If you ever wanted to analyze some genetic code, this is a really cool technique that can eventually get you there. If you’re familiar with Aqua Teen Hunger Force, here’s your overall algorithm:

1. Extract DNA in shot glass
2. ???
3. Analyze in drinking straw
4. Profit

In other words, there isn’t a tutorial yet that fully explains how to get from extraction to analysis, but be on the lookout. We’ve got steps 1 and 3 covered, so keep reading to learn about those parts.

Let’s start with a quick explanation of how to extract our own DNA (the shot glass technique):

Despite its exotic-sounding name, DNA is ubiquitous – it can be found in every cell of every living thing and almost everywhere on the planet. Nonetheless, we rarely come face-to-face with the molecule itself – and it’s not because DNA is difficult to find or isolate! In this instructable, we’ll show you how to isolate your own DNA with little more than some dish soap, table salt, high-proof alcohol, a shot glass, and a bit of your own saliva.

It only takes a couple of minutes, and after you’ve isolated your own DNA, you can either drink it back down in a tasty “DNA shot” (great party trick) or better yet, purify it further for more analysis*.

Materials & Set Up

* 1/4 of a shot glass full of your saliva
* several drops of dish soap (look for sodium laurel sulfate in the ingredients)
* a pinch of table salt (1/16 of a teaspoon)
* some contact-lens cleaning solution, meat tenderizer, or pineapple juice (optional)
* Ice-cold 120-proof+ liquor (overproof rum works well)

The next step explains how to perform electrophoresis on food coloring, which is a far cry from DNA, but it’s a step in the right direction. (See “step 2. ????”, above.) Most of the tools for analysis, with the notable exception of Agar gel, might be lying around your house. Agar gel can be picked up at a science/hobby shop (maybe in your town but certainly online), or possibly at a specialty foods store.

My understanding is that this step involves dying your sample for analysis, so that you can visually inspect it to see which portions have separated out. Apparently, such genetic dyes are “expensive or toxic”, according to some of the comments I’ve been reading. So, read the following for its coolness, but keep in mind that it still needs to be tweaked to actually apply to DNA.

RTFA: http://maradydd.livejournal.com/417631.html

Gel electrophoresis is one of the most versatile, widely used tools in a microbiologist’s or geneticist’s toolbox. It’s used for separating out DNA, RNA or protein molecules (that you presumably isolated in a previous step of your experiment) based on their molecular weight, so that you can analyze the molecules, clone them, amplify them with PCR, sequence them, lots of different things.

Electrophoresis does require some equipment to perform — an inner tray which holds the gel, an outer tray which holds a “running buffer” solution (which keeps things cool and keeps pH stable), electrodes, and a power supply (50V-150V is pretty common). You can buy a gel box from a commercial supplier, though they’re not cheap, and a fancy power supply will set you back even more; Bio-Rad has some nice ones, but they run to the thousands of dollars.

Happily, there are solutions for the biohacker on a budget.

Keep reading for a good introduction to this process, mostly using a drinking straw, 9V battery, Agar Gel, and some alligator clips. The protocol for performing a simple electrophoresis on food coloring is here:

Gel electrophoresis is used to separate DNA or RNA molecules by size. For this experiment, the gel is inside a plastic drinking straw.

Since this is a DIYbio experiment, I emphasize that all of the materials came from regular shops, including Radioshack and an Asian grocery store in Sacramento, CA. This experiment is designed to create a faster and smaller alternative to traditional gel electrophoresis.

At this point, these instructions are for imaging food coloring – take these instructions and figure out how to do DNA, RNA, proteins, and genome fingerprinting.

…continuing…

1. Cast a gel in a straw
2. Load sample
3. Place straw in gel box with running buffer
4. Run the gel

There you have it – a skeletal framework that almost (but not quite) lets you look at the relative quantities of samples in an agar medium. If you have been following this project through certain mailing lists, then this post probably isn’t for you. However, if you know about these subjects but you haven’t heard about the Do-It-Yourself approach, maybe you can contribute!

Via BoingBoing.

RTFA: http://www.nsf.gov/discoveries/disc_summ.jsp?cntn_…

Earlier this year, consumers around the world noticed higher food prices as the cost of most grains escalated. In many parts of the developing world, rice, a crucial staple for billions of people, became too expensive or not available at all, triggering large-scale hunger and food riots that destabilized entire countries and regions.

