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Base Pairs Season 1


  2018 Platinum PR Awards Winner

  2018 Webby Award nominee

Cold Spring Harbor Laboratory’s award-winning podcast, Base Pairs, tells stories that convey the power of genetic information—past and present.

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Bonus episode: Molecules and a mission

We are Base Pairs, the podcast about “the power of genetic information.” Why did we choose this name? In this bonus episode, we explain the molecules and the metaphor.

AA: Hi! I’m AndreaBS: And I’m Brian

AA: A little while back, we asked you, our fans and friends, to vote on what the name of this podcast should be.

BS: Hundreds of you voted, and at the end, the name Base Pairs came out on top.

AA: But we realized that at least some of our listeners are probably wondering about that name.

BS: Yeah… “Base Pairs” does take a little explaining… so that’s why we’re here talking to you now.

BS: Base pairs are molecules.

AA: End of explanation.

BS: Yeah, that’s all we wanted to tell you.

AA: Seriously though, base pairs are way more than just a bunch of molecules. They are the paired molecules that make up DNA and allow it to serve as coded instructions for the cell, kind of like how binary code provides the instructions for computers.

BS: Except it’s more like a quaternary code – can you believe that’s a real word? What a word.

AA: True, it’s a good one. But yeah, there are these four chemical bases—you’ve probably seen them represented with the letters A, T, C, and G—and they make up the fundamental “language” of inheritance.

BS: The instructions a cell needs to function properly are spelled out in the sequence of long strands of these bases.

AA: In DNA, these strands get paired off. Each base is drawn to another, always the same way –

BS: C, Cytosine, always pairs with G, guanine; A, adenine, pairs with T, thymine. So the base pairs that form are C-G and A-T. Combinations of these pairs, all the way across the genome.

AA: And the result is that spiral-staircase-like double-helix structure James Watson and Francis Crick discovered one February morning in 1953.

BS: It’s absolutely amazing that so much of the complexity of life can be distilled into a simple language with only four letters.

AA: And that’s a big part of what we aspire to on this podcast: to distill the fascinating but complex research that goes on at Cold Spring Harbor Lab into more simple language. Not dumbed down—just streamlined.

BS: Yeah, because for many of us, scientific jargon really might as well be another language. We want to overcome that language barrier to bring you great science stories.

AA: And we invite you, dear listeners, to let us know how we’re doing by commenting on our blog, at labdish.cshl.edu. There, you’ll also find a great video from our DNA Learning Center of James Watson explaining how tin models of the base aided the discovery of DNA’s double helix structure.

BS: This is Base Pairs: stories about the power of genetic information… the monthly podcast coming to you from Cold Spring Harbor Laboratory. Stay tuned for more science stories.

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Episode 7: The brain atlas

One in six people suffers from a mental disorder, and yet, compared to cancer and infectious disease, neuropsychiatric treatment options have barely improved since the 1950s. But why is that? In this episode of Base Pairs, we explore some of the problems neuropsychiatric drug discovery faces… and how a single, simple method may help.

AA: Hey, all. I’m Andrea.BS: And I’m Brian.

AA: And this is Base Pairs, the podcast about the power of genetic information.

BS: So put your thinking caps on because today, I wanted to start with the discussion about thinking or what can go wrong with thinking.

AA: Yes, it is a special 2016 Election Edition of Base Pairs. Okay, not really. We’re actually going to talk about neuropsychiatric disorders today. Those familiar but still puzzling illnesses like depressions, schizophrenia, and bipolar-disorder that affect 1 in 6 people across the globe.

BS: That’s according to the World Health Organization, and it’s stunning statistic. In the U.S. alone, things get even worse. The NIMH reports-

AA: That’s the United States National Institute for Mental Health.

BS: According to them, of all the potential years lost to illness, disability, or death among U.S. citizens, 20% were effected by a neuropsychiatric disorder. It’s the largest percentage, topping heart problems, cancer, injuries, even respiratory disease.

AA: Meaning mental problems are the biggest foe to quality of life for U.S. citizens, and those stats are similar in Europe.

BS: And here’s the kicker. Despite being such an impediment to public well-being, the number of distinct treatment options for the mentally-ill have barely increased from where they were decades ago.

RM: There really hasn’t been a drug with a truly novel mechanism of action for treatments of any brain disorder, especially in psychiatry, in probably 50 or 60 years.

BS: That’s Rob Malenka, a professor of Psychiatry and Behavioral Science at Stanford University. I recently spoke with him about what many call the drought of neuropsychiatric drug discovery, and his frustration is palpable.

RM: I think it’s absurd because while the medications we use in psychiatry and in neurology are often quite effective and helpful, there are still millions of patients who are suffering, who don’t get adequate treatment, and so at some point, you have to say, “Well, maybe we should change the strategy,” but I want to be right upfront, I am a founder of a biotech called Circuit Therapeutics because I became so frustrated with the lack of innovation in big corporation, big pharma, and I will talk a little bit about why I think that is.

BS: Rob, with his academic background, is one side to an important coin. I wanted a perspective from someone from pharma as well, wondering if they had anything different to say, so I reached out to Dr. Raymond Hill.

So Dr. Hill, can I call you Ray?

RH: Oh, Ray is fine. I’m a pharmacologist. I’ve worked in the pharmaceutical industry for nearly 30 years. I had the honor to be President of the Pharmacological Society about 3 years ago now.

AA: If you haven’t guessed from the accent, that’s the British Pharmacological Society, but while Ray spoke to us from London, where he enjoys his retirement as a visiting professor at Imperial College London, his knowledge of drug discovery spans years and continents alike.

RH: If you think back to the 1950’s when the first drugs that were useful in treating psychiatric disease were discovered, that was a result of brilliant empirical observations by scientists and clinicians who were working with patients and realized that drugs that were being given to treat one condition, in fact, benefited the psychiatric condition that the patient actually suffered from.

BS: Think about what Ray is saying here. He’s saying that some of the first neuropsychiatric drugs discovered over 60 years ago are still used today. Drugs like lithium for bipolar disorder and the first generation of anti-psychotic medicines, and the thing is-

AA: They were discovered accidentally. It’s wild.

BS: It is. At the time, you can see how this was a breakthrough. With hardly any understanding of the brain, nevermind mental illness, even having a little understood treatment option was huge. These discoveries became the stepping stones for neuropsychiatric pharmacology. With experts trying to reverse engineer and improve these serendipitous solutions.

AA: That seems like a good plan, but I think I see the problem already. An approach taken decades ago may not be the best option today. Science as we’ve learned time and time again is always changing.

RM: People have spent decades trying to figure out the true therapeutic mechanism of action of the tricyclic antidepressants, which have been around for 50 years or the drugs like Prozac, and the problem with that approach is people have been working on that for 50 years.

BS: That’s Rob again, and as you can probably tell, he thinks dwelling on the same drugs, the same accidental solutions is what’s holding progress back in the long run.

RM: And if they keep doing what they’re doing, and I’m using the generic “they” for Big Pharma, they all claim they’re doing new stuff and innovative stuff, but the truth is they really aren’t. They’re actually very conservative. Many of the Pharma are dominated by the business development people who are saying, “We need a new drug for this indication or that indication within 10 years that’s gonna be a blockbuster.” I hope I’m making sense here.

AA: He’s making a lot of sense actually. New discovery is always slow going, and with an organ as complex as the human brain, to ask a pharmaceutical company to put a decade or more into anything other than the drugs and approaches they’re familiar with is asking them to gamble.

