Earlier today I emailed all of the participants in the recent Reading Genes workshop. Here is what I said:

Thanks so much for participating this weekend in the diy-genotyping workshop. I personally had a great time working with all of you and I learned a wonderful amount preparing and running the event. It was a bit of an experiment, and if some or all of the results are negative, rest assured that I will figure out what went wrong and invite you back for a successful second try.

Today I’m purifying everyone’s PCR products for sequencing. I’m using an enzyme I bought from Affymetrix (the ExoSAP-IT kit) to do the purification. The sequencing machine wants 12 uL (micro-liters) of each person’s purified PCR Product. So, I’ll take 12 uL of unpurified PCR mix from each person’s tube, add it to a new tube, and also add 4.5 uL of the magical ExoSAP-IT mix.

Theoretically, the included enzyme will chew up any remaining non-PCR-product DNA and remove their phosphate backbone. The genomic DNA we copied, the primers, and the DNA nucleotide building blocks that we built the copy from (the As, Gs, Cs, and Ts) will be changed from being nucleoTIDES to nucleoSIDES. I can’t give the sequencer tubes with active ExoSAP-IT, since it would probably mess up the sequencing reactions (we’re using “Sanger sequencing”, which is like a specialized kind of PCR + gel electrophoreses), so I’ll denature the ExoSAP-IT after it does its work by heating the entire mix to 80 C for 15 minutes.

So that’s the plan. I’ll let you know how the sequencing goes.

On April 24th and 25th, 2010, we helped Cambridge Science Festival participants amplify one of their own genes by hand for DNA sequencing. The Cambridge Science Festival folks blogged about it and we got a shoutout in the Boston Globe. Even the Phoenix thought it was cool.

There were three phases to the workshop: First, we isolated genomic DNA DIY-style (and with a Chelex boiling extraction suggested by Kay Aull on Sunday), then performed PCR with primers designed to amplify two difference genes: a 418 bp region of exon 18 of BRCA1, or most of TAS2R38. Chelex are essentially micro-beads coated with a resin of EDTA, which is a chelating agent often used to absorb multivalent metal ions like Mg+2, an essential cofactor for enzymes like Polymerase and DNAses. When doing a genomic extraction, chelating ambient Mg+2 is one way to inhibit cellular DNAses from chewing up the exposed genome.

We then added a small amount (1 uL) of the genomic isolate to 44 uL of PCR Mastermix (containing NEB Phusion DNA polymerase, dNTPs, buffer, optimizers, Mg2+, etc) and 5 uL of the primers to PCR tubes and ran a 30-cycles of PCR in my hand-me-down thermocycler (thanks, Harvard!).

I’ve got the samples in a -20 C freezer at the moment waiting for cleanup and sequencing.

Tinsley & Tinsley spool genomic DNA onto a toothpick after doing a (DIY genome extraction)[http://www.instructables.com/id/5-minute-DNA-Extraction-in-a-Shot-Glass/].

The BOSSLAB signed up for the Cambridge Science Festival this year, offering to help participants sequence one or two of their own genes, by hand, diy-style. Here’s basically what we told them:

The two genes we’ll be testing are BRCA1 (wikipedia) and TAS2R38 (wikipedia). BRCA1 encodes a protein that helps repair DNA and prevent cancer. TAS2R38 encodes a protein that detects a family of bitter-tasting compounds called glucosinates, commonly encountered via PTC taste strips in biology classrooms.

If you are interested in gene patents (or the lack thereof), read this blog post summarizing a recent paper, “Metastasizing patent claims on BRCA1”. The University of Utah’s Learn.Genetics program has an excellent introduction to “The PTC gene”, (TAS2R38). In general, their site has a good overview of genetics (good to read if you are a biology novice). Additionally, I like this 3D animation explaining PCR; Have a look.

Check out the wikipedia articles and explore NCBI’s reference pages for each, if you have time

There are three steps to the workshop:

First, I’ll provide an overview of the techniques we’re going to use, provide some social context regarding the two genes we’ll be sequencing, and explain what the results will be good for.

Second, each of us will extract our genomic DNA from spit samples, and then we’ll use the Polymerase Chain Reaction to selectively amplify just the region we are interested in.

On Monday, I’ll do the third step, which is to drop our PCR products (DNA) off for sequencing. On wednesday, I should get the results back, which I will send to you.

