Difference between revisions of "Team:FAFU-CHINA/Modeling"

Revision as of 12:18, 18 September 2015

侧边栏

Background

Apiculture in the world

No one knows since when did humans begin to attempt to domesticate honeybees, just like no one knows exactly how important these little creatures can be to human civilization and world environment.

Honeybees may be most famous for the stored honey they serve up, but there are a few more useful things they do as well. They produce beeswax, which gives us the manufactures of candles and many other sorts of products. They produce royal jelly, which is extremely famous for preserving people’s health. Moreover, they pollen plants, which is the most fundamental ecological process and makes everything in nature possible.

Today, in China, apiculture is a vital economic generator for the country, producing average 245,000 metric tons and estimating at 238,000 metric tons of consumption in honey per year. In America, it creates 210,000 direct jobs for people, and it is a crucial element of U.S agriculture, which relies on apiculture for pollination. it is impossible to define the economic value of apiculture. According to a data released by Times, almost 1/3 of food of the world is dependent on honeybee’s pollination. If all the honeybees die out, thousands of plants will follow, which could leads to millions of people starving in the following years.

Einstein once said that’if all the bees die out, humans will follow a few years later.’ It is unsettling to inform you that, honeybees have started to disappear. In recent years，beekeepers have witnessed an annual 30% losses in their colonies. For the Europe alone, bees are greatly declining, from 5 million hives in 1988 to 2.5 million today. Since 2006, a phenomenon called Colony Collapse Disorder has spread to every corner of the world. We don’t exactly know what is causing it. The only thing we know is that it is pretty serious, and measures must be taken immediately.

Sacbrood Virus

Sacbrood Virus has been a scourge to apiculture over the world for almost half of a century. Sacbrood Virus is a typical RNA virus. It causes failure of larval pupation, and results in larval death. With SBV accumulating beneath larval skin, Infected larva changes in color from pearly white to pale yellow, forming a brown gondola-shaped scale after death. Different Sacbrood virus samples originate from various geographic regions. In China, it is classified as Chinese Sacbrood Virus (CSBV). According to a research from Jilin University, in some provinces of China, 60 percent of bee tribes carries CSBV, and the death rate of larvae is almost 100 percent during outbreaks.

CSBV is one of the main causes of the significant decrease of Chinese honeybee populations in the past 40 years. So far, no effective control method exists for this bee disease, besides the prevention strategy, the only one beekeepers adopting currently. FAFU-China team aims to investigate the possibility of controlling this disease through silence of CSBV’s RdRp (RNA-dependent RNA polymerase) gene by using RNA-interference technology.

RNA-interference

The RNA-interference naturally exists in many eukaryotes, including honeybees. It plays an crucial role in defending somatic cells against viruses. The biological process is known for it’s ability to inhibit gene expression by causing the destruction or silence of specific messenger-RNA molecule.

Double-stranded ribonucleic acid (dsRNA) molecules is essential to RNA-interference. In the very beginning, the Dicer enzyme initiates the biological process by cleaving dsRNA into small interfering RNA (siRNA). Next, the small interfering RNAs are soon separated into two single strands. The positive-strand which is also known as guide-RNA is then integrated into an active RNA-induced silencing complex, RISC. RISC can bind to it’s target mRNA by base-pairing and cleave it, preventing the mRNA from producing a protein.

Theory

Replication of CSBV

As a typical RNA virus, CSBV’s replication process is initiated once the messenger RNAs of CSBV, which is CSBV’s original genetic information, are injected into somatic cells. However, a essential complex for the replication of genetic information of CSBV is lacked in the somatic cells of honeybees, RNA dependent RNA polymerase, RdRp in short. RdRp can be synthesized directly by ribosome of honeybees using mRNA of RdRp as temperate. With the existence of RdRp, the replication of genetic information of CSBV can be completed and CSBV will soon spread out infect the whole organism.

This year，FAFU-China aims to investigate the possibility of controlling this disease by inhibiting the expression of RdRp gene through RNA-interference.

CSBV.Silencer 1.0

We designed a engineered bacteria capable of producing double-stranded RNA of RNA dependent RNA polymerase （RdRp）to initiate the process of RNA-interference. We inserted the RdRp gene into plasmid L4440, and inserted T7 promoters in the upstreams of both strands of the plasmid. two contemporary messenger-RNAs of RdRp can be synthesized simultaneously after T7 polymerases detect the promoters in both strands and start the transcription from 5 prime to 3 prime.

The contemporary messenger RNAs will then bind together into double stranded RNA by base-pairing. Long dsRNA of RdRp is then cleaved by Dicer enzyme and short small interfering RNA is formed. small interfering RNA will soon separate into two single strands. One is called passenger RNA, which is soon degraded. And the other strand called guide RNA will then integrated into an RNA Induced Silencing Complex, RISC in short. RISC then binds to the specific sequence of mRNA of RdRp and destruct it, thereby preventing it from being used as translation template to produce RdRp.

We transferred plasmid L4440 into E.coli so that dsRNA of RdRp can be largely produced. Then we mixed our product, CSBV.Silencer, into forage of honeybees, and feed it to infected hives. After the infected honeybees take in CSBV.Silencer, the replication process of CSBV in will be destructed in the somatic cells of honeybees, for the essential RdRp complex can not be formed.

CSBV.Silencer 2.0

On the basis of CSBV.Silencer 1.0, we decided to improve our product,out of two concerns.

In the field of food industry, safety concern is always a sensitive problem. E.coli is always taken as potential pathogen by consumers unconsciously，and because of that, we decided to replace E.coli by Yeast which originally exists in honey.

If we want to transfer CSBV.Silencer into honeybees, we need to consider the influence imposed by immune system and digest system. We need to find a way to prevent our product from being degraded by immune cells and digestive solution. The need to enable the engineered bacteria getting through the digest system without being harmed also requires us to replace the E.coli by using eukaryote as carrier.

However, if we want to use eukaryotic system to produce the dsRdRp, there is still a problem needed to be solved. In eukaryotic system, there is no T7 polymerase, which causes failure in transcription of L4440, leading dsRdRp unable to be synthesized. To solve this, we have another plasmid capable of producing T7 polymerase, PyES2.

After galactose induces Gal1 promoter, activating RNA polymerase to transcript the gene of T7 RNA polymerase, mRNA of T7 RNA polymerase can be expressed and T7 polymerase is produced. the produced T7 polymerase can go back to the T7 promoter in the upstream, and continue making more T7 polymerases. The circulation of making T7 polymerase ensures the abundance of T7 polymerases, which actually accelerates the process of producing dsRdRp.

Our next product, CSBV·Silencer 2.0, will be the engineered yeast containing plasmid PyES2 and plasmid L4440. However, in this stage, we have only come up with the idea and are still trying to recombine the plasmid PyES2. As long as we have the recombined plasmid PyES2 ready, we will then transfer PyES2 and L4440 into yeast, and have our product applied to practice.

Meanwhile,we noticed that IPTG could induce the expression of dsRdRp in HT115, and galactose could improve the efficiency of GAL1 in eukaryotic system

Easier to spread

Eusocial insects like ants, honeybees, bumble, termites have the habit of cooperative care of young. The larvae in the family are unable to forage and feed themselves, and because of that, the food delivered by workers are essential. this habit enables CSBV.Silencer flow through the whole insect family rapidly.Through the mechanism, CSBV.Silencer can be diffused easily and the effect can be detected rapidly.

Similarly, the mechanism can be adopted in the prevention of other virus disease of eusocial insects or biological control. We are planning to develop a medicine of termite control through silence of certain gene. We predict that the medicine can be delivered with food throughout the whole colony, and achieve the purpose of pest control.

Protocol

Whole RNA Extraction

We use Trizol to extract the whole RNA of CSBV,and the detail protocol is showed as bellow:

1.Take 50-100mg tissue stored in -80℃ or liquid nitrogen. Grind the tissue into powder in mortar with liquid nitrogen. Transfer the powder into a 1.5ml EP tube(RNase-Free).

2.Add 500μl Trizol, vortex to mix thoroughly and let the tube sit at room temperature for 10 min.

3.Centrifuge at 12,000 x g for 10 min at 4℃.Transfer the supernatant into a new 1.5ml EP tube(RNase-Free).

4.Add 100μl chloroform, vigorously shake with hand for 15s and then let the tube sit at room temperature for 10 min.

