A lot of people have been asking “How do I get started in DIYBIO?”. The answer is not easy. Biology is a broad field, ranging from studying entire ecosystems, to the chemicals that allow life to continue. But I have done my fair share of DIY molecular biology, and I have begun to write up protocols and reviews of equiptment- which I will begin to share on this site on the DIYBIO protocols page, and on BOSSLAB.
Enjoy! More posts on how to get started to come.
Every now and then I run into or chat with people who are really excited about DIYBIO, and it is really these people who get me excited about what I do at BOSSLAB. I just wanted to give a shutout to a few people who have recently been awesome:
Cellfyre is from Oregon, and intends to start a DIYBIO group out there! According to her twitter, “Everybody is handed a coupon for scientific knowledge at birth. Many have forgotten to redeem theirs. To create awareness I advocate #DIYBio, #STEM, and #PLoS“. She came down to BOSSLAB (last week? hard to tell with finals going on) and we talked about what it is like to run a DIYBIO lab, sourcing equipment, and getting people excited. You can (and should) check out here twitter here! If you are in Oregon, tweet at her!
Andreas Sturm is a student who works somewhere in Europe (I am unsure of where), and is very ambitious in the development of hardware. His do it yourself bio-hardware blog should be up soon- I will definitely share it here once it is up! Since bio-engineering of any kind is very taboo- to the point of being illegal- he has to work closely with his university to do even transformations! But he still persists in being curious and hacking up useful tools.
Chris Templeman is an engineer and presumably owns Templeman Automation in Somerville. It turns out he was the driving force behind the sub $200 (if i recall correctly) PCR machine that was released by cofactor bio a while back. He is smart, excited about biology, so keep an eye out for him. He is also behind a pretty sweet multitouch computing table kickstarter, here.
Today, amid the project crises going on for my various classes, I got some very good and very exciting news: my engineered microbial systems project seems to be going well!
A little background on the project and team:
Our team consists of three people: Neal Singer (MechE), Jea Young Park (E:Bio) and myself (MechE). Our professor is Jean Huang, who is awesome and exceedingly good at juggling multiple projects and inspiring us to do cool things. The goal of our team was to (in the span of a month), clone a gene from p. Atlantica into e. Coli. It sounds like it should be simple and routine, but it is actually quite a process. The good news is it seems to have worked!
How do we know it worked? Check out these gels:
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The “top” of the gel is side with the wells closest to the edge. From left to right, we ran the PCR products from samples of plasmid from transformants in wells 1-9, and the 10th one was a positive control of PCR product of genomic DNA. The idea is that if the plasmid contains the gene, we would see a band near the positive control which definitely contains a copy of the gene. And the result is that we do! This means that when we ligated the plasmid and the newly cloned gene, some of the copies re-circularized without the gene, and some of the copies incorporated the new gene, and some of those copies of the gene ended up in bacteria that we have growing in the lab.
Sweeeeeeeeeet.
Jason Bobe moderates a discussion with George Church and Geraldine Hamilton about personalized medicine microfluidic devices
Today I attended the Genomes Environments and Traits Conference. It was awesome! There were talks on all manner of technical breakthroughs from faster and cheaper sequencing, to single-cell sequencing (WITH 3D protein/DNA localization on the intracellular level!!!), to hackable drug delivery kits for 3rd world countries.
The more exciting part for me personally was running into all kinds of DIYBiologists. It was awesome to finally meet them in person! Ellen Jorgensen from GeneSpace was there, as well as Joseph Jackson from BioCurious, and (obviously) Jason Bobe from the Personal Genome Project. There were also some people from the BOSSLAB group there (woo! not sure if they want to be mentioned by name). I even found somebody from Olins’ neighbor college, Wellesley, and I spotted at least one Babson Jacket in the crowd.
Anyways, this conference got me more excited about biology and science, and this summer at BOSSLAB.
Students in REVOBots
For schematics and code, check out the revobots page here. For video of the bot, look here.
