Skip to main content

Team DBL iGEM 2016 Fundraiser

May 14th, 2016 UPDATE!

We’re in (to iGEM that is)! Now the fun begins. Thank you everyone that helped us raise the funds to apply and enter the competition. We’re having our first project meeting today (http://www.meetup.com/denverbiolabs/events/230852325/). Find out more about our proposed project at http://denverbiolabs.com/igem/.

dbl-igem-swag

May 7th, 2016 UPDATE!

We’re in!

igem-welcome-2016

 

April 18th, 2016 UPDATE!

We have registered for iGEM!! Thank you to everyone who has donated so far! With your help we have raised enough money to register for the competition, and we will be receiving our kit of “biobricks” soon. We have received incredible support for the project through this campaign, corporate sponsorships, and generous donations of equipment and mentoring, and we could not be more grateful. We plan to continue our fundraising efforts as the project gets underway – consider donating via our “Support” page at denverbiolabs.com, and we will keep you updated on our progress. Thank you again!”

February 12, 2016 UPDATE! 

We received an anonymous donation of $2500 to support our project and the donor has also generously agreed to match all funds raised through this campaign from now until the end of February up to an additional $2500! So now we need your support more than ever – please share our fundraiser, spread the word, and contribute if you can!

Every day approximately 830 women die from preventable causes related to pregnancy and childbirth. 99% of these maternal mortalities occur in developing countries. Postpartum hemorrhage accounts for 6% of maternal mortalities worldwide, and in Africa and Asia, where most maternal deaths occur, PPH accounts for more than 30% of all maternal deaths (WHO).

Several studies have convincingly demonstrated that the use of oxytocin injection – a drug used to induce or augment labor – significantly reduces the risk of PPH (Prendiville et al.1999). A 2001 report on safe motherhood strategies also states: “There is no doubt that oxytocin should be promoted as the drug of choice in preventing and treating abundant bleeding after delivery, [however] the principal problem is that the drug (oxytocin) is seldom readily available for routine use during labour.”

Denver Biolabs is creating a team for the 2016 iGEM competition that will set out to use synthetic biology techniques to increase the supply and production of oxytocin for use in under-resourced maternity facilities. We will learn and leverage protocols such as Gibson and Restriction Enzyme cloning, protein isolation, bacterial transformation, Western blotting, PCR, and immunoprecipitation to engineer bacteria to cost-effectively produce oxytocin. We also want to explore issues of supply chain and needle-based drug-administration by prototyping single-injection systems and on-site oxytocin-production kits. The broad backgrounds of our team members (electrical engineering, biology, chemistry, mechanical engineering, computer science, philosophy, law, and the list goes on) gives us an interdisciplinary leg-up to make real progress on these issues, and enter iGEM with a very compelling project solution.

What is iGEM?

IGEM_official_logo

iGEM – the international genetically engineered machines competition – is an annual synthetic biology competition hosted in Boston. Teams work for months to solve real-world challenges by creating novel genetically engineered systems in the areas of energy, environment, food and nutrition, manufacturing, health and medicine, and many others. The iGem Foundation president, Randy Rettberg states that: “iGEM is much more than an annual competition, the iGEM Giant Jamboree is also an international incubator for the synthetic biology industry that has spun out more than 20 competition projects into new startups.”

The registration fee to receive the iGEM parts registry and compete as a community lab is $4000. This does include the per-person conference registration fee of $695. To send a subset of our team to Boston in October of next year we are also in need of funding for flights and individual conference registrations. Any funding that exceeds our goal will be put toward acquiring the necessary equipment, reagents, and supplies to conduct our experiments and prototype our ideas, as well as providing the opportunity for more our team members to attend the competition in October..

We would greatly appreciate your support in helping us achieve our goal of competing in iGEM, solving a critical human problem, and growing as a community to promote and engage in impactful DIYbio.

https://www.generosity.com/fundraisers/denver-biolabs-igem-team

disecting-owl-pellets

Owl Pellet Dissections: Discovering the Bipedal Mouse Bat!