RH: It’s a huge risk, and there are many more addressable things that one can do in metabolic disease or cancer that a lot of companies are finding more attractive, and I think it’s no accident that diseases where there are addressable targets but where there is still a large clinical need, such as cancer and diabetes, are the sorts of areas where most major companies are concentrating their resources.

BS: And here’s the point where both Ray and Rob’s explanations for the lack of neuropsychiatric drug discovery, the reasons we have seen so few new drugs for mental illness over the last five decades. They begin to almost seamlessly blend.

RM: I wanna be fair. I think there are many, really great scientists working in drug discovery for the brain at many different pharma, both large and small, who are dedicated, who are creative, who really want to have an impact on human health and are doing their work for all the right reasons. However, they face many political challenges working in a corporate environment. That includes competing for resources with other therapeutic areas that are very important, like oncology, but relatively speaking, relatively, are much easier to understand and develop drugs for.

RH: I mean if you look at the other end of the spectrum. The way we’re approaching cancer now is, in a very mechanistic way, based on a fairer understanding of the molecular biology of particular [Chuma 00:08:46] types. In the case of mere psychiatry, we know almost nothing. I mean, if you look at a disorder like Schizophrenia, if you [troll 00:08:56] the literature, you could come up with as many as a thousand candidate genes that might have something to do with the disease, but there’s no clear correlation with an easily addressable target that would allow scientists in the pharmaceutical industry to start a new drug discovery project.

BS: You see the problem? For decades, trying to find a new drug target for a mental disorder has been like trying to plan a meal without knowing what you have in the pantry or going for a hike without knowing the trail. It can be done, but it’s going to take time and will be very risky.

RM: You know, what I tell my lab all the time is, “You know, the brain is complex.” But that doesn’t mean we should be nihilistic and give up. I think there are approaches that are more valuable than others.

AA: Maybe, and call me out if I’m wrong here, but maybe it’s time to get a look at that pantry to get to know those trails.

BS: Maybe it is.

TZ: My own research, until about five or six years ago, focused largely on studying the behavior of rats performing auditory decisions and trying to tease apart the circuits that are responsible for these auditory decisions. And in the course of that work, what I realized was that we were really stymied by our lack of understanding of the actual circuitry.

AA: That’s Dr. Anthony Zador, a professor whose lab is based right here at CSHL.

BS: We call ’em Tony.

TZ: So we had great tools for manipulating classes of neurons for asking whether one collection of neurons might play one role in a behavior and another class of neurons might play another roll, but what we didn’t really know were what the classes were, who their partners were, who these neurons talked to, where they sent their information.

AA: If you follow neuroscience at all, you probably know where this conversation is heading. To really move forward, people like Tony figured they were going to need a map of the brain, a concept popularly called the Connectome.

TZ: Part of that started to change, maybe five years ago, when the Allen Brain Institute decided to systematically go through and map the long range connections of a mouse brain, and they did that by injecting a tracer in each of about a thousand different regions of the brain of a thousand different mice and then following where that tracer went, and that has been an incredibly useful resource for my lab and many other labs to have an overall view of the architecture of a mouse brain.

However-

AA: However, this really seems like just a start. General regions of the brain? Doesn’t sound as detailed as I’d have hoped.

BS: That’s right. This visual approach, while informative, can’t tell you much at all about what individual neurons are doing inside those general regions.

TZ: One way to think about it is as though you’re going to an airport, and you see the counters for a dozen different airlines, and that airport flies pretty much everywhere in the world, but if you go to a particular airline, that particular airline will only serve probably a subset of the locations, so if you go to Georgian Airlines, you’ll be able to fly to the Middle East but probably not to San Diego, and if you go to Icelandic Airlines, you might not be able to find a flight to Peru.

So each of those little airlines corresponds to a neuron in this analogy. Overall, the airport will probably serve many or most locations in the world, but the individual neurons don’t send their information everywhere.

BS: It stands to reason that to catch the right flight, you really need to determine where each airline is sending its planes. So that’s what Tony set out to do, to match each individual neuron’s connections.

AA: But wait, Brian, it’s been estimated that the average human brain has anywhere between 80 and 100 billion neurons, a number so immense that no one has even been able to come up with a more accurate figure yet. So you’re telling me that Tony hopes to trace all of them?

BS: Remember how we are a podcast about genetic information? We’ve gotten pretty deep in this neuroscience stuff, so I thought I’d remind you. Human chromosomes range in size from about 50 million to 300 million base pairs. Imagine the immense number of possibilities that can come from that, and yet-

AA: The Human Genome Project.

BS: The Human Genome was published in its entirety on April 14, 2003, and since then, genome sequencing has gotten much faster and much, much cheaper.

TZ: So the idea that I had was that, if we stop thinking about neuroanatomy solely as problem of microscopy, if we stop thinking about maps as a map that you can visualize, if we can convert the problem into a problem of high throughput DNA sequencing, then we’d be able to look at the individual connections of thousands and potentially hundreds of thousands or millions of neurons at once. And so when I had that idea, about six years ago now and have been working on it pretty doggedly since, and recently, it’s started to pay off.

BS: Taking cues from genome sequencing, Tony and his lab recently mapped about 50,000 neurons in the central cortex of a mouse, and it only took one mouse and a couple of days to complete.

TZ: So we developed a technique called [MAPSeq 00:15:15]. The “Seq” stands for sequencing, and the map coincidentally is an acronym for Multiplexed Analysis of Projections.

AA: Apparently, one of the keys when developing a new technique is to give it a catchy name.

TZ: So in this technique, what we do is we label every neuron with a random sequence of DNA. We call it a barcode, and the idea is that these random sequences, there’s so many of them that the chances that two neurons get the same random barcode are infinitesimally small, so each neuron now has a unique identifier.

AA: From what I’ve heard, these barcodes are a lot like what you would see at a supermarket. What makes one can of soup different than another, a single stream of numbers, and yet, it let’s Stop & Shop know that [Joe-Shmoe 00:16:18] bought a can of creamy mushroom and not chicken noodle.

BS: Maybe he’s making green bean casserole.

AA: Science, Brian. We were talking about science.

BS: Gastronomy is a science.

AA: Neuroscience. Genetics. Barcodes.

BS: Right. I’ll let Tony handle this.

TZ: Right, so how do we barcode the neurons? Well, turns out that if you want to deliver a gene to a neuron, a gene that that neuron doesn’t normally express, what you can do is make a virus that encodes whatever it is you want to express.

BS: It’s a pretty common technique, and these viruses are not the kind that can get you or I sick. All the machinery that normally helps a virus wreak havoc on a cell has been taken out, and all that remains is a hallow shell.

TZ: If you like gutted viruses and the space left over, the space created by gutting them, we use for inserting the cargo of interest that we would like to deliver to the neurons.

BS: Each of Tony’s virus particles carries a unique barcode sequence made up of 30 RNA letters or nucleotides. When the virus is injected in a brain region of interest, unique barcodes are taken up individually by neurons in that region.

AA: So now you’ve got a bunch of neurons individually barcoded. That’s obviously not the end of it though. If I were to go back to the airline metaphor, that’s just bunch of marked airplanes sitting at their terminals. What happens next?

BS: Next, like with a lot of science, you wait.

TZ: 48 hours. This is a fast acting virus, so in 48 hours, the virus can infect the neuron, can cause this protein to be expressed, cause the barcode to be expressed, and it also even drives the barcodes out to the synapses.

AA: Synapses are where the signal carrying cables of neurons meet.

BS: Yeah, and those cables are what neuroscientists call axons. Now, to find out where those barcodes went.

AA: That is, what other neurons are at far end of the axons sent out by the barcoded neuron.

