Life Lately & Weight and Wellness Lecture #2: The interplay between poverty and obesity.

How’s it hanging Homo sapiens? How’s the weather where you are? I don’t mean to brag, but Seattle is in the midst of some uncharacteristically marvelous meteorological conditions.

Oh STOP it...no, no, no...DON'T STOP!
Oh STOP it…no, no, no…DON’T STOP!

The mighty weather gods, Cliff Mass of UW and Thor of Asgard, are truly smiling upon the Emerald City from on high.

Or from on my sheets, in the case of Thor. Yes I'm a 26-year old Ph.D. candidate who sleeps on "Avengers" sheets...no I haven't dated anyone in a while, why do you ask?
Or from on my sheets, in the case of Thor. Yes I’m a 26-year old Ph.D. candidate who sleeps on “Avengers” sheets…no I haven’t dated anyone in a while, why do you ask?

I started this particular Sunday with a slow-but-scenic 10 mile run.

Hey! Remember how this used to be a running blog?
Hey! Remember how this used to be a running blog?
It is HARD to argue with the sunrise over the Montlake cut.
It is HARD to argue with the sunrise over the Montlake cut.

After completing this morning’s mileage, I struck out for my favorite coffee shop, fully intending to put the finishing touches on the last chapter of my thesis.

PRODUCTIVITY!
PRODUCTIVITY!

However, now that my Americano is in hand, I’ve decided it would be MUCH more fun to check in with you lovely people, my gentle readers. My thesis can remain a 93-pages-of-single-spaced-text-that-doesn’t-have-references-inserted-yet albatross around my neck, for the time being.

PRODUCTIVITY?
PRODUCTIVITY?

Last Tuesday I attended a fantastic talk by Dr. Adam Drewnowski, a faculty member in UW’s School of Public Health. The lecture was the second of an ongoing “Weight and Wellness” series, exploring issues at the intersection of public health, food policy, culture, and society.

IMG_6775

Tuesday’s talk was the perfect follow up to Michael Pollan’s opening address about our general national eating disorder: a fascinating seminar titled “Obesity and Poverty: Linking Food, Health, and Incomes.” Dr Drewnowski conducts beautiful epidemiological research to create high-resolution maps and investigate the interplay between income, access to grocery stores, food behaviors, obesity rates, and socioeconomic status. His research shows that local property values are one of the best predictors of diet-related pathologies, such as diabetes. He makes the argument that the obesity epidemic is not simply a side-effect of rising income inequality, but rather a direct consequence of economic disparities. The food system in America today perversely creates conditions where people who can afford to spend the least on food consume MORE calories than those with money to spare.

IMG_6789

The average person on supplemental nutritional assistance (SNAP, or food stamps) receives $29 per week to spend on food. Gwyneth Paltrow recently attempted to understand how low-income people try to get by in this country by undertaking her own “food-bank challenge.” If Gwyneth only ate the ingredients she purchased for an entire week, according to Dr. Drewnowski’s calculations, she would be surviving on just over 800 calories per day.

SEVEN limes!?
SEVEN limes!?

Even for incredibly thin white women whose work doesn’t demand intense physical labor, 800 calories is barely enough to survive. While it’s easy to laugh at Gwyneth’s naiveté (and some excellent pieces have been written about what $29 per week ACTUALLY looks like for low-income people), I applaud her attempts to raise awareness of the difficult choices people in poverty must make regarding food. For people living in extreme poverty, eating fresh, healthful, plant-based meals every day is simply not realistic. Eating well not only costs more, but high-end grocery stores AREN’T located in low-income neighborhoods.

Have you EVER in your life seen a Whole Foods next to a taco bell?
Have you EVER in your life seen a Whole Foods next to a taco bell?

One of the most fascinating insights from Dr. Drewnoski’s talk was the relationship between where people get their groceries and their likelihood of being overweight. Obesity rates among Whole Foods shoppers are SEVEN times lower than those at discount grocery stores like Albertsons and QFC. While it is easy for well-educated, high-income food advocates (like Michael Pollan) to issue platitudes like: “eat food, not too much, mostly plants,” poverty makes a healthful plant-based diet unattainable.

Corn-syrup and soy oil are technically plants.
Corn-syrup and soy oil are technically plants.

Dr. Drewnoski pointed out that heavily processed, high-calorie foods are cheap, convenient, and satisfying. (While snakily pointing out, as I have mentioned before, that all of these junky-products technically come from plant-based corn syrup). He outlined some of his current research and reform efforts, including new pricing schemes for SNAP based on energy versus nutrient density. Overall it was a thought-provoking talk, with a wealth of information, and a beautiful data-based approach to addressing public health. I left feeling amazingly grateful that I have the time and financial resources to eat a healthful diet. I’m looking forward to the rest of the talks in this lecture series; the food system in America is clearly in need of a serious overhaul, and it’s fascinating to hear perspectives from public health researchers on the front-lines.

I'm also looking forward to eating this purple broccoli I bought at the farmer's market yesterday!
I’m also looking forward to eating this purple broccoli I bought at the farmer’s market yesterday!

I hope that everyone reading this feels similarly blessed, and maybe inspired to take notice and take action when congress attempts to further slash the budget for supplemental nutritional assistance.

Ugh...THIS guy's plan, again.
Ugh…THIS guy’s plan, again.

For this little blogger it’s time to press publish on this post, write a chapter about DNA lesions for my thesis, then get outside and enjoy a sunny Seattle Sunday.

STOP IT, Seattle...No...never stop!
STOP IT, Seattle…No…never stop!

Have a WONDERFUL weekend!

My Evening with Michael Pollan

Happy Thursday fan-boys and fan-girls! I’m brimming over with excitement because last night I saw one of my personal heroes up-close(ish) and in the flesh!

Unfortunately Elvis is still, ostensibly, deceased.
Unfortunately it wasn’t Elvis. 

Yesterday evening I attended a talk by Michael Pollan, as part of the University of Washington School of Public Health’sWeight and Wellness” lecture series.

This seems right up my alley...
This seems right up my alley…

The School of Public Health is sponsoring a series of invited speakers to discuss issues at the intersection of food, culture, agriculture, economics, health, and equality. When I saw that one of my favorite authors would be kicking off the conversation I snatched a (five dollar) ticket like a grizzly bear grabbing a salmon.

Being a grad student has its fringe benefits.
Being a grad student has its fringe benefits.

Pollen’s Talk was titled: “Our National Eating Disorder.” He opened up the evening with the sobering statement that unhealthy diets in America have effectively reversed 100 years of progress in public health. After detailing some unsettling statistics about rates of diet-related pathologies, such as obesity and type II diabetes (which reduces patients’ lifespans by seven years, on average), Pollan posed the questions: How did we get to this point? Why are chronic diseases turning into an American lifestyle? and What can we do to turn our dietary crazy-train  around?

O beautiful, for spacious thighs, for amber waves of high-fructose corn syrup....
O beautiful, for spacious thighs, for amber waves of high-fructose corn syrup….

Pollan identified three key areas where the American food system is severely broken: agricultural policy, food marketing, and food ideology. In other words the way we produce food, the way food is sold to us and the way we think about food are all severely skewed in this country. To illustrate his point, Pollan held up two products, and asked the audience to identify which represented the “healthy” choice: a fruit-flavored yogurt, or a can of coca-cola?

Wait...this is a trick question, right?
Wait…this is a trick question, right?