A few weeks ago, we welcomed some new DBL members to our community with latex gloves and owl vomit (aren’t we gracious hosts?!) More fun than it sounds, we promise. Kelsie led us through a dissection activity where we “uncovered” the bones of digested creatures who had the unfortunate fate of being on the owl menu that day. The pellets themselves were mostly-solid masses of fur, hair and feathers, and the bones were delicately encased inside. Some of us tried to play digested creature bingo using our handouts, and others got a bit more creative…

If you enjoyed “playing detective” with the owl pellets, we know you’ll enjoy the forensic biology workshop series we are planning for January! Teaser: there will be blood and a crime-scene :)

rons-workshop-06

Catching Up: Recap of DBL’s Synthetic Biology Workshops

The symbiotic relationship between Denver Biolabs and Inworks** has provided a space for innovation in biotechnology and synthetic biology – a space that has not previously existed in the greater Denver area. This unique space and partnership has created many opportunities for innovation in the biology/technology space. In the last several months, Denver Biolabs and Inworks teamed up with IndieBio, a biotech accelerator in the SF Bay Area, and Arcturus BioCloud, an automated wet-lab in the cloud, to provide some amazing hands-on synthetic biology workshops in Denver.

Genetic Tools for Bacteria Yeast and Plants, Plasmids and Strains

ron-workshop

Ron Shigeta, co-founder and Chief Science Officer of IndieBio, led the DBL community in a two day workshop on the incredible opportunities of synthetic biology, how to construct plasmids and transfect cells, and some of the hands-on steps involved in the process. Twenty-six participants streaked plates, pipetted plasmids into E.coli cells, and learned how to do basic protocols without expensive lab equipment.

Ron’s workshop highlighted some of the amazing iGEM (International Genetically Engineered Machines) projects of previous years including smell and color producing bacteria induced by various environmental conditions, agar plates that “grow” photographs, and bacteria that can fill pot-holes and cracks in cement! By the end of second day, the possibilities of synthetic biology seemed endless, and DBL was infused with excitement and momentum…but remained limited in terms of resources for carrying out experiments in Inworks’ “baby biolab” (More on this later).


Arcturus BioCloud Synthetic Biology Workshop

arcturus-workshop

Jaime and Don, CEO and CSO of Arcturus BioCloud, respectively, carried DBL’s momentum forward with another workshop at Inworks just weeks after our exciting workshop with Ron. Arcturus BioCloud is one of IndieBio’s first accelerated companies, and focuses on automated wet-lab processes that can be programmed using an online interface.

Don gave a wonderful introduction to synthetic biology and where their platform accelerates innovation. After his intro, participants logged into the Arcturus BioCloud website, and conducted the same experiment as they did the previous week at Ron’s workshop by clicking a few drop-downs, selecting their genes, and hitting “assemble”. No pipettes, no plates, and no messes for me to clean up. It was FANTASTIC! The even more amazing part was that within 10 hours of submitting our experiments, Arcturus’ robots had created our plates and sent us live photos of our colonies, happily growing and glowing. Unlike our by-hand, prone-to-human-error (a lot of it) experiment the week before, which had varying success and no expression of green fluorescent protein; the same experiments conducted on Arcturus BioCloud gave us 100% success rate. Everyone who submitted an experiment, got a vividly glowing plate, which arrived in the mail within a week (pictures below).

Talk about an “ah-ha” moment. Arcturus is revolutionizing biology, and the educational and research potential for the platform is mind-blowing. Having Arcturus’ platform available for DBL and Inworks members will allow us to pursue opportunities for creating iGEM teams and doing our own synthetic biology experiments that would not have been possible (or reliable) before.

To get a better sense of what’s possible with their system, check out their presentation from IndieBio SF Demo Day 2015.

** Denver Biolabs has the incredible fortune of being able to meet and utilize the facilities at Inworks, a new interdisciplinary initiative at the University of Colorado Denver | Anschutz Medical Campus. Inworks is a space for interdisciplinary teams to tackle hard problems that matter using the resources and capabilities of the Inworks Design and Prototyping Lab. In addition to the milling machine, CNC router, 3D printers, sewing machines, and laser cutter, Inworks houses a small, but functional biotech lab. The initial inventory of the Inworks biolab – three microscopes and a box of pre-made slides – has grown substantially thanks to the DIY-approach of Denver Biolabs members. We have built a centrifuge using the electronics shop, 3D printers, and laser cutter in the Inworks lab; we are working on an incubator using Inworks’ Arduino kits; and we have initial plans laid out for constructing many of the growing number of open source bio tools available on sites such as GaudiLabs and biodesign.cc.

 

dbl_openfuge_11

OpenFuge Build Progress 1

For the past few weeks the Biotools group has been working on building a modified OpenFuge Centrifuge. The enclosure body is made out of 1/8″ hardboard and 1/4″ acrylic. All the parts were exported from Solidworks and cut to spec by RJ using an Epilog laser cutter. The next steps involve getting the electronics and hardware built and tested. Come join us in September if you are interested in contributing or working on any of our other biotools projects. We have alot happening and could always use the help. Stay tuned!

