UW iGEM 2016

"What if the population of Scientists in the world doubled or tripled?"

-Dr. Josiah Zayner, founder of the ODIN

A scientist that I look up to founded a startup that could serve as a great resource for iGEM teams called the Open Discovery INstitute or "the ODIN" for short.  

With iGEM, OpeWetware, and the spread of biohackerspaces accross the globe (HiveBio, Genspace, Biocurious...) there's obvious support for open access to science, specifically biology.

 HiveBio in Seattle, 2015 iGEM  competition, Openwetware

The ODIN is an online store  for molecular biology lab equipment and supplies (including media, reagents, enzymes...).  The startup seems to have a fundamental purpose of giving people access to science. It's able to sell products at very inexpensive prices because it buys them in bulk from manufacturers or other suppliers, kind of Costco-like.

"Many academics I know think that people outside of labs don't want to do science or have no way to contribute. This is untrue."

ANOTHER GREAT YEAR OF OUTREACH

iGEM is as much about spreading synthetic biology as it is about practicing it. Every year, we educate K-12 students in synthetic biology, promoting interest in the biological sciences and sharing our love for research with younger members of the community.

Thanks to everyone who volunteered or visited us at outreach this year :D

Although previous UW iGEM teams preferred taking an abstract approach to outreach activities (e.g. http://2012.igem.org/Team:Washington/Outreach) , we decided to go more hands-on with an interactive strawberry DNA extraction.  This is actually a great activity for other iGEM teams and really anyone interested in doing a biology demonstration. 

Strawberries are octoploids, meaning each of their cells carries eight copies of DNA!  That’s a lot considering we’re diploid organisms, each of our cells only carries 2 copies. Thus, it should be really easy to see the strawberry DNA once it is extracted.  

IGEM is a wonderful opportunity for student scientists, but it wouldn't be possible without help from others. Together we raised $1,100 in just 9 days! May 1st was the registration deadline for our 2016 team and we made it, thanks to all of your support!  

You’ve helped fund novel biotech research, give students the opportunity to change the world through bioengineering, and engage the greater community in the art of synthetic biology.  As a certain team member likes to put it, you have “saved the world” and for this, we thank you.

We raised money not only through our crowdfunding campaign but also with these flyers.  We printed a stack of them to bring to each outreach event, raising awareness of our education program and gaining support for our team.  Feel free to print some of your own to post in other places :D 

iGEM is an international synthetic biology foundation and competition dedicated to fostering education and an open scientific community.

The UW team is recruiting new members. We welcome people from various academic backgrounds and no previous lab experience is required!  Compete with teams from around the world, meet other budding researchers, and learn more about synthetic biology, engineering design, and their real-world applications.

The dawn of a new season is upon us!  Join us on Tuesday or Wednesday to learn more about what we do as a team and how you too can get involved in hands on biotech research. 

If you are interested, attend one of the info sessions:

Tue, Jan 26 @ 6:00pm in Foege N130

Wed, Jan 27 @ 7:00pm in MolES 115

TOURING A BIOTOXIN LABORATORY

To take the tour click on the search button at the top right corner of the first picture and use the right and left arrow keys to navigate between images.  

Our team just visited Washington’s Department of Health to discuss collaborating on our current project.  In order to work with hazardous toxins, we need to experiment in an environment specific to our purpose, one tailored to compensate for the risks taken when working with paralytic shellfish poisoning.  

This is why after arriving, we headed on over to the Environmental Health laboratory situated inside.  Here we met the scientists who helped us take the first step in actually developing our Lab on a Strip as user friendly technology rather than a proof of concept system.  

We’re lucky to have been given such an informative tour of their laboratory. To learn more about the tour and get a better glimpse of their space click on the search button at the top right corner of each picture.  Take an especially good look at their wall of shellfish! 

Image source: iGEM Foundation & Justin Knight

“Dude this wasn’t supposed to happen.”-W&M Haha :D 

Congratulations to the undergrad overall jamboree winners,the William & Mary iGEM team!! Their project focused on characterizing the amount of noise or variability from the most commonly used promoters on the iGEM registry. This information is so useful! Sometimes a greater amount of intrinsic noise can actually be favorable or unfavorable based on the goals of the system.  Also, thank you so much for your pen pal outreach system :D we didn’t use it but a bunch of other teams did. 

STAY ORGANIZED AND CATCH ‘EM ALL

Overwhelmed by the number of exciting projects to see? Tired of tangibility? No worries! Guidebook is a really useful iOS app that lets convention committees, schools, and other institutions transfer their scheduling information to a digital platform….and lucky for us…iGEM has a guidebook :D 

we have someone to thank for this, either the iGEM committee itself or a dedicated team/member. I personally don’t know but would really like to acknowledge him/her/it in this post so if anyone has a clue please comment with your valuable Intel. Don’t know how to use guidebook? 