See you soon!

Mac

oscillator:

juliasegal:

antiheroe:

(via ihatesilkepil)

What if design is hard too?

DIYbio-boston got together on 13 Dec 2009 and hacked on $10 USB microscopes at the bosslab - awesome!

@molecularist blogged about the 22 Nov 09 diybio-boston meetup at sprout and recently posted a great little video of the tour. You can see us setting up Sprout and touring through the mobile lab.

Caroline and Micah, the crack designers behind http://weareagoodcompany.com/, are developing some illustrations and logos for diybio and the bosslab.

The idea is to create diybio logo and a complement of graphical motifs and decorations to garnish http://diybio.org, and to remix onto http://bosslab.org and all the other diybio-ish sites out there in the world that might be interested in some cool artwork. Carol and Micah are approaching this project with remixability in mind and I can’t wait to see what they come up with.

Here are some notes we came up with while brainstorming today:

initial notes

cuddly, happy, friendly, fun, game-like, toys

non-institutional:

• GRAFITTI
• NO LAB COATS! (too clinical)
• Indiana Jones was a scientist…
• GIRLTALK (was a molecular biologist, once upon a time)

illustrative elements could be part of a larger diagram

or furry microbes flying out of box (bosslab) or generic DIYbio headquarters

one possible treatment: retro game theme

encompassing sitewide image like vimeo illustration ( http://www.vimeo.com/927062 )

but simpler like http://www.offworld.com

main style is retro arcade game

elements of game are diybio concepts - a little lab with toy/pixelated lab equipment (some of it can be steampunk :) - iconic / sprite treatments of the other concepts

this retro sciece game look will help disrupt endemic science-phobia :)

Background

Harvard iGEM 2008 team website (DIY aesthetic)

Adventures in Synthetic Biology comic (look for the pdf, not the link to Nature)

SEED’s Synthetic Biology crib sheet

Hackteria.org - Open Source Biological Art, DIYbio

60-second defininition of synthetic biology

Synthetic biology abstraction hierarchy (look closely at datasheet)

Drew Endy explains synthetic bio in 10 minutes

http://www.ars-synthetica.net/archive/ - synthetic biology blog focusing on social issues, beautiful site design

Biobricks catalog (get an idea of the current parts collection)

metabolic networks are deliciously complicated

systems biology graphical notation - neato but engineers don’t sketch with it yet in practice

Major Themes

• DIY / Lo-Fi (retro) / indie
• science
• engineering
• bio-art

Synthetic Biology

• modularizing biological systems

• programming biological systems

• legos

• interfaces (hardware, functional, software)
• black boxes
• abstraction
• documentation data sheets

• pictures of molecular diagrams

• circuits, circuit components

• easier to use individual parts

• easier to build complex systems

naturalism / steampunk

• old school amateur science
• engraving illustrations, wood plates (http://www.droplet-microscopy.org/) — RETRO styles could be effective at disarming the unconscious barrier endemic in society to the unknown of SCIENCE, and hip, cool, fun, and a tip of the hat to victorian-era amateur scientist gentlemen
• punk style from 80s - stitching their own clothes, safety pins
• retro-rainbows! SCIENCE+YMCA logo! BIO-ATARI! http://polytroncorporation.com/ — (see their t-shirt design http://polyshop.store-08.com/browse/t-shirts/mens/ )

DIY & hardware

• Lo-Fi
• pixelated
• indie
• make magazine
• instructables
• duct tape
• toolbox
• old computer hobbyists in their garages

actual hardware

• pipets + tips (“the wrench of biology”)
• 1.5, 2, 15, 50 ml tubes
• culture plates
• lots of orange-capped glassware
• centrifuges
• vortexer
• spectrophotometer
• scale
• autoclave

Groups that might remix the illustrations

• diybio blogs
• diybio local labspaces / coworking spaces
• sticker artists
• igem teams

On Sunday diybio-boston peeps met up at sprout.

We took a tour of the shipping container lab and transported a bunch of equipment and basic reagents over to the labspace we’re setting up at Sprout.

First up: putting together a “biobrick playing card” transformation workshop. I’m going to procure the supplies over the next week. After the workshop, we’ll focus on optimizing the supplies and the protocol so it is as diy-friendly as possible.

Tag pictures with “bosslab” if you’ve got ‘em.