Well folks, it is about time I wrapped up REVOBots, which turned out to be just as much work as expected; which is to say that it took more time and effort that I had planned. And as expected, attendance dropped off towards the end of the semester as our project based classes go into full swing and spring (and the opportunity to lounge around outside) starts to warm up the weather.
REVOBots 5 ended up being an explanation about some code that I wrote, and an introduction to EagleCAD. I have attached the code to the revobots 6 pdf because if fits in better there.
A student testing a 'bot in the dark
REVOBots 6 was a build day dedicated to making the revobots go. There were two critical failures on my part before revobots 6:
That said, the bots still work at 5 volts, albeit with a drastically shorter motor life. But operating at 5V this seemed to cause too much of a current drain on the power supply, so we got some weird twitchy behavior during the class. Since then I have developed a cheap fix using two 2n3906 NPN transistors, and a smattering of decoupling caps.
Top view of the 'bot
What is a decoupling cap though? Doesen’t the five dollar arduino already have them?
The answer to the second question is yes, but the cap was not big enough. The problem the circuit was having was that the batteries were trying to output a constant voltage. This means that as current demands changed in the circuit, the battery had to adjust the output current. With the microcontroller taking only a few miliamps, the circuit is not drawing much power. BAM! Motor turns on and what happens? The battery needs to supply more current, but can’t. Then the mcu shuts down as it looses power, sending a short pulse to the motor. So bigger decoupling caps were needed to smooth out the power supply, which the caps do by charging up to 5V, and then discharging if the voltage drops due to sudden current demand.
So the symptoms were: mcu turning on and off, which I could tell because the status LED I had attached was flickering.
The prescribed cure was: Find all the capacitors on my floor, and stick them across the power rails.
Result: REVOBot works! Check it out here! (In this video it is running away from light because I have the motors running in reverse).
Really bad photo. I apologize...
I was at the mini-maker faire today representing DIYBIO Boston, and all I got was this really bad photo…
Just kidding! I also talked to a bunch of AWESOME MAKERS and excited participants. I even got to help Gui and Molly of Artisans Asylum lift a giant motorized barbers chair onto a truck, and see a bunch of <6 year olds run dyes from M&Ms in agarose gels.
If you are looking for my bio work because you met me at the festival, click here to see the things I have done with biology.
What happens when you let your saltwater tank evaporate off for a month or so, then do a water change?
…
The punchline here is BABIES. It turns out that some sea animals, in this case featherdusters, some kind of worm, and snails all like to reproduce when they are put under stress. Specifically the salinity dropped from 40+ PPT (S.G. 1.032) to 28-30 PPT (S.G. 1.021), the temperature probably dropped as I added room temperature or colder water. I also agitated the tank with a turkey baster to help the filter pick up snail waste and to dislodge some stubborn algae.
Anyways, here are some pictures of the creatures I noticed, including some nocturnal bristleworm looking things, and copeopods, which I missed in my last post about the denizens of the tank.
Baby snail!
These guys crop up with some regularity actually. I suspect some of them dont make it, and others rapidly grow up. Occasionally I see some that are just 1-2mm long, this one was about twice that size.
Just a blurry view of my aquarium...or is it?
At first glance, this is just a really bad photo of the aquarium where the AF decided to focus on the glass. But when I looked closer…
Upon closer inspection, there is a baby tube worm/featherduster!
I noticed teeny tiny feelers coming out of this guy. When I tapped the glass, he snapped back into his coil-thing, just like the featherduster! I can only assume that they are related. I can’t wait for these to grow up; there are a whole bunch of them sprinkled around the aquarium.
This appears to be a bifurcated bristleworm
This guy may not be a baby, but it certainly caught my attention with its weirdly bifurcated body. It seems to be due to trauma and not genetic, because one side is much longer and the bifurcation did not seem to be symmetrical.
Last but not least, a copeopod
This guy (to the right of the pink thing in the middle) is a copeopod. These are ALL OVER the tank, and they feed on pretty much anything. They like to pester the featherdusters (the burrow/shell of which can be seen directly below the ‘pod).
Thats all for now. Tomorrow I may go chiton hunting somewhere on the shore of mass, so there may be forthcoming posts about that!