5.Centrifuge at 12,000 x g for 15 min at 4℃. Transfer the upper colourless aqueous phase into a new 1.5ml EP tube(RNase-Free).

6.Add 250μl isopropanol, turn the tube upside down many times for around 10 min, and let it sit at room temperature for 10 min until the white floccule arise,and then centrifuge at 12,000 x g for 10 min at 4℃.

7.Discard the supernatant,add 500μl,75%ethanol with DEPC,and mix thoroughly.Centrifuge at 7,500 x g for 5 min at 4℃ and discard the supernatant.

8.Dry it at room temperature or in the bechtop for 15 min.

9.Add 15-20μl RNase-Free water to dissolve RNA when the precipitate become transparent.

10.Store RNA at -80℃.

RT-PCR and PCR

We amplify DNA of CSBV by RT-PCR and PCR. And the detail systems and programs are showed as bellow:

1.RT-PCR（using M-MLV Reserve Transcriptase kit bought from Promega company

ComponentVolume(μl)

Whole RNA of CSBV4.0

dNTP Mixture(10mM)4.0

Reserve primer2.0

70℃ pre-denaturation10min

Component(add in order) Volume(μl)

5×M-MuLV buffer4.0

RNase free water4.5

M-MLV Reserve Transcriptase1.0

42℃1h

72℃15mins

Store cDNA at -20℃

2.PCR

(1)System(50μl)

10×PCR Buffer5.0μl

2.5mM dNTP Mix2.0μl

Template(cDNA)2.0μl

Primer F2.0μl

Primer R2.0μl

Dream Taq DNA pol0.5μl

ddH2O36.5μl

Volume50.0μl

(2)Program

94℃5min

94℃30s

55℃(Tm-5℃)30s

72℃T(1min/kb) 2 34

72℃10min

16℃∞

qPCR

We use GoTaq? qPCR Master Mix Kit(buy from Promega company) and Eppendrof Mastercycler? ep realplex Real-Time PCR to do qPCR.

(1)System(20μl)

SYBR Premix Ex TaqTM 2×mix10.0μl

Template(cDNA)1.0μl

Primer F0.4μl

Primer R0.4μl

RNase-Free water8.2μl

Volume20.0μl

(2)Program

95℃2min

95℃20s

60℃20s

72℃30s

72℃10min

16℃∞

Plasmid Extraction

We use E.Z.N.A. Plasmid DNA Mini Kit I bought from OMEGA bio-tek company to
extract plasmids and the detail protocol is showed as bellow:

1. Isolate a single colony from a freshly streaked selective plate, and inoculate a culture of 1- 5 mL LB medium containing the appropriate selective antibiotic. Incubate for ~12-16 hours at

37°C with vigorous shaking (~ 300 rpm).

2. Centrifuge at 10,000 x g for 1 minute at room temperature

3. Decant or aspirate and discard the culture media.

4. Add 250 mL Solution I/RNase A. Vortex or pipet up and down to mix thoroughly.

5. Transfer suspension into a new 1.5 mL microcentrifuge tube.

6. Add 250 mL Solution II. Invert and gently rotate the tube several times to obtain a clear lysate. A 2-3 minute incubation may be necessary.(Avoid vigorous mixing)

7. Add 350 mL Solution III. Immediately invert several times until a flocculent white precipitate forms.

8. Centrifuge at maximum speed (≥13,000 x g) for 10 minutes. A compact white pellet will form. Promptly proceed to the next step.

9. Insert a HiBind DNA Mini Column into a 2 mL Collection Tube.

10. Transfer the cleared supernatant from Step 8 by CAREFULLY aspirating it into the HiBind DNA Mini Column. Be careful not to disturb the pellet and that no cellular debris is transferred to the HiBind DNA Mini Column.

11. Centrifuge at maximum speed for 1 minute.

12. Discard the filtrate and reuse the collection tube.

13. Add 500 mL HB Buffer.

14. Centrifuge at maximum speed for 1 minute.

15. Discard the filtrate and reuse collection tube.

16. Add 700 mL DNA Wash Buffer.

17. Centrifuge at maximum speed for 1 minute.

18. Discard the filtrate and reuse the collection tube.

19. Centrifuge the empty HiBind DNA Mini Column for 2 minutes at maximum speed to dry the column matrix.

20. Transfer the HiBind DNA Mini Column to a clean 1.5 mL microcentrifuge tube.

21. Add 30-100 μl Elution Buffer or sterile deionized water directly to the center of the column membrane.

22. Let sit at room temperature for 1 minute.

23. Centrifuge at maximum speed for 1 minute.

24. Store DNA at -20°C.

Gel Extraction

We use E.Z.N.A. Gel Extraction Kit bought from OMEGA bio-tek company to recover our target fragments after AGE and the detail protocol is showed as bellow:

1. Perform agarose gel/ethidium bromide electrophoresis to fractionate DNA fragments. Any type or grade of agarose may be used. However, it is strongly recommended that fresh TAE buffer or TBE buffer be used as running buffer. Do not reuse running buffer as its pH will increase and reduce yields.

2. When adequate separation of bands has occurred, carefully excise the DNA fragment of interest using a wide, clean, sharp scalpel. Minimize the size of the gel slice by removing extra agarose.

3. Determine the appropriate volume of the gel slice by weighing it in a clean 1.5 mL microcentrifuge tube. Assuming a density of 1 g/mL, the volume of gel is derived as follows: a gel slice of mass 0.3 g will have a volume of 0.3 mL.

4. Add 1 volume Binding Buffer (XP2).

5. Incubate at 60°C for 7 minutes or until the gel has completely melted. Vortex or shake the tube every 2-3 minutes.

6. Insert a HiBind DNA Mini Column in a 2 mL Collection Tube.

7. Add no more than 700μl DNA/agarose solution from Step 5 to the HiBind? DNA Mini Column.

8. Centrifuge at 10,000 x g for 1 minute at room temperature.

9. Discard the filtrate and reuse collection tube.

10. Repeat Steps 7-9 until all of the sample has been transferred to the column.

11. Add 300 mL Binding Buffer (XP2).

12. Centrifuge at maximum speed (≥13,000 x g) for 1 minute at room temperature.

13. Discard the filtrate and reuse collection tube.

14. Add 700μl SPW Wash Buffer.

15. Centrifuge at maximum speed for 1 minute at room temperature.

16. Discard the filtrate and reuse collection tube.

17. Centrifuge the empty HiBind DNA Mini Column for 2 minutes at maximum speed to dry the column matrix.

18. Transfer the HiBind DNA Mini Column to a clean 1.5 mL microcentrifuge tube.

19. Add 30-50μl Elution Buffer or deionized water directly to the center of the column membrane.

20. Let sit at room temperature for 2 minutes.

21. Centrifuge at maximum speed for 1 minute.

22.Store DNA at -20°C.

CTAB Extraction of dsRNA

1.Pipet 2mL bacterium suspension, centrifuge at 5,000rpm for 1 minute.

2.Discard the supernatant, add 500μl TE Buffer(10mmol· L-1Tris, 1mmol· L-1EDTA,PH7.5) and resuspend.

3.Add 30μl 10%SDS,mix thoroughly and put it in 37℃ incubator for 1h.

4.Add 100μl NaCl(5mol· L-1), mix thoroughly.

5.Add 80μl CTAB/NaCl, mix thoroughly, 65℃ water bath for 10min.

6.Add isometric phenol/ chloroform/isoamylol mixture(25:24:1), mix thoroughly and centrifuge at 12,000rpm for 5 minute at 4℃.

7.Transfer the supernatant into a new 1.5 mL microcentrifuge tube. Add 3/5 volume of it isopropanol. Centrifuge at 12,000rpm for 10 minute at 4℃.

8.Discard the supernatant, add 500μl 75% ethanol, vortex to mix thoroughly, and centrifuge at 6,000rpm for 5 minute at 4℃.

9.Vacuum dry for 10minute, and digest with DNase(1U), RNase(1U) respectively.

10.Store dsRNA at -80℃ or use for next experiment immediately.

Dual-enzyme digestion

1.Vector 10.0μl

Restriction enzyme(EcoR1,Pst1) 0.5μl

Buffer(10×H) 2.0μl

ddH2O 7.0μl

Volume 20.0μl

37℃ metal bath,8h or overnight.

2.Recover target fragments by gel extraction.