In May of this year, a group of computational biologists at the University of Washington began to tap the collective power of more than 1 million desk top computers to better understand the protein structures of rice plants …, the Nutritious Rice for the World project … Led by Ram Samudrala, an associate professor and computational biologist at the University of Washington, the project taps the World Community Grid, a distributed computing system created by IBM that links up computers all over the planet. The grid combines the spare power of computers not in use to handle large-scale computational problems such as analyzing rice genomics.

The project is one of five initiatives being tackled by the World Community Grid right now and, according to Samudrala, it is taking up about a third of the grid’s current capacity. By using the collective power of the grid, Samudrala and his collaborators estimate the project will be completed in two years, considerably faster than the 200 years they estimate it would take a conventional computer system to complete the same job.

Ultimately, the combined power of these computers should allow the researchers to map out the 30,000 to 60,000 rice protein structures and better understand their related functions. Armed with this information, plant biologists should be able to begin to provide the world’s farmers with rice varieties that can grow with less water, resist insects and diseases and provide a more nutritious meal.

… Given the large number of people who eat rice as their primary source of grain, this research could go a long way in tackling some of the food security challenges currently facing the human race.

This project demonstrates the power for great good that can be achieved through pure nerdiness. If you’re a bio-geek, you will probably enjoy checking out Prof. Samudrala’s website. The site is chalk chock full of goodies, including software downloads (and a web API!) to model genomes, proteins, et al. (: http://software.compbio.washington.edu/ Using their online “Bioverse” java app, I generated this DNA sequence of E. Coli and its closest evolutionary relatives … oh E. Coli: So good for the lower intestines; so bad for the stomach!

RTFA: http://www.sciencedaily.com/releases/2008/05/08050…

An analysis of the genome, published today in the journal Nature, can help scientists piece together a more complete picture of the evolution of all mammals, including humans.

The platypus, classified as a mammal because it produces milk and is covered in a coat of fur, also possesses features of reptiles, birds and their common ancestors, along with some curious attributes of its own. One of only two mammals that lays eggs, the platypus also sports a duck-like bill that holds a sophisticated electrosensory system used to forage for food underwater. Males possess hind leg spurs that can deliver pain-inducing venom to its foes competing for a mate or territory during the breeding season.

“The fascinating mix of features in the platypus genome provides many clues to the function and evolution of all mammalian genomes,” says Richard K. Wilson, Ph.D., director of the The Genome Center at Washington University and the paper’s senior author. “By comparing the platypus genome to other mammalian genomes, we’ll be able to study genes that have been conserved throughout evolution.”

The platypus represents the earliest offshoot of the mammalian lineage some 166 million years ago from primitive ancestors that had features of both mammals and reptiles. “What is unique about the platypus is that it has retained a large overlap between two very different classifications, while later mammals lost the features of reptiles,” says Wes Warren, Ph.D., an assistant professor of genetics, who led the project.

Comparison of the platypus genome with the DNA of humans and other mammals, which diverged later, and the genomes of birds, whose ancestors branched off an estimated 315 million years ago, can help scientists fill gaps in their understanding of mammalian evolution. The comparison also will allow scientists to date the emergence of genes and traits specific to mammals.

Things are getting crazy. This article includes a link to the raw DNA data. I find that fact, by itself, to be insane. …not to mention the fact that this is an insight into the craziest “mammal” in existence: the platypus.

RTFA: http://technology.newscientist.com/article/dn13252…

Two artificial DNA “letters” that are accurately and efficiently replicated by a natural enzyme have been created by US researchers. Adding the two artificial building blocks to the four that naturally comprise DNA could allow wildly different kinds of genetic engineering, they say.

Eventually, the researchers say, they may be able to add them into the genetic code of living organisms.

The diversity of life on earth evolved using genetic code made from arrangements of four genetic “bases”, sometimes described as letters. They are divided into two pairs, which bond together from opposite strands of a DNA molecule to form the rungs of its characteristic double-helix shape.

The unnatural but functional new base pair is the fruit of nearly a decade of research by chemical biologist Floyd Romesberg, at the Scripps Research Institute, La Jolla, California, US.

Romesberg and colleagues painstakingly created a library of nearly 200 potential new genetic bases that are slight variations on the natural ones. Unfortunately, none of them were similar enough in structure and chemistry to the real thing to be copied accurately by the polymerase enzymes that replicate DNA inside cells.

Erm… the horror? As in: oh shit chaos? Yes?