well with 2% SDSand boil at 99℃for 5 min.
+
3) Lyse the cells by mixing well with 2% SDS and boil at 99℃ for 5 min.
</p>
</p>
<p>
<p>
-
4) Centrifuge for 1 min in maximum speed andobtain supernatant .
+
4) Centrifuge for 1 min in maximum speed and obtain supernatant .
</p>
</p>
<p>
<p>
-
5) Dilute the supernatant to desiredconcentrations.
+
5) Dilute the supernatant to desired concentrations.
</p>
</p>
<p>
<p>
Line 1,325: Line 1,023:
</p>
</p>
<p>
<p>
-
7) Add 5ul 0.5mM MQAE dissolved in DMSOafterwards.
+
7) Add 5ul 0.5mM MQAE dissolved in DMSO afterwards.
</p>
</p>
<p>
<p>
Line 1,331: Line 1,029:
</p>
</p>
<p>
<p>
-
9)Measure the fluorescence by microplatereader using 350 nm absorption wavelength and 460 nm emission wavelength
+
9)Measure the fluorescence by microplate reader using 350 nm absorption wavelength and 460 nm emission wavelength
</p>
</p>
<p>
<p>
-
Later found that the halorhodopsin’s colour affect the measurement ofthe MQAE fluorescence, need to change to centrifuge for 1 h in maximum speed at4℃and obtain supernatant after boiling with SDS to separate the halorhodopsinfrom the cell lysate.
+
Later found that the halorhodopsin’s colour affect the measurement ofthe MQAE fluorescence, need to change to centrifuge for 1 h in maximum speed at 4℃ and obtain supernatant after boiling with SDS to separate the halorhodopsin from the cell lysate.
</p>
</p>
<p>
<p>
Line 1,340: Line 1,038:
</p>
</p>
<p>
<p>
-
<strong><u>Excitation of bacteria to trigger thehalorhopsin</u></strong>
+
<strong><u>Excitation of bacteria expressing halorhopsin</u></strong>
</p>
</p>
<p>
<p>
Line 1,349: Line 1,047:
</p>
</p>
<p>
<p>
-
1) Usealuminum foil to wrap start cultures.
+
1) Use aluminum foil to wrap start cultures.
</p>
</p>
<p>
<p>
-
2) Excite thebacteria using either 405, 530, 670 nm lasers with the confocal microscope withlive cell imaging for 2 min.
+
2) Excite the bacteria using either 405, 530, 670 nm lasers with the confocal microscope with live cell imaging for 2 min.
</p>
</p>
<p>
<p>
-
3) Adjust tothe target laser power.
+
3) Adjust to the target laser power.
</p>
</p>
<p>
<p>
Line 1,361: Line 1,059:
</p>
</p>
<p>
<p>
-
<strong><u>Controlledbacterial cell movement measurement</u></strong>
+
<strong><u>Controlled bacterial cell movement measurement</u></strong>
</p>
</p>
<p>
<p>
Line 1,373: Line 1,071:
</p>
</p>
<p>
<p>
-
Anti- E. coli antibody (Bioon)
+
Anti- <i>E. coli</i> antibody (Bioon)
</p>
</p>
<p>
<p>
-
Antibody coating buffer solution - Protein Amagnetic bead binding buffer (New England BioLabs)
+
Antibody coating buffer solution - Protein A magnetic bead binding buffer (New England BioLabs)
</p>
</p>
<p>
<p>
Line 1,403: Line 1,101:
</p>
</p>
<p>
<p>
-
3) Addanti- E. coli antibody and incubate at 4C overnight with gently shaking.
+
3) Add anti- E. <i>coli</i> antibody and incubate at 4C overnight with gently shaking.
</p>
</p>
<p>
<p>
Line 1,409: Line 1,107:
</p>
</p>
<p>
<p>
-
5)Addition of the E. coli cell to resuspend the magnetic bead and incubate for 2hour room temperature with gently shaking.
+
5)Addition of the <i>E. coli</i> cell to resuspend the magnetic bead and incubate for 2 hour room temperature with gently shaking.
</p>
</p>
<p>
<p>
-
