Difference between revisions of "Team:Auckland MOD/Notebook"
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<h3>Identifying the Urea Metabolic Pathway</h3> | <h3>Identifying the Urea Metabolic Pathway</h3> | ||
<p>The team met with Nijat again after researching further into his suggestions. <i>H. pylori</i> high affinity urease will be a bit difficult to introduce as it would need special approval to be inserted into <i>A. thaliana</i>. It's also a human pathogen and has a different accessory proteins (so it's very complicated!). We need to look into another way of upregulating urease. </p> | <p>The team met with Nijat again after researching further into his suggestions. <i>H. pylori</i> high affinity urease will be a bit difficult to introduce as it would need special approval to be inserted into <i>A. thaliana</i>. It's also a human pathogen and has a different accessory proteins (so it's very complicated!). We need to look into another way of upregulating urease. </p> | ||
| − | <p> We’ve decided that we want to upregulate the <b>AtDUR3</b> gene then the urease or rate-limiting accessory protein. There is limited research around upregulating urease activity: one of the urease accessory proteins, <b>UreG</b>, might be our best luck as an alternative to expressing urease with all accessory genes. | + | <p> We’ve decided that we want to upregulate the <b>AtDUR3</b> gene then the urease or rate-limiting accessory protein. There is limited research around upregulating urease activity: one of the urease accessory proteins, <b>UreG</b>, might be our best luck as an alternative to expressing urease with all accessory genes. Rachel and Stephen have been researching which glutamine synthetase gene we might upregulate. <b>GS1;2 isogene</b> appears to be the most successful in producing glutamate from ammonia at the highest capacity. </p> |
| − | + | ||
<h3> Beginning Work in the Plant Lab</h3> | <h3> Beginning Work in the Plant Lab</h3> | ||
<p> We've selected Greta, Prokhor and Stephen to undergo the plant lab induction in mid-May. They will be responsible for growing our <i>A. thaliana</i> plants in this PC2 lab, with aid of the lab supervisor, Nathan Deed. </p> | <p> We've selected Greta, Prokhor and Stephen to undergo the plant lab induction in mid-May. They will be responsible for growing our <i>A. thaliana</i> plants in this PC2 lab, with aid of the lab supervisor, Nathan Deed. </p> | ||
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<p> <b> Rest of June: </b> We've had reports of yellowing leaves, indicating stress to the plants. We've been advised to apply hydroponic solution directly to the yellowing plants. The plant facilities had a heating malfunction on the 25th, so we had to move them to the temperature controlled room. No plant damage was observed. </p> | <p> <b> Rest of June: </b> We've had reports of yellowing leaves, indicating stress to the plants. We've been advised to apply hydroponic solution directly to the yellowing plants. The plant facilities had a heating malfunction on the 25th, so we had to move them to the temperature controlled room. No plant damage was observed. </p> | ||
<h4>Getting started with our BioBrick Characterisation</h4> | <h4>Getting started with our BioBrick Characterisation</h4> | ||
| − | <p> <b> Early June: </b> Had a meeting with 2017 iGEM team lab members, Judith and Jess, to get a better idea of how we can work more efficiently. They suggested not to continue from their BioBrick project this year, but instead do a fluorescent or chromoprotein. We've chosen <b>BBa_E0020</b> from 2004 - we’ll be finding out at what pH we observe the highest fluorescent intensity. | + | <p> <b> Early June: </b> Had a meeting with 2017 iGEM team lab members, Judith and Jess, to get a better idea of how we can work more efficiently. They suggested not to continue from their BioBrick project this year, but instead do a fluorescent or chromoprotein. We've chosen <b>BBa_E0020</b> from 2004 - we’ll be finding out at what pH we observe the highest fluorescent intensity. We've met with our lab supervisor, Jasper, to go over our lab protocol and familiarise ourselves to the BioBrick standard system. </p> |
| − | + | ||
<img src="https://static.igem.org/mediawiki/2018/7/73/T--Auckland_MOD--PC1_StackedPlates.jpeg"> | <img src="https://static.igem.org/mediawiki/2018/7/73/T--Auckland_MOD--PC1_StackedPlates.jpeg"> | ||