Linkage and transformation

1.Linkage system(10μl): Target fragment 4.0μl, Vector 1.0μl, 5×Buffer 2.0μl, T4 ligase 1.0μl, ddH2O 2.0μl. 4℃, overnight.

2.Add the product of linkage into 50μl DH5αcompetent cell, pipet up and down gently to mix thoroughly, and put it on ice for 30min.

3.Heat in 42℃ water bath for 90s, and take it out immediately and put it on ice for at least 2min.

4.Add 200μl LB medium without any selective antibiotic. Incubate for 45min at 37℃with vigorous shaking (~ 220 rpm).

5.Pipet 150μl bacterium suspension and smear it on LB plate with the appropriate selective antibiotic. Culture in 37℃ incubator,overnight.

CSBV.Silencer 2.0

Preliminatry experiment

The effect of different homologous dsRNA of CSBV to the expression of CSBV’s mRNA.

To find the most effective homologous dsRNA of CSBV for our project, we tested the pupation rate of honeybee larvae under different dsRNA. We added different homologous dsRNA of CSBV (dsHelicase, dsProtease, dsRdRp and dsVP1) into forage and fed to the infected larvae. After 12 hours, We fed the larvae with extracted fluid of CSBV, and kept feeding it in the following day. According to the statistics we collected, infected larvae fed with dsRdRp have the highest pupation rate among all the experimental groups.

The effect of CSBV.Silencer in curing the disease

We fed the infected hives with our CSBV·Silencer, and collected the following statistics under the help of professional beekeepers from College of Bee Science.

1.The decrease of the number of infected larvae.

Compared with the control group, it is quite obvious that the infected larvae in medium concentration group and in high concentration group dropped dramatically by 91.44 percent and 94 87.91 percent after 14 days while the infected larvae in control group showed 65.82 percent increase after 7 days.

2.The effect of dsRdRp on the number of sealed brood.

The number of sealed brood is another indicator of the effect of CSBV. It is an necessary stage of larval pupation. In this graph, the number of sealed brood in medium concentration and high concentration increases by about 23.68% and 30.10% after 21days. Similarly, the result witnesses a significant improvement in the pupation rate.

3.The increasing population.

We counted the number adult honeybees to study the changes of population.The changes are just as you see. For the high concentration group alone, the growth of population had reached almost 60% in just 21 days. On the contrary, the control group showed a 27.78% decrease after 21 days.

These statistics directly proved that, our product, CSBV.Silencer 1.0 does have a remarkable effect in the treatment to Sacbrood disease.

The effect of galactose to induce GFP expression at different concentrations and different time.

1.The galactose at three different concentrations can induce GFP expression efficiently and have little influence on the level of GFP

We transformed GFP-pYES2 into the yeast and let the recombinant strain grow to mid-log phase in YEPD medium containing 2% glucose. And then we transferred it to medium, containing 2%, 0.1% or 0.02% galactose, and assayed for GFP fluorescence.

According to the statistics we collected, we find that the production of GFP protein is quite high even though at 0.02% galactose and with the increase of its concentration, the level of GFP have no remarkable change.

2.GFP production sharply increases and a peak shows up in about 24h under the induction of galactose.

The yeast transformants were grown in YEPD medium. At a cell density of 2 ×107 ml-1, cultures were washed and galactose added to a final concentration of 2% and the fluorescence value of samples was measured every 5h.

As the diagram shown, we can find that GFP production sharply increases in 10h and a peak shows up in about 24h and then it decreases gradually.

In conclusion, we can find using 0.02% galactose to induce the expression of GFP in 24h is a reasonable and efficient way to get the most production of GFP protein. It means that we can induce the expression of T7 RNAP gene efficiently under the same condition.

Notebook

2015.6.8

Today was the first day that we began our project in the lab after we made a scientific plan. Firstly, we extracted the whole RNA of CSBV by Trizol. As we all know, RNA is easy to be digested in the environment. Therefore although we did this quickly, there were still some samples without RNA fragment. But we did again and the result was satisfied at that time. It was encouraging!

2015.6.9

Today we made RT-PCR with four sets of reverse specific primers and the RNA of CSBV to synthesize homologous cDNA(CSBV Helicase、Protease、VP1 and RdRp respectively). Then dsDNAs was amplified with four sets of specific primers by PCR. It went through smoothly. So far, we got the target fragments successfully. Also,we used GFP F/R to amplify GFP gene.

2015.6.10

We utilized T7 RiboMAXTM Express RNAi System kit and dsDNAs as templates to synthesize dsRNAs(dsHelicase、dsProtease、dsVP1、dsRdRp and dsGFP), but there were only dsHelicase and dsGFP we could get. We tried again and still failed. It took our whole day to find the reason. Tomorrow we will ask our advisor for some solutions and do it one more time.

2015.6.12

After figuring out the problem, we eventually got the all right dsRNAs. Another part, we began to prepare the larvae of Chinese honeybee which was offered by our institute of bees.

2015.6.13

We put dsRNAs into fodder of the larvae of the honeybee to feed them. Then after 12h, we fed them another fodder with CSBV extracting solution. We did so twice before they got normal fodder.

2015.6.17

During three days, we observed the change of percentage of pupation and collect and analyse data. Meanwhile,RT-qPCR was done to detect the effect of different dsRNAs to CSBV. According to the result, we found that dsRdRp made a remarkable influence on the replication of CSBV. So we decided to use dsRdRp to inference CSBV.

2015.6.19

We used cDNA of RdRp and specific primers(Not1-F/Pst1-R、EcoR1-F/Pst1-R) to synthesize RdRp gene. However, after agarose gel electrophoresis(AGE), we could not find our target fragment.

2015.6.20

We changed a better DNA polymerase and set the annealing temperature to 60℃. Finally we got the RdRp gene.

2015.6.22

We picked the colonies to do PCR and sent the positive sequencing(M13).

2015.6.24

Today we got the result of sequencing. After comparing with data in NCBI, we only had two 100 percent samples. We started to do double enzyme digestion(Not1 and Pst1、EcoR1 and Pst1) to cut vector L4440、pSB1C3 and RdRp-T recombinant plasmid.

2015.6.25

We made RdRp gene link with T vector in 25℃, 15min and then transformed it into DH5α,a kind of competent cell, which was cultured in 37℃,overnight.

2015.6.26

We made it! And we immediately did gel recovery. Then we began to link RdRp with L4440 and pSB1C3 using T4 ligase, 4℃, overnight.

2015.6.27

We did transformation. However,we forgot to make LB medium with CmRR. So the transformation of RdRp-pSB1C3 could only be done tomorrow.

2015.6.29

Today there was two news. The good one was we successfully got recombinant plasmid RdRp-L4440 while the bad one was nothing grew on the plate with CmRR. We thought maybe it was because RdRp did not link with pSB1C3 successfully. Anyway we would do it again tomorrow.

2015.7.2

On the one hand, we still could not link RdRp with pSB1C3 so that there still nothing on the plate. We wonder if it was because of the efficiency of ligase or anything. On the other hand,we prepared another competent cell,HT115,which included T7 RNAP gene in its genome. It was used as engineering bacteria for expressing dsRdRp.

Also, considering the biosecurity of E.coli, we decided use yeast as the final transformation target. So we want to recombine another vector,T7 RNAP-pYES2.

2015.7.3

We transformed RdRp-L4440 into HT115,culturing in 37℃. Overnight. And T7 RNAP gene was amplified by PCR(EcoR1-F/Xho1-R).

2015.7.4

Today we used IPTG, which was divided into two groups with different concentrations(0.4mmol/ml、0.8mmol/ml), to induce the expression of dsRdRp in HT115 for 5h. Then we collected the bacteria to extract dsRdRp by CTAB. According to the result of AGE, dsRdRp had been expressed in HT115 successfully, even though its concentration was a little bit lower. It was really a good news for us!

2015.7.5

We added engineering bacteria with expressed dsRdRp, which was divided into three groups with different concentrations(low、mediate and high), into the fodder of the infected swarms. And another infected swarm was fed normal fodder. Since now, we will obverse the change of population of them, the mortality, and the number of sealed brood and collect data every weeks until we get the obvious result.

2015.7.7

Considering we have not gotten RdRp-pSB1C3 yet,we decided to link T7 RNAP gene to pSB1C3 first. So we used specific primers(EcoR1-F/Pst1-R) to synthesize T7 RNAP gene by PCR.

2015.7.8

Transformation again!

