Team:NAIT Edmonton/Logbook
First Day in Lab!
Our team got the overview of our work space for the summer. We were geared and ready to start the iGEM adventure!
May 4
Research into Silver Staining
Before beginning a project, it is of great importance to fully understand what it is you are planning to research. Our team focused on understanding the basics and chemistry of silver staining completely.
May 4 to 8
Formation of Color in Silver Staining
What was the scientific basis of color formation post silver staining?
May 11 to 15
Spruce Grove High School Lab
Students taking Biology 30 at SGHS came to NAIT today and we were lucky enough to be able to T.A for them.
May 21
Alberta Innovates and geekStarter
Team NAIT went on a road trip to the University of Calgary!
May 24
Research Continued...
Getting our wiki set up and looking for sponsorships.
May 25 to 29
Getting Our Timeline Set Up
Time is ticking! We are already into the second month of the summer!
June 1 to 5
techLife and NAIT Photoshoot
We had a photoshoot with NAIT's techLife magazine. Thank you to Ms. Linda Hoang and Blaise for your patience!
June 11
Ongoing Research and Practice
Perfecting our silver stain techniques!
June 12
Sequences Ordered!
First four sequences of our own design ordered from IDT!
June 16
Met the President!
No, not Obama. We met NAIT's President! Dr. Glenn Felthan and NAIT's VP External and CDO, Mr. George Andrews were most accommodating.
June 18
Article on Synthetic Biology in Canada
Submitted an article for Team iGEM Amoy China.
June 20
Plasmid and Sequence Digestion
A plasmid double digestion was performed along with digestion of four of our sequences. The sequences used were Arginine, Lysine, Glutamic Acid and Cysteine samples.
June 22
Sequences Arrived!
Research, Presentations and Practice
"If we knew what it was we were doing, it would not be called research, would it?" - Albert Einstein
June 22 to 25
Presentation to the Office of Research and Innovation
Today, we were lucky enough to have ORnI hear, assess and critique our preliminary presentation for iGEM. We are so happy to know that we have the full support of so many amazing individuals at the Office of Research and Innovation and at NAIT.
June 26
Happy Canada Day!
Pumping out those Sequences
This week, our team really focused on creating a variety of sequences for testing. Equipped with the knowledge from our literature searches in prior weeks, we crafted each sequence carefully and diligently. As a team, we created and ordered over 25 this week!
June 29 to July 3
And so the cloning begins...
Dr. Marcet helped us get started with cloning! But first, we had to test our enzymes to see if they will properly linearize our plasmid!
July 6
Expressing our Custom Sequences in our E. coli
Got our sequences inserted (hopefully) and now we want to grow our bacteria!
July 10
Team BBQ!
We had an awesome Sunday barbecue! The sun was shining bright, we had cold drinks and great company - A perfect day.
July 12
Maya Monday
Slowly cranking out those animations! Stay tuned!
July 13
Experiment and Protocols Flowchart
Drafted and published the first version of our experimental protocols and design! You can view it here.
July 16
Officially Registered!
SO EXCITED!!!!!!!!!
July 20
AITF and geekStarter Workshop
NAIT is off for the 6 hour drive to visit a workshop hosted by our co-Albertan team, Team Lethbridge!
July 24 to 26
Team Re-Branding
Today, we stepped away from our original iGEM inspired logo and tried to come up with a new team identity so that we could stand out from the crowd and our team would leave a lasting impression in iGEM.
July 30
NAIT Photoshoot and Mini-Prep
We had another photo shoot with our institution! Eduardo and Joy managed to escape early, because of a plasmid mini-prep.
July 31
Let's Work Together!
Our team is new to iGEM so we are helping out others as best we can. We've completed many surveys and given feedback to many teams!
August 6
Title and Abstract.. Submitted!
Today was the due date for the final abstract and title for iGEM's brochures and websites.
August 7
Officially Argentum!
Received our new logo concepts from our friend and design advisor, Derek Lue. We changed the layout of our Wiki to what you see now!
August 10
Abbie's Back!
Abbie’s last day working her full-time summer student position as a lab tech for Keyera AEF. Time to get into the lab and work on the project!
August 14
Go, Team NAIT, GO!
