Difference between revisions of "Team:Auckland MOD/Notebook"
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<img src="https://static.igem.org/mediawiki/2018/f/f3/T--Auckland_MOD--lab.jpg"> | <img src="https://static.igem.org/mediawiki/2018/f/f3/T--Auckland_MOD--lab.jpg"> | ||
| − | < | + | <h4>Getting started with our BioBrick characterisation</h4> |
| + | <p> <b> Week 22: </b> Had a meeting with 2017 iGEM team lab members, Judith and Jess, to get a better idea of how they operated in the lab and how we can be more efficient. Jess was responsible for the BioBrick work (which was unsuccessful), and suggested not to continue from their BioBrick project this year, but instead do a fluorescent or chromoprotein for our characterization requirements. | ||
| + | Found an engineered fluorescent protein, <b>BBa_E0020</b> from 2004, which has been characterized by its allergenicity in one of last year’s iGEM team (Baltimore BioCrew). We’ll be finding out at what pH we observe the highest fluorescent intensity. Wrote out a basic protocol to share with the rest of the BioBrick team, Sneha and Jeremy. | ||
| + | <p> <b> Week 23: </b> We've met with our lab supervisor, Jasper, to go over our lab protocol and familiarise ourselves to the BioBrick standard system. We still don’t know exactly how we’re going to measure the changes in fluorescence (maybe flow cytometry?), but we’ve been given the green light to do our transformations. We plan on doing them as soon as possible before exam study gets in the way, so that we can carry on after we finish our exams. </p> | ||
<p><b> Week 24: </b> Finally jumping into the lab with Jeremy and doing 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> Week 24: </b> Finally jumping into the lab with Jeremy and doing 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> Week 25</b> 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> | + | <p><b> Week 25:</b> 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> |
| + | <img src="https://static.igem.org/mediawiki/2018/f/f3/T--Auckland_MOD--lab.jpg"> | ||
</div> | </div> | ||
</div> | </div> | ||
Revision as of 06:21, 24 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.
Title
some sort of extra mumbo jumbo
February
February
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.
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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.
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.
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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, using the enzymes DUR3, UreG and GS1;2.
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
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.
June
June
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.
Getting started with our BioBrick characterisation
Week 22: Had a meeting with 2017 iGEM team lab members, Judith and Jess, to get a better idea of how they operated in the lab and how we can be more efficient. Jess was responsible for the BioBrick work (which was unsuccessful), and suggested not to continue from their BioBrick project this year, but instead do a fluorescent or chromoprotein for our characterization requirements. Found an engineered fluorescent protein, BBa_E0020 from 2004, which has been characterized by its allergenicity in one of last year’s iGEM team (Baltimore BioCrew). We’ll be finding out at what pH we observe the highest fluorescent intensity. Wrote out a basic protocol to share with the rest of the BioBrick team, Sneha and Jeremy.
Week 23: We've met with our lab supervisor, Jasper, to go over our lab protocol and familiarise ourselves to the BioBrick standard system. We still don’t know exactly how we’re going to measure the changes in fluorescence (maybe flow cytometry?), but we’ve been given the green light to do our transformations. We plan on doing them as soon as possible before exam study gets in the way, so that we can carry on after we finish our exams.
Week 24: Finally jumping into the lab with Jeremy and doing 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.
Week 25: 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.
New 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.
New 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.
July
July
Designing our gene constructs
We’re starting to design our GS1;2 construct to transform into Agrobacterium, with help of our PI and other researchers in SBS. 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.
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.
Starting our investor presentations!
Had our first investor presentation with 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.
Working through the BioBrick lab
Week 27: 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.
Week 28: 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 characterizing the RFP in the composite BBa_I3241 Brick.
Week 29: 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!
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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© MOD 2018