Soda pretty clearly lacks any redeeming nutritional value. However, despite the presence of protein and calcium, the yogurt contains MORE SUGAR, ounce-for-ounce than the can of coke. Can we genuinely call that yogurt a “healthy” choice? Why are food-companies cramming all of this corn syrup into everything anyway? Do either of those things have gluten in them? What’s a confused consumer to do?

Buy sugar-free yogurt...duh
Buy sugar-free yogurt…duh

To address the question of how America arrived in our current state of food-confusion, Pollan gave a fascinating overview of policy and food-marketing trends stretching back to the Nixon era. Ever since the 70s the dominant goal of agricultural legislation in this country has been to facilitate the production of PLENTIFUL and CHEAP commodity crops.

Ah yes...king corn, we meet again.
Ah yes…king corn, we meet again.

Pollen was quick to point out (as I have also noted, when I talked about why I believe in labeling GMO food) that the abundance of corn and soy produced in this country “ARE NOT corn-on the cob and edamame.” These commodity crops are basically inedible, produced purely for processing into high-fructose corn syrup and soy oil. I was surprised to learn that soy oil composes 10% of the calories in the typical modern American diet!

Corn==>Candy corn!
Corn==>Candy corn!

The perverse nature of agricultural policy in America, however, turns economics upside-down and backwards. Political leaders love cheap food, the political turmoil in India and Egypt during 2008’s global rice crisis illustrate how disruptive price increases in food products can be. Therefore, although food prices overall have decreased, the overabundance of supply is heavily subsidized to increase production even further, leading to further price reductions. The average American spends LESS on food today than they did in the 1970s (which has helped cushion the national decline in average wages), even though we are eating WAY more than we ever have before.

Evolution?
Evolution?

In order to deal with the overabundance of food-supply, industry has come up with clever ways to increase American demand. Pollan gave several examples of how food-marketing competes for “stomach-share” and endeavors to “transcend the fixed stomach,” convincing consumers to buy (and eat) more processed food than they could possibly need.

Ladies and gentlemen of the jury, I present exhibit M...for McNugget
Ladies and gentlemen of the jury, I present exhibit M…for McNugget

Pollan’s talk wasn’t all doom-and-gloom. After elegantly outlining what’s WRONG with the American food-system, he offered some suggestions for how the country can move forward and put things RIGHT. Pollen repeated his call for a national food policy, designed to ensure that everyone in America has enough and that food should be healthy, rather than our current situation which is engineered to keep commodity prices low and farmers employed. To address the over-abundance of processed crap he suggested a tax on junk-food (a la Mayor Bloomberg’s efforts), with concomitant efforts to encourage good food choices. As he so eloquently stated: “you cannot subsidize broccoli, but you can subsidize demand.” Finally, he offered up some of his own “Food Rules” that he has collected to aid in making personal decisions about what to eat.

Mostly plants
Hint: Mostly plants

I’m a huge fan of Michael Pollan’s entire ethos (I think that my recipes attest to a deep passion for fruits and veggies). It was awesome to hear one of my favorite authors talking about his topic. I haven’t heard of any of the other speakers in this lecture series, but I might decide to check out a few of the talks in the upcoming weeks.

HAPPY EATING!

What’s your favorite plant to eat?

Ascensions

Hello, bunnies! Did you have a hip-hop-happy Easter?

I had an egg-cellent time!
I had an egg-cellent time!

I hope you took some time to meditate upon the most holy ascension ever witnessed by man. I am, of course, referring to the recent rise of Bertha, the giant tunnel-boring drill that got oh-so-very stuck underneath Seattle’s Alaskan Way Viaduct.

As incredible as the above video is, I do believe that they missed out on a GOLDEN opportunity when selecting the soundtrack.

In all seriousness, I hope that everybody had an enjoyable easter/passover/vernal equinox/festival of the pagan goddess Eostre, depending on whatever tradition you and your family choose to celebrate the emergence of spring.

Seattle can really turn it OUT at the end of winter.
Seattle can really turn it OUT at the end of winter.

I must apologize that I have gone so long without posting. Things have been, as always, busy over here on my end. I took a trip to Washington D.C.

I'm trying to become more presidential.
I’m trying to become more presidential.

I also moved!

The answer to the question: "Will that fit into my subaru?" Is always: "yes"
The answer to the question: “Will that fit into my subaru?” Is always: “yes”

I’ve found some time to have some fun. I went to see an amazing performance by The Seattle Men’s Chorus.

IMG_6756

They sang “Tyler’s Suite” (a work celebrating the life of Tyler Clementi, the Rutgers student who took his own life after experiencing cyber-bullying) as well as “I Am Harvey Milk” (a biographical operetta about the nation’s first openly gay elected official). The performance was incredible, the singing was amazing, exuberant, tragic, and ultimately inspiring.

Throughout all of this I’ve been writing my thesis and finishing up the last few experiments for a new manuscript. I’ll probably be posting less frequently during the coming weeks. Somehow writing on my blog just isn’t terribly relaxing after spending 10 hours writing my thesis at work.

I may have skipped directly to step 3.  source: http://phdcomics.com/comics/archive.php?comicid=1776
I may have skipped directly to step 3.
source: http://phdcomics.com/comics/archive.php?comicid=1776

I hope everyone’s week is off to a WONDERFUL start.

What’s the weather like where you are? Has Spring sprung? 

When genome editing meets the germline…

Hello movers, shakers, and policy-makers!

What's up Barack!? It's Sam.
What’s up Barack!?

Today’s post is inspired by a pair of editorials in Nature and Science calling for a worldwide moratorium on genome editing in the human germline. I highly recommend reading both pieces; the authors each contributed to developing the TALEN zinc-finger nuclease and CRISPR/Cas9 technology for use in genetically modifying human cells. Both TALENs and CRISPRs are systems that may be engineered to cut DNA in a specific spot, the cut can then be used to introduce a change in the genome by hijacking a cell’s own repair capabilities (see my previous post on Genome Editing, or this excellent review by Jennifer Doudna for a more detailed explanation). These technologies are not exactly new, in fact the field has an established track record of successfully producing viable transgenic primates and edited human cell lines with both techniques, why are scientists suddenly calling for a stop to this type of research?

The first transgenic primates produced with CRISPR (source, Niu et al. Cell, 2014)
The first transgenic primates produced with CRISPR (source, Niu et al. Cell, 2014)

The authors are not calling for a blanket ban on genome-editing itself; the technology shows considerable promise for treating incurable genetic diseases. Last year Yin et al. successfully used CRISPR to correct hereditary tyrosinemia (a blood disease) in adult mice. Another group used TALEN to remove a gene in human T-cell lines, which effectively rendered the cells immune to HIV. The biotech industry is paying attention to these academic successes: Novartis recently acquired the small CRISPR-focused start-up Intella biosciences, with the express purpose of developing genome-edited stem-cell therapies for cancer. Editas, a boston based firm, aims to apply CRISPR-mediated genome editing to correcting Sickle-Cell Anemia. The F.D.A. has strict regulatory guidelines in place to oversee the thousands of gene-therapy clinical trials currently underway in the United States.

The future IS now.
The future IS now.

The key distinction between the amazing advances described above and the research that is currently making genome-editors in general very nervous is the type of tissue targeted for tinkering. All of the efforts to correct blood diseases or cure HIV introduce changes into the genomes of somatic cells in specific adult tissues. Any alterations in somatic cells are not passed on to the next generation. However, advances in genome editing, combined with expertise in in vitro fertilization could allow researchers to change the DNA in embryos before implantation. Any resulting edited offspring would carry the alteration in every single cell in their entire body, including the germline, so any changes would then be passed on to their progeny.

