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                     <p>Your place:&nbsp;<a href="https://2015.igem.org/Team:Nankai">Home</a>&nbsp;&gt;&nbsp;<a href="https://2015.igem.org/Team:Nankai/Description">Project</a></p>
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                     <p>Your place:&nbsp;<a href="https://2015.igem.org/Team:Nankai">Home</a>>&nbsp;&gt;&nbsp;<a href="https://2015.igem.org/Team:Nankai/Practices">Human Practice</a></p>
 
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<h2 class="page-title">Project Description</h2>
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<h2 class="page-title">Human Practice</h2>
 
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<h4>Human Practice: An Amazing Summer！！ </h4>
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<p>As Peter Carr puts it, "Human Practices is the study of how your work affects the world, and how the world affects your work." This summer, Nankai iGEM team worked our best to put the spirits of collaboration and sharing into practice. Not only have we attended many important activities<a name="No1"> and</a> conferences, but also a new information-sharing platform— iShare has become reality. Let’s see what our team did in this amazing summer.</p>
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<h4>What is γ-PGA?</h4>
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<p>Poly-γ-glutamic acid (γ-PGA) is an important, naturally occurring polyamide consisting of D/L-glutamate monomers. Unlike typical peptide linkages, the amide linkages in γ-PGA are formed between the α-amino group and the γ-carboxyl group. γ-PGA exhibits many favorable features such as biodegradable, water soluble, edible and non-toxic to humans and the environment. Therefore, it has been widely used in fields of foods, medicines, cosmetics and agriculture and many unique applications, such as a sustained release material and drug carrier, curable biological adhesive, biodegradable fibres, and highly water absorbable hydrogels.</p>
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<h4>1. What is iShare?</h4>
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<h4>How can we produce it?</h4>
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<p>During the summer, we ran into many problems when we were working on our experiments. The lack of materials for instance, is one major difficulty that occurred to us. To continue our project, we had to acquire those materials from other laboratories, which involved us into intellectual property issues..</p>
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<p>Strains capable for producing γ-PGA are divided into two categories based on their requirement for glutamate acid: glutamate-dependent strains and glutamate-independent strains. Glutamate-independent strains are preferable for industrial production because of their low cost and simplified fermentation process. However, compared with glutamate-dependent strains, their lower γ-PGA productivity limits their industrial application.Therefore, the construction of a glutamate-independent strain with high γ-PGA yield is important for industrial applications.</p>
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<p>Thanks to the current system of material transformation, we managed to put all the things we needed together. Most of the laboratories would share their resources with us if we sign the material transfer agreement with them. However a small community as Nankai University is, it still took us a long time to find the right materials we needed. We could imagine how difficult if an iGEM team seeks for information about certain materials among the hundreds of previous teams.</p>
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<h4>Who can produce it?</h4>
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<p>As far as we have concerned, iGEM has already established a functional platform for all the participators to share Bio-bricks that have been submitted since the birth of the event, which is absolutely an excellent work for resources sharing. But there is no information about other materials related to the Bio-bricks, such as bacteria strains, antibodies, enzymes and so on. So our suggestion is that iGEM design a special webpage or a section on wiki for iGEM teams to list the materials they use in their experiments. In addition, iGEM teams could label the materials which they are willing to share. And teams who are interested in those materials could contact the owner for more information or a way to acquire the materials. In this way, future teams could have more resources for similar work and may come up with more improvements, while all iGEM need to do is to provide an information platform like “iShare”.</p>
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<p>Bacillusamyloliquefaciens LL3, isolated from fermented food, is a glutamate-independent strain, which can produce 3-4 g/L γ-PGA with sucrose as its carbon source and ammonium sulfate as its nitrogen source. The B. amyloliquefaciens LL3 strain was deposited in the China Center for Type Culture Collection (CCTCC) with accession number CCTCC M 208109 and its whole genome has been sequenced in 2011. In this study, we aimed to improve the γ-PGA production based on the B. amyloliquefaciens NK-1 strain (a derivative of LL3 strain with its endogenous plasmid and upp gene deleted).</p>
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<p>A mature system of all-round resources sharing could definitely make iGEM a better community. Before it could be accomplished, let’s make the first step by setting up an information sharing platform to promote material sharing. Team Nankai has already designed a model for i-Share. See more information<a name="No2"> on</a> our wiki, and join us to make iShare better and better!See iShare wiki platform <a href="https://2015.igem.org/Team:Nankai/Practices/iShare">here</a>!</p>
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<h4>What did we do?</h4>
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<p>In order to improve γ-PGA production, we employed two strategies to fine-tune the synthetic pathways and balance the metabolism in the glutamate-independent B. amyloliquefaciens NK-1 strain. Firstly, we constructed a metabolic toggle switch in the NK-1 strain to inhibit the expression of ODHC (2-oxoglutarate dehydrogenase complex) by adding IPTG in the stationary stage and distribute the metabolic flux more frequently to be used for γ-PGA precursor-glutamate synthesis. As scientists had found that the activity of ODHC was rather low when glutamate was highly produced in a Corynebacterium glutamicum strain. Second, to balance the increase of endogenous glutamate production, we optimized the expression level of pgsBCA genes (responsible for γ-PGA synthesis) by replacing its native promoter to seven different strength of promoters. Through these two strategies, we aimed to obtain a γ-PGA production improved mutant strain.<a href="https://2015.igem.org/Team:Nankai/Experiments">Click for more detail.</a></p>
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<h6><a href="https://2015.igem.org/Team:Nankai/Description">Description</a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Practices"><a href="#No1">iShare Description</a></a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Experiments">Experiments & Protocols</a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Practices_iShare survey"><a href="#No2">iShare survey</a></a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Results">Results</a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Practices_Communition and Collaboration"><a href="#No3">Communition and Collaboration</a></a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Design">Design</a></h6>
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                                                 <p>Preparing for LB medium.</p>
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                                                 <p>Cultured LL3.</p>
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                                                 <p>iShare Wikipage</p>
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                                                 <p>In the progress of fermentation.</p>
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<h6>References</h6>
 