We're getting an overwhelming amount of support from NAIT. We're even getting golf shirts to wear in Boston!
Argentum ... Re- IM[Ag]INE 'd
Turns out, we cannot use Argentum as our team name. There is a local company that has trademarked that brand and we do not want to get into any trouble.
August 19
Watch our Intro Video!
We have a new respect for anyone who has to be in front of the camera as their career.. This less-than-two-minutes video took us a few hours to shoot and edit.
Watch it! August 20
iGEM Banner
Final banner design finished and ready for sending to iGEM HQ. We cannot wait to see our banner hanging at the Hynes Convention Centre.
Collaboration with our New Application Track
As you know, we're a first-time team. We reached out to our Track mates and asked them to help us out.
August 26-28
Digestion of Sequences
All our sequences (23) were digested and in doing so each were cleaved at specific sites to later ligate with our plasmid, pSB1C3.
August 26
Digestion of Plasmids + rSAP
We digested our pSB1C3 plasmids to cleave each at specific restriction sites to be able to insert our sequences of interest.
August 28
Presentation.. Round Two!
We presented to NAIT's Office of Research and Innovation again to give them a rundown on our current progress for our project.
August 28
Sequence and Plasmid Ligation
Ligation was conducted on our sequences of interest to join and bind with our plasmid pSB1C3 (T7+RBS) backbone.
August 29
Transformation!
From ligation, all novel sequences were transformed and plated. We counted a total of 302 colonies from this experiment. (THEY ARE ALIVE!!!!)
August 31 to September 2
Colony PCR
Four 96 well plates and many agarose gels later... We obtained the colonies that showed to have taken up our sequences!
September 2
Grew Our Colonies
To ensure our colonies would produce adequate protein when induced, we prepared them for harvest during their log phase of growth.
September 5
IPTG Induction of Proteins
We're starting to see the light at the end of the tunnel! We induced our proteins with IPTG when they had an absorbance of approximately 0.8.
September 8
Back to School for NAIT students!
Noooooooooo
september 8
Ni NTA Kit Purification!
Received our Ni-NTA kit from the University of Alberta.
September 10
IM[Ag]INE Shirts have Arrived!
Additionally, we finished pelleting and purifying more samples of our proteins. Unfortunately, not all of them showed a concentration in the NanoDrop.
September 11
Preliminary Results
After four months of work, we completed the last step of our experimental design - SDS PAGE and Silver Staining of our synthetic proteins.
September 13
Experimental Validation
We ran more gels in order to validate our preliminary results. Regrettably, the gels failed to run properly and we were unable to finish in time.
September 14
The End of our Lab Journey
And so it ends. Today, we pulled the plug on all remaining lab work and running experiment. Now, it's time to focus on our Wiki, Poster and Presentation.
September 15
Wiki FREEZE!!!!!
Had a blast browsing through our fellow iGEM team's tweets about #WikiFreeze. We're definitely scrambling. AHHH!!!!
September 18
DestiNAITion: Boston
Lab Selfie!
Week 1 - May 4 to 8
On week one, we focused on finding literature about the specific chemistry of silver staining. In general, we did not find any literature about the specific, molecular interactions of the silver stain dye with proteins. Many of the articles even stated that the exact mechanism of silver staining remains unknown.
Week 2 - May 11 to 15
This week, we researched on the scientific basis of color. More specifically, we looked into how the interaction between silver, protein and the polyacrylamide gel produces a certain color. We found that the size of silver nano-particles and the refraction of light is how we perceive different colors. We also tried to look into the electron cloud and how electron excitation produces certain wavelengths of light.
Lab with SGHS
This week, we also helped out Spruce Grove High School with a fun biology lab! We experimented with electrophoresis in agarose gel and visualized DNA strands from a mock crime scene. Additionally, we streaked plates with Serratia marcescens. Overall, the high school trip was a success and we got along really well with the students!
geekStarter Workshop
We attended the geekStarter workshop hosted by Alberta Innovates at the University of Calgary on Sunday, May 24. We presented questions about iGEM to a panel of experts. We also got one on one "speed-mentoring" with the experts as well as an exclusive group meeting with each of the four experts. Meeting the University of Lethbridge team was also quite cool!
After meeting with the experts, we decided to put the literature review on the back burner so that we could proceed with actual, physical experiments.