BS: Right. To do that, Tony and his team, just like all mappers of the mouse brain, have to sacrifice the test animal, and in this case, find out where in the brain all those barcodes were carried by the virus, the place where each neuron’s axon formed a synapse with another neuron. But instead of looking for a visual trace, as with optical methods that can only trace one or two neurons per animal per experiment, Tony’s method uses RNA sequencing to find the final synaptic destinations of the many thousands of barcodes that infected neurons in the source region, that original brain area of interest.

TZ: And that way, we can get more information in a single experiment than anyone has ever had before. We can get the [all-to-all 00:19:17] conic activity of about 50,000 neurons from a single specimen, and we can get that at single neuron resolution.

AA: Wow, and this is all in about 48 hours and using one mouse and not thousands? Yeah, I can see how this is a game changer.

BS: Still, there’s a lot of questions left to ask. One big one being, “So what can we gain from this?”

TZ: And the answer is we don’t know what we’re gonna know, so if you asked 15 years ago when people were sequencing the human genome, “What good is the human genome gonna be?” There are a lot of possible answers. In the end, the day that the human genome was released, I would say, there was no real headline. The headline that I read was, “Human Genome Has About 20,000 Genes,” but you know what, my life was no different with the knowledge that it had 20,000 genes, not 5,000, and not a 100,000.

So the day the human genome was released, I don’t think we knew that much. That said, genomics has transformed how we do biology. It has provided a solid foundation. It’s changed the way that everything in modern biology is done. I suspect that it’ll be the same when we have the Connectome. So in the most optimistic scenario, the day that we finish the mouse Connectome, we’ll slap our foreheads and say, “Ah! Now it’s obvious. Now we see that that’s how the brain works.”

And sure, I sure hope that’s the case, but I don’t think so. I think instead, what it will serve to do is constrain our hypotheses about how the brain works. We’ll know that no, it can’t possibly be this way because the circuitry is just not available for that, and it’ll guide us toward thinking of other classes of hypotheses.

So in five years, when we have the Connectome of a mouse, we’ll start a set of experiments by sitting down at a computer and just sort of thinking through some of the circuitry that might be involved in whatever behavior we’re interested in. And immediately, we’ll rule out 99 out of our hundred choices or maybe 98, and maybe we’ll be left with 2 or 3 or 4, and those will be the ones that we’ll spend our time actually studying with other sorts of tools.

So that’s how I think it’s going to impact what we do.

AA: What I’ve gleaned from all this is that even with a Connectome, even with a high-resolution atlas of an entire brain, we still don’t have enough to spark a revolution in drug discovery. It’s a revolution of another kind, a necessary change in how neuroscience will be done moving forward.

BS: That’s right. It may be that neuroscience has to evolve first to start asking new questions, and it will be the answer to those questions, questions we don’t even know yet, that will set the stage for a neuropsychiatric revolution. It’s not gonna happen overnight, but I’m personally convinced that Tony is at the starting point of this new journey.

AA: And as for our friends, Ray and Rob, what do they think of all this?

RH: And I think that may be the reality, that we just have to wait for people like him to do their work and come up with the beautifully elegant maps that the rest of us can then use to cherry-pick targets, where I can say there’s a simple-minded drug discover, “This is a terrific hypothesis, let’s try and discover a drug that works here.” But you know, you can’t do it until the work is completed.

RM: So I think the kind of foundational Connectome mapping that people are doing, I think we have to do it. I am a passionate believer in that none of us is smart enough to know where the big breakthroughs are come from, and the best use of money is to support the best basic science on issues relevant to neuropsychiatric disorders because that’s where, if you look at the history of biomedical research, that’s where major breakthroughs come from.

Blah blah blah. I’ll shut up finally.

BS: So, I could talk to Rob for the rest of the day, but we usually try to keep these episodes short and sweet.

AA: But you know, maybe you guys want to hear more from us. Maybe you’d like longer episodes, and we want to know that, so we’d love for you guys to review us on iTunes and let us know what you guys are liking, what you’d like to hear more of. And this is a really great time to do that because-

BS: It’s the last episode of the season. We’re gonna take two month siesta?

AA: Yeah, we’ll be back on March 15, 2017.

BS: 2017.

AA: It’ll be next year already.

BS: And our New Year’s Resolution will be to improve this podcast, so hop over to iTunes, hop over to Lab Dish and please tell us what you think.

AA: Yeah, please. We really, really would love to hear from you.

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Episode 6: When antioxidants are pro-cancer

Recent research on antioxidant levels in the cells of pancreatic cancer patients is homing in on a new, safer avenue for treatment. And it’s not what you’d think based on the reputation antioxidants have gained in popular culture.

BS: Hey, I’m Brian Stallard.AA: And I’m Andrea Alfano.

BS: And this is Base Pairs, the podcast about the power of genetic information. We’re on our sixth episode now and somehow, we haven’t talked about cancer yet.

AA: I can’t believe it either. Scientists have been able to learn so much about cancer through genetic information.

BS: I mean, even in our daily lives we hear about this. Over the summer you probably saw ads for sunscreen that protects against some of the UV radiation that can damage your DNA and give rise to skin cancer. And then at the doctor we’re told about genetic tests for cancer genes, like the breast cancer gene BRCA1.

AA: Breast cancer is a great example of how genetic information has revolutionized the field of cancer research.

BS: It is. The survival rate for breast cancer has been increasing significantly over the past few decades. It’s up by roughly 25 percent, though that varies depending on what stage the doctors catch it at.

AA: That’s so important. Catching cancer at stage 1, before it’s had much of a chance to establish itself, and catching it at stage 4, when it’s already spread or metastasized throughout the body, are completely different situations.

BS: For breast cancer, genetic testing can give some families a heads-up. And mammograms—x-rays of the breasts—those have also really helped with early detection. While there’s controversy about how often to go for mammograms, that starts to seem less relevant once a woman or her doctor feels a lump.

AA: But cancer can also arise in places deep within the body, like in the pancreas—places where you can’t feel for lumps. Pancreatic cancer is incredibly difficult to catch early, partly because of this. And because it’s so hard to detect, the survival rate is really low. Only about 7 percent of patients live five years past diagnosis. Dannielle Engle, a postdoc researching pancreatic cancer in the lab of Dr. David Tuveson here at CSHL, knows this all too well.

DE: So I’m one of those people who has a very personal reason why I’m in the lab, and that’s because both my father and my uncle passed away from pancreatic cancer. Both my father and my uncle had stage four pancreatic cancer at the time of diagnosis.

BS: Stage four—that is not the stage you want to find cancer at.

AA: Not at all. It’s heartbreaking to hear how little there is to do for these patients.

DE: It just—it’s all over at that point. It’s so widely metastatic and they’re just also so sick at that point that even if we had effective therapy to give them it’s usually kind of hard to tolerate and so there’s very little that we can do besides makes these patients comfortable at the time of diagnosis. And I think that’s what a lot of people don’t realize, is that we have patients that only live for weeks after the time of diagnosis.

BS: Wow, so it’s kind of too late for chemo at that point, since by stage 4 the cancer has spread and usually can’t be brought under control by chemo.

AA: Basically, yeah. So there’s not a lot to do for these patients right now. But Dannie and her colleagues in Tuveson Lab are working on this problem. Some of them recently published a paper that describes a new potential avenue for treatment—one that only kills cancer, and leaves healthy cells unscathed. It has to do with antioxidants, which I think most people have heard of by now.

BS: Yeah, they destroy “free radicals” and prevent damage to DNA. Health food ads talk about them all the time.