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<p>1. Ashiuchi, M., Misono, H., 2002. Biochemistry and molecular genetics of poly-γ-glutamate synthesis. Appl. Biochem. Biotechnol. 59, 9–14.</br>
 
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2. Kunioka, M., 1997. Biosynthesis and chemical reactions of poly(amino acid)s from
 
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microorganisms. Appl. Microbiol. Biotechnol. 47, 469–475.</br>
 
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3. Shih, I.L., Van, Y.T., 2001. The production of poly(γ-glutamic acid) from microorganism and its various applications. Bioresour. Technol. 79, 207–225.</br>
 
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4. Li, C., 2002. Poly(L-glutamic acid)--anticancer drug conjugates. Adv. Drug Deliver. Rev. 54, 695–713.</br>
 
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5. Liang, H.F., Chen, C.T., Chen, S.C., Kulkarni, A.R., Chiu, Y.L., Chen, M.C., Sung, H.W., 2006. Paclitaxel-loaded poly(γ-glutamic acid)-poly(lactide) nanoparticles as a targeted drug delivery system for the treatment of liver cancer. Biomaterials. 27, 2051–2059.</br>
 
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6. Richard, A., Margaritis, A., 2001. Poly (glutamic acid) for biomedical applications. Crit. Rev. Biotechnol. 21, 219–232.</br>
 
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7. Park, Y.J., Liang, J., Yang, Z., Yang, V.C., 2001. Controlled release of clot-dissolving tissue-type plasmmogen activator from a poly(L-glutamic acid) semi-interpenetrating polymer network hydrogel. J. Control. Release. 74, 243–247.</br>
 
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8. Cao, M.F., Geng, W.T., Liu, L., Song, C.J., Xie, H., Guo, W.B., Jin, Y.H., Wang, S.F., 2011. Glutamic acid independent production of poly-γ-glutamic acid by Bacillus amyloliquefaciens LL3 and cloning of pgsBCA genes. Bioresour. Technol. 102, 4251–4257.</br>
 
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9. Geng, W.T., Cao, M.F., Song, C.J., Xie, H., Liu, L., Yang, C., Feng, J., Zhang, W., Jin, Y.H., Du, Y., Wang, S.F., 2011. Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-γ-glutamic acid. J. Bacteriol. 193, 3393–3394.</br>
 