6) Themagnetic beads were transferred to a new tube and rinsed with fresh cell medium
+
6) The magnetic beads were transferred to a new tube and rinsed with fresh cell medium
</p>
</p>
<p>
<p>
-
7) Thecells are attached with magnetic particles and subjected to movement bymagnetic field.
+
7) The cells are attached with magnetic particles and subjected to movement by magnetic field.
</p>
</p>
<p>
<p>
-
8) Thenumber of cells captured by fixed antibody-tagged magnetic particles aremonitored by disrupting the antibody through heat or chemical and detectedspectrophotometry or microscopy.
+
8) The number of cells captured by fixed antibody-tagged magnetic particles are monitored by disrupting the antibody through heat or chemical and detected spectrophotometry or microscopy.
</p>
</p>
<p>
<p>
-
9) The bacterial cell tagged on magneticparticles, which can be observed with bare eyes with a dark brown colour, wasattracted by a fixed magnetic field and the movement rate is calculated bydistance over time until all brown colour particles bind on the wall
+
9) The bacterial cell tagged on magnetic particles, which can be observed with bare eyes with a dark brown colour, was attracted by a fixed magnetic field and the movement rate is calculated by distance over time until all brown colour particles bind on the wall
</p>
</p>
<p>
<p>
Line 1,430: Line 1,128:
</p>
</p>
<p>
<p>
-
<strong><u>Laserexcitation protocol</u></strong>
+
<strong><u>Laser excitation protocol</u></strong>
</p>
</p>
<p>
<p>
Line 1,490: Line 1,188:
</p>
</p>
<p>
<p>
-
1) Grow transformed bacteria <em>BL121(DE)</em> in LB with 0.4 M of NaCl inthe presence of antibiotic at 37°C.
+
1) Grow transformed bacteria <em>BL121(DE)</em> in LB with 0.4 M of NaCl in the presence of antibiotic at 37°C.
</p>
</p>
<p>
<p>
-
2) Collect 500 μl of bacterialsample with OD600 reaches 0.4.
+
2) Collect 500 μl of bacterial sample with OD600 reaches 0.4.
</p>
</p>
<p>
<p>
-
3) Transfer the bacterial sample tocell chamber.
+
3) Transfer the bacterial sample to cell chamber.
</p>
</p>
<p>
<p>
-
4) Excite bacterial sample by laserconfocal scanning microscope (FV1000D, Nikon).
+
4) Excite bacterial sample by laser confocal scanning microscope (FV1000D, Nikon).
</p>
</p>
<p>
<p>
Line 1,508: Line 1,206:
</p>
</p>
<p>
<p>
-
7) Power of laser: 0-65%; 5% asinterval.
+
7) Power of laser: 0-65%; 5% as interval.
</p>
</p>
<p>
<p>
-
8) Collect 200 μl of excitedbacterial sample.
+
8) Collect 200 μl of excited bacterial sample.
</p>
</p>
<p>
<p>
Line 1,544: Line 1,242:
</p>
</p>
<p>
<p>
-
2) Collect 500 μl of bacterialsample with OD600 reaches 0.4.
+
2) Collect 500 μl of bacterial sample with OD600 reaches 0.4.
</p>
</p>
<p>
<p>
Line 1,550: Line 1,248:
</p>
</p>
<p>
<p>
-
4) Excite bacterial sample by laserconfocal scanning microscope (FV1000D, Nikon).
+
4) Excite bacterial sample by laser confocal scanning microscope (FV1000D, Nikon).
</p>
</p>
<p>
<p>
Line 1,556: Line 1,254:
</p>
</p>
<p>
<p>
-
6) Length for excitation: 0-600s;30s as interval.
+
6) Length for excitation: 0-600s; 30s as interval.
</p>
</p>
<p>
<p>
Line 1,562: Line 1,260:
</p>
</p>
<p>
<p>
-
8) Collect 200 μl of excitedbacterial sample.
+
8) Collect 200 μl of excited bacterial sample.
</p>
</p>
<p>
<p>