Week 4 - May 25 to 29
This week, we focused on perfecting our silver staining techniques. We are currently troubleshooting our gels because the stain comes out quite dark and with a lot of background staining.
We started reaching out to local start-ups and companies looking for sponsorship and further funding.
Our team also started drafting versions of our wiki on this week. As we are not familiar with the mediaWiki interface, this task proved to be quite difficult. It did, however, go live later in the week. A lot of work is still necessary for the wiki because at this time, there was no content - just a template.
Week 1 - June 1 to 5
This week, we worked on and finalized the DNA sequences to be sent to IDT.
We also continued perfecting the silver staining techniques outlined by our principal investigator. Unfortunately, we are still experiencing difficulties in background clarity. We tried to switch out the vessels used during staining because we thought that residual silver was affecting our gels. However, even new pyrex containers did not make a difference in our final stained products. We are thinking now that the BioRAD Silver Stain Plus kit that was provided for us contains defective reagents.
Week 2 - June 8 to 12
This week, we really decided to focus our efforts into perfecting our silver stain techniques. Additionally, we divided all the tasks we have to do from now until Boston and divided them according to each of our team members strengths.
We also changed the look of our wiki this week. We opted for a more centralized design. Our new logo went live this week as well (we had to change it due to branding issues with our institution). We took inspiration from the separated protein bands in SDS-PAGE and we are quite happy with how it turned out.
On June 11th, we were joined by Ms. Linda Hoang and Blaze from our institution in a professional photo shoot for NAIT's techlife magazine. The majority of us had never been in a photoshoot before so it was quite the experience. Our mentors, Marcelo and Mattéa laughed at us at every step of the way. They also joined the shoot at the end.
Joy and Marcelo started diligently working on or PyMOL and Maya animations this week.
Genetic Engineering NOW: An introspective look at synthetic biology in Canada
by Team NAIT 2015
Synthetic Biology (SynBio) is a multidisciplinary branch of science that combines biotechnology; evolutionary, molecular and systems biology; biophysics; and electrical engineering. In many ways, it is related to transgenesis; however, unlike transgenesis, which exchanges existing genes from one organism to another, synthetic biology allows scientists to write and synthesize novel genetic codes and insert them into a living organism (The Canadian Biotechnology Action Network, n.d.). Organisms that express the new genetic codes can then be used to create a molecule of human interest. From cleansing our environment to producing novel medications to treat currently incurable diseases, these genetically engineered organisms can potentially help us solve a multitude of pertaining problems in the future.
However, since synthetic biology is a novel field in research, it needs to gain the trust of the public in order to be successful (Bubela, Hagen, & Einsiedel, 2012). Public awareness and involvement in synthetic biology will help facilitate its acceptance into society as well as aid in focusing it in the development of specific products that are necessary for the community (Bubela, Hagen, & Einsiedel, 2012). Synbiota, a young canadian company that began as an iGEM Team, developed DNA design software that helps in the designing, assembling, testing and reiterating of genetic circuits created by its users (Synbiota, 2015). Their vision is to create an open ecosystem in which synthetic biology parts and protocols can be generated, exchanged, and be made accessible to the public (Synbiota, 2015). The transparency and public involvement in Synthetic Biology will help to alleviate some of the misconceptions and distrust of the new, emerging science.
In addition to public acceptance, SynBio also needs to be supported in industry. Since the year 2000, Genome Canada, a nonprofit organization that applies genomics and genomicbased technologies to create social and economic benefits for Canadians, has invested $2.3 billion CAD to decipher and understand the mechanism of economically important plant, microbial, and animal genomes (Genome Canada, 2015) (Quirion, Martin, Meulien, LePage, & Bell, 2014). Moreover, a fraction of that money has been used in developing technological toolkits that can improve the study of synthetic biology (Quirion, Martin, Meulien, LePage, & Bell, 2014). With regards to research centres, the Concordia Centre for Applied Synthetic Biology (CASB), in Montréal, is the first dedicated SynBio centre in Canada. Its main goals are to discover and understand the mechanisms of this novel science, and to research and develop tools, protocols, and technologies that allow the scientific community come up with solutions for current environmental and health matters (Concordia University, n.d.). It additionally deals with societal, legal, and ethical concerns with regards to SynBio in order to allow the conscientious development of this scientific field (Concordia University, n.d.). For synthetic biology to become a successful discipline, multiple areas of expertise must synergize (Quirion, Martin, Meulien, LePage, & Bell, 2014). Along with biotechnology, research in law, business, social sciences, and humanities is necessary to resolve the ethical, supply chain management, societal, and cultural adaptation issues that will arise with the current and future development of synthetic biology (Quirion, Martin, Meulien, LePage, & Bell, 2014).