2015.7.9

As usual, pinking the positive colonies, PCR and sequencing. We hope everything goes smoothly.

2015.7.11

According to the result of sequencing, there was no sample 100 percent matching. We did transformation again.

2015.7.13

The second sequencing was completely failed because the sequencing company could not get any plasmid. We thought maybe the replication of plasmid in competent cell(DH5α) was inefficient, so we changed another one,T1,bought from Transgene company.

2015.7.14

This time we sent plasmid rather than bacteria. Although the concentration of the plasmid was a little bit lower, it was enough to do sequencing.

2015.7.15

Considering the lower fidelity of the enzyme used for T7 amplification before, we changed into a better one called KD Plus and restarted to PCR, linking and transformation.

2015.7.16

The third sequencing still showed nothing right. We were a little disappointed, but we exactly knew that failure was a normal phenomenon in the lab.

2015.7.18

Eventually,we got the matching sample after using KD Plus. Immediately, we began to do double enzyme digestion(EcoR1/Xho1、EcoR1/Pst1).

2015.7.19

After gel recovery, we linked our target fragments to relative vectors with T4 ligase, 4℃, overnight.

Meanwhile, we collected data about the index of the condition of swarms again, which was used to analyze the effect of dsRdRp by Excel later.

2015.7.20

Transformation, plate coating,37℃, overnight.

2015.7.21

Pinking the positive colonies, PCR detection, and then plasmid extraction. It was smooth! So, we got T7 RNAP-pYES2 and T7 RNAP-pSB1C3 successfully. We stored them in -20℃.

2015.7.23

Today we went to observe the condition of swarms, and it was happy to see that the experimental groups turned to a healthier development comparing with control group. It meant that using dsRdRp expressed in E.coli to prevent and cure CSBV was working. Next, we would continue to collect more data until we draw the scientific conclusion.

2015.7.26

With the development of our project, we gradually have realized that even if using yeast can solve the problem of biosecurity, there are still other troubles, such as less expression of dsRdRp in yeast, easier to loss plasmids in yeast and harder to digest the cytoderm of yeast for Chinese honeybees.

So we need a better plan to deal with these to make a more practical production. That was what we would consider deeply in future work.

2015.7.27

Today we decided to constract RdRp-pSB1C3 again, because we thought T7 RNAP-pSB1C3 may be not a new part any more. So, we did linking. We decided if it is failed just like before this time. We had to change T4 into a faster ligase..

2015.7.29

As predicted, there was still nothing on the plate.(please tell us why you cannot grow out,bacteria!)

2015.8.1

We got the preliminary result of index of swarms. Next few days we would detect the expression quantity of CSBV in offspring.

2015.8.2

We made the figure of the effect of dsRdRp on the number of sac-like larvae. It showed that the number of infected larvae which were fed with HT115-dsRdRp in mediate and high concentration was remarkably less than the control group.

2015.8.5

Other two figures were made out, which showed the effect of dsRdRp on the number of sealed brood and the population of a colony respectively. They demonstrated the similar conclusion.

2015.8.8

We detected the CSBV-carried rate of offspring by RT-PCR. After AGE, it showed that the CSBV-carried rate of first and second filial generation was 30% and 20% respectively, which was obviously declined.

2015.8.12

We detected the expression quantity of CSBV in offspring by RT-qPCR. We found with the decreasing of CSBV. The expression quantity of RdRp gene declined either, which meant that dsRdRp really could inhibit the replication of CSBV.

Last final month

Even though we were succeed in using dsRdRp expressed in proeukaryotic system to prevent and cure CSBV, we still had to take care of some problem we met. So next stage we will try to constract another plasmid with suicide gene to control the concentration of engineering bacteria. Further more, we want to use CRISPR-Cas9 system to make RdRp gene inserted into the genome of E.coli. So that we can solve the problem of biosecurity.

Communication Design

Communication design is a mixed discipline between design and information-development which is concerned with how media intermission such as printed, crafted, electronic media or presentations communicate with people.

A5源码

Communication Design

Communication design is a mixed discipline between design and information-development which is concerned with how media intermission such as printed, crafted, electronic media or presentations communicate with people.

Communication Design

Communication design is a mixed discipline between design and information-development which is concerned with how media intermission such as printed, crafted, electronic media or presentations communicate with people.

Communication Design

Communication Design

Communication design is a mixed discipline between design and information-development which is concerned with how media intermission such as printed, crafted, electronic media or presentations communicate with people.