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10. Feng, J., Gao, W.X., Gu, Y.Y., Zhang, W., Cao, M.F., Song, C.J., Zhang, P., Sun, M., Yang, C.,  Wang, S.F., 2014a. Functions of poly-gamma-glutamic acid (γ-PGA) degradation genes in γ-PGA synthesis and cell morphology maintenance. Appl. Microbiol. Biotechnol. 98, 6397–6407.</br>
 
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11. Uy, D., Delaunay S., Germain, P., Engasser, J.M., Goergen, J.L. 2003. Instability of glutamate production by Corynebacterium glutamicum 2262 in continuous culture using the temperature-triggered process. J. Biotech. 104, 173-184.</p>
 
 
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<h5>2. iShare Survey </h5>
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<p>Before a functional platform could be established, we surveyed its popularity among iGEM teams this year. Questionnaires were sent to 281 iGEM teams separately and 82 of them were filled and retrieved. Statistics and analysis of the questions are as following.</p>
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<p>Most of those teams were undergraduate teams (76.14%), some were graduate teams (20.45%) and two were high school teams (2.27%). </p>
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<h6>Q1. Which section is your team in?</h6>
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<p>Also most teams surveyed were from Asia (53.41%), some were from North America (21.59%) and Europe (18.18%), 5 teams were from South America (5.68%) and one team from Africa (1.14%).</p>
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<p>As we explained, “ishare” wants promotes communication and material sharing between iGEM teams. However interactions between teams are greatly limited by the distances of teams. It’s easier for us to reach those teams that are close to us, teams in Asia, but it’s pretty clear that we still need help in organizing real material sharing events on anther continental.</p>
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<h6>Q2. Which region is your team in?</h6>
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<p>Among those teams interviewed, 77% of them had difficulty finding experimental materials related to their projects and about 53% of those troubled teams said their project was greatly delayed due to the lack of materials. </p>
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<p>It’s usually very difficult for a new team to start on their project. We experienced this inconvenience last summer and that was where the idea of “ishare” came from. Information on wiki could sometimes be too overwhelming, and most of the time we never know how to contact a team by just reviewing their wiki. Therefore it would be great if “ishare” can provide a chance for two-way communication as, a supplement for team wiki. Teams who join “ishare” could put project description and e-mails on it, so that teams with similar interest could find and help each other.</p>
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<h6>Q3. Have you met any difficulties in finding experimental material related to your project?</h6>
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<p>In the meantime, 34.09% of teams found it difficult to repeat or improve previous iGEM projects, 56.82% of teams thought it was hard to say and only the 6% of the teams said it would be easy to do so.</p>
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<p>iGEM has already established a functional platform of biobricks on registry, and iGEM teams are recommended to use and improve those parts. However information related to those biobricks is often ignored on registry, such as information about bacteria strains, antibodies, enzymes and so on. How can another team acquire certain bacteria strain, when the biobrick is better expressed in this strain than it is in E.coli? Can other teams get this strain directly from the original team, or is it possible that they obtain it from a third party? If those information could be well collected and presented on the platform, independently or as a supplement for registry, “ishare” would be of great help for teams to repeat and improve previous projects, independently or as a supplement for registry.</p>
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<h6>Q4. How difficult do you think it would be to repeat or improve previous iGEM projects?</h6>
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<p>Like we expected, 84.09% of the teams agreed that a resource sharing platform like "ishare" would help on solving the problems above.</p>
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<h6>Q5. Would a resource sharing platform help in improving previous iGEM project?</h6>
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<p>And 84.09% of the teams would like to join “ishare”.</p>
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<h6>Q6. Would you like to be part of iShare?</h6>
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<p>In addition, we questioned about team’s preference about sharing materials. 78.41% of the teams would like to share bacterial strains, 57.95% of them would like to share cells strains, 67.05% of them would share enzymes, 55.68% of them would share antibodies, 80.68% of them would share plasmids and another 21.59% would share other materials. </p>
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<p>Showed in the histogram below, teams were generous about real materials they would offer. In the meantime the actual process of sharing the material for instance shipment of bacterial strains may still be troublesome. However it won’t remain as a problem for long, as long as teams are truly involved in “ishare”. There could dozens of solutions between different teams, and in the future, a wider list of material’s information would be presented on “ishare”.</p>
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<img src="https://static.igem.org/mediawiki/2015/9/9a/IShare_HP_iShare_Survey7.png">
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<h6>Q7. What kind of material do you expect to get or share on iShare?</h6>
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<p>Now "ishare" is fully functional and 4 iGEM teams have already provided information of materials related to their project on the platform. We want to show iGEM HQ that this is a trouble solving idea. We hope in the future "ishare" could be presented on the upstream of wiki server <a name="No3">and</a> be put into actual use.</p>
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<p>If you want to participate in the survey, Click <a href="http://www.sojump.com/jq/5722679.aspx">here</a>.</p>
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<h5>3. Collaborations and Conferences </h5>
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<p>This year is the second year of team Nankai participating in iGEM. We have been working with other teams more frequently than before. Tianjin University is our neighbor and intimate partner, and we share a lot on experiments, projects design and human practice. What’s more, during summer vacation, team Nankai had a meetup with team ZJU and team SYSU in Zhejiang University to exchange ideas on iGEM 2015.
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<h6>Nankai University & Tianjian University</h6>
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<p>Until now, we have built up the collaboration with TJU, ZJU and SYSU. In the near future, we will further communicate with more universities and build up collaborations. We have the same wish for a better tomorrow! Let’s communicate and collaborate!</p>
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<h6>Meeting in Zhejiang University: team Nankai, team ZJU and team SYSU</h6>
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<p>What’s more, to promote team's public engagement, we showed up in the iGEM meet up held by Peking University this summer. Besides, we took part in the 3rd Symposium of Bohai-RIM Microbiology and presented our work to other participants.</p>
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<p>During those conferences, we got precious suggestion from experts and other iGEM teams. In the meantime it has broaden our horizons on synthetic biology. </p>
 