Here are some photos from the build process:

snapgeneviewer-pglo

Newsletter, Events, & Logistics

Hello DBL! (I know this post is long, but please read, we have a lot of exciting news!)

Upcoming events:

(You will be able to register for these at www.inworks.com next week and there will also be a link to register on the DBL meetup page. I will remind everyone again once the links are up!)August 27th – Ron Shigeta from Berkeley Biolabs and IndieBio (http://www.indiebio.co/) in San Francisco will be at DBL doing a plasmid workshop. We will learn how to use restriction enzymes and insert genes. This will be a hands-on workshop, but please bring your laptops as well because some of the work will be using a software program called “SnapGene”.

September 10th – Jaime Sotomayor and Andres Ochoa from Arcturus BioCloud (https://www.arcturus.io/) will be at DBL doing an intensive synthetic biology workshop. At the end of the workshop, you and your partner/team will submit experiments to the Arcturus Biocloud platform and we will all receive our ACTUAL samples back in the mail a couple weeks later. This is going to be a GREAT workshop and we hope to have everyone here for this. There is a fee for this workshop – $80 per sample, so pair up to create and submit your samples in order to bring the per-person price down. More on this closer to the date.

DBL Meeting Logistics:

  • Our website is live and we are posting project updates weekly – please comment or respond with questions/ideas/ (www.denverbiolabs.com)
  • Health Devices Group! – remember that we had homework last week. Please come prepared to present what you’ve found on your question(s) to the group.
  • If you and your group would like to organize alternative meeting times to work on your projects via the meetup site, please email me and I will make you an event organizer on meetup.com.
  • Once a month, we are going to do project update presentations. The first one will be July 30th! Work with your groups to figure out who will give the update to the entire group. We could turn these into “potlucks” and have a more social focus – I suggest starting at 6pm and ending around 8pm. Feedback welcome :)
  • Mailing List Sign Up Instructions!!
      * For the NEWS mailing list – please enter your email address on the sidebar of our website under “Newsletter” (www.denverbiolabs.com)
      * To sign up for the Community mailing list:
      1. Click here: http://lists.denverbiolabs.com/mailman/listinfo/community_lists.denverbiolabs.com
      2. Fill out form with email / password and click Subscribe.
      3. You will get an email confirmation. Reply as instructed.
      4. You should get a welcome email.
      5. Send an introduction email to the list when you are subscribed at community@lists.denverbiolabs.com.

Inworks Memberships:

We have a new membership system at Inworks for community members to use the lab space and get qualified on our equipment. This might be helpful if your group wants to use the Inworks facility for their projects beyond the Thursday night meetup times. Check out our membership application at http://www.inworks.org under “Membership”. We can discuss this at tomorrow night’s meetup if anyone/group is interested.

Thanks and hope to see you all soon!

Best,
Heather & Denver Biolabs Team

Samples after spinning: Left - untreated, Right - 1ml blood, 0.5ml ethanol

Spinning things up and breaking things down

There was a lot going on at DBL last night. The enthusiasm, curiosity, and laughter was great, and progress was made on all fronts!

Health Devices Group

The Health Devices group continued to work on the real-time blood alcohol sensor design and implementation. The Bitalino sensors came last week, and we did some initial playing around with using the OpenSignals software to capture and visualize accelerometer data from the sensors.

We also continued our brainstorming session for form-factor, functionality, and goals for our design. Brad helped structure the discussion using a criteria matrix, and we narrowed it down to either a watch, a ring, a phone case/application, or some sort of (micro-needle?) patch device.

Lastly, we got to play with BLOOD! Jen kindly brought us a bag of chicken livers and a whole lot of chicken blood to go with them. Chloe brought the Eppendorf tubes and helped Max prepare our samples (blood + ethanol in different quantities). Then, we used the 3D printed centrifuge piece that the BioTools Group made a few weeks ago to spin the blood+alcohol mixtures down using the drill. Our first test revealed that the RPMs of the hand drill weren’t really cutting it. However, we did see a pretty drastic difference between untreated samples and the sample of 1ml of blood + 0.5ml of ethanol. The second test, we used the drill press at 1850 RPMs and got a pretty drastic difference between our samples. Lysis! The goal of this test (besides the “super cool” factor of playing with high-speed devices and blood) was to explore how to extract/differentiate alcohol from blood and measure the ratio, because blood alcohol levels are measured in mass per volume. We will continue thinking about this and our results next week.