[clip of POM Wonderful ad: https://www.youtube.com/watch?v= _HAk9zK8gTg]

AA: Right. Free radicals are basically oxidants, which, as the names suggest, are the kinds of molecules that antioxidants neutralize. Antioxidants are definitely important. But there’s more to know than what the ads tell you…

[clip 0:04 – 0:33 from Consumer Reports video: http://www.consumerreports.org/cro/2013/03/antioxidants-more-is-not-always-better/index.htm

AA: That clip is from a video by Consumer Reports. Scientists quoted in that video and across the scientific community say that our relationship with antioxidants is not so simple.

CC: I think like most of the general public, my view on antioxidants initially was that it’s good because it prevents aging, also prevents damage to our cells.

BS: That’s Christine Chio, a postdoc who works in the same lab as Dannielle and studies pancreatic cancer.

CC: The concept that I had initially was that you want to increase antioxidants to prevent cancer, to reduce progression. But as I slowly entered the field and I read the literature and I did some research myself, I realized that it’s quite the opposite—that while antioxidants might be good in certain settings in preventing aging, that’s also very much beneficial for the cancer cells.

BS: Antioxidants can benefit cancer cells. They definitely don’t mention that in the health food ads.

AA: Definitely not. But it’s really important to note that we are talking about situations where cancer already exists or is in the process of beginning — not in healthy people. These findings don’t apply to healthy people eating antioxidant-rich foods, so don’t throw away your blueberries or anything. Healthy cells in our bodies are constantly working to maintain a balance of oxidants and antioxidants that they need to survive.

BS: Still, it seems important.

AA: Agreed. This is one of the many examples of why talking to the public about science is so important.

BS: And the Tuveson Lab actually does quite a bit of it.

AA: They do! Sometimes it’s through large events like the Lustgarten Foundation’s annual pancreatic cancer awareness and fundraising walk, but sometimes it’s just sitting down with patients and their families over a meal—like when Dannielle recently sat down for lunch with the incredible Carol Whalen. After the immense tragedy of losing both her husband and daughter to pancreatic cancer, Carol immersed herself in scientific research on the disease, and has been meeting with Dannielle for years. As I sat eating my sandwich with them, Carol was furiously taking down notes and asking tons of questions.

CW: [crinkling of potato chip bags] Can you talk while eating? You have to multitask, Dannielle. There was an article in Newsweek about Dr. Chio, who found that antioxidants in the tumor or the tumor cell in the pancreas through working with organoids.

DE: Yes, Christine in our lab.

CW: What do you think of that?

DE: Well, I think what she’s found makes a lot of sense. And this is something that I think the clinic hasn’t quite caught up with the science.

AA: Christine is studying the effects that antioxidants have on cancer cells by looking into their DNA.

CC: I took a genetic approach in studying the effects of antioxidants. I study a gene called NRF2. So it is a master regulator of antioxidants in the body. In other words, when this protein is active, it leads to the production of antioxidants. And so the approach that I took was to try to genetically remove this gene, and by doing so, we can increase oxidants in the cells, and we ask “what are the effects to the cancer cells when we do this?”

BS: So they got rid of the gene for NRF2 in cancer cells. Meaning less antioxidants, and more oxidants.

AA: Right. In healthy, normal cells N-R-F-2 or “nerf” 2 serves as the guardian against stress to the cell. When the cell detects stress, like from UV radiation, for example, the NRF2 gene gets turned on. When certain foreign substances enter the cell, NRF2 gets turned on. It helps protect cells. Which sounds like a good thing, right? But then again…

CC: If you think about it from the perspective of a cancer cell, you would also realize that something like this would be very much desirable in a cancer cell to protect itself from the chemotherapeutics that we try to apply to the patient, for example. So there are many mechanisms through which NRF2 could, I guess, create chemo resistance.

BS: That makes so much sense. Cancer cells are like healthy cells in a lot of ways, but much more selfish and greedy. Of course they would take advantage of the good things that antioxidants can do for them.

AA: This blew my mind when I learned about it because it makes so much sense, just intuitively, and yet it’s so counter to the messages that we hear about antioxidants. This idea isn’t based solely in intuition, though. A growing body of evidence supports the idea that antioxidants can help cancer cells survive—a body of evidence that Christine and her colleagues are adding to.

CC: We found that when we increase oxidative stress [AA: That’s the kind of stress that antioxidants neutralize] through removing NRF2 there is a decrease in the activity of making proteins in cancer cells. So protein synthesis—or the making of proteins—is a very important procedure in any cell. This is true for normal cells, and this is MUCH more so for cancer cells. And when we do this [AA: when they remove NRF2, thereby LOWERING antioxidant levels] cancer cells don’t grow as well and some of them cannot survive, and therefore we think this might be a novel therapeutic approach that we can take.

BS: But don’t the healthy cells need antioxidants?

AA: Yes. But not as much as cancer cells do. Cancer cells are like normal cells on steroids, you might say

CC: The reason why we think this works is because when we applied the same strategy on normal cells we found that the effect is much, much less severe in the normal setting, and this is because the cancer cells have a much heavier dependence on the process of protein synthesis, or protein making.

[AA: Right, because they’re dividing so much.] Right. [AA: So every time they divide they need to make new little machines that keep the cell running, right?] That’s right. [AA: Ok, that makes sense.]

BS: Hold on. So cancer cells divide a lot. That’s why they’re so problematic. And that means they have to make lots of new proteins, because these molecules do lots of jobs and every new cell needs its own set. And to make proteins, cells need antioxidants.

AA: Exactly. To divide more, a cell needs more antioxidants.

BS: Did they observe this effect in humans?

AA: Kind of. They haven’t tried this out in the clinic with real patients yet. But they did do tests on cells from real patients. This research is a new strategy, so they have to do a lot of testing in the lab before they can come up with a drug that’s ready for people to try. Instead, they used this super cool new system for studying the pancreas, both when it’s healthy and when there’s cancer.

CC: We have this beautiful platform of organoids which allows us to study normal cells, precancerous cells, and cancer cells.

AA: Organoids are basically balls of cells that they grow from small samples taken from either humans or mice. They put these samples in a dish that mimics the environment in the body, and this allows the cells to divide and grow in 3D, which is really important. This is what Carol Whalen really came to see during her latest lab visit with Dannielle. You’ll also hear Megan, a lab technician, and Carol’s husband, Mike Whalen.

DE: So when you look in the plate from the side—this is a well, and then what you’ll see is basically a little dome In this dome, you’ll see little tiny bubbles. And these bubbles are little spheres of cells that are the patient’s tumor cells growing as organoids. And so what we’re going to do is show you some normal and some malignant. And Megan, which one do we have on the microscope right now?

Meg: This is the normal.

DE: So I’ll just take a quick look to orient you guys and then what you can do is sit at this microscope and if you look in here, you’ll see a bunch of little bubbles. So feel free to sit down and take a look You see those? You see how they’re very neat and tidy? They’re all hollow, they’re all very thin-walled, and they all look very similar?

MW: They’re all different sizes.

DE: They’re all different sizes, but they’re all kind of the same shape, right? Take a look at these. These are kind of an example of our most aggressive, malignant-looking organoids. So when you look in there what do you see?

CW: Oh my gosh! Huge difference!

DE: And so tell me what differences you see.

CW: Well the size—well the number of large ones is lower, many more small, very small—some are teensy! And many are very dark throughout. Some are even different shades of gray throughout. And it looks like—I don’t know, it looks like some are kind of clumping together.

DE: Yes. So what is happening is—so a normal organoid is a hollow sphere with a single cell layer. These are solid. These are completely filled in.

AA: The head of this lab, David Tuveson, played a key role in developing this organoid system, which is used across a variety of cancers today—not just pancreatic cancer. Christine told me about why organoids are so powerful.