Don't edit me...
Don’t edit me…

The idea of genome-edited embryos and designer babies seems like a scene from a science fiction story. However, biotech firms such as OvaScience are working to improve the efficiency of successful IVF by modifying a mother’s eggs. The U.K. recently approved embryonic mitochondrial transfers (a.k.a three-parent children) to treat incurable genetic disorders of the cell’s energy factories. Neither of these advances are examples of targeted embryo-editing, however, a provocative piece from MIT’s Technology Review cites unnamed sources purporting that “such [germline editing] experiments had already been carried out in China and that results describing edited embryos were pending publication.”

Communist mutants!
Communist mutants!

Adding to the general unease, a recent publication in Science combined CRISPRs with gene-drive technology to generate a heritable mutation in fruit-flies that spread rapidly through the population in subsequent generations. In other words, we know how to make make genetic changes that are heritable, and highly transmissible. Scientists see a potential Pandora’s Box opening up all over our chromosomes, if this research is allowed to continue unchecked.

What could possibly go wrong?
What could possibly go wrong?

This isn’t the first time scientists have convened to consider something new and scary; in 1975 the Asilomar Conference issued common-sense guidelines for research using Recombinant DNA Molecules. We’re approaching the 40 year anniversary of this seminal meeting, recombinant research is alive and well, and despite the doomsday predictions, we haven’t inadvertently created a manmade Andromeda Strain.

Although we did produce a Kardashian...which might be just as bad
Although we did produce a Kardashian…which might be just as bad

I’m skeptical that Chinese scientists are on the cusp of publishing about modified mutants. I HIGHLY doubt that any reputable journal would agree to publish such blatantly unethical research. No institutional review board at a major academic institution would EVER approve a such a study. If a rogue scientist, working in isolation DID somehow successfully bring a CRISPR-modified embryo to term tomorrow they SHOULD be exiled from academia, and the details of the findings SHOULD be buried away from public consumption. The world isn’t ready for germline genome editing…yet.

We're BARELY ready for somatic cell editing...but that ship has sailed.
We’re BARELY ready for somatic cell editing…but that ship has sailed.

I applaud the exhortations for more careful consideration. I agree that scientists, ethicists, and policy-makers need to carefully consider exactly what is acceptable and what are the best practices governing genome-editing research. I’m encouraged that meetings devoted to this very topic are happening worldwide. I also don’t believe that the technology ought to be rejected outright. If a parent knows that they carry a genetic allele that will cause their children to develop cystic fibrosis or aggressive breast cancer, correcting the problem before birth through embryonic editing could decrease the societal burden of incurable diseases. Although pop-science pieces fan the flames of false controversy by imagining “designer babies” or “eliminating the gay gene (er…gay-8-megabase region on the X-chromosome),” the realistic applications of the technology could substantially improve peoples’ lives.

No WAY are we getting rid of the gay gene...but we might be able to eliminate HIV
No WAY are we getting rid of the gay gene…but we might be able to eliminate HIV

However, ethical concerns remain, even if this technique is only ever applied in the service of promoting human health. One of my main questions is: who will benefit from this technology? DNA sequencing and in vitro fertilization are EXPENSIVE. If embryonic genome editing does become widely available, are we setting ourselves up for a future where the burden of genetic disorders falls disproportionately upon the poor? What types of diseases are candidates for treatment by genome editing? Certainly disorders that would otherwise be lethal, such as Huntington’s Disease seem like prime candidates; what about severe developmental disabilities such as autism? What about congenital blindness? Is it ethical to “correct” mutations that don’t necessarily kill afflicted individuals, but do carry a societal cost?

Help us out, Abe, we need some guidance.
Help us out, Abe, we need some guidance.

I’m excited to see high-profile scientists engaging the ethical questions. I think genome-editing has enormous potential, but like any technology, it needs to be considered in terms of its applications. I don’t think a blanket ban or all-purpose endorsement is appropriate; this research SHOULD proceed…with immense caution. I think that the concluding paragraph of the Asilomar Meeting‘s report is as applicable today as it was in 1975:

“the standards of protection should be greater at the beginning and modified as improvements in the method-ology occur and assessments of the risks change”…”future research and experience may show that many of the potential biohazards are less serious and/or less probable than we now suspect.”

 

 

 

The Arctic Apple: a GMO that aspires to reduce food waste

Happy Sunday scholars and sledders.

bobsled
This bobsled looks lost…

 

I hope everyone is having a merry and mathematical weekend! Did you celebrate Pi Day yesterday? Did you read any of the multitudinous articles about the marvelous irrational ratio of a circle’s circumference to its diameter? Did you bake any pies yourselves?

American as apple pie!
American as apple pie!

My favorite flavor of pie is definitely rhubarb, but today I want to discuss a different fruit-filling: apples, specifically, the genetically modified Arctic Apple that was recently approved for sale by the F.D.A.

Nice segue...
Nice segue…

The arctic apple offers an interesting case study into the ongoing GMO debate. Arctic Apples are cisgenic GMOs- they don’t have any genes from another organism added into them, rather they have been manipulated not to go brown when sliced or bruised (similar to the Simplot potato, that I discussed previously). The trick that allows arctic apples to remain pristine even after hours left out in the air is called gene silencing through RNA interference (RNAi).

RNA interference shuts down an undesirable process by taking advantage of a cell’s own defense mechanisms. As you all remember from basic biology, the cell’s genetic information is stored in the sequence of double-stranded DNA within its nucleus. When a cell wants to make a particular protein, it opens up the corresponding stretch of DNA, then transcribes that region into a single-stranded RNA molecule. That RNA molecule is then sent outside of the nucleus (into the region of the cell called the cytosol, which is where most of the interesting just-and-bolts chemistry takes place to keep us alive).

You guys, Eukaryotic cells are SO complicated.
You guys, Eukaryotic cells are SO complicated.

A machine in the cytosol called a ribosome reads the RNA to make a proteins (which is called translation). Cells are accustomed to their own double-stranded DNA staying in the nucleus, and single stranded RNA floating around the cytoplasm. However, cells are constantly under attack from invading genetic material. Viruses try to take over cells by injecting their own genomes into the mix and hijacking the machinery.

When viruses attack!
When viruses attack!

Viruses come in all shapes and sizes, but some store their own genetic information in the form of double-stranded RNA.

Ebola virus looks like spaghetti!
Ebola virus looks like spaghetti!

Therefore, double-stranded RNA inside a cell’s cytoplasm is a signal that something may be seriously wrong. When a cell senses double-stranded RNA, it quickly grabs onto the offending molecule, and either chews up or sequesters away that piece of RNA, in an effort to avoid inadvertently making viral proteins. This process is pretty similar to how bacteria target invading phages for degradation using CRISPR.

Different name for the proteins, same general idea.
Different names for the proteins, different targets, but same general idea.

The scientists who created the arctic apple took advantage of RNAi to trick the fruit’s cells into turning off one of their own genes. Apples go brown when cut due to the action of an enzyme called polyphenol oxidase (PPO). Just as the name suggests, PPO oxidizes things; when apple cells rupture, the enzyme reacts with oxygen in the air and phenol compounds inside the fruit, producing the unsightly brown color. Engineers introduced a complementary copy of the PPO gene into the Arctic Apple. The extra copy produces a special single-stranded RNA called a small interfering RNA. The small interfering RNA binds the normal PPO RNA inside the plant’s cytosol, making it double-stranded. The plant’s own defenses then kick in to prevent any PPO protein from ever getting made, effectively squelching the process that causes apples to brown. It’s important to note that, although the RNAi strategy is designed to target four particular copies of the PPO gene, there are ten total versions of PPO within the apple genome. We don’t know WHAT all of these extra copies are doing, or if there’s any cross-talk between the engineered silencing system and these extra alleles.