Welp, we’ve got a surprise for you: a protocol! I’m sure you haven’t seen a lot of those lately. Anyway…

Guidebook Set Up for iGEM Scheduling

Click on this link: https://guidebook.com/g/iGEM2015/

Click “Download in the App Store”.

Click “get” at the top right corner of the page and then click “install” (The app is free). 

Dodge security…or type in your password etc…

Go to your home screen. Cool! the installation progress of your app is displayed through a pie chart :)

Wait for your pie chart to disappear:(

Click the guidebook app icon.

Search “iGEM” and select.

Wow look around that panel. So much organized information!

INTO THE WORLD OF ELECTROPHORESIS 

Gel electrophoresis can be used to execute a variety of tasks.  We’ve actually just finished using it to verify the plasmid for our theophylline pathway before sending it off to be sequenced.  

After placing selected restriction enzymes into each solution of DNA, we run a gel and wait until the dye is about 80% down the gel.  Sybr Safe, which stains our nucleotides, has been added to the TAE buffer and Agarose gel; when we view the gel in UV light, our DNA strands should glow.  I don’t have a picture of our gel so here are a couple found online….just look at how pretty they are :)  

Side Note: The DNA strands in these gels are glowing pink because instead of using Sybr Safe these people used Ethidium Bromide to stain their strands.

Image source: https://askabiologist.asu.edu/agarose-gel-electrophoresis

So How Does Gel Electrophoresis Work? 

What this process does is separate DNA strands by size.  This is actually really helpful when you think about it.  We can use it for purification, verification, gene sequencing etc…  but how does it work?

DNA is a negatively charged molecule thus, it is attracted to a positive charge. During gel electrophoresis a current is run through the gel/TAE (purified water/buffer); the opposite end of the gel is positively charged, while the end with the DNA is negatively charged. 

We’ve been vigorously working in the lab all summer…This year, we’re building a diagnostic device that houses genetically-modified yeast capable of detecting small molecules. Eventually, we hope to make this system generalizable to a variety of molecules including hormones and toxins.  

This is the first step toward an easy-to-use test kit that you could be using in your home in a just a few years.  It could be used locally to screen for shellfish toxins in your Puget Sound oysters, or globally to test for drinkable water in low-resource areas.

Our long-term goal is to improve the safety of local food products by giving the consumer the ability to test for harmful substances in the products they buy.  We feel that there are many problems in public and environmental health, both in the Northwest and in the world, that could be solved through the coupling of synthetic biology and paper-based diagnostics.  

Image source: http://www.innatthemarket.com/blog/wp-content/uploads/2011/01/Stock-Pike-Place-Sign.jpg 

We'd like to say an enormous THANK YOU to Juno Therapeutics for their generous sponsorship of our team. Juno is currently developing some incredible cellular immunotherapies for cancer treatment.

Keep up the good work, and thanks again for your support! 

Before various outreach events, we  had to come up with a few ideas to intrigue the scientists of tomorrow.  Members of our team thought of awesome backstories tied in with some simple biological demonstrations  that had to do with a little  Détective  Noir-esque drama.  

These ideas were originally intertwined into one elaborate scheme built by Anastasia. I’ve typed up my favorite and the most versatile of the three.  Here is one of the fun and easy-to-do activities to get the younger community and even yourself engaged in the amazing world of bioscience!  

The Painter and the Homicide : A Twist on the Basic Strawberry DNA Extraction

Image source: http://4.bp.blogspot.com/-OfwPFYXbxZ4/UX6-bCejTLI/AAAAAAAAADU/EEE4hsGjRNg/s1600/Red+top+tube.JPG

A sticky red substance was found on suspect 1’s shoes, and on suspect 2’s shirt.  They both claim it is red paint.  Suspect 1 says he was painting his living room (and on inspection, it is indeed red).  Suspect 2 says painting is his hobby, and his apartment displays this.  Agent 2 wants to know: does the sample have DNA in it (this would indicate it is blood)?

Materials:

Strawberries

Salt

Dishwashing detergent

Ziploc Bags

Spoon or something to mix solution

Glass Test Tubes

Rubbing alcohol

Spoon for transferring strawberry/paint solutions to the test tubes

Something for transferring alcohol to the test tubes

Procedure For Blood Sample Preparation: 

Place the strawberries into a plastic bag and close.

squish the strawberries up for a few minutes.  

Add about 10ml of detergent to the bag and close.

Squish the new solution up for about 5-10 minutes.  

Pour the liquid (not the extra chunks) into a test tube.  

For the paint sample, mix red food coloring and detergent in a separate test tube. 

How it Works:

The structure of detergent molecules is very similar to the bilayer structure of strawberry cell membranes.  This is due to the polarity of the molecules forming these structures.  The polarity of molecules is responsible for so many things in science, because it helps determine molecular structure and structure helps determine function.  We’re actually using polarity to dissolve the strawberry cells’ membranes.