RESOURCES:

  • Some high-level info about how BAC can be measured: http://bloodalcoholcalculator.org/detecting-blood-alcohol-concentration-in-the-human-body/
  • An easy step-by-step on determine BAC using time, % alcohol, and weight: http://www.wikihow.com/Calculate-Blood-Alcohol-Level

HOMEWORK: At the end of the meeting we each took on a question from the previous session to tackle and bring info back to the group. We will start with going over these next week (see this post if you forgot which question you had!)

Computational Biology Group

David and Peter worked on configuring Python coding environments on their laptops. This was followed by doing some paired programming on a bioinformatics script that analyzes genomic data from 23AndMe.

Lab Fundamentals Group

Max has been watching the growth of our pond-water samples (microcosms) on agar plates. Last night he discovered that the most growth was on the penicillin-treated plate. Initially, this caused some concern as we thought we may be growing antibiotic-resistant bacteria (“super bugs”), but with some more investigation, Max discovered we were simply growing mold.

The lab fundamentals group also got to use their new skills last night to prep the blood samples for the health devices group and weigh the samples once they finished spinning. It’s been great having the groups collaborate and work together to make progress on all the projects!

See everyone next week!

Chloe breaking down the brainstorm!

Getting specific: How is alcohol actually detected in blood?

Health Devices Group: Blood Alcohol Sensor

 

This week we narrowed our focus to answering some specific questions about HOW alcohol is actually measured in blood. We came up with some questions that will hopefully help direct our design for the sensor:

* How is blood alcohol actually measured? (g/dL is the unit of measurement)
* How is alcohol metabolized in the body?
* What is the boiling point of alcohol?
* What is the resonating frequency of alcohol?
* How much (and more details) does alcohol change the pH of blood?
* How long does each alcohol molecule and byproduct stay in the body?

 

Let’s spend this week diving into these questions more and seeing what we can find out about the actual processes behind determining blood-alcohol levels. Here’s one website we found that might help us get started: http://www.azdefense.com/blog/blood-alcohol-testing/. Post others in the comments!

 

Next week we are going to use the drill-centrifuge that the BioTools group 3D printed to try and separate different substances out of blood (namely ethanol). Jen is bringing the blood!
foodsci_caviar_09

Alcohol Detector, Centrifuge, Honey Caviar, and Coffee

Health Devices

The Health Devices group started focusing on developing a real-time, non-invasive blood alcohol detector that can transmit data to a smartphone. Some of the potential uses of this type of device are: to help individuals track their own blood alcohol levels, to help reduce injuries and accidents from drunk driving, to reduce underage drinking, and to monitor recovering alcoholics. We were basing our design ideas off of the judging requirements of this competition: https://www.challenge.gov/challenge/a-wearable-alcohol-biosensor/. Next week, we hope the Bitalino health sensor kit will be here (http://www.bitalino.com/index.php/plugged-kit) and we can start tracking some of our ECG, accelerometer, and temperature data. We also found some great resources to read more about how breathalyzers work and how blood alcohol levels can be detected via other bio-markers or proxies.

Building Biotools

The Biotools group decided last week to build a centrifuge based on the dremelfuge and OpenFuge open source projects. In the past week they printed out some test pieces for the dremelfuge. The original dremelfuge model wasn’t available so Scott replicated it in Solidworks and RJ printed it out in Nylon using a Markforged printer. The two parts here hold the same size eppendorf tubes. The left one can be hooked onto a dremel and the right can be put into a hand drill. We’ll test them out and report back soon.

scott-demelfuge-02

Computational Biology

Michelle gave a great presentation to the group of genome mutation basics, and we decided to start working on next generation gene sequencing and machine learning to generate hypotheses from the data.

compbio_michelle

Food Science

In the Food Science lab we created honey caviar using agar, as well as a scientifically-derived recipe for French Press coffee. In the French Press portion, we determined that the 300 year old design of coffee grinders produce more consistent grind size as opposed to modern day blade grinders. We also quantified the loss of water retained in the coffee grounds to be ~11% after pressing.

Lab Fundamentals

The lab fundamentals group spent a little time investigating the creatures growing in the microcosms they started a few weeks ago. Max spent a few hours chasing down interesting organisms. Chloe demonstrated how to make agar and fill petri dishes with and without nutrients. These will provide a test bed for microorganisms to grown next week.