HT_artic_apples_comparison_jef_150213_4x3_992
There’s kind of a lot we don’t know, other than the fact that it seems to work…

The Arctic Apple breezed through regulatory approval; as a cisgenic GMO its difficult to make any convincing arguments that the product poses any possible human health risk. I’ve read some breathless claims that double-stranded RNA can be recovered from the digestive tract after being consumed orally. However, given that humans don’t have a PPO gene and the siRNA doesn’t seem to be getting taken up by human cells, I can’t think of any biological reason why a small bit of RNA passing through your intestines (the important word here is THROUGH) would pose any risk at all to human health.

This is probably where that siren is ending up...
This is probably where that siRNA ends up.

I have to couch my statement with the caveat that human health is incredibly complicated, and we don’t really know anything about what dsRNA does to our systems because the technology just hasn’t been around for very long. It’s controversial whether mammals even use RNA interference to defend themselves from viruses at all! I could potentially imagine a scenario where the dsRNA might shift something in our microbiome, and cause some strange unforeseen consequence (our microbiome does LOTS of things for us, including alter how our liver processes drugs).

It's always all about the bacteria, isn't it?
It’s always all about the bacteria, isn’t it?

However, as I have argued before, the impact on human health is largely beside the point when considering an individual GMO. I sincerely doubt that this technology really poses a threat to anyone’s safety. A more important and more interesting question to consider is: How will large scale implementation of a product influence our food system as a whole?

Think globally, act spicily.
Think globally, act spicily.

I personally strongly object to GMOs that promote increased pesticide usage and poor farming practices. I also worry that a single monolithic company holds proprietary patents over the majority of our agricultural products. Round Up Ready corn and soybeans are two of the most egregious GMO offenders, responsible for a steady flow of glyphosphate onto the ground and coins into Monsanto’s coffers.

Ugh...these guys...
Ugh…these guys…

An orchard of Arctic Apples, by contrast, would be indistinguishable from any other arboretum. Non-organic apples are among the most pesticide-sprayed snacks on the market, but that’s incidental to the discussion of this particular product. The company that developed The Arctic Apple, Okanagan Specialty Fruits, is a small biotechnology and agriculture firm based in British Columbia. Okanagan specialty fruits was recently acquired by the Maryland based company Intrexon, which I see as an encouraging shift away from the evil empire of Monsanto single-corporation market-dominance currently in place.

hh
I’ll get you my pretty! With my pretty GMO corn!

I’m ambivalent about what the GMO trait itself does for the apple. There’s some evidence that the activity of PPO helps protect plant seeds from pathogens, but apple trees seem to be able to grow juts fine when the gene is silenced. In terms of human health, a brown apple is JUST as nutritious and delicious as a pristine, just-sliced fruit. PPO activity merely causes cosmetic defects, why did Okenagan Specialty Fruits spend YEARS developing a way to turn off this gene? Representatives at the company are optimistic that Arctic Apples will help reduce food waste. Food waste comprises a massive proportion of the material languishing in landfills across America. Each year up to 1.3 million tons of food gets thrown away, uneaten. Fruits and vegetables are the most commonly wasted food items, and most of the waste arises simply because of cosmetic defects. American are throwing away 40% of the food we purchase; we toss to 1,700 calories per day of perfectly edible products in the trash. The marketing team behind the Arctic Apple claims that a non-browning fruit will reduce food waste. The apples don’t bruise, so supermarkets will throw away less fruit inadvertently blemished during shipping. They company conducted a market survey which found that 55% of consumers rate apple browning as “a big issue.” They also hope that this product will sell like gangbusters in the pre-sliced fruit market.

Pre-sliced fruit: more evidence that Americans are lazy and willing to pay three times as much for anything wrapped in plastic
Pre-sliced fruit: because Americans are lazy and willing to pay a 300% mark up for  anything wrapped in shiny plastic

I think that food waste is a travesty, although I’m a more than a little skeptical that a non-browning apple will really significantly halt the flow of fruits and veggies into landfills. I think that strong messaging about buying less, and not rejecting fruits just because they look funny will do more to reduce food waste than this one GMO. The biggest success stories in food waste reduction (like Harvard’s efforts in its dining halls) come from changing consumer habits, not necessarily the food itself.

Tragically, Carmen Miranda's Tutti-frutti hat is likely an example of food waste.
Tragically, Carmen Miranda’s Tutti-frutti hat is likely an example of food waste.

Additionally, there are other effective ways to prevent the PPO enzyme in apples from turning them brown. The acidity in lemon juice does the trick; coumarin (which naturally occurs in cinnamon) will work as well. I even found a paper that isolated a PPO inhibitor from Blue Mussels. Whether a brown apple is more objectionable than an apple covered in eau-de-mollusk remains an ongoing topic of debate.

Why Mussels produce a PPO inhibitor is a question beyond my pay-grade
Why Mussels produce a PPO inhibitor is a question beyond my pay-grade.

I don’t believe that the Arctic Apple is really going to do much for food waste (though it would be great if it does). However, I think it is an important development, even though it hits supermarket shelves in 2017, and the public appears to have already lost interest.

Maybe if we called it an ArKtiK apple?
Maybe if we called it an ArKtiK apple?

Primarily, I hope that the Arctic Apple can start to shift the national conversation about GMOs, by introducing consumers to a familiar, non-threatening, photogenic product.

Who's afraid of a little apple?
Who’s afraid of a little apple?

I hope that eventually we can become sophisticated enough in our discourse to really discuss the merits of a particular GMO individually, rather than falling back on blanket statements. Right now we seem stuck shouting either: “ALL GMOs ARE EVIL AND MONSANTO WILL MURDER OUR CHILDREN” or “GMOs ARE USEFUL AND SAVE FARMERS MILLIONS OF DOLLARS AND YOU’RE A DIRTY HIPPY IF YOU DISAGREE.”

I am, of course, a damn dirty hippy, but I don't think all GMOs are bad.
I am, of course, a damn dirty hippy, but I don’t think all GMOs are bad.

The Arctic Apple, a likely harmless, but potentially not very useful, GMO is interesting because it shifts the script to a conversation about food waste. I’m rooting for the product to hit supermarket shelves, and for consumers to realize that, indeed, this GMO is likely largely indistinguishable from any other apple. Starting a conversation about WHY we throw away so much food every year would be an added benefit. Finally, I’m more than a little excited about the prospect of a small Canadian upstart unseating king-corn Monsanto from its GMO throne.

Mostly because I REALLY love Canada
Mostly because I REALLY love Canada

I’ll be following Okanagan specialty fruits and Intrexon as they move forward with this product. If nothing else, it’s a clever application of genome editing technology. Hopefully we can start paying more attention to what GMOs actually DO and spend less time deciding whether they are universally BAD or GOOD.

What do you think about the Arctic Apple?

What do you think about food waste? Isn’t it atrocious how much we throw away?

Run commuting for fun and profit…or maybe just fun

Good morning sunshines! I did something weird today!

Hello world!
And what else is new?

Specifically I combined two activities: my morning run and my daily commute. Typically I ride my bike to work, but today I decided to shake up my routine and try something new.

I'm sorry, lover.
Don’t worry, I still love you.

Run-commuting allowed me to wake up about an hour later than my usual time.