<p><b> Mid-June: </b> Finally jumping into the lab to do our plating and preparatory steps for the transformation into competent <i>E. coli</i> strain, DH5α. We’re all starting to feel the pressure of upcoming exams which is getting in the way of lab progress. Right now, the priority is to grow our transformed <i>E. coli</i> and get them on ice so we can experiment on them later in July. </p> | <p><b> Mid-June: </b> Finally jumping into the lab to do our plating and preparatory steps for the transformation into competent <i>E. coli</i> strain, DH5α. We’re all starting to feel the pressure of upcoming exams which is getting in the way of lab progress. Right now, the priority is to grow our transformed <i>E. coli</i> and get them on ice so we can experiment on them later in July. </p> | ||
| − | |||
<img src="https://static.igem.org/mediawiki/2018/9/95/T--Auckland_MOD--CFP_PCRgel1.jpeg"> | <img src="https://static.igem.org/mediawiki/2018/9/95/T--Auckland_MOD--CFP_PCRgel1.jpeg"> | ||
| + | <p> Our first transformation of our BioBrick has been successful! We’re now waiting for our primers (from our IDT free DNA supply) to arrive in the mail so we can run colony PCR and confirm our insert is being expressed. </p> | ||
</div> | </div> | ||
</div> | </div> | ||
Revision as of 01:14, 30 July 2018
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Notebook
It's been a busy year! Take a look at the progress we've been making in our project: both in and outside of the lab.
January
January
Recruitment: We Want You!
As everyone comes back after the summer break, we begin recruiting new 2018 Team MOD members. The handover process from 2017 iGEM Team SECA means we're slowly building an iGEM alumni here at UoA. They've been really helpful mentoring us as we start our new project in terms of sharing research documentation, transferring financial accounts, and having a small team cheering for us from the sidelines.
Fundraising
Had a meeting with Alastair Harris (Alumni from iGEM 2017) to organise financial accounts with our partner, Chiasma. Jessica Chiang, an Alumni from iGEM 2016, is also the CEO of Chiasma. We talked about almost everything to do with iGEM and the Giant Jamboree, including presenting to Chiasma for constructive feedback. Contacted Shaun Lott to confirm the rollover of some more funding from Return on Science.
February
February
Registering Our Team
Began the iGEM team registration process, however problems with transferring bank account authority prevented us from paying iGEM (we therefore missed the early registrations). Confirmed primary lab space with Austen Ganley and secondary lab space with Jo Putterill if we need to do work on a plant model. Completed the iGEM Resource Description form. Nearly finished sorting out our financial account - thanks to iGEM alumni Jessica Chiang and Sheree Clifton from Chiasma (one of our university partners).
Contacted Matthew Mayo-Smith, a summer lab student recommended by our PI, Jo Putterill, due to his knowledge of plant molecular methods. Matthew was unsure whether he’d be at Auckland Uni this year but is keen to help if needed.
We also had the opportunity to talk about iGEM at an academic symposium hosted by the Science Student's Association here at UoA. This was a great experience to inspire other future scientists to see the potential of synthetic biology through a commercial lens.
Improving the Wiki System
Followed up with Suzie and Traci from iGEM HQ about improving their wiki-handin system. They were well impressed with our website initiative but are having trouble implementing changes. We’re giving it one last push and offering all the help we can! The goal here is to allow teams to submit both a wiki and a private website to allow best practice web design and development for students.
March
March
Identifying a National Problem
As a team we've all come together to discuss potential project ideas. Everyone has their own specific interests ranging from plant physiology to wine microbiology - it's great to see a diverse range of options. We've identified waterway pollution as a huge problem in New Zealand: each year we're seeing more incidences of toxic algal bloom formation in the summer and have begun searching potential ways to use synthetic biology to combat this issue.
Subtitle
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
April
April
Refining our Biological Solution
After carrying out our own research, we've looked into the effects of dairy run-off entering the water system. Discussion with our PI and researchers within the university has helped narrow down the chosen metabolic pathway we might upregulate. We've chosen Arabidopsis thaliana as our model organism and plan on increasing the uptake and breakdown of excess urea in the soil.