Latest revision as of 18:57, 28 October 2011

Protocols Contents



1. Cloning

1.1 PCR Amplification of the gene

1.2 Double Digestion

1.3 PCR Purification

1.4 Agarose Gel electrophoresis

1.5 Ligation

1.6 Gel Extraction

1.7 Bacterial Transformation

1.8 Inoculation

1.9 Extraction of Plasmid DNA

2. Electrodesfunctional test

3. Bacteria light-couple electricity generation

4. Measuring voltage vs. sodium chloride concentrationrelation of mixing entropy electrode

5. Cell growth optimization

5.1 Preparation of growth medium

5.2 Inoculation

5.3 Salt concentration test

6. Measurement of chloride concentration in bacterial lysate using fluorescent dye N-(ethoxycarbonylmethyl)-6-methoxyquinoliniumbromide (MQAE)

7. Excitation of bacteria expressing halorhopsin

8. Measurment on controlled bacterial cell movement

9. Laser excitation protocol

9.1 General, wavelength

9.2 Laser power

9.3 excitation length

 

 

Cloning

PCR Amplification of the gene

 

- Reagents

1) PCR SuperMix High Fidelity

22 U/ml DNA polymerase mixture in:

- 66 mM Tris-SO4 (pH 9.1 at 25°C)

- 19.8 mM (NH4)2SO4

- 2.2 mM MgSO4

- 220 μM dGTP

- 220 μM dATP

- 220 μM dTTP

- 220 μM dCTP

- stabilizers

2) Forward and Reverse Primer

3) DNA template

 

- Protocols

PCR Assembly from Reaction Components:

1) Set up reaction tubes on ice.

2) Add the following components in any order to each reaction tube:

a) 45 μl PCR SuperMix High Fidelity

b) Primer solution (200 nM final concentration of each is recommended)

c) Template DNA solution (Total volume of primer and template solutions added can be 0.5-5 μl)

3. Mix contents of tubes and cover with mineral or silicone oil. Depending on the model of thermal cycler used, mineral or silicone oil may notbe necessary.

4) Cap tubes and load thermal cycler at 94°C.

5) Start cycling program file

 

*Thefollowing general procedures are suggested as guidelines for use of PCRSuperMix High Fidelity. Assembly of the reactions on ice from pre-chilledcomponents is recommended. Final reaction volumes described below is areapproximately 50 μl. Reaction size may be altered to suit user preferences.

 

**Recommended Cycling Program

1 cycle of:  94°C for 30 seconds (Pre-amplification denaturation)

30–35 cycles of:

 94°C for 30 seconds (Denaturation)

 55–68°C for 30 seconds (Annealing)

 68–72°C for 60 seconds per kb target length(Extension)

 Use of 68°C during extension step of PCR is strongly recommended for fragments > 5 kb in length

 

Double Digestion

 

- Reaction mixtures

Total volume 50μl

37.6μl Insert/Vector + ddH2O*

5μl 10X NEB Buffer3

5μl 10X BSA

1.2μl Enzyme 1

1.2μl Enzyme 2

*Water is addedfirst and the template the last

 At least 200ng DNA should be added

 

- Protocol

Reaction mixture at 37oc for 2 hours

Buffer Chart

or http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/buffer_activity_restriction_enzymes.asp

 

PCR Purification

 

- *Protocol

1) Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix. It is not        necessary to remove mineral oil or kerosene.

2) If pH indicator I has been added to Buffer PB, check that the color of the mixture is yellow. If the color of the mixture is orange or violet, add 10 µl of 3 M sodium acetate (pH 5.0), and mix. The color of the mixture will turn to yellow.

3)Place a QIAquick spin column in a provided 2 ml collection tube.

4) To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60s.

5)Discard flow-through. Place the QIAquick column back into the same tube.

6) To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.

7)Discard flow-through and place the QIAquick column back in the same tube. Centrifugethe column for an additional 1 min. Protocol

8)Place QIAquick column in a clean 1.5 ml microcentrifuge tube.

9) To elute DNA, add 50 μl Buffer EB (10 mM Tris·Cl, pH 8.5) or water (pH 7.0–8.5) to the center of the QIAquick membrane and centrifuge the column for 1 min. Alternatively, for increased DNA concentration, add 30 μl elution buffer to thecenter of the QIAquick membrane, let the column stand for 1 min, and then centrifuge.

10) If the purified DNA is to be analyzed on a gel, add 1 volume of Loading Dye to

5 volumes of purified DNA. Mix the solution by pipetting up and down before loading the gel.