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Latest revision as of 23:33, 18 September 2015

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Human Practice

Human Practice: An Amazing Summer！！

As Peter Carr puts it, "Human Practices is the study of how your work affects the world, and how the world affects your work." This summer, Nankai iGEM team worked our best to put the spirits of collaboration and sharing into practice. Not only have we attended many important activities and conferences, but also a new information-sharing platform— iShare has become reality. Let’s see what our team did in this amazing summer.

1. What is iShare?

During the summer, we ran into many problems when we were working on our experiments. The lack of materials for instance, is one major difficulty that occurred to us. To continue our project, we had to acquire those materials from other laboratories, which involved us into intellectual property issues..

Thanks to the current system of material transformation, we managed to put all the things we needed together. Most of the laboratories would share their resources with us if we sign the material transfer agreement with them. However a small community as Nankai University is, it still took us a long time to find the right materials we needed. We could imagine how difficult if an iGEM team seeks for information about certain materials among the hundreds of previous teams.

As far as we have concerned, iGEM has already established a functional platform for all the participators to share Bio-bricks that have been submitted since the birth of the event, which is absolutely an excellent work for resources sharing. But there is no information about other materials related to the Bio-bricks, such as bacteria strains, antibodies, enzymes and so on. So our suggestion is that iGEM design a special webpage or a section on wiki for iGEM teams to list the materials they use in their experiments. In addition, iGEM teams could label the materials which they are willing to share. And teams who are interested in those materials could contact the owner for more information or a way to acquire the materials. In this way, future teams could have more resources for similar work and may come up with more improvements, while all iGEM need to do is to provide an information platform like “iShare”.

A mature system of all-round resources sharing could definitely make iGEM a better community. Before it could be accomplished, let’s make the first step by setting up an information sharing platform to promote material sharing. Team Nankai has already designed a model for i-Share. See more information on our wiki, and join us to make iShare better and better!See iShare wiki platform here!

iShare Description
iShare survey
Communition and Collaboration

IShare Logo

iShare Wikipage

2. iShare Survey

Before a functional platform could be established, we surveyed its popularity among iGEM teams this year. Questionnaires were sent to 281 iGEM teams separately and 82 of them were filled and retrieved. Statistics and analysis of the questions are as following.

Most of those teams were undergraduate teams (76.14%), some were graduate teams (20.45%) and two were high school teams (2.27%).

Q1. Which section is your team in?

