GelGreen: As Good As Advertised

Check out the bands on the right! Its a DNA ladder. Its pretty smiley because I was running at high amperage just to test the new stain.

I ordered some GelGreen from Phenix research the other day, because they sell it in .1 ml quantities, unlike the other suppliers in the US, and because they will just take my money and ship me things without a probing questionnaire or having to call or email them (again, unlike the other US distributors).  The .1 ml quantity also sells at the same cost/unit as the .5 ml quantity!  Combined with my ability to illuminate it with some cheepo blue LEDs from ebay, incredibly low toxicity and cell permeability, and stability at room temperature in water, I would recommend it as an alternative to Carolina’s “Carolina Blu” DNA stain, which is awful.  It also makes a fine alternative to ethidium bromide if you don’t want to have hazardous chemicals around, or if you don’t want to have to buy expensive UV gel documentation equipment.
I guess my only question for Biotum is…why the heck is it called GelGreen?  Nothing about it is green, as far as I can tell.  Its Fluorescence is really more of a yellowy color, according to the datasheet.

Click here to find out more about GelGreen

And Here to buy GelGreen from Phenix Research

DIYBIO – FBI Outreach Conference, San Fransisco

Actually, we were in Walnut Creek, but it is close enough to call it San Fransisco!

As it turns out, the FBI and other defense organizations (Hello, DTRA) are pretty interested in DIYBIO.  Coming away from the conference, it seems like the FBI is  interested in exactly what you would expect: preventing bad guys (nefarious actors!) from doing Bad Things.  The Defense Threat Reduction Agency on the other hand, is interested in buying technology from people who start in “garages”, or DIY environments, to use for defense work.

The room was pretty full! I didn’t know there were this many diybiologists!  (some of these people are FBI agents/wmd coordinators.  Hard to tell the difference in this photo)

The main focus of the conference was on the interaction between law enforcement and DIY biologists.  It seems to be that the FBI is not concerned with DIY biologists, and that the FBI certainly does not view the DIYBIO “movement” as a threat.  The position of the Bureau is that local DIYBIO folks should get a hold of their local WMD coordinator,  It was also reassuring to know that the FBI hires PHD biologists and a lot of scientists to work in their WMD department- it would be nice if policy makers were just as well informed.

There was also a good discussion about the media- it turns out that both the FBI and DIYBIO folks both tend to kind of dislike the media, because as one attendee put it “They overestimate our abilities, and underestimate our ethics”.  There were some good talks given on how to engage the press in a a way that cannot be misconstrued, and how to do due diligence when someone wants to cover your space.  Rachel had an anecdote from when the BBC approached them to do a piece on the DIYBIO activities at MADLAB/MCR:

The approach that we got. we are interested in debate, is't that lovely, PCR machines, exclamation points. This is what we read: we're going to do a piece on bioterror and flu virus research. And we knew that, we knew that we were going to be portrayed as extreme. We're the only group that can kind of say these things, we weren't the right people, but we were going to be their people anyway, and it was. This is what showed up in the BBC website.. "growing concern about DIYbio.. FBI, oh there you are". Biological threat, all in the same sentence.
( quote from transcript typed by Bryan Bishop )

I thought it was very useful that we had Dan Grushkin, Rachel Turner, and Sascha Karburg -who have both done quite a bit of journalism- to tell us how the journalism works.  It is important to have both sides of the story to really understand what is going on, so DIYers can engage the press more tactfully.

Speaking of Sascha, we got to enjoy his documentary on DIYBIO at the end of the first day.  After a few years in the making, it looked pretty awesome!  I didn’t understand what they were saying most of the time, as it was in German, but the images definitely told a story.

I think that the highlight of the conference was finally seeing who was out there, and what they were up to.  If you want, you can read transcripts here, courtesey of Brian Bishop.

countries from left to right:
USA, The Netherlands (behind the benches), Finland, Denmark, Germany, Turkey

The last day we all went down to Biocurious to play with some DNA.  Biocurious walked everyone through the basic procedure for a chemical transformation, but the real highlight here was working with people from other places, and actually building a plasmid with the Genomikon kit.

Overall it was fun to meet everyone, and exciting to see what the rest of the diybio folks are up to.  I think finally meeting the European counterparts helped bring the community together.  And it was certainly good to learn that the FBI won’t be knocking on our door any time soon.

FBI-DIYBIO Outreach Workshop

I have been invited to California to the FBI-DIYBIO outreach workshop.  Day one is tomorrow.  As I sit here slurping at the last of of my large java-chip frappacino (with whipped cream) at Bryant and Mariposa, I have to say that I am pretty psyched to see Biocurious, and meet all the other DIYBIO folks to compare notes.  I will be posting my notes here on what happens!

How Do I Get Started In DIYBIO?

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.

Gene Cloning: Successful!

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.

Genomes, Environments and Traits Confrence!

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.

Mini-Maker Faire @ Cambridge Science Festival!

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.

Baby Sea-Animals, Everywhere.

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!

Deizens of the Saltwater Tank

Despite having added only live rock and snails, the 5 gallon hex tank is showing an amazing amount of macro biodiversity.  This is a short post to document what is growing in there!

A multitude of dwarf cerith snails

These guys are the workhorse of the algae fighting army.  There are many of them, in many shapes and a variety of sizes.  They like to crawl up and down the sides of the tank, and will occasionally congregate there.  Sometimes they hitch a ride on the back of larger snails!

This big guy is a florida cerith!

If I had to pick the coolest looking species of snail in the tank, it would be the Florida cerith.  Between their green coloration and rippled shell, they are hard to beat!  Not to mention these snails can self-right themselves!  These are are the largest snails in the tank.

This is the nassarius snail, in the middle. it looks like he is hitching a ride on a Florida cerith

If you zoom in you can tell this is a nassarius on a florida cerith snail.  The nassarius is easily distinguished by its single long stalk that probes for algae.  These guys are speedy!

Heres a nerite snail

My nerites are identifiable by the deep grooves that run along their round shells.  they have two long feelers, unlike the nassarius.  These guys are also very speedy.  Here, the nerite is harassing a dwarf cerith.

This is a featherduster

This guy was quite the find! It came as a hitchhiker on some live rock I bought.  It seems to have grown some since the rock was introduced, and it certainly is less skittish now.  there is another one on the same rock with a green/purple coloration, but it is hard to get a picture of that one because it is shy and very well hidden.

Cyanobacteria!

I thought this stuff was algae, but I was wrong!  It turns out to be purple cyanobacteria.  Its HUGE, and the snails seem to nibble at it from time to time.  I really don’t mind it, although it is considered a pest.

Thats all for now!  Maybe I will notice more stuff as time goes on.