IMPORTANT: Ensure that the elution buffer is dispensed directly onto the QIAquick

membrane for complete elution of bound DNA. The average eluate volume is 48 µl

from 50 µl elution buffer volume, and 28 µl from 30 µl elution buffer.

*Protocol adopted from QIAquick PCR purification kit protocol

 

 

 

Agarose Gel electrophoresis

 

- Set gel

1) Dissolve 0.55g Agarose into 55ml 0.5X TBE buffer.

2) Microwave (high power, 800W) for 1 minute.

3) Cool it down using running water for 1 minute.

4) Add 1μl GelRed

5)Pour the solution to tightened tank with gates and gel comb and allow it to solidify.

6)Transfer the gel to gel tank once it is set hard.

 

-Run gel

1)Orient the gel with wells facing the black negative electrode. Check if the gel is covered by TBE buffer in the tank. If not, add TBE buffer to cover it to about 1mm.

2) Mix loading dye and the insert/plasmid before adding to the wells. For example, if the DNA we have got is 45μl, and the loading dye we have got is 10X, then add 5μl of loading dye to the samples. Mixture should be in blue.

3)To run the gel, add all samples to the wells of gel. Then add 1kb DNA ladder to a separate well. 1μl should be enough for detection under UV.

4)Connect the electrodes to the power supply with correct colour. Set the power supply to 120V. Check if there are bubbles on the negative electrodes.

5) Allow it to run for about 40 - 60 mins. To avoid running the band off the gel, the yellow band (position of the smallest fragments) should stay on the gel.

 

*Gel Extraction

 

1. Excise the DNA fragment from the agarose gel with a clean, sharp scalpel.

2. Weigh the gel slice in a 2 ml centrifuge tube. Add 3 volumes of Buffer QG to

1 volume of gel (100 mg ~ 100 μl).

3. Incubate at 50°C until the gel slice has completely dissolved (around 10  min). Mix by vortexing the tube every 2 mins during the incubation.

4. After the gel slice has dissolved completely, check that the color of the  mixture is yellow. If the color of the mixture is orange or violet, add 5-10 μl of 3 M sodium acetate (pH 5.0), and mix until it turns to yellow.

5. Add 1 gel volume of isopropanol to the sample and mix (for DNA fragments  <500 bp and >4 kb).

6. Place a QIAquick spin column in a provided 2 ml collection tube.

7. To bind DNA, apply the sample to the QIAquick column, and centrifuge for 30 s. (The maximum volume of the column reservoir is 800 μl. For sample volumes of more than 800 μl, simply load and spin again).

8. Discard flow-through and place QIAquick column back in the same  collection tube. Collection tubes are re-used to reduce plastic waste.

9. Add 0.5 ml of Buffer QG to QIAquick column and centrifuge for 30 s toremove all traces of agarose.

10. To wash, add 0.75 ml of Buffer PE to QIAquick column, stand for 2 mins and centrifuge for 30 s.

11. Discard the flow-through and centrifuge the QIAquick column for anadditional 30 s and air-dry for 2 mins (This step can ensure all ethanol is removed and the column is NOT over-dry)!

12. Place QIAquick column into a clean 1.5 ml microcentrifuge tube.

 

13. To elute DNA, add 35 μl of 50 oC ddH2O to the center of the QIAquick

membrane, wait 2 mins and centrifuge the column for 2 mins at maximum speed.

*extracted from CUHK iGEM2010 protocol

 

Ligation

 

- Reaction mixture

Total volume 20μl

2μl 10X ligation buffer

1μl T4 DNA ligase

14μl Vector

3μl insert

 

- Protocol

Allow the reaction to be taken place at 16oC overnight, or 22oC for 1 hour.

 

Bacterial Transformation

 

- Transformation of E. coli (DH5α or BL21(DE)) with plasmid DNA

1) Thaw competent cell on ice.

2) Add 50 ~ 100 ng DNA to competent cell culture.

3) Put in ice for 30 min.

4) Heat shock at 42oC for 1 minute.

5) Put in ice for 2 min.

6) Add 1 ml LB broth medium.

7) Incubate at 37oC for 90 min with shaking (~ 250 rpm).