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-{{FAFU-CHINA}}
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+<div class="com">
+<div class="com__content">
+	<section class="com__section com__section--text">
+        <div style="background-color:rgba(255,255,255,0.2);">
+   <br>
+                 <br>
-<h2> Modeling</h2>
+                 <center><div><B>Background<B></div></center>
+                 <br>
+                 <br>
+                 <img src='https://static.igem.org/mediawiki/2015/a/a0/FAFU-CHINA_BG.png'>
+                 <center><div><B>Apiculture in the world<B></div></center>
+                 <br>
+                 <img src='https://static.igem.org/mediawiki/2015/8/88/FAFU-CHINA_Background_%283%29.png'>
-<div class="highlightBox">
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>No one knows since when did humans begin to attempt to domesticate honeybees, just like no one knows exactly how important these little creatures can be to human civilization and world environment. </div>
-<h4>Note</h4>
-<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Honeybees may be most famous for the stored honey they serve up, but there are a few more useful things they do as well. They produce beeswax, which gives us the manufactures of candles and many other sorts of products. They produce royal jelly, which is extremely famous for preserving people’s health. Moreover, they pollen plants, which is the most fundamental ecological process and makes everything in nature possible.</div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Today, in China, apiculture is a vital economic generator for the country, producing average 245,000 metric tons and estimating at 238,000 metric tons of consumption in honey per year. In America, it creates 210,000 direct jobs for people, and it is a crucial element of U.S agriculture, which relies on apiculture for pollination. it is impossible to define the economic value of apiculture.
+According to a data released by Times, almost 1/3 of food of the world is dependent on honeybee’s pollination. If all the honeybees die out, thousands of plants will follow, which could leads to millions of people starving in the following years. </div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Einstein once said that’if all the bees die out, humans will follow a few years later.’  It is unsettling to inform you that, honeybees have started to disappear. In recent years，beekeepers have witnessed an annual 30% losses in their colonies. For the Europe alone, bees are greatly declining, from 5 million hives in 1988 to 2.5 million today. Since 2006, a phenomenon called Colony Collapse Disorder has spread to every corner of the world.  We don’t exactly know what is causing it. The only thing we know is that it is pretty serious, and measures must be taken immediately.</div>
+                 <br>
+                 <br>
+                 <center><div><B>Sacbrood Virus<B></div></center>
+                 <img src='https://static.igem.org/mediawiki/2015/a/a0/FAFU-CHINA_BG.png'>
+                 <img src='https://static.igem.org/mediawiki/2015/e/e3/FAFU-CHINA_Background_%280%29.png'>
+                 <img src='https://static.igem.org/mediawiki/2015/f/f6/FAFU-CHINA_Background_%281%29.png'>
+ <img src='https://static.igem.org/mediawiki/2015/a/a3/FAFU-CHINA_Background_%282%29.png'>
+                  <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Sacbrood Virus has been a scourge to apiculture over the world for almost half of a century. Sacbrood Virus is a typical RNA virus. It causes failure of larval pupation, and results in larval death. With SBV accumulating beneath larval skin, Infected larva changes in color from pearly white to pale yellow, forming a brown gondola-shaped scale after death. Different Sacbrood virus samples originate from various geographic regions. In China, it is classified as Chinese Sacbrood Virus (CSBV). According to a research from Jilin University, in some provinces of China, 60 percent of bee tribes carries CSBV, and the death rate of larvae is almost 100 percent during outbreaks. </div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>CSBV is one of the main causes of the significant decrease of Chinese honeybee populations in the past 40 years. So far, no effective control method exists for this bee disease, besides the prevention strategy, the only one beekeepers adopting currently. FAFU-China team aims to investigate the possibility of controlling this disease through silence of CSBV’s RdRp (RNA-dependent RNA polymerase) gene by using RNA-interference technology.</div>
+                 <br>
+                 <br>
+                 <center><div><B>RNA-interference<B></div></center>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>The RNA-interference naturally exists in many eukaryotes, including honeybees. It plays an crucial role in defending somatic cells against viruses. The biological process is known for it’s ability to inhibit gene expression by causing the destruction or silence of specific messenger-RNA molecule.</div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Double-stranded ribonucleic acid (dsRNA) molecules is essential to RNA-interference. In the very beginning, the Dicer enzyme initiates the biological process by cleaving dsRNA into small interfering RNA (siRNA). Next, the small interfering RNAs are soon separated into two single strands. The positive-strand which is also known as guide-RNA is then integrated into an active RNA-induced silencing complex, RISC. RISC can bind to it’s target mRNA by base-pairing and cleave it, preventing the mRNA from producing a protein.</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div><B>Theory<B></div>
+<br>
+<br>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <center><div><B>Replication of CSBV<B></div></center>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>As a typical RNA virus, CSBV’s replication process is initiated once the messenger RNAs of CSBV, which is CSBV’s original genetic information, are injected into somatic cells. However, a essential complex for the replication of genetic information of CSBV is lacked in the somatic cells of honeybees, RNA dependent RNA polymerase, RdRp in short. RdRp can be synthesized directly by ribosome of honeybees using mRNA of RdRp as temperate. With the existence of RdRp, the replication of genetic information of CSBV can be completed and CSBV will soon spread out infect the whole organism. </div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>This year，FAFU-China aims to investigate the possibility of controlling this disease by inhibiting the expression of RdRp gene through RNA-interference.</div>
+<br>
+                 <br>
+                 <center><div><B>CSBV.Silencer 1.0<B></div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>We designed a engineered bacteria capable of producing double-stranded RNA of RNA dependent RNA polymerase （RdRp）to initiate the process of RNA-interference. We inserted the RdRp gene into plasmid L4440, and inserted T7 promoters in the upstreams of both strands of the plasmid. two contemporary messenger-RNAs of RdRp can be synthesized simultaneously after T7 polymerases detect the promoters in both strands and start the transcription from 5 prime to 3 prime.</div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>The contemporary messenger RNAs will then bind together into double stranded RNA by base-pairing. Long dsRNA of RdRp is then cleaved by Dicer enzyme and short small interfering RNA is formed. small interfering RNA will soon separate into two single strands. One is called passenger RNA, which is soon degraded. And the other strand called guide RNA will then integrated into an RNA Induced Silencing Complex, RISC in short. RISC then binds to the specific sequence of mRNA of RdRp and destruct it, thereby preventing it from being used as translation template to produce RdRp. </div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>We transferred plasmid L4440 into E.coli so that dsRNA of RdRp can be largely produced. Then we mixed our product, CSBV.Silencer, into forage of honeybees, and feed it to infected hives. After the infected honeybees take in CSBV.Silencer, the replication process of CSBV in will be destructed in the somatic cells of honeybees, for the essential RdRp complex can not be formed. </div>
+                 <br>
+                 <br>
+                 <center><div><B>CSBV.Silencer 2.0<B></div><center/>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>On the basis of CSBV.Silencer 1.0, we decided to improve our product,out of two concerns. </div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>In the field of food industry, safety concern is always a sensitive problem. E.coli is always taken as  potential pathogen by consumers unconsciously，and because of that, we decided to replace E.coli by Yeast which originally exists in honey. </div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>If we want to transfer CSBV.Silencer into honeybees, we need to consider the influence imposed by immune system and digest system. We need to find a way to prevent our product from being degraded by immune cells and digestive solution. The need to enable the engineered bacteria getting through the digest system without being harmed also requires us to replace the E.coli by using eukaryote as carrier.  </div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>However, if we want to use eukaryotic system to produce the dsRdRp, there is still a problem needed to be solved. In eukaryotic system, there is no T7 polymerase, which causes failure in transcription of L4440, leading dsRdRp unable to be synthesized. To solve this, we have another plasmid capable of producing T7 polymerase, PyES2. </div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>After galactose induces Gal1 promoter, activating RNA polymerase to transcript the gene of T7 RNA polymerase, mRNA of T7 RNA polymerase can be expressed and T7 polymerase is produced. the produced T7 polymerase can go back to the T7 promoter in the upstream, and continue making more T7 polymerases. The circulation of making T7 polymerase ensures the abundance of T7 polymerases, which actually accelerates the process of producing dsRdRp. </div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Our next product, CSBV·Silencer 2.0, will be the engineered yeast containing plasmid PyES2 and plasmid L4440. However, in this stage, we have only come up with the idea and are still trying to recombine the plasmid PyES2. As long as we have the recombined plasmid PyES2 ready, we will then transfer PyES2 and L4440 into yeast, and have our product applied to practice.</div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Meanwhile,we noticed that IPTG could induce the expression of dsRdRp in HT115, and galactose could improve the efficiency of GAL1 in eukaryotic system</div>
+                 <br>
+                 <br>