Feeling fresh! Looking tired
Feeling fresh! Looking tired

I suited up in spandex, and took Porter for a walk in lieu of my typical warm-up routine.

Doggy business waits for no runner
Doggy business waits for no runner.

Once Porter completed her morning “act of congress,” I was off to the races!

Or rather, off to my lab.
Or rather, off to my lab.

I took a circuitous route from my house to the health sciences building where I work in order to make sure my morning run-commute covered adequate mileage. One short hour and seven miles later I arrived at the rear entrance to my lab.

Wake up and smell the science!
Our building is quite lovely in the morning. 

I’m fortunate because I work in a big research complex with EXCELLENT shower facilities.

I'm one of those things!
I’m one of those things!

I also always keep a change of clothes and a towel stashed in my desk in case of emergencies.

Emergency towel; emergency snowboots in case of a blizzard; emergency wine in case of...Wednesday
Emergency towel; emergency snowboots in case of a blizzard; emergency wine in case of…Wednesday.

I recognize that my experiment in run-commuting would have been impossible without the luxuries of access to showers at work and a flexible schedule. Within a matter of minutes I transformed myself from a smelly-sweaty runner person:

You look ridiculous!
You look ridiculous!

Into a (somewhat) respectable scientist-person:

You still look ridiculous...but intellectual
You still look ridiculous…but intellectual

Once I had lathered, rinsed, and repeated, it was time to rehydrate:

Electrolytes, they're what plants (and runners) crave.
Electrolytes, they’re what plants (and runners) crave.

Caffeinate:

The most important piece of equipment in our entire laboratory.
The most important piece of equipment in our entire laboratory.

And, most importantly, carbohydrate:

Breakfast of champions.
Breakfast of champions.

As a side note, I received that Vigilant Eats instant oatmeal as part of an “athlete-fuel” sampler box I ordered from TheFeed.com. While I appreciate the ethos of the product (whole grains, no refined sugar, non-GMO sourced ingredients, exciting antioxidants, etc…), overall I found the flavor to be overwhelmingly sweet for my tastes. I’m certainly not opposed to putting chocolate in my oatmeal, but I think I’ll stick to the dark stuff in the future.

If there's one thing I do not do...it's mess around with my chocolate.
If there’s one thing I do not do…it’s mess around with my chocolate.

After re-fueling and re-recaffeinating…

I live in Seattle, don't judge me.
I live in Seattle, don’t judge me.

I started my experiments for the day.

Today I'm interested in DNA topology!
Today I’m interested in DNA topology!

I enjoyed run-commuting for sheer novelty value. Although the endeavor did require some forward planning (i.e. stashing clothes in my desk), I liked starting the day with a change to my typical routine and an extra hour of sleep. I’ll likely run to work occasionally in the future; however, I definitely prefer bike-commuting to phedippides-ing to work.

Although I wouldn't object to being more like Steve Reeves...
Although I wouldn’t object to being more like Steve Reeves…

What I liked about run-commuting was arriving at work early, and making use of my building’s excellent showers.

Seriously, the water pressure is better than I get at home.
Seriously, the water pressure is better than I get at home.

However, run-commuting does carry a few drawbacks. I usually go out for my miles in around 5:00 am, which ensures that the streets are empty. I embarked upon my run-commute at 6 am this morning, and I was mildly annoyed by some traffic along the route.

The world's smallest violin plays a tragic symphony for me.
The world’s smallest violin plays a tragic symphony for me.

Additionally, and most egregiously, run commuting in the morning means taking the bus home in the evening.

I HATE the bus
I HATE the bus

My favorite thing about my normal two-wheeled means of transportation is that it affords me the freedom to leave work whenever I want. Traveling by pedal-power, I am beholden to nobody’s schedule. I chafe under the tyrannical regime of king-county metro’s timetable!

For FREEDOM!
For FREEDOM!

I know that thousands of competent adults and children ride the bus to work every day. I also know that I am EXTREMELY privileged to have so many different commuting options. I can afford to live within the Seattle city limits and my schedule is flexible enough that I can roll into work fifteen minute late with minimal consequences if I get a flat tire.

Or if, you know, I get distracted and decide to bike to Narnia.
Or if, you know, I get distracted and decide to bike to Narnia.

Barb Chamberlain wrote an excellent piece for Bicycle Alliance of Washington unpacking the invisible knapsack of bike-privilege. I’m exceedingly grateful every day that my commute isn’t spent stuck in traffic, sucking smog, but rather is an activity I genuinely enjoy.

I hate traffic even MORE than the bus.
I hate traffic even MORE than the bus.

In summary: run commuting was a fun experiment, but biking to work still holds the number one spot in my heart. Chocolate in oatmeal is a good idea, but should only be attempted by trained professionals. Coffee is mandatory. And finally, even though my house’s hot water heater is truly pathetic, overall I am an extremely lucky guy.

The hyacinths are blooming!
The hyacinths are blooming!

Have a WICKED Wednesday!

What’s your commute like? Do you bike, run, swim, or kayak? How can I get over my irrational fear of public transportation?

 

 

Highlights from #KSDNA, part two

Good morning Americans!

I’m excited to share the highlights from the second half of my trip to Canada for the Keystone Symposia joint meeting on DNA Repair & Genome Maintenance and Replication & Recombination. You can find my my previous posts (covering CRISPRs, Synthetic Lethality, and my highlights from the first two days of the conference) in the aforementioned links. If you’re sick of hearing about this madcap microbiologist’s misadventures in the mountains, I’m sorry, but fret not!

Fret not, but do be cautious!
Fret not, but do be cautious!

 

This blog will soon be returning to its regularly scheduled programming! I’ve been watching the news coverage surrounding the approval of the arctic apple (a GMO fruit that doesn’t go brown when sliced) and I, of course, can’t wait to add my own two cents (or two-thousand words) into the conversation.

I LOVE apples!
I LOVE apples!

However, that’s a matter for another day. For now, let’s go over some of the exciting things I learned during my final days in Whistler.

Such as: this is the symbol of Canada. I don't know what it's supposed to be, either
Such as: this is the symbol of Canada. I don’t know what it’s supposed to be, either

I will admit that many of the talks I attended in the second half of the conference were a bit outside my wheelhouse. An entire plenary session was devoted to “The Interface Between Chromatin and Genome Maintenance.” Chromatin refers to how DNA is packaged within the nuclei of cells.

DNA packaging is critical to keeping our cells humming along. A single base pair of DNA is tiny, measuring in at just about 0.34 nanometers long. However, each and every human cell contains 6,400,000,000 base-pairs worth of genetic information stored within the two copies of each of our 23 chromosomes. That means that each and every single one of our cells has just about 2 meters of genetic-spaghetti wound up inside its nucleus. Eukaryotes wrap their DNA around proteins called histones, to make structures called nuclesomes, which are themselves arranged into higher order structures called chromatin.

Tightly wound DNA Source: https://www.mun.ca/biology/scarr/Fragile_X_chromosome.html
Tightly wound DNA
Source: https://www.mun.ca/biology/scarr/Fragile_X_chromosome.html

However, any time the cell needs to use a particular stretch of DNA, whether to copy it or turn on a particular gene, the nucleosomes must be rearranged to expose the information of interest. Bacteria (which happen to be my bread and butter) don’t really have histones. There are proteins called SMC (for Structural Maintenance of Chromosomes) in bacteria, that seem to play a role in keeping everything organized, but these proteins certainly aren’t subject to the same complex, multi-level regulation that occurs on histones to shape Eukaryotic chromatin.