8) Spread plate (with suitableantibiotics):

9) Spin down the remaining cells and discard large amount supernatant (1ml), then resuspend cells.

10) Incubate at 37oC overnight until colonies are obtained.

 

Inoculation

 

- Protocol

1) Pick colonies & culture in 2~ 3 ml LB broth with antibiotics.

2) Incubate at 37oC for 12-16 hours with shaking at 250rpm.

 

Extraction of Plasmid DNA (Miniprep)

 

- Protocol

1. Resuspend pelleted bacterial cells in 250 µl Buffer P1 and transfer to a micro-

centrifuge tube.

2. Add 250 µl Buffer P2 and mix thoroughly by inverting the tube 4–6 times and incubate 2 min at room temperature. Do not vortex!

3. Add 350 µl Buffer N3 and mix immediately and thoroughly by inverting the tube

4–6 times.

4. Centrifuge for 10 min at 13,000 rpm in a table-top microcentrifuge. A compact white pellet will form.

5. Apply the supernatants from step 4 to the QIAprep spin column

6. Centrifuge for 30–60 s. Discard the flow-through.

7. Recommended: wash the QIAprep spin column by adding 0.5 ml Buffer PB and

centrifuging for 30–60 s. Discard the flow-through.

8. Wash QIAprep spin column by adding 0.75 ml Buffer PE and centrifuging for

30–60 s.

9. Discard the flow-through, and centrifuge for an additional 1 min to remove residual

wash buffer.

10. Place the QIAprep column in a clean 1.5 ml microcentrifuge tube.

add 50 µl Buffer EB (10 mM Tris·Cl, pH 8.5) or water to the center of each QIAprep

spin column, let stand for 1 min, and centrifuge for 1 min to elute the DNA.


Electrodes functional test

 

- Protocol

Put electrodes to 100 ml double distilled water, measure the voltage by multimeter between two electrodes until the reading becomes steady. Then, put electrodes to 100 ml, 0.4 M sodium chloride solution. Parallel connect a voltmeter and an ammeter (both are multimeter actually) between the two electrodes to measure voltage and current. Take the readings every minute.

When the voltage reading achieve steady, replace sodium chloride solution with double distilled water. While keep taking readings every minute. Put the electrodes in fresh water again. Keep taking the readings every minute until the voltage achieve steady.Plot voltage vs. time and current vs. time. Calculate the power for every time point. Estimate the total electric work.

 

Bacterialight-couple electricity generation

 

- Protocol

The experiment was conducted within a Class 2 biosafety cabinet and under sterile condition. Before each experiment the electrodes (4 ply carbon cloth, 3x4 cm each) were rinsed twice by immersing in tap water for 1-2 minutes, then wrapped with aluminium foil and autoclaved at 121⁰C for 25 minutes. Other instruments such as multimeter were wiped thoroughly with 70% ethanol before the experiment starts. The electrodes were fixed at the wall of the beaker with maximum possible separation (~3 cm) and connected to a RIGOL DM3051 digital multimeter with unshielded cable. The background open-circuit potential was about -0.1 to +0.2 mV.

25 mL of e. coli bacterial suspension (see below) were poured into the 100mL beaker. We define the moment where pouring was completed as t=0. Potential reading was then taken every minute afterwards using automatic data logging function of the multimeter. The experiment was done at room temperature.

To minimize the impact of external lighting on the experiments, most lights in the laboratory was turned off and the front glass of the biosafety cabinet was completely blocked by a polystyrene board after the bacterial suspension has been added. This is what we define as “dark condition” (<0.5 lux). The “light condition” was achieved by illuminating the beaker with a white LED (appox. 4160 lux at the beaker). The LED was a few centimeters above and aside from the beaker.

 

Measuring voltage vs. sodium chloride concentration relation of mixing entropy electrode

 

- Protocol

To start with, 0.6M stock sodium chloride solution was prepared by dissolving 5.310g of sodium chloride (Sigma Aldrich, Lot no: 090M01531V) in a small beaker and subsequently transferred into a 100 mL volumetric flask and made up to the graduation mark using deionized water. Other concentrations of sodium chloride solutiosn were prepared by mixing proper proportions of stock solution and deionized water in a 100 mL measuring cylinder.

