Difference between revisions of "Team:BNU-CHINA/Team"

Line 475: Line 475:
 
                         <li>
 
                         <li>
 
                             <h5>Materials:</h5>
 
                             <h5>Materials:</h5>
−
                            <!--少一张表格-->
 
 
                             <table class="table table-condensed">
 
                             <table class="table table-condensed">
 
                                 <tbody>
 
                                 <tbody>
Line 493: Line 492:
 
                                     <tr>
 
                                     <tr>
 
                                         <td>Stacking Gel(4%) </td>
 
                                         <td>Stacking Gel(4%) </td>
−
                                         <td>pH=6.8 500ul
+
                                         <td>pH=6.8 500\(\mu\)l
 
                                         </td>
 
                                         </td>
 
                                         <td>500 \(\mu\)l</td>
 
                                         <td>500 \(\mu\)l</td>
Line 579: Line 578:
 
                             <p>Divide the NGM solid medium (d = 6 cm) equally into two parts (drawing on the surface of the culture dishes).
 
                             <p>Divide the NGM solid medium (d = 6 cm) equally into two parts (drawing on the surface of the culture dishes).
 
                             </p>
 
                             </p>
−
                             <p>Put 50 ul compound of different concentration and DMSO as contrast respectively on the two parts. Make 3 repeats of each concentration.
+
                             <p>Put 50 \(\mu\)l compound of different concentration and DMSO as contrast respectively on the two parts. Make 3 repeats of each concentration.
 
                             </p>
 
                             </p>
−
                             <p>Flush nematode from the plate with M9 and inoculate 20 ul (about 30 nematodes) into the center of the medium.
+
                             <p>Flush nematode from the plate with M9 and inoculate 20 \(\mu\)l (about 30 nematodes) into the center of the medium.
 
                             </p>
 
                             </p>
 
                             <p>Incubate at 20&#176C for 1hr, and then place them at 4&#176C refrigerator for 1hr.
 
                             <p>Incubate at 20&#176C for 1hr, and then place them at 4&#176C refrigerator for 1hr.
Line 686: Line 685:
 
                             <h5>The incubation condition of caenorhabditis elegans N2 wild type:
 
                             <h5>The incubation condition of caenorhabditis elegans N2 wild type:
 
</h5>
 
</h5>
−
                             <p>Generally incubated at 20&#176C. Grow slowly at 16C and grow fast at 25C while egg laying amount declines.</p>
+
                             <p>Generally incubated at 20&#176C. Grow slowly at 16&#176C and grow fast at 25&#176C while egg laying amount declines.</p>
 
                         </li>
 
                         </li>
 
                         <br/>
 
                         <br/>
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                             <h5>Protocol:
 
                             <h5>Protocol:
 
                                 </h5></li>
 
                                 </h5></li>
−
                         <p>Inoculate NGM medium with 150~200 ul OP50, incubate at 37&#176C for 12hr. Cut down a square of NGM(about 1cm x 1cm) with nematodes.
+
                         <p>Inoculate NGM medium with 150~200 \(mu\)l OP50, incubate at 37&#176C for 12hr. Cut down a square of NGM(about 1cm x 1cm) with nematodes.
 
                         </p>
 
                         </p>
 
                         <p>Put the square on the NGM medium with OP50 and let the surface with nematodes adown to contact the medium.
 
                         <p>Put the square on the NGM medium with OP50 and let the surface with nematodes adown to contact the medium.

Revision as of 01:01, 13 September 2015

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Team:BNU-CHINA - 2015.igem.org

Team Beijing Normal University

1. Attribution

Project Design and Wet Lab Experiments

Under the supervision of Prof. Zhu Xudong, Prof. Yang Dong, and Prof. Xiang Benqiong etc, nearly all team members have taken part in the project designing process, especially those of wet lab group.Beichen Gao , Yuanyi Dai , Yufei Cao and Jia Li are the group leaders who mainly design the experimental patterns and guide the different parts of the experiments.

Modeling

Cheng Li is the leader of modeling group, who mainly enrolled in designing the device 2.0. Yuan Yin , Qiuyue Yuan and Xueting Zhao also do a great many works in the modeling group, such as information searching, paper writing and equipment appilication.

Wiki Construction

Jiajun Zhang , who has led the web design group to build the wiki, together with group members Zhiyao Chen and Chengfei Peng complete the main work in database construction and maintenance.

Graphic design

Lu Xu( group leader), Lee and Yalei Cao really do a fantastic work in graphic and web design. They all make great efforts in designing our team logo, website, poster, souvenir, T-shirt and so on.

Human practice

Meng Tang , the leader of human practice group, has organized a series of activities for Policy and Practice, like survey and publicize in some middle schools etc. Some group members as Yuanyi Dai,Jia Li , Jiajun Zhang , Beichen Gao , Zhiyao Chen , Jingyu Zhao , Xiaofei Feng also play a significant role in planning and organizing the activities . Other group members also take an active part in some other activities of human practice.