CC: So the development of this 3D culture is revolutionary because we now can maintain the genetic integrity of the cancer cells. And more importantly, this 3D culture supports the growth of normal cells. So now we have the ability to compare side-by-side normal cells and cancer cells.

BS: Scientists couldn’t get normal cells to grow in a flat Petri dish before? That’s incredible—being able to compare a drug’s effects on cancer cells with effects on normal cells is critical.

AA: It really has been revolutionary. This organoid system made it possible for Christine and her colleagues to do much more rigorous tests on potential new drugs that kill cancer—but not healthy cells—by lowering levels of antioxidants. They first tested the idea that lowering antioxidants could kill cancer by removing the NRF2 gene. But since we can’t exactly go around changing humans’ genes, for a variety of reasons, they set out to find a drug that has this effect.

CC: When we first found that this drug has an effect only in the cancer cells, I think that was the most exciting moment. But we think that this is still not the best drug combination because we can only achieve a modest improvement in survival. And the hope is that by studying these combinations in organoids and also in our mouse model, we can identify a better therapeutic combination.

BS: This is really just the beginning for this potential new therapy, then.

AA: Indeed. While it’s important to recognize that this work is still in an early stage, it’s an exciting start. And when dealing with a disease like this, where patients have such dismal options, new treatment ideas like this are pretty much the only source of hope. That’s also a big part of why Dannielle, is so passionate about spreading the word about pancreatic cancer research.

DE: I think one of the big problems with pancreatic cancer research is that we just need more people doing it. There’s a lot of work to be done and we need to encourage more young people to become scientists and to work on this problem, and I think that’s where participating in outreach and just talking about what I do has become very important to encouraging that in the future.

BS: She’s really like a missionary for pancreatic cancer research.

AA: Really. She’s an ambassador for the Lustgarten Foundation and is constantly looking for ways to spread the word about pancreatic cancer research—even talking with her mom on the phone has become an exercise in making her science accessible.

DE: I spend a lot of time practicing what I’m going to talk about with my mom, who’s not a scientist. She’s an accountant. So I spend a lot of time, like, on the phone explaining my research to her, so she understands very well what I do as a lay person. And so I think it’s important to talk about our research, just, like, to our friends and our family to make it more normal and accessible and they’ll be wanting to talk about with their friends so that we can eventually raise awareness of this disease and, you know, try and make a bigger difference.

AA: Dannielle and Christine are certainly doing their part, and so is everyone in their lab. I think it’s easy for people to imagine that scientists become detached from the people they’re supposed to serve, and in some cases that may be so. But not in this lab.

DE: My father passed away right when I started graduate school, so almost 10 years ago now. And it’s definitely very empowering. I do take my experimental failures I think a little bit harder because of it, but at the same time I have a unique drive and motivation to really fight pancreatic cancer because it’s personal with me. It’s really messed with my family and I’ve seen what it does to other families. And so I think as a scientist it’s important that we remember why we’re here and it’s definitely for those patients and families.

AA: The room where Dannielle and the rest of the team keep the organoids is what you would probably expect a lab to look like—sort of sterile and impersonal, with white walls and lots of equipment. But as Dannielle showed Carol around the room, the feeling that anything about that room is impersonal quickly washed away.

DE: So we have actually two incubators full right now. These are just more patients. And so right now, so you can see that some of them require very tender loving care, so Megan annotates those as being fragile. So you have to watch them very carefully to adjust to their needs. So something that Megan can attest to is that we’re here every day of the week. Sometimes our specimens come in at 8pm and we come in to isolate them, and we’re here until sometimes two in the morning.

Meg: Yeah [laughing] Takes a few hours.

CW: Just remember you’re doing it for us!

Meg: Yeah, I know!

DE: We’re here. We’re dedicated, and I think our success rate has to do with the fact that we are—we recognize how important it is.

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Episode 5: "Sink or swim"

When he was just 27 years old, Adrian Krainer, now a professor, was offered the opportunity to run his own lab. Now, research from his lab has contributed significantly to the development of what promises to be the first drug therapy for a deadly disease affecting infants.

AA: Hey, I’m Andrea Alfano.BS: And I’m Brian Stallard.

AA: And this is Base Pairs, the podcast about the power of genetic information. But this episode is a little different from the others we’ve done. We wanted to give you listeners a better sense of what it’s like to sit down and talk with one of these amazing scientists—you’ll see what I mean.

BS: Last time, we talked about how that power can help save lives by enabling us to produce more food, which we’re really going to need as the human population continues to grow. But Andrea, you’ve been talking to someone who has seen how genetic information can save lives in a much more direct way.

AA: I have. It’s amazing.

BS: Now, I would think that has something to do with detecting harmful mutations, or identifying genetic disease, so that doctors know which treatment to give.

AA: That’s right. But. There’s more.

BS: More?

AA: A lot more. This is not like anything you’ve heard of before, because there has never been a treatment like this. And this treatment is only possible because of basic research on how our cells use the information stored within our DNA. It’s not an approved treatment yet—applications will soon be filed with regulators in the US, Europe and Japan. But, we can say for sure that there are babies who have received this drug who were unlikely to live past age two, and they are now four years old.

BS: That’s incredible! So this scientist you’ve been talking with, the guy who did much of the basic research behind this new medicine, that’s Professor Adrian Krainer right? He just celebrated 30 years of working at CSHL this year, and when he started working here, he had never even heard about this disease that kills infants,. Like a lot of our scientists, he was MUCH more focused on that timeless pursuit of new knowledge about biology—fundamental stuff.

AA: Yeah, so I wanted to know how that happens. How do you go from studying broad, basic processes in biology to helping save the lives of very real people with a particular disease? For Adrian, it meant going way back.

AK: I think that—well, I was motivated to go into biology around high school. I was interested in genetics when I first was exposed to classical genetics, Mendelian genetics, I thought it was extremely interesting. I had a lot of fun with it.

AA: Who’s Mendel again?

AK: So Mendel—So Gregor Mendel was an Austrian monk and he was doing experiments with peas and other plants and he discovered how traits are passed from one generation to the next and he showed some rules for it—dominance and recessive—the types of traits and the manner in which they are inherited. So I had a lot of fun with that topic and I thought that I should go into it and do research. So I grew up in Uruguay, in South America, and so that’s where I went to high school, and that interest in science and research prompted me to come to the U.S. to study.

AA: So you always—you kind of started out wanting to do basic research in particular?

AK: Yeah, to the extent that I understood what that consisted of. And uh, at Columbia I majored in biochemistry. And then I did my PhD in biochemistry at Harvard, that’s when I started to study RNA splicing and because of the research that I did I always maintained a close link between the new basic knowledge we were gaining and the relevance to genetic diseases. I feel that I do a kind of genetics, or molecular genetics, so I didn’t deviate too much from what I had in mind when I went into college. Now of course I didn’t even know that splicing existed then.

BS: Splicing. I just learned about this recently. It’s a very strange process. I think the fact that I produce this podcast actually really helped me to understand how it works, because the kind of splicing that Adrian studies—splicing together bits of molecules that carry genetic information in the cell—is like the kind of splicing that I do to put together the bits of audio in this podcast.

AA: You know, you’re right—it is similar.

BS: So from my understanding, splicing goes like this: You have your DNA, which contains the information in all of your genes. But for gene to do its job, the cell first makes a copy of that information in the form of RNA. RNA is a molecule that’s related to DNA, but it’s better suited to editing. It’s like when I copy and convert an audio file from, say, an mp3 file to a WAV file. Same information, different format.

AA: Right, and it’s for editing purposes that the cell makes this RNA copy.