The sodium manganese electrode and the inert electrode, with the dimension of 3x4 cm each, were immersed in a random sequence into different concentrations of salt water, which was contained within a 100 mL beaker. The solution used each time was approximately 25 mL. Less than 1 cm of each electrode was immersed in the solution, but the entire electrode should be wet.

Three potential readings were taken after the potential reading became steady with a RIGOL DM3051 digital multimeter. This procedure is duplicated with another batch of stock solution to give 6 replicates at each concentration. It could take 30 minutes to a few hours for the potential to become steady, depending on the previous salinity that the electrode was exposed to. Sometimes the tendency for electrodes to repel or attract to each other can be observed. Thereby the electrodes must be fixed carefully to avoid undesirable short-circuit.

 

Cell growth optimization

Preparation of growth medium (500ml LB (Luria Broth), 500ml 1M NaCl LB and 500ml 1M KCl LB)

 

- Protocol

1) Weigh 12.5g LB powder and add the powder into a 500ml bottle.

2) Add 500ml distilled water to the bottle.

3) Autoclave the solution.

4) 29.22g NaCl and 37.25g KCl is added respectively to prepare 500ml 1M NaCl LB and 500ml 1M KCl LB.

 

Inoculation

 

-Protocol

1) Add 5ml LB solution to a falcon.

2) Add 5ul antibiotic K.

3) Add 2.5ul IPTG.

4) Pick a single colony from plate spread with DH5α transformed with pET27b HR and add it into the falcon.

5) Put the start culture inside the incubator at 37℃ and shaking 200rpm.

6) Collect thestart culture the other day.

 

Salt concentration test

 

- Protocol

 

A. Preparation of 6 sets of solution:

0.1-1M NaCl with IPTG

0.1M-1M NaCl without IPTG

0.1M-1M KCl with IPTG

0.1M-1M KCl without IPTG

0M salt with IPTG

0M salt without IPTG

1) Prepare the medium as shown:

[Salt]/M

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

LB +1M salt/ml

0

0.4

0.8

1.2

1.6

2.0

2.4

2.8

3.2

3.6

4

LB/ml

4.0

3.6

3.2

2.8

2.4

2.0

1.6

1.2

0.8

0.4

0

 

2) Add 2ul IPTG (only applicable to those with IPTG, otherwise go to step 3).

3) Add 40ul of DH5α transformed with pET27b HR start culture into each tube.

4) Use a test tube rack to hold all the tubes and put the rack inside the incubator at 37℃. and shaking 200 rpm(?).

 

 

B.Measurement of absorbance

1) Set the wavelength of spectrophotometer to 600nm.

2) Set blank with 1ml LB solution.

3) Pipette up and down to mix the solution by P1000 pipette.

4) Transfer 1ml solution to a cuvette.

5) Record the OD600.

 

C. Measurement of bacterial growth curves

1) Inoculate the cells overnight.

2) Autoclave conical flasks with 100 ml LB solution.

3) Measure the OD600 and calculate the relative amount of bacteria needed and add into the conical flasks (usually 1% inoculums).

4) Measure the OD600 after adding the bacteria intothe conical flasks. This is time 0.

Measure the OD600 every half hour for eight hours.

 

Measurementof chloride concentration in bacterial lysate using fluorescent dye N-(ethoxycarbonylmethyl)-6-methoxyquinoliniumbromide (MQAE)

 

- Protocol

1) Culture the cells overnight.

2) Centrifuge for 1 min in maximum speed andcollect the cell pellet.

3) Lyse the cells by mixing well with 2% SDS and boil at 99℃ for 5 min.

4) Centrifuge for 1 min in maximum speed and obtain supernatant .

5) Dilute the supernatant to desired concentrations.

6) Add 95ul of each sample to 96well-microplate.

7) Add 5ul 0.5mM MQAE dissolved in DMSO afterwards.

8) Incubate for 1 hour at 37℃.

9)Measure the fluorescence by microplate reader using 350 nm absorption wavelength and 460 nm emission wavelength

Later found that the halorhodopsin’s colour affect the measurement ofthe MQAE fluorescence, need to change to centrifuge for 1 h in maximum speed at 4℃ and obtain supernatant after boiling with SDS to separate the halorhodopsin from the cell lysate.