Source: Hirano, T. Nature Reviews Mol Cell Biol, 2006
Source: Hirano, T. Nature Reviews Mol Cell Biol, 2006

Even though I was outside my comfort zone during some of the sessions, I learned A LOT. Without further, further ado, here are my highlights from part two!

Took you long enough
Took you long enough

=> Iestyn Whitehouse gave a talk covering chromatin dynamics during lagging strand replication. He has set up an awesome system to specifically sequence nascent lagging strand DNA. After establishing proof of principle in yeast cells, he’s started to investigate replication in the worm C. elegans, as a model for more complex organisms. It turns out that we still don’t know a whole lot about where in the genome replication gets going in higher metazoans, and his system is the perfect tool to address the question.

=> Michelle Debatisse gave a provocative talk about what causes common fragile site instability. Common fragile sites are regions in the genome that are especially prone to breaking and mutating. These regions are linked to all sorts of diseases, such as fragile X syndrome. Fragile sites tend to be located in very long genes, which has led to the model that collisions between replication and transcription cause their instability. Debatisse presented evidence that, although there is an interplay between the two processes at play, premature replication termination in long genes drives common fragile site instability, rather than collisions with the transcription machinery.

=> I learned about two techniques (that are both a few years old at this point) during this session: Repli-seq, which allows scientists to sequence only newly replicated DNA; and Nascent-RNA seq, which lets researchers specifically figure out where and when RNA polymerase is transcribing genome-wide.

=> Dale Wigley‘s presentation about the structure and function of the bacterial double-strand DNA break repair machineries AddAB and RecBCD was mind-expanding. The RecBCD helicase/nuclease machine has been seized by creationists as an example of something so elegant, that it is simply “too complicated to have evolved.” Wigley showed some awesome structural and biochemical data demonstrating precisely how RecBCD DID, in fact, evolve, and how it works on the DNA.

=> Ken Marians is just an amazing biochemist. Full stop. His talk on the protein requirements for nascent strand regression at stalled replication forks was a thorough, methodical, dissection of in vitro DNA dynamics.

Source: Gupta et al., JBC, 2014
Source: Gupta et al., JBC, 2014

=> Johannes Walter gave a very clear talk about the mechanisms of vertebrate replication termination. His experimental system (studying replication of two interlinked plasmids in Xenopus egg extracts) is seriously clever, and the idea that two replisomes might just blow right past each other when forks converge is something I had never before considered.

=> Philipe Pasero found that SAMHD1, which is classically thought to be an anti-HIV restriction factor, plays a role in genome maintenance. Who doesn’t love a protein multi-tasker?

swiss_army_knife

=> Andres Aguilera, the king of R-Loops, gave a talk demonstrating how these RNA-DNA hybrid structures alter chromatin compaction. R-Loops are a big deal in my bacterial world; I had no idea they could also mess with how human chromosomes are packaged.

Source: Aguilera & Garcia-Muse, Mol Cell, 2014
Source: Aguilera & Garcia-Muse, Mol Cell, 2014

=> Joseph Jirincy‘s talk offered an answer for the age old question: How does the mismatch repair machinery know which stand contains the correct base? E. coli bacteria stick a methyl group modification on their DNA; if the replisome makes a mistake in the newly copied DNA, the machine that fixes the error knows which DNA strand is the parent copy (because the new strand won’t be methylated yet). Therefore the proteins use the old strand as a template to correct the improperly inserted base. Eukaryotes (and most bacteria, in fact) don’t do methylate. Jirincy has found that misincorporated ribonucleotides (RNA building blocks) in newly replicated DNA might serve as the signal that tells the mismatch repair machinery which DNA strand is which.

=>Jesper Svejstrup‘s multi-level proteomic, genomic, transcriptomic, DNA-damage specific screen made my head spin with its complexity. His finding that RNA polymerase travels a smaller distance along the lengths of genes after UV exposure is fascinating. He’s already identified a ton of interesting factors with his septuple-omic screen; I’m sure his list of candidate factors is longer than the length of all the DNA inside a human body.

=> The final evening of the conference featured a DJ dance party. We answered the age-old scientific question: how many Ph.D.s does it take to remember how to do the macarena?

Yeahhhhhh....
Yeahhhhhh….scientists got DOWN

Overall I had a fantastic time in Whistler. I learned more than I ever could have anticipated. I made connections with scientists from all over the country. I laughed, I danced, I even got to sneak off and go skiing!

Although there was so little snow, I almost cried.
Although there was so little snow, I almost cried.

I hope you enjoyed reading my highlights from the conference. Writing them down has certainly helped me to cement the experience in my brain. Keystone Symposia puts on amazing scientific meetings, I hope that I will have the chance to attend many more of these events in the future!

Science and Scenery? Sign me UP!
Science and Scenery? Sign me UP!

 

 

Highlights from #KSDNA 2015 (part one)

Hello from Seattle! Shockingly, the border patrol let this suspicious-looking scientist back into the states after my whirlwind week in Whistler, B.C. for the Keystone Symposium joint meeting covering DNA Replication & Recombination and Genomic Instability & DNA Repair.

duty-freedom
Aaaaaahhhh, freedom

I had a phenomenal week. The conference organizers put together an amazing docket of talks, the poster sessions were chock-full of exciting research-in-progress, and it was fantastic to socialize with scientists from all over the globe. I even got to go skiing!

Conditions weren't so hot, but OMG look at that VIEW!
Conditions weren’t so hot, but OMG look at that VIEW!

I could easily write thousands of words about any one afternoon of the conference (and I, in fact, did, ramble on extensively about CRISPRs and synthetic lethality); however, I wanted to take a moment to briefly highlight some of my favorite moments from the first part of the week. I definitely will be re-visiting some of these topics in more depth later (and re-cap the second half of the conference as well). For now, here’s a list (in chronological order) of things that blew my mind during my first two days in Whistler, with links to further information, where appropriate.

 

Did I mention the mind-blowing scenery?
Did I mention the scenery?

=> John Diffley (who does SERIOUSLY impressive work reconstituting replication initiation in vitro) casually mentioned in his talk that over the course of a half hour’s time, each and every human being synthesizes over 10 billion meters of DNA in their cells.

=> Mike O’Donnell recently reconstituted and solved the structure of the Eukaryotic replication fork. He published the architecture of the leading strand this past summer, and told us some surprising facts about how the protein players on the lagging strand are arranged at the meeting.

=> James Berger (who did some truly elegant work to demonstrate that the helicase-loader protein in bacteria breaks open the helicase protein’s hexametric ring structure to put it on the DNA) has started to learn some really interesting things about regulation of replication initiation by phage proteins. As I mentioned in my CRISPR post, phages are EVERYWHERE; Berger called these abundant entities “biological dark matter,” they’re in almost all bacterial genomes, but we still don’t understand everything they’re doing.

Phages are so cool.
Phages are so cool.

=> Antoine van Oijen is doing some AMAZING work to visualize individual polymerase molecules inside living cells. His findings might revolutionize how we think about the spatiotemporal regulation of Y-Family polymerases. Given that my own research has revealed some new roles for these molecular in B. subtilis, I was particularly excited to learn about the peculiar way these proteins behave in E. coli.

=> Tom Steitz might win the “most quotable” award during his candid talk covering the architecture of the bacterial replisome (in particular the arrangement of primase in regards to the helicase). His talk was the first time I ever heard a nobel prize winner say “Everything below here is believable, I’ve been very skeptical about the rest, but it might be right,” when describing his own structural model.