Set up a meeting with Dr Nijat Imin who specialises in nitrogen activity in plants. We were already thinking of upregulating AtDUR3 urea transporter and incorporating H. pylori’s urease that has a high affinity. He's informed us that ammonia is toxic in high amounts and gave us a few transporters that would be able to redirect it to other parts of the plant. He is excited about the project and is willing to give us more support throughout the year.
Lab induction time! We've all had to complete our safety training so we can jump into the PC1 facilities for our lab work.
Looking Beyond the Lab
If we're looking at a product for dairy farmers, it's important to start thinking about market validation. Rachel has begun speaking to social scientists in the university to get an idea of how to conduct a focus group, and how to engage with students as part of our community engagement efforts.
May
May
Identifying the Urea Metabolic Pathway
The team met with Nijat again after researching further into his suggestions. H. pylori high affinity urease will be a bit difficult to introduce as it would need special approval to be inserted into A. thaliana. It's also a human pathogen and has a different accessory proteins (so it's very complicated!). We need to look into another way of upregulating urease.
We’ve decided that we want to upregulate the AtDUR3 gene then the urease or rate-limiting accessory protein. There is limited research around upregulating urease activity: one of the urease accessory proteins, UreG, might be our best luck as an alternative to expressing urease with all accessory genes. Rachel and Stephen have been researching which glutamine synthetase gene we might upregulate. GS1;2 isogene appears to be the most successful in producing glutamate from ammonia at the highest capacity.
Beginning Work in the Plant Lab
We've selected Greta, Prokhor and Stephen to undergo the plant lab induction in mid-May. They will be responsible for growing our A. thaliana plants in this PC2 lab, with aid of the lab supervisor, Nathan Deed.
Late May: We received training for entry procedures, plant sowing, logging our sowed/bleached plants, and seed sterilisation. We've successfully sowed our first round of 24 wild-type A. thaliana seeds. We watered the plants with 1:10 hydroponics solution and recorded planting dates.
Sharing our Experiences with Synthetic Biology
Hadleigh, Prokhor, Greta and Sneha went to St. John’s School in Mairangi Bay to teach our first lesson for the community engagement project. We taught two classes of Year 6 students how to conduct a basic scientific experiment and gave them the task of coming up with their own solutions to the polluted waterways issue. We then introduced GM and the concept of DNA to them - they asked a lot of questions!
For Team MOD, experiences like this really put our work into perspective. We want to share the potential we see in GMOs with the rest of New Zealand - this can happen at any level, from the big guys up in parliament to kids in the classroom.
June
June
Thinking about our Business Model
Spent the entire week working towards our Return on Science presentation, really diving into the commercial aspects of our project and thinking about GMO policy in New Zealand which is exciting! We’ve also spoken to our secondary PI, Shaun Lott, about the future of iGEM in terms of next year’s team and getting recognition from the university as a contribution to the BSc degree.
Tending to our Shoots
Early June: Our first algal bloom has been reported. As a result we've cleaned and exchanged our trays for new clean ones. We've been continuously watering our plants and recording growth every few days.
Rest of June: We've had reports of yellowing leaves, indicating stress to the plants. We've been advised to apply hydroponic solution directly to the yellowing plants. The plant facilities had a heating malfunction on the 25th, so we had to move them to the temperature controlled room. No plant damage was observed.
Getting started with our BioBrick Characterisation
Early June: Had a meeting with 2017 iGEM team lab members, Judith and Jess, to get a better idea of how we can work more efficiently. They suggested not to continue from their BioBrick project this year, but instead do a fluorescent or chromoprotein. We've chosen BBa_E0020 from 2004 - we’ll be finding out at what pH we observe the highest fluorescent intensity. We've met with our lab supervisor, Jasper, to go over our lab protocol and familiarise ourselves to the BioBrick standard system.
Mid-June: Finally jumping into the lab to do our plating and preparatory steps for the transformation into competent E. coli strain, DH5α. We’re all starting to feel the pressure of upcoming exams which is getting in the way of lab progress. Right now, the priority is to grow our transformed E. coli and get them on ice so we can experiment on them later in July.