BS: Yes. Once the DNA sequence is copied in the different “format” of RNA, there are extra bits of sequence that need to be edited out—meaningless gibberish. It’s like when I edit out sections of audio that aren’t relevant to our story.

AA: At first the RNA sequence of a gene is like a raw recording that still has a bunch of outtakes.

BS: Right. I use an audio editing program to cut those out and then splice together the bits that we need – but only those bits. The cell’s equivalent of such an editing program is an amazing piece of molecular machinery called the spliceosome, which removes the bits of sequence that are mucking up the “message.” This machine pastes together the bits of sequence containing the instructions for making a protein.

AA: Yeah, and those sequences that are mucking up the message – you can think of them as “interfering” sequences. And that’s why biologists called them introns. Those get spliced away. In the same vein, the sequences that get expressed to the cell’s protein factories are called exons. Those get stitched together to form the gene’s fully edited RNA message.

BS: So at the end of the process, you get a sequence of letters that make a coherent message. Or in our analogy, a podcast that you’ll understand.

AA: This is the process that we’re talking about when we say “splicing.” A co-discoverer of splicing, Rich Roberts, actually worked here at CSHL. He and Philip Sharp of MIT simultaneously discovered splicing in 1977, and later shared a Nobel Prize. Ok, back to Adrian—and our story of how an amazing drug for very sick children was invented.

AK: The work that I did as a Ph.D. student was to develop a system to study the biochemistry of RNA splicing. So we were able to get RNA splicing to happen in the test tube, using extracts from cell nuclei.

AA: So you got to meet Rich Roberts when you came here, right?

AK: Yeah, so actually we met in 1985. So I came to Cold Spring Harbor in 1986, so in ’84 however I gave a talk at the RNA Processing meeting here when I was still a graduate student. So that’s how Rich knew about my work, through that presentation I gave.

AA: And Rich Roberts is one of the scientists who won the Nobel Prize.

AK: Yeah, so Roberts and Sharp won the Nobel Prize later in 1993. So it was a landmark discovery and a paradigm shift. And so Rich went to that meeting and that’s when he suggested to me to come here as a Cold Spring Harbor Fellow. And so eventually I came here—30 years ago, in July of 1986.

AA: And you were actually the first fellow, right? Or one of them.

AK: Yes, that’s right. I was the first fellow. So the idea is to bring a young scientist, straight after the Ph.D. and let them function independently and sink or swim on their own. And generally they have a mentor, and so Rich Roberts was my mentor.

RR: Jim and I don’t know whether Joe, but some people anyway, decided that we would have a program for really good post-docs and call them Junior Fellows in exactly the system that they have at Harvard.

BS: That’s Rich Roberts himself, Nobel Prize-winner and co-discoverer of splicing.

RR: You find really good people and you pretend that they are very special. You bring them in and give them some extra money and resources and so on. I thought Adrian would be perfect for this. We could bring him in under that auspice. He could work in conjunction with my lab, be independent, do whatever he wants to do. I kind of like it when people in my lab do what they want to do rather than what I tell them to do. It was perfect. I met Adrian, convinced him to do it. The rest is history, as they say.

AA: History, indeed. But when I talked to Adrian I learned that if it weren’t for this Fellows program, that history could have been very, very different—for Adrian, and especially for those kids who are alive today because of the drug that came out of his research.

AK: If I went and did a standard postdoc somewhere, I probably would have switched to something completely different and I was very attached to this work.

AA: What was it about this that made you so interested in splicing? Like, was it that it was such a puzzle to figure out?

AK: Yeah, yeah. It did seem like a completely new frontier and you really want to know how it works and having spent a few years learning very novel things about it, it’s kind of addictive—you really then want to know the other aspects of it and in greater detail. And so the Cold Spring Harbor Fellow position gave me the opportunity to continue that work, and my previous mentor was very supportive of that. And so, then I thought, “Ok, great. I’ll come here and try to purify the spliceosome, or identify some components of it.”

AA: What was it like to figure out in a test tube what all of these little—machines, basically, are that are in your cells all the time?

AK: It’s like solving a puzzle, so it’s very rewarding. So, I mean it’s technically very difficult to get there and you don’t get the answers overnight. You have to generate ways to look at it, or assays, you have to generate reagents, you have to purify components—typically this has to be done in a cold room because proteins or enzymes are very sensitive and they don’t—you know, they don’t last in an active form very long, you have to keep things—you have to work very carefully and precisely.

AA: Were you working in a literal cold room?

AK: Yeah, certainly I did a lot of work in the cold room. You put a coat on and, you don’t have to stay there for hours on end but you go in and out constantly. So it is very, very labor intensive. And it’s kind of an art, I would say. But at the end of this exercise, which can take weeks or months or years, you may purify a component. You start with an extract that has thousands of proteins and you manage to get a pure component where you’re able to say here there’s only one protein. And that really is required, because if I don’t add it to this reaction, splicing doesn’t happen.

So we did that, and then the first postdoc who I hired here was a Japanese fellow Akila Mayeda—it was his turn to go into the cold room. — Mayeda, that postdoctoral fellow, purified a protein that’s called a splicing repressor. And so for example, for certain exons, if they can be excluded or skipped during splicing, when that factor is present at higher levels, that exon will tend to be skipped.

BS: Why would the cell want to repress the splicing of a certain exon? I thought those are the parts that are supposed to be expressed.

AA: They are. So this is the really ingenious part of splicing. Those exons, the expressed bits? They are what provide the instructions for building different proteins, which are the workhorses of the cell.

BS: Yeah, basically they do everything! They help us digest our food, keep us safe from invading viruses and bacteria, carry messages from cell to cell…

AA: Yes. There are lots of different kinds that are specialized to do a lot of different jobs. But there is some overlap—some parts of different proteins are the same. So the cell does this clever thing: it uses the instructions in some of the same exons to build different proteins.

BS: And it does that by repressing the splicing of certain exons, so they don’t get included in the final message?

AA: Exactly. This is one of the reasons that humans can be so complex even though the human genome is not much bigger than that of a fly.

BS: Genius!

AA: It is! Except…mistakes can happen. And one such mistake, a splicing mistake, turns out to prevent these children we’ve been mentioning from living past the age of two. They have a disease called spinal muscular atrophy, or SMA for short. Adrian learned about this at an NIH workshop in 1999.

AK: What happens is that motor neurons—and these are nerve cells that are responsible for the ability to move voluntary muscles, so they go from the spinal cord to the various muscles in your extremities and anywhere that you can move in a voluntary manner. But in this disease, motor neurons are unhealthy and they gradually die. And as the muscle loses the motor neurons that innervate it, then the muscle atrophies. And so over time—

AA: And so atrophy is when—?

AK: Well the muscle ceases to function and then it just disappears, essentially. And then although this can take a long time, so over time the patients lose their ability to move their extremities and they also have trouble breathing because the diaphragm and the rib muscles are necessary to move the rib cage to breathe, and holding the head is difficult.

AK: In ’99 there was a workshop at the NIH. And the work in the field in that time had shown that—so there are two genes involved in SMA. The genes are called SMN for survival of motor neuron, but there is SMN1 and SMN2. And they knew by then that the SMN1 gene is the most important gene and in patients it’s missing or it’s mutated to the point that it’s nonfunctional. And in that situation, the SMN2 gene becomes essential.

AA: So they make the same thing, these two genes?

AK: Yeah, I’ll get to that. So in patients they are strictly dependent on SMN2 to make this protein that is essential for life, SMN. So it is essential for motor neuron survival, as the name implies. Now, the SMN2 gene is not as good or as potent a gene as SMN1 and this has to do with splicing. And that’s what I learned about in 1999 when I went to that workshop. So there is a number of exons, and exon 7, instead of being included in RNA splicing of the SMN2 gene, it tends to be skipped.