Nonetheless, the development of this science challenges the present regulatory framework, laws, and public opinion (Bubela, Hagen, & Einsiedel, 2012). In order to constitute relevant regulations pertaining synthetic biology, policy makers must oversee every advancement made in this field and weigh out its risks and benefits (Bubela, Hagen, & Einsiedel, 2012). An analysis on the current regulations must be done to address the gaps in law, and to create new legislations that ensure that the public and scientists will both be protected (Bubela, Hagen, & Einsiedel, 2012). Currently in Canada, any product synthesized by biotechnological means is treated as any other product: regulation is initiated based on the innovative trait of the product (European Commision, 2014). Risk evaluations are done in a scientific and productbased form by Health Canada, the government agency that assesses and manages the risks of health, food, and environmental/industrial products (European Commision, 2014).
With regards to the future of SynBio in Canada, Montréal’s Concordia University held a workshop to discuss how synthetic biology can be integrated into Canada's future, creating a rough outline of its plan of action in October 2014. This outline involved crosssectoral alliances, and the direction of money towards research and development in this particular area. Furthermore, in November 2014, Genome Canada gathered Parliamentary representatives, senior public servants, and representatives of industry, academia, and research agencies to discuss how genomics and synthetic biology could influence the country’s resource sectors and, at the same time, protect and preserve the environment (Quirion, Martin, Meulien, LePage, & Bell, 2014).
Canada is definitely making a conscious effort to advance the new field of SynBio. The First Research Excellence Fund, which was recently introduced into the Canadian Budget, aims to empower postsecondary research institutions. By helping researchers develop into a highly qualified workforce with worldleading capabilities, Canada can stay internationally competitive in the research scene while remaining uptodate with cuttingedge technology a benefit to all Canadians (Merson, 2014). The proposed budget will deliver $200 million CAD annually by 2018, meaning that within the next decade, the fund will provide approximately $1.5 billion CAD to help establish Canadian universities and postsecondary institutions as global leaders in research and innovation. (Merson, 2014).
Like the United Kingdom and America before it, Canada has begun to see the importance of Synthetic Biology and how this new science can revolutionize the future of our societies. From eliminating world hunger to adapting to rapid climate change, Synthetic Biology has the potential to solve many of the present challenges that we face. However, many factors contribute to the success of a science in Canada; such as public opinion and lawful regulation. Although difficult to establish a new, groundbreaking science in Canada, investing in Synthetic Biology has been regarded as a necessary risk and a research priority.
Weekly Recap
Much of our time this week was dedicated to perfecting and polishing the preliminary presentation we plan to give on Friday, June 26 to NAIT's Office of Research and Innovation (formerly novaNAIT). Eduardo stepped up to the plate to deliver this presentation solo.
On June 24, Joy, Kevin and Jo met up with Armen, a bioinformatician from the University of Alberta. They discussed how programs such as PyMOL and PDBePISA may be of help for simulating our project. Armen will most likely be working most closely with Joy and Kevin for the project. The meeting was quite fruitful and we consider ourselves lucky to have such an experienced individual on board with our project.
June 25, we had our second meeting with NAIT's VP External and CDO, Mr. George Andrews. The CEO of Guardian Chemicals, Mr. Stewart Roth, was also present and gave us very valuable advice about the future steps necessary for our project. In addition to Mr. Roth and Mr. Andrews, we were also lucky to be joined by NAIT's Executive of Marketing and Communications (Susan Cline), Brand Manager (Sana Al Jamea) and techLife Editor (Scott Messenger) - all of whom gave sound advice for us as we go forward. Stay tuned for the cool collaborations we may do with our institution.
This week, our team also heard back from a University in Columbia about an exciting opportunity to collaborate. More on this in later weeks.