=> Steve Kowalczykowski‘s in vitro work visualizing recombination (specifically RAD51 loading by BRCA2) is a technical tour de force.

=> Daniel Durocher’s talk on the cell-cycle regulation of DNA double-strand break repair was mind expanding for this microbiologist. Bacteria are always in S-phase, it was cool to think that us multi-cellular organisms decide to repair our DNA by different mechanisms, depending on when the damage occurs. Durohcer also raised a, quite salient, question of nomenclature: how should scientists refer to genome-edited “knock-out” cell lines to avoid confusion with other genetic approaches?

=> Ralph Scully gave a great short talk about recombination after replication runs into a roadblock. He invoked “The Good, The Bad, and The Ugly,” as well as Facebook to make his points. I always appreciate the value of a good metaphor for effective scientific communication.

=> My boss, Houra Merrikh, totally crushed her talk, and presented some provocative evidence that DNA replication rates inside living cells might be much more dynamic than previously thought.

My boss is kinda awesome. Remember that time we got picked up in a patriotic limo?
My boss is kinda awesome. Remember that time we got picked up in a patriotic limo?

=> Francesca Storici demonstrated that yeast can use an RNA template to direct DNA repair by homologous recombination. I cannot overstate how truly strange and amazing this finding is for the DNA-repair field, or the innovation and creativity required to convincingly demonstrate these results.

=>Last, but not least. I presented my poster (Replication restart after conflicts with transcription requires recombination in B. subtilis) on Tuesday evening! I had a great time talking about my results with experts in the field, and I got some excellent feedback.

EXPLAINING replication restart requires red wine in H. sapiens
EXPLAINING replication restart requires red wine in H. sapiens

Stay tuned for my highlights from the second half of the conference! There will be glacier-skiing, R-Loops galore, and scientists getting DOWN on the dance floor!

#KSDNA: Genome editing workshop (CRISPRs in Wonderland)

Hello again from wonderful Whistler!

This moose has a Ph.D. in foraging
This moose has a Ph.D. in foraging

I’m having a splendid time at the Keystone Symposia’s DNA Repliaction and Recombination meeting. I’ve heard some amazing talks, and drank MANY teeny-tiny mugs of coffee.

Seriously, Keystone? Scientists require FAR larger doses of caffeine for productive thinking
Seriously, Keystone? Scientists require FAR larger doses of caffeine for productive thinking

I wanted to use this post to give a rundown on a workshop I attended yesterday covering Genome Editing. The workshop consisted of a series of short presentations given by a mixture of junior investigators and researchers from biotech firms. The talks all covered ongoing progress in the field of genome editing. We learned about technologies that sound like they could have been ripped from the pages of a Margaret Atwood novel, yet the reality is that science is stranger and more amazing than fiction.

This novel, specifically. (Which is INCREDIBLE)
This novel, specifically. (Which is INCREDIBLE)
Although the fact that you can buy a CRISPR off the shelf is pretty incredible too.
The fact that you can buy a CRISPR off the shelf is pretty incredible too.

I’m not going to talk about any of the unpublished or proprietary data that I saw at the workshop, but I did want to give a brief summary of the amazing progress we’ve made in custom DNA-tinkering, and the incredible biology behind the innovation. The term “genome editing” could encompass a wide variety of techniques and tools, however, for the most part, the talk focused on current efforts to introduce specific changes into the DNA sequences of living cells. Researchers are already using these technologies to make transgenic organsims (like glowing worms or custom mutant monkeys).

Source: Tzur et al. Genetics, 2013
Source: Tzur et al. Genetics, 2013

The long-term goal for genome editing, however, is to create cures for genetic diseases like sickle-cell anemia or cystic fibrosis. These disorders arise due to very specific mutations in very particular genes. Researchers are trying to figure out a way to alter the offending alleles to healthy sequence inside living cells. This turns out to be an extremely tricky problem. Genomes are enormous: there are three billion base pairs of DNA inside of every human cell. Almost any time you attempt to change one particular region of the DNA you end up messing with something else, somewhere else, which can have disastrous effects.

 

Genetic engineering gone wrong? As far as I know, the Weekly World News isn't doing biotech research
Genetic engineering gone wrong? As far as I know, the Weekly World News isn’t doing biotech research…

A new technology called CRISPR offers a way to target very specific regions of the genome. The first papers demonstrating genome editing with a CRISPR in human cells were published in Science in 2013. However, I hesitate to call CRISPR a new technology, mostly because humans aren’t NEARLY clever enough to create this amazing tool on their own. Rather, CRISPR is the latest example of Homo sapiens stealing adapting a feature of bacterial physiology that evolved over the course of several billion years.

You think you're SOOOO clever, don't you.
You think you’re SOOOO clever, don’t you.

 

I should take a giant step backwards to define what CRISPRs are and how they work. These systems are, at their core, a pattern of DNA sequence that is found in the genomes of 40% of all bacteria and 90% of archaea. The region always consists of a few protein-coding genes (named cas for CRISPR-associated) next to an extended series of short repeated sequences, intermingled with an oleo of spacers. These repeats are what gives rise to the awkward acronym CRISPR, which stands for Clustered Regularly Interspersed Short Palindromic Repeats.

 

They look like this
They look like this

Widespread whole genome sequencing led to the observation that CRISPRs can be found within many bacterial chromosomes, but their function remained mysterious until 2006 when some very clever researchers in the dairy industry realized what this strange segment of DNA does. CRISPRs function as a bacterial immune system to protect microbes from malicious phages.

EEeeeeeeK!
EEeeeeeeK!

 

Phages are viruses that infect bacteria. In the fight against phages, bacteria are hopelessly outnumbered and outgunned. Phages outnumber bacteria by a factor of 10 to 1 and kill up to 50% of the bacterial biomass on earth each day. There are a LOT of bacteria on the planet, but according to the latest estimates there are more phages on Earth than there are stars in the universe. Because bacteria are constantly targeted by phages, they have evolved mechanisms to protect themselves from new invasive elements. CRISPRs are a unique and elegant system that gives bacterial cells inherited memory of encounters with phages, allowing them to efficiently kill off the virus during subsequent encounters. In other words, CRISPRs are a bacterial adaptive immune system.

 

So how does this chuck of genetic information protect bacteria from phages? After all, a CRISPR is pretty much just a bunch of repeated DNA sequences with interspersed spacers. The magic of CRISPR is that the interspersed spacers match regions within phage genomes. Those spacers in the bacteria’s genome are small chunks of DNA that the bacteria stole from invading phages and (in a process that remains mysterious to this day) stuck onto their own chromosomes. These sequences let bacteria recognize and destroy phage DNA the next time it enters the cell. Bacteria recognize invading phages by first making the whole CRISPR region into one big, long RNA. That RNA gets cut up into individual pieces by the CRISPR-associated proteins. Each of the little bits of RNA binds to a collection of proteins, which then go into seek-and-destroy mode. If the proteins and RNA bind to a matching piece of invading DNA, together the complex chops up that DNA, which kills the phage.

 

I'm passing fond of CRISPR because I wrote about it for my off-topic second year Ph.D. exam proposal
How all of this works. Source: My 2nd year topics exam proposal

My brief description doesn’t really do justice to the years of elegant experiments required to demonstrate how this process works. Much of the research was funded by the dairy industry because invading phages can totally DEVASTATE large-scale fermentations required for yogurt production and cheese-making.

Phages can TOTALLY screw up your breakfast
Phages can TOTALLY screw up your breakfast

Even though we have a pretty good grasp of how these systems recognize and chop up invading DNA, mysteries remain, including the fact that in many bacteria the CRISPR appears to be non-functional. However, I’m not here to probe the deep questions about CRISPR biology, I’m here to tell you about how we’ve harnessed this bacterial immune system for genome editing.