AA: So you had spent all of this time meticulously figuring out what—ingredients, basically, the cells needs to create different splices—

AK: Different splices and what are the sequences they recognize and what are some of those key ingredients that do that selection.

AA: Right, and then you go to this conference and they’ve noticed that there are these differently spliced RNAs—

AK: Yeah, spliced forms and a gene that’s not fully functional, has a nucleotide change within the exon, and that seems to be determining for the exon not to be recognized efficiently.

AA: So did you realize that right away? While you were at the conference, did you have the thought?

AK: I said that it was very interesting and I told people that we were studying something very similar, and that I don’t know anything about this disease, but I probably should just start maybe studying in this area and see what we can contribute.

AA: All of that basic research that Adrian and his team did, all of those hours spent in the cold room—that gave them the basic understanding of splicing that they needed to figure out how to correct the splicing error that gives rise to SMA. They came up with an idea for a drug, which they later developed with a company called Ionis Pharmaceuticals. The drug prevents the skipping of exon number 7 that makes SMN2 protein inadequate. The drug is called Nusinersen, and it’s the first of its kind: no existing drug works by fixing a splicing error.

BS: We’re going to save the details of how the drug works for a later episode. We’ll do that show once the drug makes its way through the FDA. It will hopefully be approved, but there is some good news right now.

AA: This past August, Ionis ended a Phase III trial in infants early because the results were so positive.

AK: Just looking at the patients who have received drug for variable period of time and looking at how they’ve done, particularly in reaching developmental milestones, like sitting, rolling, holding the head, even being able to walk, I mean these are very young—and in this trial, infants enrolled as early as six weeks of age, and older. So there was already striking or statistically significant differences between the treatment and the control groups, and therefore they felt you couldn’t continue the trial to completion.

AA: Does that happen a lot?

AK: No (laughs), not usually. I mean, things have to be very clear cut.

AA: What was it like to see that for the first time? You know, this thing that started out with you mixing things in a test tube.

AK: Oh, it’s an amazing path, and from what I gather, it’s not one that one can expect to see many times in one’s career. I go to a couple of SMA meetings every year and I meet patients and clinicians and their families and so I understand the impact and the need and—you know, it was always very motivating to come back to these meetings. I still view that what we do is very basic science, but then it has immediate, or a very strong impact on health. It’s very rewarding, let’s just say.

AA: So I mean, you said that this kind of thing doesn’t exactly happen all the time in a scientific career, or it doesn’t happen at all. So what kind of advice do you have for young scientists, especially basic scientists?

AK: I’ve found it very rewarding to work at the interface of the basic science and the direct applications. We didn’t necessarily set out to come up with a cure for something, we didn’t feel like we were in a position to do that, but in the process of doing the work, you know, then opportunities arise. — When this work started I only had a minimal understanding of what a motor neuron was. But I think that’s an exciting part of science—when you’re following what you have a passion for, it forces you to learn different things along the way, depending on where the science takes you.

AA: Learning about Adrian’s amazing career has really made me think about how important it is to support young scientists and help them pursue their passions. After all, if Adrian hadn’t gotten the Fellow position at CSHL, there’s a good chance that he would have ended up studying something else instead of continuing to study splicing. And then who knows if there would be Nusinersen?

BS: Wow. Yeah, I can only imagine how the families of the children in those clinical trials feel about that. But I know for a fact how one important person feels about it. CSHL’s president, Bruce Stillman, feels very strongly about supporting young scientists.

BStill: One of the reasons why Cold Spring Harbor Laboratory is really so successful is that we spend a lot of time and effort investing in the careers of young people. This was the case with Adrian Krainer, who came as a Cold Spring Harbor Fellow in 1986, and the Cold Spring Harbor Fellows program has been incredibly successful. Another Fellow, Carol Greider, went on to win the Nobel Prize for medicinal physiology in 2009. By investing in the careers of young people, allowing them and giving them the resources to do really whatever they want, can really lead to profound discoveries. Both in basic science, and as you’ve seen with Adrian Krainer’s work, in the clinic.

AA: So, here’s to young people—the young scientists, and the very young people in that clinical trial, who will hopefully continue to benefit from these profound discoveries on splicing.

BS: And to many more profound discoveries.

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Episode 4: The people problem

Nearly ten billion people will walk the Earth by 2050, and for some of the poorest and fastest growing countries, that could mean a bleak and hungry future. Josef Schmidhuber of the FAO and CSHL Professor David Jackson explain what has gone wrong, and how delving into the mysteries of plant genetics can help.

BS: Hey all, I’m Brian, and with the help of my co-host Andrea…AA: Hey there.

BS: We’ve already talked a lot about genes, research, and how all that impacts us, people.

AA: So far we’ve dived into the discovery of new diseases, revolutions in farming, and the evolution of humanity.

BS: This time we’re going to talk some more about that very last bit.

AA: Which bit?

BS: The last bit. The impact bit.

AA: The people bit?

BS: The people bit! People, people, people, people, people, people…

AA: People. I think we get it.

BS: People are everywhere and we’re always growing … growing physically, growing as a species, and most noticeably, growing in number.

Currently the globe place host to an estimated 7.3 billion people and that’s no number to sneeze at … or do, because by 2050, the United Nations expects global populations to total up to a stunning 9.7 billion people.

AA: And to put that in perspective, it would take more than 3 hundred years just to count to 9.7 billion out loud. (Brian counting in background)

AA: Even more worrying, is that it won’t be the healthiest or wealthiest countries that grow the most. According to the FAO…

BS: That’s the Food and Agricultural Organization of the United Nations.

AA: The great majority of population growth will happen in developing nations.

JS: If you look into the population projections that are currently available, we essentially have 13 countries that have population growth rates above 2.5 percent in the future.

BS: That’s our friend Josef, a high-profile analyst who works for the FAO.

JS: My name is Josef Schmidhuber. I’m the deputy director of the Markets and Trade Division.

BS: Alongside his colleagues, Josef works to understand food availability and market trends, which in turn tells him what kinds of difficulties the world’s most vulnerable countries are due to face.

JS: These are countries like Senegal, Burundi, Tanzania, Mali, Central African Republic, Uganda, Angola, Zambia and Niger.

AA: And if you think he sounds worried, he is.

JS: So if you look at their total population today, this is around 320 million. These are just 13 countries. If we look at their populations in 2050, it will increase to 835 million. If we look into their population by the end of the century, 2100, their population will have swollen to 1.8 billion people. Okay?

If you take the country with highest growth rate, that’s Niger, currently at around 20 million people, it will be at 72 million people by 2050 and 210 million by 2100. Clearly, that’s unsustainable.

BS: Unsustainable, meaning that as things stand, these incredible population spikes can’t last.

JS: Right, because a country like Niger doesn’t have the agriculture resources, doesn’t have the land, the water, and everything that is required to actually produce the food that it requires for 200 million people from a domestic base.

At the same time, with the exception of production of uranium, it hardly has the non-agricultural resources to import the food that it would require to feed its population.

There are two alternatives. Either the country will be dependent, in that they will significantly sit on foreign assistant, or these population projections don’t come true simply because there is permanent malnutrition and hunger.

AA: It’s not a pretty picture Josef is painting here, and with climate change and political unrest sweeping across the globe, he admits the situation could get even worse.

BS: But, he did tell us that there is hope.