+                 <center><div><B>Easier to spread<B></div><center/>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Eusocial insects like ants, honeybees, bumble, termites have the habit of cooperative care of young. The larvae in the family are unable to forage and feed themselves, and because of that, the food delivered by workers are essential. this habit enables CSBV.Silencer flow through the whole insect family rapidly.Through the mechanism, CSBV.Silencer can be diffused easily and the effect can be detected rapidly.</div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Similarly, the mechanism can be adopted in the prevention of other virus disease of eusocial insects or biological control. We are planning to develop a medicine of termite control through silence of certain gene. We predict that the medicine can be delivered with food throughout the whole colony, and achieve the purpose of pest control.</div>
+                 <br>
+                 <br>
+                 <center><div>Protocol</div><center>
+                 <div style="text-align:left">Whole RNA Extraction</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We use Trizol to extract the whole RNA of CSBV,and the detail protocol is showed as bellow:</div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>1.Take 50-100mg tissue stored in -80℃ or liquid nitrogen. Grind the tissue into powder in mortar with liquid nitrogen. Transfer the powder into a 1.5ml EP tube(RNase-Free).</div>
+                 <div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>2.Add 500μl Trizol, vortex to mix thoroughly and let the tube sit at room temperature for 10 min.</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>3.Centrifuge at 12,000 x g for 10 min at 4℃.Transfer the supernatant into a new 1.5ml EP tube(RNase-Free).</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>4.Add 100μl chloroform, vigorously shake with hand for 15s and then let the tube sit at room temperature for 10 min.</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>5.Centrifuge at 12,000 x g for 15 min at 4℃. Transfer the upper colourless aqueous phase into a new 1.5ml EP tube(RNase-Free).</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>6.Add 250μl isopropanol, turn the tube upside down many times for around 10 min, and let it sit at room temperature for 10 min until the white floccule arise,and then centrifuge at 12,000 x g for 10 min at 4℃.</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>7.Discard the supernatant,add 500μl,75%ethanol with DEPC,and mix thoroughly.Centrifuge at 7,500 x g for 5 min at 4℃ and discard the supernatant.</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>8.Dry it at room temperature or in the bechtop for 15 min.</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>9.Add 15-20μl RNase-Free water to dissolve RNA when the precipitate become transparent.</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>10.Store RNA at -80℃.</div>
+<br>
+<div style="text-align:left">RT-PCR and PCR</div>
+<div style="text-align:left">We amplify DNA of CSBV by RT-PCR and PCR. And the detail systems and programs are showed as bellow:</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left">1.RT-PCR（using M-MLV Reserve Transcriptase kit bought from Promega company</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Component</span>Volume(μl)</div><!--有问题，4,4,2，要跟volume对齐。-->
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Whole RNA of CSBV</span>4.0</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>dNTP Mixture(10mM)</span>4.0</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Reserve primer</span>2.0</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>70℃ pre-denaturation</span>10min</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Component(add in order)	</span>Volume(μl)</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>5×M-MuLV buffer</span>4.0</div>  <!--版面啊版面啊版面啊。-->
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>RNase free water</span>4.5</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>M-MLV Reserve Transcriptase</span>1.0</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>42℃</span>1h</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>72℃</span>15mins</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Store cDNA at -20℃</div>
+<br>
+<div style="text-align:left">2.PCR</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left">(1)System(50μl)</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>10×PCR Buffer</span>5.0μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>2.5mM dNTP Mix</span>2.0μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Template(cDNA)</span>2.0μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Primer F</span>2.0μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Primer R</span>2.0μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Dream Taq DNA pol</span>0.5μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>ddH2O</span>36.5μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Volume</span>50.0μl</div>
+<div style="text-align:left">(2)Program </div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>94℃</span>5min</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>94℃</span>30s</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>55℃(Tm-5℃)</span>30s</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>72℃</span>T(1min/kb)  2  34</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>72℃</span>10min</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>16℃</span>∞</div>
+<br>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>qPCR</span></div>
+<div style="text-align:left">We use GoTaq? qPCR Master Mix Kit(buy from Promega company) and Eppendrof Mastercycler? ep realplex Real-Time PCR to do qPCR.</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left">(1)System(20μl)</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>SYBR Premix Ex TaqTM  2×mix</span>10.0μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Template(cDNA)</span>1.0μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Primer F</span>0.4μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Primer R</span>0.4μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>RNase-Free water</span>8.2μl</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>Volume</span>20.0μl</div>
+<div style="text-align:left">(2)Program </div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>95℃</span>2min</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>95℃</span>20s</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>60℃</span>20s</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>72℃</span>30s</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>72℃</span>10min</div>
+<div style="text-align:left"><span style="display:-moz-inline-box; display:inline-block; width:350px;"><span style="display:-moz-inline-box; display:inline-block; width:25px;"></span>16℃</span>∞</div>
+<br>
+<div style="text-align:left">Plasmid Extraction</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left">We use E.Z.N.A. Plasmid DNA Mini Kit I bought from OMEGA bio-tek company to <div style="text-align:left">extract plasmids and the detail protocol is showed as bellow:</div>
+<div style="text-align:left">1. Isolate a single colony from a freshly streaked selective plate, and inoculate a culture of 1- 5 mL LB medium containing the appropriate selective antibiotic. Incubate for ~12-16 hours at</div>
+ <div style="text-align:left">37°C with vigorous shaking (~ 300 rpm).</div>
+<div style="text-align:left">2. Centrifuge at 10,000 x g for 1 minute at room temperature</div>
+<div style="text-align:left">3. Decant or aspirate and discard the culture media.</div>
+<div style="text-align:left">4. Add 250 mL Solution I/RNase A. Vortex or pipet up and down to mix thoroughly. </div>
+<div style="text-align:left">5. Transfer suspension into a new 1.5 mL microcentrifuge tube.</div>
+<div style="text-align:left">6. Add 250 mL Solution II. Invert and gently rotate the tube several times to obtain a clear lysate. A 2-3 minute incubation may be necessary.(Avoid vigorous mixing)</div>
+<div style="text-align:left">7. Add 350 mL Solution III. Immediately invert several times until a flocculent white precipitate forms. </div>
+<div style="text-align:left">8. Centrifuge at maximum speed (≥13,000 x g) for 10 minutes. A compact white pellet will form. Promptly proceed to the next step.</div>
+<div style="text-align:left">9. Insert a HiBind DNA Mini Column into a 2 mL Collection Tube.</div>
+<div style="text-align:left">10. Transfer the cleared supernatant from Step 8 by CAREFULLY aspirating it into the HiBind DNA Mini Column. Be careful not to disturb the pellet and that no cellular debris is transferred to the HiBind DNA Mini Column.</div>
+<div style="text-align:left">11. Centrifuge at maximum speed for 1 minute.</div>
+<div style="text-align:left">12. Discard the filtrate and reuse the collection tube. </div>
+<div style="text-align:left">13. Add 500 mL HB Buffer.</div>
+<div style="text-align:left">14. Centrifuge at maximum speed for 1 minute.</div>
+<div style="text-align:left">15. Discard the filtrate and reuse collection tube.</div>
+<div style="text-align:left">16. Add 700 mL DNA Wash Buffer.</div>
+<div style="text-align:left">17. Centrifuge at maximum speed for 1 minute.</div>
+<div style="text-align:left">18. Discard the filtrate and reuse the collection tube.</div>
+<div style="text-align:left">19. Centrifuge the empty HiBind DNA Mini Column for 2 minutes at maximum speed to dry the column matrix. </div>
+<div style="text-align:left">20. Transfer the HiBind DNA Mini Column to a clean 1.5 mL microcentrifuge tube.</div>
+<div style="text-align:left">21. Add 30-100 μl Elution Buffer or sterile deionized water directly to the center of the column membrane.</div>
+<div style="text-align:left">22. Let sit at room temperature for 1 minute.</div>
+<div style="text-align:left">23. Centrifuge at maximum speed for 1 minute.</div>
+<div style="text-align:left">24. Store DNA at -20°C.</div>
+<br>
+<div style="text-align:left">Gel Extraction</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left">We use E.Z.N.A. Gel Extraction Kit bought from OMEGA bio-tek company to recover our target fragments after AGE and the detail protocol is showed as bellow:</div>
+<div style="text-align:left">1. Perform agarose gel/ethidium bromide electrophoresis to fractionate DNA fragments. Any type or grade of agarose may be used. However, it is strongly recommended that fresh TAE buffer or TBE buffer be used as running buffer. Do not reuse running buffer as its pH will increase and reduce yields. </div>
+<div style="text-align:left">2. When adequate separation of bands has occurred, carefully excise the DNA fragment of interest using a wide, clean, sharp scalpel. Minimize the size of the gel slice by removing extra agarose.</div>
+<div style="text-align:left">3. Determine the appropriate volume of the gel slice by weighing it in a clean 1.5 mL microcentrifuge tube. Assuming a density of 1 g/mL, the volume of gel is derived as follows: a gel slice of mass 0.3 g will have a volume of 0.3 mL.</div>
+<div style="text-align:left">4. Add 1 volume Binding Buffer (XP2).</div>
+<div style="text-align:left">5. Incubate at 60°C for 7 minutes or until the gel has completely melted. Vortex or shake the tube every 2-3 minutes.</div>
+<div style="text-align:left">6. Insert a HiBind DNA Mini Column in a 2 mL Collection Tube.</div>
+<div style="text-align:left">7. Add no more than 700μl DNA/agarose solution from Step 5 to the HiBind? DNA Mini Column.</div>