 

We took advantage of this part!  Source: My 2nd year qualifying exam proposal
We took advantage of this part!

It turns out, shockingly, that you can make a CRISPR system from scratch and get it to target any DNA sequence that you want. CRISPRs in bacterial genomes are made up of repeats interspersed with spacers that match different phages. However, it’s reasonably easy to change the spacers to match any stretch of DNA that your heart desires. CRISPRs cut DNA matching the spacer sequence, which is great for killing phages, and also allows us to delete almost any gene we want with remarkably high efficiency. However chopping up a genome into little bits is probably not the best way to edit out mutations to cure diseases. Luckily, scientists have figured out how to mess with the part of CRISPR that chews up the invading DNA. One group used a version of a CRISPR that doesn’t cut at all stuck to a fluorescent-GFP tag figure out exactly where different genes localized in living cells.

Source:
Source: Chen et al. Cell, 2013

In order to edit genomes researchers made versions of CRISPR that find a target DNA sequence, make a single cut, and then stop.

 

It looks like this. Source: Hsu et al. Cell, 2014
It looks like this.
Source: Hsu et al. Cell, 2014

Why would introducing a break in the DNA in a specific location allow us to edit genomes? The answer lies in how cells repair breaks in the DNA, which is a process called homologous recombination. This series of DNA gymnastics fixes broken DNA using an undamaged template.

Recombination is...complicated.
Recombination is complicated, and requires lots of sharpies

Normally that template is exactly the same as the broken DNA, so any mutations present in the original will still be there. However, the innovative idea behind genome editing with CRISPR is to force the cells to base their repairs upon a DIFFERENT stretch of DNA. The idea is to make a single cut inside a mutated gene, then have the cells repair the cut using an un-mutated, healthy template. Voila! Offending mutation erased, original function restored!

Source: Hsu et al. Cell, 2014
Source: Hsu et al. Cell, 2014

 

The idea is exciting, but we are certainly a few years away from being able to erase mutations inside patient cells. However I heard some exciting talks about ongoing efforts to improve the repair efficiency, change the cutting activity, and apply the system to different genetic disorders. I was particularly excited by Cecilia Cotta-Ramusinos’ talk about using CRISPR to correct mutations that cause sickle-cell anemia. Cecilia works at a biotech company named Editas, who are performing some thrilling research using CRISPR technology. The future looks bright!

#KSDNA Plenary Speaker Stephen Jackson: PARP Inhibitors, Synthetic Lethality & Lynparza

Hello from sunny, scenic, British Columbia!

IMG_6425

I’m blogging after my first day at an awesome scientific conference: The Keystone Symposia joint meeting covering DNA Replication & Recombination and Genomic Instability & DNA Repair. The talks today were all top-notch. I wanted to give a run-down of some of the radical research I’ve seen thus far, but I don’t want to hit you, my readers, with a firehose of data, so instead I think I’ll summarize the plenary session, and leave the rest of the genomic gymnastics for another post.

There were CRISPRs...get stoked
There were CRISPRs…get stoked

Our first speaker, Stephen Jackson, kicked off the conference with an exhortation for collaboration. He encouraged scientists working on similar topics to reach out and promote synergy rather than trying to scoop each other. I really appreciated his message of cooperation: the point of conferences is the productive exchange of ideas, not a giant scientific pissing match. Jackson made a point to acknowledge all of the other researchers who contributed to the work he presented during his talk. He mentioned that a night in the bar with Alan Ashworth led to the screen of small molecule DNA-repair inhibitors against many mutant cell lines that gave rise to a recently approved cancer drug

Jackson gave a retrospective of 25 years of research leading to one of the hottest new cancer drugs on the market right now: Lynparza (olaparib).This compound is exciting because it is a first-in-class PARP-inhibitor drug especially for personalized cancer medicine. Traditional cancer treatments, like chemotherapy and radiation, kill cancer by destroying any rapidly dividing cells within the body. This blunt approach works reasonably well for fast growing tumors, but it causes NASTY side effects. Hair, skin, and cells in the gut all also happen to also be fast-growing, which is why Chemo hits people like a sledgehammer. Additionally, chemotherapy and radiation don’t take into account the innate differences between different types of tumors. These approaches won’t work on all tumors (like Chondrosarcomas…Hi Mom!) On the surface it’s obvious that breasts and bones and brains are RADICALLY different body parts, and therefore treating cancers of each organ identically is insane. We wouldn’t wear brassieres as hats, why would we treat a breast and a brain tumor with the same drug? However, even within a single type of tissue, different genetic mutations can give rise to different kinds of cancers. The premise behind personalized medicine is that each type of tumor carries its own particular set of changes that contribute to causing disease.  

As we get better and better at sequencing genomes we’ve started to better understand the underlying causes of different kinds of cancers; concomitantly,  clinicians are becoming more and more adept at targeting these specific differences to destroy tumor cells. One particularly aggressive type of cancer is distinguished by defects in the BRCA genes. The BRCA genes are vital for DNA break-repair. Lynparza inhibits a different DNA repair protein called PARP; PARP inhibitors are highly effective for treating cancers with BRCA mutations. The concept of treating cancer with a drug that prevents DNA repair is, at first glance, a shocking strategy. After all, isn’t cancer CAUSED by DNA damage? Don’t defects in DNA repair genes (like BRCA) LEAD TO cancer? Wont there be lots MORE DNA damage in cancer cells if you treat them with this inhibitor?

The fact that cancers carrying BRCA mutations are defective for DNA repair is precisely the phenomenon behind Lynparza’s success. The idea behind this strategy is that normal human cells have many different pathways to deal with DNA damage; there are back-up mechanisms in place if Lynparza takes down PARP. Cancer cells, by contrast, have lost most of their repair capability (due to mutations in BRCA, or other genes) and thus don’t have many options to fix their DNA. Therefore, DNA repair inhibitors become potent poisons specifically for cancer cells. This concept, where a particular deficiency only becomes a problem in the context of another defect is called synthetic lethality.

Jackson talked about the extensive findings that helped uncover Lynparza’s synthetic lethal effect for cancers with BRCA mutations, and showed the data from phase II clinical trials demonstrating its dramatic efficacy. Not only did the researchers observe prevention of disease progression in 34% of patients, the side effects associated with Lynparza are a walk in the park compared to conventional chemotherapy. The FDA just granted accelerated approval status to Lynparza for treatment of advanced ovarian cancers, based on promising results from these Phase II clinical trials.

The talk, of course, contained lots more mechanistic details about which components of the DNA Damage Response do what, and how scientists in Stephen’s group (and others) figured all of this out. I really enjoyed seeing a multi-decade long story where basic science (mechanisms of DNA repair) eventually led to an awesome new cancer drug.

I could go on, and on, and ON about what else I saw today (There were TWO Plenary speakers…a whole session on single-molecule studies of the replisome…a workshop on genome editing…CRISPRS! I’m in DNA-nerd heaven). However, after explaining synthetic lethality, I think that I want to go to bed so that I’m bright eyed and bushy tailed for my poster presentation tomorrow.

I’ll keep writing up some of the cool stuff I see all this week (I might even sneak in some skiing as well).

Skis, snacks, passport...all VITAL things to bring to a conference in Canada
Skis, snacks, passport…all VITAL things to bring to a conference in Canada

In the meantime, I hope everybody’s having a killer Monday!