Also most teams surveyed were from Asia (53.41%), some were from North America (21.59%) and Europe (18.18%), 5 teams were from South America (5.68%) and one team from Africa (1.14%).

As we explained, “ishare” wants promotes communication and material sharing between iGEM teams. However interactions between teams are greatly limited by the distances of teams. It’s easier for us to reach those teams that are close to us, teams in Asia, but it’s pretty clear that we still need help in organizing real material sharing events on anther continental.

Q2. Which region is your team in?

Among those teams interviewed, 77% of them had difficulty finding experimental materials related to their projects and about 53% of those troubled teams said their project was greatly delayed due to the lack of materials.

It’s usually very difficult for a new team to start on their project. We experienced this inconvenience last summer and that was where the idea of “ishare” came from. Information on wiki could sometimes be too overwhelming, and most of the time we never know how to contact a team by just reviewing their wiki. Therefore it would be great if “ishare” can provide a chance for two-way communication as, a supplement for team wiki. Teams who join “ishare” could put project description and e-mails on it, so that teams with similar interest could find and help each other.

Q3. Have you met any difficulties in finding experimental material related to your project?

In the meantime, 34.09% of teams found it difficult to repeat or improve previous iGEM projects, 56.82% of teams thought it was hard to say and only the 6% of the teams said it would be easy to do so.

iGEM has already established a functional platform of biobricks on registry, and iGEM teams are recommended to use and improve those parts. However information related to those biobricks is often ignored on registry, such as information about bacteria strains, antibodies, enzymes and so on. How can another team acquire certain bacteria strain, when the biobrick is better expressed in this strain than it is in E.coli? Can other teams get this strain directly from the original team, or is it possible that they obtain it from a third party? If those information could be well collected and presented on the platform, independently or as a supplement for registry, “ishare” would be of great help for teams to repeat and improve previous projects, independently or as a supplement for registry.

Q4. How difficult do you think it would be to repeat or improve previous iGEM projects?

Like we expected, 84.09% of the teams agreed that a resource sharing platform like "ishare" would help on solving the problems above.

Q5. Would a resource sharing platform help in improving previous iGEM project?

And 84.09% of the teams would like to join “ishare”.

Q6. Would you like to be part of iShare?

In addition, we questioned about team’s preference about sharing materials. 78.41% of the teams would like to share bacterial strains, 57.95% of them would like to share cells strains, 67.05% of them would share enzymes, 55.68% of them would share antibodies, 80.68% of them would share plasmids and another 21.59% would share other materials.

Showed in the histogram below, teams were generous about real materials they would offer. In the meantime the actual process of sharing the material for instance shipment of bacterial strains may still be troublesome. However it won’t remain as a problem for long, as long as teams are truly involved in “ishare”. There could dozens of solutions between different teams, and in the future, a wider list of material’s information would be presented on “ishare”.

Q7. What kind of material do you expect to get or share on iShare?

Now "ishare" is fully functional and 4 iGEM teams have already provided information of materials related to their project on the platform. We want to show iGEM HQ that this is a trouble solving idea. We hope in the future "ishare" could be presented on the upstream of wiki server and be put into actual use.

If you want to participate in the survey, Click here.

3. Collaborations and Conferences

This year is the second year of team Nankai participating in iGEM. We have been working with other teams more frequently than before. Tianjin University is our neighbor and intimate partner, and we share a lot on experiments, projects design and human practice. What’s more, during summer vacation, team Nankai had a meetup with team ZJU and team SYSU in Zhejiang University to exchange ideas on iGEM 2015.

Nankai University & Tianjian University

Until now, we have built up the collaboration with TJU, ZJU and SYSU. In the near future, we will further communicate with more universities and build up collaborations. We have the same wish for a better tomorrow! Let’s communicate and collaborate!

Meeting in Zhejiang University: team Nankai, team ZJU and team SYSU

What’s more, to promote team's public engagement, we showed up in the iGEM meet up held by Peking University this summer. Besides, we took part in the 3rd Symposium of Bohai-RIM Microbiology and presented our work to other participants.

During those conferences, we got precious suggestion from experts and other iGEM teams. In the meantime it has broaden our horizons on synthetic biology.

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Nankai IGEM Team 2015