Chandra Clarke

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Custom Genome Engineering… At Home

November 13, 2015 By Chandra Clarke Leave a Comment

Diverse_e_Coli

Project: DIY CRISPR Kits

A molecular biophysicist has just launched a crowdfunding project that will allow you to do CRISPR-based genetic editing at your kitchen table.

Dr. Josiah Zayner, who received his PhD from the University of Chicago where he studied protein engineering, is currently working for NASA, where he is a Research Fellow in NASA’s Synthetic Biology. In his spare time, he has taken to designing and creating kits for people to do the same sort of thing he does. “Budget and funding issues at NASA necessitate that I mostly work alone. I figured there has to be another way where more people can contribute to science,” said Zayner.

CRISPR stands for “clustered regularly interspaced short palindromic repeats.” In layman’s terms, this means that we have found a protein (Cas9) that can use an RNA guide to make highly specific cuts in DNA. Unlike many previous editing and engineering techniques, this one is highly accurate and easy to use. (For a backgrounder on CRISPR, check out http://www.newyorker.com/magazine/2015/11/16/the-gene-hackers.)

“This allows unprecedented abilities to edit and engineer DNA,” Zayner said. “The reason it is such a great synthetic biology tool is the specificity and general applicability. One can target almost any DNA region in almost any organism and the time to do this is an order of magnitude less than before with other genetic engineering techniques.”

Zayner has several kits on offer including a Bacteria DIY CRISPR Kit, a Yeast DIY CRISPR Kit, and some related kits, like creating light-controlled bacteria, and glow-in-the-dark bacteria projects.

If you miss his IndieGoGo project, you can also check out his store at The ODIN.

 

Photo credit: Mattosaurus, via Wikimedia Commons. e. Coli bacteria.

 

 

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Down The Garden Path

March 20, 2014 By Chandra Clarke Leave a Comment

It seemed like a good idea at the time.

The first item on my “to do” list today was “fix up garden.” Having done most of the hard work last fall, it was just a matter of clearing out winter debris, pulling a few stray plants, and planting the spring bulbs.

Two hours work, tops, right?

That was before my kids got involved.

I figured this was one of those projects my children and I could do together. So, first came the prep. My family is fair-skinned, so I broke out the sunscreen, sunglasses, and a hat. My kids took the slathering and accessorizing without complaint. I was lulled into a false sense of security.

Then it was off to the garage to get the tools. You should know my youngest son has a fixation with buttons; he is particularly fond of the garage because the door is automatic. It’s big, it’s very noisy, and you operate it with a button.

Twenty minutes later, after thoroughly exploring every angle at which you can halt the progress of a garage door, we managed to get the tools into the front yard. Among other things, I brought out two rakes: one was toddler-sized, new and bright green, while the other is ancient, unwieldy, and held together with duct tape. Of course, they all wanted mine.

They picked up the knack of raking in no time. Unfortunately, there being a great deal more rake handle than kid, their technique left me with a cauliflower ear, a bruised elbow, and a poked gut. They weren’t particularly interested in the patch of lawn I’d shown them either, preferring to rake the garden just like mummy. Sadly, the lily of the valley fared worse than I did — it’s just as well I was pulling it out anyway.

I finally convinced them to switch rakes, and I thought we were making good progress. Then I realized they were taking great armloads of leaves and throwing them *back* into the flower beds and dissolving into giggles. I decided it was time to demonstrate how much fun bagging leaves could be.

That was when they decided to explore the juniper. Juniper are not nice bushes. They’re very prickly and scratchy, and they have thin branches which make it impossible to push off and stand up. Toddlers are not very patient about this sort of thing. Fortunately, my daughter is not allergic to them; me, I get a bright red, stinging rash on contact. We won’t go into how I got the black eye, except that it has to do with impatient toddlers flailing about before they realize they’ve been rescued.

After fishing her out, pausing for a snack, finishing the raking, stopping for a nappy change, bagging the leaves, and feeding them lunch, it was time to plant. I gave each of them their very own pot full of dirt and a trowel, which they thought was great. And for fifteen minutes, I was able to work quickly and quietly, digging holes and dropping in bulbs according to the pattern I’d plotted out in my head.

Did I mention toddlers have the ability to teleport?

One minute she was happily flinging dirt onto the grass; the next minute she was beside me, having already rearranged all of the “onions!” I’d just planted and added a few choice items of her own. I will have anemone squeezed in between the freesia, tigridia mixed in with the mirabilis, and tulips shooting up beside the Fisher Price gas station action figure.

I will not say much about what happened when it was time to water the garden, except that I learned three things:

1) My shoes are not waterproof. 2) Diapers really *are* very absorbent. The brand we use can hold approximately 38 lbs of water without falling off. 3) Upturned pant cuffs, pockets and sleeves are apparently great places to hide handfuls of dirt.

So here I sit, bruised, battered, itching like mad, and contemplating an evening of mud-caked laundry … after I’ve dealt with the bathtub, which now holds most of the garden’s topsoil.

Would I do it again?

Only if I can find where they planted my rake.

Photo by John-Mark Smith on Unsplash

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Citizen science explained

March 16, 2014 By Chandra Clarke 1 Comment

Last month, I had the pleasure of speaking at a TEDx conference, where I explained the concept of citizen science to a very receptive and enthusiastic audience. Check it out, and please share it with your networks!

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Personal biology

July 10, 2013 By Chandra Clarke Leave a Comment

centrifuge with handwheel.
A very basic centrifuge with handwheel. (Photo credit: Wikipedia)

“DIYBio” got it’s start in 2008, when a group of enthusiasts got together and asked the question: Can molecular biology or biotechnology be a hobby? There was already evidence to suggest that it could be, including instructions posted online for how to isolate DNA using stuff you find in your kitchen. And at least one tinkerer, John Kanzius, who had no prior knowledge of the field, had invented a potential cancer therapy which is being tested and  investigated today. Practitioners believe that the movement has the potential to bring new technologies to bear on biological issues faster than traditional methods allow.

Today, members of the DIYBio community are working on projects like cell-pickers and centrifuges, and they’re involved in things like Genspace, previously covered on this blog.

It’s no surprise that “do-it-yourself biology” is gaining interest; nothing is more personal than your health. Internet searches for health-related questions typically number in the tens of thousands a month, and the advent of cheap, and increasingly sophisticated personal measurement devices has lead to things like the  “quantified self” or “personal analytics.”

If you’re interested in finding out more about the DIYBio movement, there are local groups from Victoria to Sydney. Check out the directory here.

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