Nothing's crisper than CRISPR
Introducing Berkeley's latest rock star, Dr. Jennifer Doudna!
Doudna is receiving all kinds of hype in the science world for her innovative contribution to the world of genetic engineering, CRISPR.
The New York Times calls it "a scientific frenzy." Science magazine dubbed it "red hot" - "The CRISPR Craze."
It's been less than two years since Berkeley biochemist Jennifer Doudna reported in Science a startlingly versatile strategy to precisely target and snip out DNA at multiple sites in the cells of microbes, plants and animals.
But since her landmark paper, more than 100 labs have already taken up the new genomic engineering technique to delete, add or suppress genes in fruit flies, mice, zebrafish and other animals widely used to model genetic function in human disease.
As you may recall, DNA is the molecule that encodes all of your hereditary genetic traits (and some uninheritable traits, but maybe we'll discuss that later); DNA is written in a four-letter language. For DNA to be implemented, a modified copy of it is made, called RNA. RNA also has four letters and each one pairs up pretty specifically with its corresponding DNA-letter. This specificity and complementarity is key to the mode of action for CRISPR.
Doudna pairs RNA with an enzyme that cuts up DNA, called Cas9. By combining a nuclease (i.e., an enzyme that cuts DNA) with a specific RNA sequence, Doudna has created a homing missile that will allow for the degradation of targeted DNA sequences.
Doudna and her colleagues were inspired by a bacterial self-defense system that, like our immune systems, is able to remember and better-incapacitate repeat attackers.
Researchers discovered that when a bacterium is invaded by a virus, it "saves" a snippet of the viral DNA--called a spacer--and inserts it into its own DNA.
If the microbe encounters the same virus again, it can convert the original viral spacer DNA into RNA. The RNA then essentially guides the Cas9 enzyme to snip the matching stretch of DNA in the new invader, disabling the virus.
CRISPR is improving research already. I can think of past experiments when I would have loved to have a tool like this. CRISPR will allow researchers to test a gene's function by providing an easy and reliable way to specifically target and knockout a gene. The majority of the human genome doesn't even encode for genes and its role is somewhat unknown; CRISPR will potentially aid in our understanding of these segments by allowing researchers to determine how a cell is affected as a consequence of eliminating such sequences. This technology will help scientists replace a gene in a cell with an alternate version, like one with improved activity or immunity to some drug or toxin. Researchers are already dreaming of using this technique to treat gene-based disorders.
And yes, "DNA" is literally in her name. How baller is that?
Secondhand smoke, schmecondschmand schmoke. Thirdhand smoke is here!
Beware! Thirdhand smoke is a thing that exists, even if my spell check is skeptical.
A study led by researchers from Lawrence Berkeley National Laboratory has found for the first time that thirdhand smoke—the noxious residue that clings to virtually all surfaces long after the secondhand smoke from a cigarette has cleared out—causes significant genetic damage in human cells.
This seems, at first glance, like the kind of no-brainer research that would be conducted at a lesser institute when they want a break from studying marshmallows. But I think this study deserves our attention because I appreciate how thoroughly and intelligently they approached the questions.
[Bo] Hang and coworkers exposed the human cells by first extracting the compounds from the paper with a culture medium then using the medium to culture the human cells for 24 hours. The concentrations of the compounds were carefully measured. "They are close to real-life concentrations, and in fact are on the lower side of what someone might be exposed to," Hang said.
Next Hang is pursuing further understanding of the chemistry of the NNA reaction with DNA bases. NNA is a tobacco-specific nitrosamine that is not found in freshly emitted secondhand smoke. "It looks like it's a very important component of thirdhand smoke."
When conducting an experiment like this, you always have to use a model; you can't expose a set of human subjects to arbitrary amounts of thirdhand smoke and then wait a few years to see any changes. (I mean, you can, but it would be pretty unreliable and your boss would probably want data and results faster than that.) Every experiment requires testing a model of the situation of interest and, while no model is perfect, these scientists were careful to test exposure concentrations that mirror real-world values.
Additionally, this study is impressive for investigating some of the unique risks presented by thirdhand smoke. Any researcher could simply (and lazily) assume the risky components are the same as the ones in nicotine and secondhand smoke; however, Hu et al. studied unique nitrosamines (like NNA) that are more prevalent in thirdhand smoke.
Unfortunately, unless you have the means to just re-upholster every room a smoker has been in, there aren't any solutions to these problems just yet. And, if you do have those monetary means, please donate to the university and to poor CGBers slaving away under Avi's rule.
Berkeley helping start startups
I can definitively say there are only two classifications of scientists: those who enjoy science for the sake of science and those who are motivated by the desire to translate their work to the world. That's it. Black and white with no in-between.
UC Berkeley is celebrating their initiatives intended to help that latter group of scientists and promote the expansion of their research from the lab bench to the rest of the world.
"One characteristic of UC Berkeley is our strong sense of social mission and engagement," says Graham Fleming, Berkeley's vice chancellor for research. "Our students and faculty have a keen desire to apply their creativity to real-world inventions that provide solutions to the most pressing global problems. The university is fostering this creativity by investing in several new programs that support the translation of new ideas into real-world solutions."
Since IPIRA's founding, more than 150 startups have been launched with intellectual-property licenses from Berkeley. And according to the private-equity research firm PitchBook, last year Berkeley ranked first in the number of grads founding startup companies with venture capital money, topping Stanford, MIT and Harvard.
In addition to IPIRA (the Office of Intellectual Property and Research Alliances), UC Berkeley boasts six programs intended to help get ideas, research, and companies off the ground, from connecting researchers to business experts, providing equipment, or just providing space.
And, if I may editorialize for a minute (and even if I may not because this is my column, so you will read my every word), I joke about the division between "science for the sake of science" and translational research (AND IT WAS SUCH A FUNNY JOKE HAHAHAHAHA), but the two are actually inherently linked. Old-timey physicist John Tyndall (no idea if he's related to former Cal O-lineman Bill Tyndall or a clone of former Cal fullback John Tyndall) was curious about why the sky was blue and by toying with that question, discovered the microbial basis for disease and new methods of food sterilization. CRISPR's Doudna was not researching with the goal of a direct application in genetic engineering; in her curiosity about the mechanism of bacterial immunity, she discovered this exciting new tool. There is a wealth of merit and translational application to scientific curiosity, whether it's from a culture of bacteria or about exploring outer space.
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