Our first transformation of our BioBrick has been successful! We’re now waiting for our primers (from our IDT free DNA supply) to arrive in the mail so we can run colony PCR and confirm our insert is being expressed.
July
July
Designing our Urea Gene Constructs
We’re starting to design our GS1;2 construct to transform into Agrobacterium, with help of our PI and other researchers, Nijat Imin and Matthew Mayo-Smith. We plan on using the Gateway reaction (using the attB sites) to introduce our gene constructs into our chosen destination vectors. From their advice, we'll be using pDONR221 as our entry vector and pB2GW7 as our destination vector.
Progress in the Plant Lab
In early July, Greta and Prokhor and completed the training for staking and bagging of our Arabidopsis plants with sprouted stems. This is done to contain the seed pods and prevent unintentional spreading of GMOs. We've also been trimming lateral shoots to optimize growth. Continuous management of algal formation and applying hydroponic solution in response to plant growth. On the 27th, the plant lab team had their seed collection training, involving the cutting of dried plant stems, freeing the seeds from their pods and collecting them for storage.
The UreG plasmid the plant lab ordered from another lab group arrived in the mail. We want to test our Gateway protocol as we wait for our IDT vectors to arrive, but first we need to find out how to add the attB sites to our plasmid.
Working through the BioBrick lab
Early-July: Received our BioBrick primers from IDT and will begin the characterisation part of our project. It would be a good idea for future iGEM teams to provide primers for the BioBrick standard in the Distribution Kit. We’re also contacting past iGEM teams that have contributed to the same BioBrick or used similar protocols that we plan on using.
Mid-July: We’ve run into some roadblocks in the BioBrick characterisation lab - spending the week troubleshooting our PCR protocol. We’ve found the polymerase we’ve been using hasn’t been that efficient, now using KAPA2G. Also looking at the BioBrick construct, our original Brick (BBa_E0020) doesn’t have a promoter so there’s no way to observe CFP expression unless we subclone it into another vector - (this seems like poor design in terms of iGEM’s standard system). For this reason we’ve switched to characterising the RFP in the composite BBa_I3241 Brick.
We’ve successfully transformed our composite RFP BioBrick into E. coli and run colony PCR to confirm. We’ll be spending the rest of the week planning our purification technique (subcloning into another vector to add a HisTag) and fluorescent characterisation under different salinities. We’ve found the transformed E. coli grow a bit slower than usual - I’ve sent out emails asking past teams that have worked with our BioBrick if they’ve encountered the same problems. Still waiting for them to reply!
Starting our Investor Presentations!
Presented our research to BioMatters! They were really receptive towards our idea in terms of it being relevant to nitrogen pollution in New Zealand. Such a cool experience connecting with people in the industry who are equally passionate about GMOs and are keen to support us!
Had our presentation with Return On Science! It’s cool to see our lab students present the entrepreneurial aspects of our project for the first time. We got some good feedback on areas of commercialization we should deeper look into - particularly around IP and our business model.
Expanding the iGEM Community
One of our contribution initiatives is to establish another iGEM team in New Zealand. We've spoken to Kyle Webster, a PhD student previously from Canterbury University, who was involved in our past iGEM teams here in Auckland. He's keen to help us get in contact with the right people in Canterbury University to spread this opportunity to other undergrads down in the South Island.
August
August
Title
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
Subtitle
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
September
September
Title
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
Subtitle
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
October
October
Title
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
Subtitle
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
November
November
Title
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
Subtitle
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
December
December
Title
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
Subtitle
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque iaculis nibh ut quam pellentesque eleifend. Quisque posuere dolor vitae quam tincidunt placerat. Suspendisse ex purus, ornare ut porta nec, interdum id diam. Morbi at mauris imperdiet, porttitor libero in, mattis magna. Pellentesque in mi tristique, congue ligula vitae, ultrices odio. Donec ac mauris nulla. Nam eu purus sed turpis congue placerat. Nunc ut lorem eu arcu auctor sollicitudin.
"Competing in iGEM required more strength, endurance, and sacrifice than any other project I have undertaken. But nothing could have prepared me more for the post graduate study I am now pursuing than formulating and completing our project as an independent scienctist."
Judith Glasson, Alumni
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