2. Collaboration

Our modeling can be divided into four parts. Firstly, in order to enable our project to be applied in life, we design a device placed in soil, which can attract and kill nematodes by modified engineering bacteria inside. Secondly, assuming there is a farmland, we take advantage of nematodes’ movement analogue simulation to find the best position where the device should be placed and the best concentration of attracting substance. Thirdly, according to this concentration, we obtain the best size of the device by calculating. At last, we establish a database to enlarge applied range of our method to kill other pests. We would appreciate that new synthetic biological and environment-friendly methods can be shared and improved with the science researchers all over the world.


3. Acknowledgement

Thanks:


Prof. Zhu Xudong, Prof. Yang Dong and Prof. Xiang Benqiong

Offered us much precious advice on the project.


Hao Xiaoran, Chi Xiaodong, Huo Liang, Ai Ying and Wang Xuan

Offered us advice on our experiments and helped us solve problems.


The College of Chemistry, Beijing Normal University

Helped us do GC-MS.


Prof. Yang Chonglin of Chinese Academy of Sciences

Offered us C.elegens and taught us how to cultivate them.


Prof. Li Hongmei of Department of Plant Pathology，Nanjing Agricultural University

Helped us to do Species identification of nematodes.

BIT-China & ZJU-China & FAFU-CHINA

Offered us some helpful advice and we also had a collaboration together.


Agricultural Service Center of Ceyu, Hebei Province

Helped us learn more information about the damage caused by local nematodes and villager’s attitude towards agricultural insecticide.


Shang Zhong National Middle School of Guizhou Province

Supported us in our voluntary education.


National Chiao Tung University &Peking University

Provided us opportunities to communicate with other teams.


Feng Xiaofei and her family in Hebei Province

Helped us get soybeans samples and did a survey in the locality.


Prof. Wang Yingdian

Discussed the bright future of our project with us.


Sponsors:



Beijing Normal University (BNU), is a public research university located in Beijing with strong emphasis on basic disciplines of humanities and sciences. It is one of the oldest and most prestigious universities in China. Our school supported us to our iGEM Journey and provided us adequate resources to complete the competition. Students of different colleges in our school took part in our team, and all these colleges supported us very much.


4. Notebook

4.1 Wet Lab


4.2 Dry Lab

Week 1

After we determined the theme of our project, we recuited more undergraduates from related colleges, including college of Mathematics, Physics and Computer Science. After a short meeting, four undergraduates joined our team. Congratulations!


Week 2-3

The first Modeling group meeting was held, during which time we introduced the International Genetically Engineered Machine Competition and our team & project to our new members.


Week 3-4

Modeling group members read some related materials and papers, including wikis of former teams especially their modeling parts as well as papers introducing nematodes.


Week 5-6

Together with members majoring in physics, mathematics and biology, we drafted an abstract settlement concentrating on how to simulate the concentration of nematodes in chemotaxis. The goal of our modeling project is to give a best attractant of concentration so that we can determine the most economical plan.


Week 7

We realized that our original assumption that we regard nematodes as static models cannot react to some essential properties of nematode moving. So we changed our minds into using dynamic methods to simulate the diffusion of nematodes in chemotaxis. We decided to apply Celluar Automata to solve the problem.


Week 8

Since we can get the solution of best concentration of attractant and the diffusion of nematodes, we decided to go towards a further step. What is needed urgently in agriculture product is a low-cost and more importantly environment-friendly device to kill nematodes. Finally our plan was to design and build a debug device.


Week 9

We built a device all by handwork! There was a big change in the process. At first, we wanted to design in CAD software and built it by 3D print. However, the cost of product by 3D print was too high. Finally, we chose traditional technology to produce devices in the future if it was verified that our device had high value of application. Of course, we also cannot afford the cost of custom-built sample. That’s why we had to make it by hand.


Week 10

Another important module of our project is to build a database which researchers and even farmers can get information of bio-pesticide easily. We started to work on it.


Week 11

We reviewed the work we had done together and made a specific plan for following days. First, we had built simulation model and we can use it to build economic model. Second, the device we had made actually was not applicable enough, which required further improvement. Third, we had built a basic frame of the database.


Week 12

We put the database on the github.com and it can be edited and added new items by all users.