+<div style="text-align:left">8. Centrifuge at 10,000 x g for 1 minute at room temperature.</div>
+<div style="text-align:left">9. Discard the filtrate and reuse collection tube. </div>
+<div style="text-align:left">10. Repeat Steps 7-9 until all of the sample has been transferred to the column.</div>
+<div style="text-align:left">11. Add 300 mL Binding Buffer (XP2).</div>
+<div style="text-align:left">12. Centrifuge at maximum speed (≥13,000 x g) for 1 minute at room temperature.</div>
+<div style="text-align:left">13. Discard the filtrate and reuse collection tube. </div>
+<div style="text-align:left">14. Add 700μl SPW Wash Buffer.</div>
+<div style="text-align:left">15. Centrifuge at maximum speed for 1 minute at room temperature.</div>
+<div style="text-align:left">16. Discard the filtrate and reuse collection tube.</div>
+<div style="text-align:left">17. Centrifuge the empty HiBind DNA Mini Column for 2 minutes at maximum speed to dry the column matrix. </div>
+<div style="text-align:left">18. Transfer the HiBind DNA Mini Column to a clean 1.5 mL microcentrifuge tube.</div>
+<div style="text-align:left">19. Add 30-50μl Elution Buffer or deionized water directly to the center of the column membrane.</div>
+<div style="text-align:left">20. Let sit at room temperature for 2 minutes.</div>
+<div style="text-align:left">21. Centrifuge at maximum speed for 1 minute. </div>
+<div style="text-align:left">22.Store DNA at -20°C.</div>
+<br>
+<div style="text-align:left">CTAB Extraction of dsRNA</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left">1.Pipet 2mL bacterium suspension, centrifuge at 5,000rpm for 1 minute.</div>
+<div style="text-align:left">2.Discard the supernatant, add 500μl TE Buffer(10mmol· L-1Tris, 1mmol· L-1EDTA,PH7.5) and resuspend.</div>
+<div style="text-align:left">3.Add 30μl 10%SDS,mix thoroughly and put it in 37℃ incubator for 1h.</div>
+<div style="text-align:left">4.Add 100μl NaCl(5mol· L-1), mix thoroughly.</div>
+<div style="text-align:left">5.Add 80μl CTAB/NaCl, mix thoroughly, 65℃ water bath for 10min.</div>
+<div style="text-align:left">6.Add isometric phenol/ chloroform/isoamylol mixture(25:24:1), mix thoroughly and centrifuge at 12,000rpm for 5 minute at 4℃.</div>
+<div style="text-align:left">7.Transfer the supernatant into a new 1.5 mL microcentrifuge tube. Add 3/5 volume of it isopropanol. Centrifuge at 12,000rpm for 10 minute at 4℃.</div>
+<div style="text-align:left">8.Discard the supernatant, add 500μl 75% ethanol, vortex to mix thoroughly, and centrifuge at 6,000rpm for 5 minute at 4℃.</div>
+<div style="text-align:left">9.Vacuum dry for 10minute, and digest with DNase(1U), RNase(1U) respectively.</div>
+<div style="text-align:left">10.Store dsRNA at -80℃ or use for next experiment immediately.</div>
+<br>
+<div style="text-align:left">Dual-enzyme digestion</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left">1.Vector                          10.0μl</div>
+<div style="text-align:left">Restriction enzyme(EcoR1,Pst1)      0.5μl</div>
+<div style="text-align:left">Buffer(10×H)                     2.0μl</div>
+<div style="text-align:left">ddH2O                           7.0μl</div>
+<div style="text-align:left">Volume                         20.0μl</div>
+<div style="text-align:left">37℃ metal bath,8h or overnight.</div>
+<div style="text-align:left">2.Recover target fragments by gel extraction.</div>
+<br>
+<div style="text-align:left">Linkage and transformation</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+<div style="text-align:left">1.Linkage system(10μl): Target fragment 4.0μl, Vector 1.0μl, 5×Buffer 2.0μl, T4 ligase 1.0μl, ddH2O 2.0μl. 4℃, overnight.</div>
+<div style="text-align:left">2.Add the product of linkage into 50μl DH5αcompetent cell, pipet up and down gently to mix thoroughly, and put it on ice for 30min.</div>
+<div style="text-align:left">3.Heat in 42℃ water bath for 90s, and take it out immediately and put it on ice for at least 2min.</div>
+<div style="text-align:left">4.Add 200μl LB medium without any selective antibiotic. Incubate for 45min at 37℃with vigorous shaking (~ 220 rpm).</div>
+<div style="text-align:left"> 5.Pipet 150μl bacterium suspension and smear it on LB plate with the appropriate selective antibiotic. Culture in 37℃ incubator,overnight.</div>
+<br>
+<br>
+                 <center><div>CSBV.Silencer 2.0</center>
+                 <div style="text-align:left">Preliminatry experiment</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">The effect of different homologous dsRNA of CSBV to the expression of CSBV’s mRNA.</div>
+                 <div style="text-align:left">To find the most effective homologous dsRNA of CSBV for our project, we tested the pupation rate of honeybee larvae under different dsRNA. We added different homologous dsRNA of CSBV (dsHelicase, dsProtease, dsRdRp and dsVP1) into forage and fed to the infected larvae. After 12 hours, We fed the larvae with extracted fluid of CSBV, and kept feeding it in the following day. According to the statistics we collected, infected larvae fed with dsRdRp have the highest pupation rate among all the experimental groups. </div>
+<br>
+                 <div style="text-align:left">The effect of CSBV.Silencer in curing the disease</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We fed the infected hives with our CSBV·Silencer, and collected the following statistics under the help of professional beekeepers from College of Bee Science.</div>
+                 <div style="text-align:left">1.The decrease of the number of infected larvae.</div>
+                 <div style="text-align:left">Compared with the control group, it is quite obvious that the infected larvae in medium concentration group and in high concentration group dropped dramatically by 91.44 percent and 94 87.91 percent after 14 days while the infected larvae in control group showed 65.82 percent increase after 7 days.</div>
+                 <div style="text-align:left">2.The effect of dsRdRp on the number of sealed brood.</div>
+                 <div style="text-align:left">The number of sealed brood is another indicator of the effect of CSBV. It is an necessary stage of larval pupation.  In this graph, the number of sealed brood in medium concentration and high concentration increases by about 23.68% and 30.10% after 21days. Similarly, the result witnesses a significant improvement in the pupation rate. </div>
+                 <div style="text-align:left">3.The increasing population.</div>
+                 <div style="text-align:left">We counted the number adult honeybees to study the changes of population.The changes are just as you see. For the high concentration group alone, the growth of population had reached almost 60% in just 21 days. On the contrary, the control group showed a 27.78% decrease after 21 days. </div>
+                 <div style="text-align:left">These statistics directly proved that, our product, CSBV.Silencer 1.0 does have a remarkable effect in the treatment to Sacbrood disease.</div>
+                 <div style="text-align:left">The effect of galactose to induce GFP expression at different concentrations and different time.</div>
+                 <div style="text-align:left">1.The galactose at three different concentrations can induce GFP expression efficiently and have little influence on the level of GFP </div>
+                 <div style="text-align:left">We transformed GFP-pYES2 into the yeast and  let the recombinant strain grow to mid-log phase in YEPD medium containing 2% glucose.  And then we transferred it to medium, containing 2%, 0.1% or 0.02% galactose, and assayed for GFP fluorescence.</div>
+                 <div style="text-align:left">According to the statistics we collected, we find that the production of GFP protein is quite high even though at  0.02% galactose and with the increase of its concentration, the level of GFP have no remarkable change.</div>
+                 <div style="text-align:left">2.GFP production sharply increases and a peak shows up in about 24h under the induction of galactose.</div>
+                 <div style="text-align:left">The yeast transformants were grown in YEPD medium. At a cell density of 2 ×107 ml-1,
+cultures were washed and galactose added to a final concentration of 2% and the fluorescence value of samples was measured every 5h.
 </div>
+                 <div style="text-align:left">As the diagram shown, we can find that GFP production sharply increases in 10h and a peak shows up in about 24h and then it decreases gradually.</div>
+                 <div style="text-align:left">In conclusion, we can find using 0.02% galactose to induce the expression of GFP in 24h is a reasonable and efficient way to get the most production of GFP protein. It means that we can induce the expression of T7 RNAP gene efficiently under  the same condition.</div>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
-<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
+<div id="Notebook"></div>
-<p>
+<br>
-Here are a few examples from previous teams:
+<center><div>Notebook</div></center>
-</p>
+<br>
-<ul>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
-<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
-<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
-</ul>
+                 <center><div>2015.6.8</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Today was the first day that we began our project in the lab after we made a scientific plan. Firstly, we extracted the whole RNA of CSBV by Trizol. As we all know, RNA is easy to be digested in the environment. Therefore although we did this quickly, there were still some samples without RNA fragment. But we did again and the result was satisfied at that time. It was encouraging!</div>
+<br>
+                 <center><div>2015.6.9</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Today we made RT-PCR with four sets of reverse specific primers and the RNA of CSBV to synthesize homologous cDNA(CSBV Helicase、Protease、VP1 and RdRp respectively). Then dsDNAs was amplified with four sets of specific primers by PCR. It went through smoothly. So far, we got the target fragments successfully. Also,we used GFP F/R to amplify GFP gene. </div>
+<br>
+               	 <center><div>2015.6.10</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We utilized T7 RiboMAXTM Express RNAi System kit and dsDNAs as templates to synthesize dsRNAs(dsHelicase、dsProtease、dsVP1、dsRdRp and dsGFP), but there were only dsHelicase and dsGFP we could get. We tried again and still failed. It took our whole day to find the reason. Tomorrow we will ask our advisor for some solutions and do it one more time.</div>
+<br>
+                 <center><div>2015.6.12</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">After figuring out the problem, we eventually got the all right dsRNAs. Another part, we began to prepare the larvae of Chinese honeybee which was offered by our institute of bees.
 </div>
+                 <center><div>2015.6.13</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We put dsRNAs into fodder of the larvae of the honeybee to feed them. Then after 12h, we fed them another fodder with CSBV extracting solution. We did so twice before they got normal fodder. </div>