Thank You, Office of Research and Innovation
We are so lucky to have the support of such amazing people at NAIT. Eduardo did a phenomenal job presenting our ideas to the Office of Research and Innovation which made them very excited for the future of our project. They gave excellent critique about our presentation and we definitely plan to consider their comments for our iGEM presentation in September. After today, we decided to schedule two more meetings before we leave for Boston! We are successfully spreading our excitement about this project!
Special thanks to those who attended: Sandra Spencer, Stacey Ohlmann, Ryan Leskiw, Wade Muri, Chris Dambrowitz, Robin Mazumder, Iain Mackie, Albana Zeko, Kelly Maher, Andrew Pryor, Laurie Allen and our wonderful mentors, Marcelo Marcet and Mattéa Bujold.
And the results for the day...
After getting our sequences ordered and delivered, it was time to start the lab work! First thing we had to do was ensure that our enzymes were properly working.
Lane 1: DNA Marker
Lane 2: Double digest of our plasmid
Lane 3: Digest of our plasmid with only one of the two enzymes
Lane 4: Digest of our plasmid with the other one of the two enzymes
Lane 5: Undigested plasmid
Looking at the gel above, the bands show that our double digestion worked and that both enzymes are functioning correctly. In Lane 2, we now have our linear plasmid and a shorter excised fragment that cannot be visualized in the gel. Lanes 3 and 4, conversely, do not contain that fragment because the plasmid only underwent a single digestion. Lane 5 enables us to see the difference between a linear plasmid and a supercoiled plasmid. (The supercoiled, circular plasmid travelled further down the gel and thus the band is seen lower).
NAIT Team Barbecue
An awesome day!
Joy even made an iGEM cake!
We also played badminton in 30 degree weather.
To see more of our photos, check out our facebook page here
AITF geekStarter Workshop at Lethbridge
We had an amazing trip to Lethbridge this weekend. We left on Friday because the drive was over six hours long! But luckily, we were all in good company and the time just flew by.
Our home for the weekend was an amazing 4-bedroom University of Lethbridge dorm apartment, Mount Blakiston. We didn't sleep much because there was always work to do but the couches were very comfortable! :D
On Saturday, July 25 (after our Tim Hortons run, of course) we showcased Project Argentum to Team Lethbridge and a panel of four experts: Mr. César Rodriguez, FSU; Mr. André Laroche, AgriFood Canada; Mr. David Lloyd, FREDsense; and Mr. Patrick Wu, Synbiota Inc. We received incredible advice on how to improve upon our presentation. Although Eduardo did an amazing job presenting, there are still many parts we can improve upon such as:
- Why our project is important
- Add more information on our sequence design
After watching UofL's awesome RNAi presentation, we had one on one talks with César and Patrick and then André and David. Cesar and Patrick helped us by going over our entire presentation and making specific suggestions. Patrick and André helped us with seeing a new, exciting potential application of our technology and rethinking our policy and practices. The last event on Saturday was a two hour session with César, discussing our project and how we can improve upon it. During this talk, we even realized we were designing our sequences completely incorrectly.
We ended our Saturday eating "Kick-Ass Burgers" at Pop's Pubhouse with Team Lethbridge, Jennifer Hill, Sarah Lee and the four experts. It was an amazing (but tiring) day.
Sunday started with a very informative Wiki/Presentation/Design Presentation from Patrick followed by a one-on-one session with him looking at our Wiki specifically.
After a short break, we had a Skype session with Ms. Jane Calvert from Edinburgh discussing Policy and Practices. We had the opportunity to ask her questions after her talk. Although Skype calls lag quite a bit, we still received helpful information from Jane.
After lunch, we had a workshop/interactive activty with David Lloyd, co-founder of FREDsense, a company that laid its roots in iGEM 2013. David helped us realize how much thought needs to be put in to a business and business plan. Additionally, he helped both Team NAIT and Lethbridge by introducing the concept of a Business Canvas to our teams and helping us fill them out. We even looked over and filled out Team Lethbridge's canvas and they looked over and added to ours.
Cesar also gave a talk today on the Imagine, Design, Create workflow. He discussed with us his other triads of thought including: Empathy, Curiousity, Ingenuity; Software, Wetware, Hardware; Imagine, Design, Create; and Passion, Creativity, Excellence. What an enlightening talk!