Week 13
Week 14
Week 15

5.1 Cloning


PCR
  • Reaction System:

    H2O 38 \(\mu\)l

    10x Taq buffer 5 \(\mu\)l

    2.5mM dNTP 4 \(\mu\)l

    Primer 1 1 \(\mu\)l

    Primer 2 1 \(\mu\)l

    Template 0.5 \(\mu\)l

    Taq 0.5 \(\mu\)l

  • Process:

    \(\begin{equation}\left. \begin{array}{lcl} {94&#176C\ 10min} \\ {94&#176C\ 30s} \\{58&#176C\ 30s} \end{array} \right\} Cycle\ 30\end {equation}\)

    94&#176C 10min

    94&#176C 30s

    58&#176C 30s

    72&#176C 2min30s

    72&#176C 10min

    10&#176C ---


    • Electrophoresis---Gel Purification
  • Material:

    Agarose gel: 1% agarose dissolved in 1 x TAE + gelstain

  • Protocol:

    We used gelstain to stain the DNA and imaged it in a Transilluminator.

    We used the gel extraction kit to get the objective fragment.


    • Digestion
    50\(\mu\)l reaction system
    Reagent 10x H buffer EcoR I Pat I Plasmid H2O
    Dosage 5 \(\mu\)l 1.5 \(\mu\)l 1.5 \(\mu\)l 15 \(\mu\)l 27 \(\mu\)l
    10ul reaction system
    Reagent 10x H buffer EcoR I Pat I Plasmid H2O
    Dosage 1 \(\mu\)l 0.3 \(\mu\)l 0.3 \(\mu\)l 3 \(\mu\)l 5.4 \(\mu\)l

    Ligation
    Ligation reaction system
    Reagent Cph8 PSB1C3 T4 buffer T4 ligase
    Dosage 14 \(\mu\)l 3 \(\mu\)l 2 \(\mu\)l 1 \(\mu\)l

5.2 Transformation

  • Material:
    • LB liquid medium
    Reagent Tryptone Yeast extract powder NaCl
    Dosage 10 g/L 5 g/L 10 \(\mu\)l

  • Protocol:

    preparation of the competent cells

    20\(\mu\)l ligation product + 50\(\mu\)l cells

    Heatshock of E.coli BW25113(42C,90s)

    Put on ice(2min)

    Add 800ul LB media and incubate for 1.5h(37C, 150rpm)

    Centrifuge at 4000rpm for 1min and remove 900ul supernatant

    Resuspend the pellets using the left supernatant

    Spread plates(with ampicillin)

    Incubate for 12~16h(37C)


5.3 Detetion


SDS-PAGE
  • Materials:
    Gel Tris-HCl Acr/Bis 30% SDS 10% ddH2O TEMED AP 10%
    Stacking Gel(4%) pH=6.8 500\(\mu\)l 500 \(\mu\)l 25 \(\mu\)l 1350 \(\mu\)l 2.5 \(\mu\)l 12.5 \(\mu\)l
    Running Gel(12%) pH=8.8 1250 \(\mu\)l 2000 \(\mu\)l 50 \(\mu\)l 1675 \(\mu\)l 2.5 \(\mu\)l 25 \(\mu\)l
    Running Gel(18%) pH=8.8 1250 \(\mu\)l 3000 \(\mu\)l 50 \(\mu\)l 675 \(\mu\)l 2.5 \(\mu\)l 25 \(\mu\)l
    Running Buffer
    Reagent Tris-HCl Glycine (w/v) SDS
    Dosage 25 mmol/L 0.192 mol/L 0.1%
  • Protocol:

    The SDS polyacrylamide gels are prepared in the so-called PerfectBlue™ Twin Double Gel System.

    After ensuring that the equipment is waterproof, the 12 % (or 18%) running gel is mixed and filled into the chamber. Pipetting about 1 ml of H2O on top of the running gel to seal the gel.

    After polymerization, the remaining H2O is removed and the 12 % stacking gel is filled on top. Insert a comb to create sample pockets.

    After the stacking gel also polymerized, 1 x running buffer is used to run the Double Gel System via the SDS gel.

    After loading the generated pockets with the samples, the stacking gel is run at 100 V and then running gel at 120 V.


Detection of Baiting Nematodes
  • Materials:

    Pure chemical compound: linalool and limonene.

    Solvent: DMSO

    Dissolve the compounds with DMSO to set a series of concentration gradient of attractant.

  • Protocol:

    Synchronize the nematodes.

    Divide the NGM solid medium (d = 6 cm) equally into two parts (drawing on the surface of the culture dishes).

    Put 50 \(\mu\)l compound of different concentration and DMSO as contrast respectively on the two parts. Make 3 repeats of each concentration.

    Flush nematode from the plate with M9 and inoculate 20 \(\mu\)l (about 30 nematodes) into the center of the medium.

    Incubate at 20&#176C for 1hr, and then place them at 4&#176C refrigerator for 1hr.

    Count the nematodes of each part under the stereoscope.

    Compare the results of different compound concentration and make a conclusion.


Detection of Killing Nematodes

    Inoculate 5mL LB liquid mediums added Chl with experimental group E.coli BW25113 (transformed with rMpl or bace16 genes) and blank control group separately. Incubate at 37&#176C, 190r.m.p for 3 hr.