+<br>
+                  <center><div>2015.6.17</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">During three days, we observed the change of percentage of pupation and collect and analyse data. Meanwhile,RT-qPCR was done to detect the effect of different dsRNAs to CSBV. According to the result, we found that dsRdRp made a remarkable influence on the replication of CSBV. So we decided to use dsRdRp to inference CSBV.</div>
+<br>
+                 <center><div>2015.6.19</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We used cDNA of RdRp and specific primers(Not1-F/Pst1-R、EcoR1-F/Pst1-R) to synthesize RdRp gene. However, after agarose gel electrophoresis(AGE), we could not find our target fragment.</div>
+<br>
+                 <center><div>2015.6.20</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We changed a better DNA polymerase and set the annealing temperature to 60℃. Finally we got the RdRp gene.</div>
+<br>
+                 <center><div>2015.6.22</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We picked the colonies to do PCR and sent the positive sequencing(M13).</div>
+<br>
+                 <center><div>2015.6.24</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Today we got the result of sequencing. After comparing with data in NCBI, we only had two 100 percent samples.
+We started to do double enzyme digestion(Not1 and Pst1、EcoR1 and Pst1) to cut vector L4440、pSB1C3 and RdRp-T recombinant plasmid.
+</div>
+<br>
+                 <center><div>2015.6.25</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We made RdRp gene link with T vector in 25℃, 15min and then transformed it into DH5α,a kind of competent cell, which was cultured in 37℃,overnight.</div>
+<br>
+                 <center><div>2015.6.26</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We made it! And we immediately did gel recovery. Then we began to link RdRp with L4440 and pSB1C3 using T4 ligase, 4℃, overnight.
+</div>
+<br>
+                 <center><div>2015.6.27</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We did transformation. However,we forgot to make LB medium with CmRR. So the transformation of RdRp-pSB1C3 could only be done tomorrow.
+</div>
+<br>
+                 <center><div>2015.6.29</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Today there was two news. The good one was we successfully got recombinant plasmid RdRp-L4440 while the bad one was nothing grew on the plate with CmRR. We thought maybe it was because RdRp did not link with pSB1C3 successfully. Anyway we would do it again tomorrow.
+</div>
+<br>
+                 <center><div>2015.7.2</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">On the one hand, we still could not link RdRp with pSB1C3 so that there still nothing on the plate. We wonder if it was because of the efficiency of ligase or anything.
+On the other hand,we prepared another competent cell,HT115,which included T7 RNAP gene in its genome. It was used as engineering bacteria for expressing dsRdRp.</div>
+<div style="text-align:left">Also, considering the biosecurity of E.coli, we decided use yeast as the final transformation target. So we want to recombine another vector,T7 RNAP-pYES2.</div>
+<br>
+                 <center><div>2015.7.3</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We transformed RdRp-L4440 into HT115,culturing in 37℃. Overnight. And T7 RNAP gene was amplified by PCR(EcoR1-F/Xho1-R).</div>
+<br>
+                 <center><div>2015.7.4</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Today we used IPTG, which was divided into two groups with different concentrations(0.4mmol/ml、0.8mmol/ml), to induce the expression of dsRdRp in HT115 for 5h. Then we collected the bacteria to extract dsRdRp by CTAB. According to the result of AGE, dsRdRp had been expressed in HT115 successfully, even though its concentration was a little bit lower. It was really a good news for us! </div>
+<br>
+                 <center><div>2015.7.5</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We added engineering bacteria with expressed dsRdRp, which was divided into three groups with different concentrations(low、mediate and high), into the fodder of the infected swarms. And another infected swarm was fed normal fodder. Since now, we will obverse the change of population of them, the mortality, and the number of sealed brood and collect data every weeks until we get the obvious result.
+</div>
+<br>
+                 <center><div>2015.7.7</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Considering we have not gotten RdRp-pSB1C3 yet,we decided to link T7 RNAP gene to pSB1C3 first. So we used specific primers(EcoR1-F/Pst1-R) to synthesize T7 RNAP gene by PCR.
+</div>
+<br>
+                 <center><div>2015.7.8</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Transformation again!</div>
+<br>
+                 <center><div>2015.7.9</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">As usual, pinking the positive colonies, PCR and sequencing. We hope everything goes smoothly.
+</div>
+<br>
+                 <center><div>2015.7.11</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">According to the result of sequencing, there was no sample 100 percent matching. We did transformation again.
+</div>
+<br>
+                 <center><div>2015.7.13</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">The second sequencing was completely failed because the sequencing company could not get any plasmid. We thought maybe the replication of plasmid in competent cell(DH5α) was inefficient, so we changed another one,T1,bought from Transgene company.
+</div>
+<br>
+                 <center><div>2015.7.14</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">This time we sent plasmid rather than bacteria. Although the concentration of the plasmid was a little bit lower, it was enough to do sequencing.</div>
+<br>
+                 <center><div>2015.7.15</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Considering the lower fidelity of the enzyme used for T7 amplification before, we changed into a better one called KD Plus and restarted to PCR, linking and transformation.</div>
+<br>
+                 <center><div>2015.7.16</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">The third sequencing still showed nothing right. We were a little disappointed, but we exactly knew that failure was a normal phenomenon in the lab. </div>
+<br>
+                 <center><div>2015.7.18</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Eventually,we got the matching sample after using KD Plus. Immediately, we began to do double enzyme digestion(EcoR1/Xho1、EcoR1/Pst1).</div>
+<br>
+                 <center><div>2015.7.19</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">After gel recovery, we linked our target fragments to relative vectors with T4 ligase, 4℃, overnight.</div>
+                 <div style="text-align:left">Meanwhile, we collected data about the index of the condition of swarms again, which was used to analyze the effect of dsRdRp by Excel later.</div>
+<br>
+                 <center><div>2015.7.20</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Transformation, plate coating,37℃, overnight.</div>
+<br>
+                 <center><div>2015.7.21</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Pinking the positive colonies, PCR detection, and then plasmid extraction. It was smooth! So, we got T7 RNAP-pYES2 and T7 RNAP-pSB1C3 successfully. We stored them in -20℃.</div>
+<br>
+                 <center><div>2015.7.23</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Today we went to observe the condition of swarms, and it was happy to see that the experimental groups turned to a healthier development comparing with control group. It meant that using dsRdRp expressed in E.coli to prevent and cure CSBV was working. Next, we would continue to collect more data until we draw the scientific conclusion.</div>
+<br>
+                 <center><div>2015.7.26</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">With the development of our project, we gradually have realized that even if using yeast can solve the problem of biosecurity, there are still other troubles, such as less expression of dsRdRp in yeast, easier to loss plasmids in yeast and harder to digest the cytoderm of yeast for Chinese honeybees.</div>
+<div style="text-align:left">So we need a better plan to deal with these to make a more practical production. That was what we would consider deeply in future work.</div>
+<br>
+                 <center><div>2015.7.27</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Today we decided to constract RdRp-pSB1C3 again, because we thought T7 RNAP-pSB1C3 may be not a new part any more. So, we did linking. We decided if it is failed just like before this time. We had to change T4 into a faster ligase..</div>
+<br>
+                 <center><div>2015.7.29</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">As predicted, there was still nothing on the plate.(please tell us why you cannot grow out,bacteria!)</div>
+<br>
+                 <center><div>2015.8.1</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We got the preliminary result of index of swarms. Next few days we would detect the expression quantity of CSBV in offspring.</div>
+<br>
+                 <center><div>2015.8.2</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We made the figure of the effect of dsRdRp on the number of sac-like larvae. It showed that the number of infected larvae which were fed with HT115-dsRdRp in mediate and high concentration was remarkably less than the control group.</div>
+<br>
+                 <center><div>2015.8.5</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Other two figures were made out, which showed the effect of dsRdRp on the number of sealed brood and the population of a colony respectively. They demonstrated the similar conclusion. </div>
+<br>
+                 <center><div>2015.8.8</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We detected the CSBV-carried rate of offspring by RT-PCR. After AGE, it showed that the CSBV-carried rate of first and second filial generation was 30% and 20% respectively, which was obviously declined.</div>
+<br>
+                 <center><div>2015.8.12</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">We detected the expression quantity of CSBV in offspring by RT-qPCR. We found with the decreasing of CSBV. The expression quantity of RdRp gene declined either, which meant that dsRdRp really could inhibit the replication of CSBV.</div>
+<br>
+                 <center><div>Last final month</div></center>
+<hr style="height:1px;border:none;border-top:1px solid #555555;" />
+                 <div style="text-align:left">Even though we were succeed in using dsRdRp expressed in proeukaryotic system to prevent and cure CSBV, we still had to take care of some problem we met. So next stage we will try to constract another plasmid with suicide gene to control the concentration of engineering bacteria. Further more, we want to use CRISPR-Cas9 system to make RdRp gene inserted into the genome of E.coli. So that we can solve the problem of biosecurity.</div>
+<br>
+<br>
+        </div>
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