 

Excitation of bacteria expressing halorhopsin

 

-Protocol

1) Use aluminum foil to wrap start cultures.

2) Excite the bacteria using either 405, 530, 670 nm lasers with the confocal microscope with live cell imaging for 2 min.

3) Adjust to the target laser power.

 

Controlled bacterial cell movement measurement

 

- Materials and Reagents

Protein A magnetic beads (New EnglandBioLabs)

Anti- E. coli antibody (Bioon)

Antibody coating buffer solution - Protein A magnetic bead binding buffer (New England BioLabs)

LB medium (USB)

Curvette (Sarstedt)

Spectrophotometer

40X bright-field microscope

 

- Protocol

1)Wash the Protein A magnetic bead with antibody coating buffer 3 times.

2)Resuspend the Protein A magnetic bead in antibody coating buffer.

3) Add anti- E. coli antibody and incubate at 4C overnight with gently shaking.

4)Wash away the excess antibody with with antibody coating buffer 3 times.

5)Addition of the E. coli cell to resuspend the magnetic bead and incubate for 2 hour room temperature with gently shaking.

6) The magnetic beads were transferred to a new tube and rinsed with fresh cell medium

7) The cells are attached with magnetic particles and subjected to movement by magnetic field.

8) The number of cells captured by fixed antibody-tagged magnetic particles are monitored by disrupting the antibody through heat or chemical and detected spectrophotometry or microscopy.

9) The bacterial cell tagged on magnetic particles, which can be observed with bare eyes with a dark brown colour, was attracted by a fixed magnetic field and the movement rate is calculated by distance over time until all brown colour particles bind on the wall

of the container.

 

Laser excitation protocol

General,wavelength

 

-Protocol

1)Grow transformed bacteria BL121(DE)in LB with 0.4 M of NaCl in the presence of antibiotic at 37°C.

2)Collect 500 μl of bacterial sample with OD600 reaches 0.4.

3)Transfer the bacterial sample to cell chamber.

4)Excite bacterial sample by laser confocal scanning microscope (FV1000D, Nikon).

5)Three wavelengths are chose: 405nm, 530 nm and 670 nm.

6)Length for excitation is 2 minutes.

7)Collect 200 μl of excited bacterial sample.

8)Spin sown bacterial sample.

9)Remove supernatant.

10)Lysis bacterial in 90 μl of 2% SDS.

11)Boil at 99°C for 10 minutes.

12)Determine the intracellular Cl- concentration by MQAE.

 

Laser power

 

-Protocol

1) Grow transformed bacteria BL121(DE) in LB with 0.4 M of NaCl in the presence of antibiotic at 37°C.

2) Collect 500 μl of bacterial sample with OD600 reaches 0.4.

3) Transfer the bacterial sample to cell chamber.

4) Excite bacterial sample by laser confocal scanning microscope (FV1000D, Nikon).

5) Wavelength chose 530 nm.

6) Length for excitation is 2minutes.

7) Power of laser: 0-65%; 5% as interval.

8) Collect 200 μl of excited bacterial sample.

9) Spin sown bacterial sample.

10) Remove supernatant.

11) Lysis bacterial in 90 μl of 2%SDS.

12) Boil at 99°C for 10 minutes.

13)Determine the intracellular Cl- concentration by MQAE.

 

Excitation length

 

- Protocol

1) Grow transformed bacteria BL121(DE) in LB with 0.4 M of NaCl inthe presence of antibiotic at 37°C.

2) Collect 500 μl of bacterial sample with OD600 reaches 0.4.

3) Transfer the bacterial sample tocell chamber.

4) Excite bacterial sample by laser confocal scanning microscope (FV1000D, Nikon).

5) Wavelength chose 530 nm.

6) Length for excitation: 0-600s; 30s as interval.

7) Power of laser: 25%.

8) Collect 200 μl of excited bacterial sample.

9) Spin sown bacterial sample.

10) Remove supernatant.

11) Lysis bacterial in 90 μl of 2%SDS.

12) Boil at 99°C for 10 minutes.

13) Determinethe intracellular Cl- concentration by MQAE.

 



"Creativity is thinking up new things. Innovation is doing new things." - Theodore Levitt

©Copyright CUHK IGEM Team 2011