We had an awesome trip! Thank you, Team Lethbridge, most especially Suneet and Graeme, for hosting an amazing event.
Who Are We? Team ARGENTUM!
Today, we met with NAIT's Branding department to try and come up with a new identity for our team. Previously, we had derived our team logo from the original iGEM logo. Sana and Derek at the Branding and Marketing office gave great advice on how we can make our team stand out. Although our original logo was nice and embodied out project well, it did not give our team its own personal identity.
We settled on a new team name: ARGENTUM. The Latin word for silver, our project is mainly about the reaction between silver staining reagents and proteins. We had already used Argentum as our project name so the transition from project name to team name was easy. Woo hoo!
NAIT Viewbook Photoshoot
The front cover of NAIT's 2016-2017 Viewbook now has some of our faces on it!
The photoshoot was on such a hot day that we had to take all the photographs in the shade. The shoot lasted almost two hours!
Luckily, Eduardo and Joy managed to escape the shoot and return to mini-prepping the backbones that we are going to use for the competition - pSB1C3. We did over 50 minipreps that day.
Final Abstract and Title Submitted - New Application Track, Here We Come!
Development and Characterization of Protein Motifs to Generate Colours upon Interaction with Silver Staining Reagents
SDS-PAGE is a very popular technique used to separate proteins based on their size. Embedded proteins, invisible to the naked eye, are then visualized by staining. Among the various staining techniques, silver staining is easy to perform and highly sensitive. However, the outcome is a series of monochromatic protein bands. Previously, we observed that some proteins inherently produce different hues post-staining. We hypothesized that specific amino acid configurations yield coloured bands after reacting with silver staining reagents. To test our hypothesis, we created numerous amino acid motifs to elucidate the sequences that would generate specific colours following silver staining. Our findings will let us generate a molecular weight marker with the innate capacity of providing users colour-coded bands post-staining without the use of impregnating dyes. Our technology will also pave the way for new types of colorimetric assays using synthetic proteins.
Argentum.. REDESIGNED
We received our new logos from our design mentor and friend, Mr. Derek Lue. We opted to keep our original idea of descending bands but we added multiple colours to it instead of using only pink and blue.
IM[Ag]INE that..
Another identity change! Our team has gone through three this summer. We are, however, very happy with this latest one and we are quite sure that this is the one we will be using in Boston.
IM[Ag]INE completely embodies our team's summer story. We started iGEM with the smallest of ideas - gaining colour - and we imagined a whole spectrum of uses and future directions. The box around Ag is a call out to the periodic table of elements and also acknowledges the fact that our research revolved around the interactions of silver ions with specific amino acids. As with our previous logos, we decided to retain the banded letters effects of multiple colours. These bands are remeniscient of the bands seen after staining in a polyacrylamide gel but, of course, they are in colour!
"Imagination is more important than knowledge. For knowledge is limited to all we now know and understand, while imagination embraces the entire world, and all there ever will be to know and understand." - Albert Einstein
New Application Buddies!
As part of our human practices we invited all the teams from our track to attempt the first ever, complete inter-track collaboration! Of the 30 teams, 7 answered the call. Over the course of one week, we conducted a series of 10-15 minute interviews on Skype, where we inquired about their iGEM 2015 journey. To learn more about how we integrated the interviews with our Human Practices project, head over to our Policy and Practices page to learn more!
Office of Research and Innovation - Presentation 2
In this presentation we went through the run down of SDS PAGE and the bio brick backbone used to create our proteins. We also went deeper in the process on how to produce the colour and specific amino acid configurations we engineered. The point for this presentation is to practice our presentation skills and also get feedback on our progress. The Office of Research and Innovation gave us excellent suggestions for improving our final PowerPoint for iGEM.
Transforming our Bacteria
From ligation, all novel sequence plates had growth which means some of those colonies may contain our custom DNA!!!
First Day of School!
Darn. We no longer have the entire institution to ourselves...
Preliminary Results!
We can see the light!!!!
AHHHH!!! The HOME STRETCH
It's a mad rush here at NAIT's HP Centre. OH MY GODDDDD.