    Mix up 800\(\mu\)l control group and 200ul experimental liquid medium Inoculate 1mL mixture mentioned above to NGM plate. Incubate upside down at 37&#176C overnight.

    Flush nematodes from the plate with M9, centrifugate (1500r.p.m,3min), abandon the supernatant and resuspend the precipitation with 3mL M9.

    Add 500ul resuspended solution to the NGM plate inoculated with mixed E.coli as mentioned above as experimental group and NGM plate with blank E.coli as control group. 37&#176C incubate overnight.

    Observe and compare the activation and size of nematodes of each group and draw a conclusion.


5.4 Nematode

  • Materials:

  • NGM medium:

    • Minimum Medium
    Reagent NaCl Bacto peptone（BD 4059002) Agar ddH2O
    Dosage 3 g 2.5 g/L 17 \(\mu\)l 975 ml

    Prepare 1mol/L CaCl2, 1mol/L MgSO4 and phosphoric acid buffer meanwhile.

    Phosphoric Acid Buffer
    Reagent KH2PO4 KHPO4 ddH2O
    Dosage 108.3 g 35.6 g/L 1 L

    Autoclave the above mentioned reagents with 120C for 30 min and then water bath them to 65C.

    Dissolve the cholesterol with ethanol to 5 mg/ml.

    Add 1ml cholesterol, CaCl2, MgSO4 and 25 mL phosphoric acid buffer into the minimum medium in order (all at 65&#176C, shake up).

    Make plate with the NGM medium, storing at 4&#176C.


  • OP50 E.coli deficit type (food of nematodes):

    • Streak inoculate OP50 on LB solid medium, Incubate at 37&#176C for 6 hr or overnight. Inoculate LB liquid medium with OP50 single colonies, and incubate (37C, 220r.p.m) overnight.


Cultivate
  • The incubation condition of caenorhabditis elegans N2 wild type:

    Generally incubated at 20&#176C. Grow slowly at 16&#176C and grow fast at 25&#176C while egg laying amount declines.


  • Protocol:

    • Inoculate NGM medium with 150~200 \(mu\)l OP50, incubate at 37&#176C for 12hr. Cut down a square of NGM(about 1cm x 1cm) with nematodes.

    Put the square on the NGM medium with OP50 and let the surface with nematodes adown to contact the medium.

    Seal and incubate upside down at 20&#176C.

    Watch the growth condition of nematodes under the stereoscope everyday and re-inoculate every 4 to 5 days to avoid the nematodes growing too densely.

    For inoculating abundant nematodes rapidly, or changing plate to provide more food and better condition for them, we can flush them with M9 and centrifuge them with 1500r.m.p for 1 min, and incubate the precipitate on a new plate.


    Synchronization
  • Materials:
    • M9 NS
    Reagent Na2HPO4 KH2PO4 NaCl 1M MgSO4 ddH2O
    Dosage 6 g 3 g 5 g 1 ml 1 L
    Bleach Buffer
    Reagent NaOCl 5M NaOH ddH2O
    Dosage 50 \(\mu\)l 100 \(\mu\)l 850 \(\mu\)l

  • Protocols:

    • We have tried several methods and two of them succeed as mentioned below, we recommend the first one by comparison.

    1. Flush and incubate

    Flush the nematodes with M9 NS

    Centrifugation (3000r.m.p, 1min)

    Abandon the supernatant, add 1mL bleach buffer to the precipitation

    Centrifugation (3000r.m.p, 1min), abandon the supernatant

    Transfer the precipitation (nematode eggs) to a NGM plate with OP50, then the eggs will incubate synchronously.

    2. Directly pick

    Transfer 30 nematodes that are under egg laying period to a new NGM plate with OP50. Generally, the egg laying nematodes can lay about 8 eggs per hour. Remove all nematodes after 2hr.

    Incubate the plate at 20&#176C for 3d and therefor can get about 300 to 400 nematodes.

    Note: all of the procedure outlined above must be conducted under sterile condition.


    Isolate nematodes from soil
  • modified Baermann funnel method:

    • 1. Place a glass funnel (d = 10~15cm) on the funnel stand linked with about 10cm rubber tube which is furnished with a flatjaw pinchcock.

    2. Cut the soil sample into matchstick shape. Package 10g(wet weight) with gauze and put it into the funnel, and then add water to immersion the sample.

    3. After 4~24 hr, nematodes leave the plant tissue and swim in the water and ultimately precipitate at the bottom due to their gravity and hydrotaxis.

    4. Open the flatjaw pinchcock, adopt about 5~15 mL liquid sample from the bottom which obtains most active nematodes of the soil sample. Check under the stereoscope and count nematodes, or centrifugate(1500 r) first and check the precipitation if the nematodes are too few.

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