JS: What is very important, is that developing countries manage to increase the productivity on the existing land and, I mentioned Niger, you don’t only have this phenomenal population growth, it’s a country which essentially has 12 million hectares of crop land available that are potentially usable and all of them are already in use. So, in order to increase production, one needs to have higher productivity.

AA: Higher productivity. He’s saying that for a country that can’t even afford to feed itself with imports. The only way to battle starvation is to somehow take one corn cob and make it two, to take an already fruitful field and make it grow more.

BS: That sounds like a tall order, perhaps even a miracle, but if you’ve listened to our second episode, you know it can be done given enough time and scientific ingenuity.

JS: So, the genetic potential for many crops still considerable. We haven’t exhausted it. We have indications that that’s the case, so it may still be a better idea to invest in R&D than into more intensive agriculture.

AA: Oh, R&D. Now we’re starting to sound like a science podcast.

BS: That we are, and this genetic potential has a lot to do with how good the farmers and scientists in a region have gotten at controlling growth.

DJ: Yeah so really what we’re doing is we’re tricking the plants. We’re fooling them into putting all their resources into one ear. Whereas, in the natural setting, that would not be good for the plant, but in an agricultural setting, that’s exactly what we need.

BS: That’s David Jackson, a professor here at CSHL, and he’s one of the world’s leading plant scientist. He spends most of his days making corn grow in ways that nature would normally avoid.

DJ: The natural ancestor or relative of corn makes very small ears, but it makes hundreds of them, and in a natural environment, that’s good for the plant because it optimizes the plant’s ability to spread seeds and to reproduce itself. But in a farmers field, it’s a very different environment. There, you want to have all of the energy, all of the seeds, concentrated in one large ear that makes it easier for the farmer to harvest.

AA: Tricking a plant to do something that it wouldn’t do in the wild may remind you of particular buzzword, but…

DJ: It’s not GMO, we’re not adding any foreign genes to the plants. We’re doing it by the same process by which breeders have been making crops for the last hundreds of years.

AA: Dave studies the development and architecture of plants and he uses corn in part because it’s a model crop that scientists are very familiar with.

BS: Remember episode two? No, really. Go listen to episode two if you haven’t. Corn, as it turns out, has been subject of crop study for over a century.

AA: Anyway, Dave uses corn not just because he wants to make more corn, he’s looking into ways to increase yield in all plants, and to do that he’s got to study crop growth on a very fundamental level.

DJ: My feeling is that most plants the basic way in which the genes work is the same, but their expression changes in different plants and that gives rise to different architectures.

AA: I like to think of Dave as an ugly corn aficionado because to prove this he chases after mutations, sometimes sifting through entire fields of corn in search of the most unsightly cobs.

DJ: We end up opening thousands of ears in a day and we look for ones that look abnormal.

Speaker 11: Let’s just see if I can find a [inaudible 00:08:28] Yes.

speaker 2: The reason is because a mutant is a way of figuring out how normal development works, right? So say you have a car, for example, you want to know how it works. If you knew nothing at all, one way to do it would be to just open up the hood and start pulling pieces out and see what happens, so that’s exactly analogous to what we do when we look for mutants. Mutants … we’ve basically pulled out one gene. We’ve inactivated it and so then we find out what happens when you inactivate that one gene.

BS: It sounds simple enough, but there’s one big catch. If, we’re comparing corn to cars, your average maize plant could have more than 32 thousand protein coding parts to experiment with and each one could be broken in different and complicated ways. Discovering these genetic tweaks one at a time seems like a pretty exhausting way to figure out how plants work.

AA: That’s true, but the alternative is the guess work that only rarely leads to resilient radishes or blue ribbon beets.

Without the crucial knowledge Dave and colleagues are working towards, breeders would never be able to unlock a plants full potential as a crop, and besides, sometimes a scientist can get very lucky.

DJ: So we got lucky. It’s like winning the jackpot kind of thing, you know?

BS: That’s Dave again, talking about a discovery recently made in his lab about stem cells. One that was a long time coming.

DJ: I’ve been working with that mutant for almost 20 years. I’m a little bit embarrassed to say, but sometimes these projects go on for a long time.

AA: And all those years of work paid off in really big way.

DJ: Yeah, so what we’ve found in our work is that the stem cells also respond to signals that come from the developing leaves and this a very new way of thinking about stem cells, because normally we think about them sort of being fairly autonomous, where they control themselves, but this suggests that the leaves, for example, which we normally think of being as quite passive in the developmental process, they’re actually sending signals back to the stem cells to instruct them how to divide.

BS: Whoa.

AA: Yeah.

BS: I get what Dave’s saying here, and it’s pretty exciting stuff, but to really convey its importance, we’re going to need to talk shop.

You’ve probably heard of stem cells, the Big Momma cells, if you will, from which all other specialized cells are born. Need a leaf cell? A stem cell divides, creating one new stem cell and one cell meant to develop specifically as a leaf cell.

AA: Yep. That’s the bit that people usually know, but what’s extra cool is that, while stem cells od their jobs, they’re constantly chatting with one another.

BS: Yeah, they’re all like, “I’ve got this cell covered boys, no need to double up. There’s lots of other work to be done!”

AA: (Laughter) Okay, Brian. I’m not sure that molecular signaling can have an accent. Actually, I don’t think that it sounds like anything, but I get your point.

What Brian’s trying to say is that stem cells keep in touch with one another so that energy isn’t wasted on dividing, unless a plant really needs a new cell of a specific type.

BS: But Dave’s lab discovered that mature cells, the cells that make up those growing leaves and roots we talked about, they’re actually sending signals to the stem cells also, giving updates on how things are shaping up where they are, and in this way, helping the stem cells know how to direct future growth.

DJ: A nice analogy of this is if you imagine the process of building a house. So, that normally starts with an architect who would make the plans, and then the architect would pass those plans onto a builder, who would then start laying the foundation and laying the bricks for the walls, for example. So this kind of signaling is analogous to thinking about a way in which those bricks are now sending signals back to the architect to tell the architect to maybe modify the plans for the house … and we think it makes a lot of sense, although it’s quite a new way of thinking about development, and it makes sense because the bricks, in that case, or in our case the leaves, are really out there in the environment, and they can sense what’s going on and they may find some mistakes that the architect has made or maybe find a better way to build the house, or, in our case, the plant.

AA: It’s a discovery that gives us a new view of plant biology that you won’t find in your high school text book, but you might be wondering how knowing this will feed the world.

BS: And this where we take our leave of the construction sight and return once again to the corn fields.

AA: Dave Jackson first discovered these leaf cell to stem cell conversations when investigating a single mutation known as FEA3, an abbreviation for Fasciated Ear 3.

DJ: You often see plants in your garden or in nature that are fasciated, so actually the word derives from a Latin term, which means club-shaped. The ears, rather than being long and skinny, actually look like a club, so they’re fatter at the top than at the bottom … and 3 means it’s the third mutant that we found which had that phenotype. There’s also a FAE1 and FAE2 and a FAE4 and a FAE5.

BS: You’ve been busy.

DJ: Yeah. (laughter)

BS: You’d have to see a FAE3 cob for yourself to really understand why geneticists have been chasing after fasciated corn for decades. Twisted and misshapen and packed full of shriveled kernels, these cobs scream mutant.

AA: Or, to circle back to Dave’s chop shop metaphor, they’re junkers just waiting to be torn apart and analyzed, and that’s exactly what he did.

DJ: As you know DNA is like a blue print, so that is read out in the cell to make proteins and we can recognize that the FAE3 gene was read out to make a kind of protein that we call a receptor, and these types of proteins that are very special in development. They’re proteins that sit on the surface of cells and respond to signals during growth.

BS: Or, to put it another way, these receptors are a lot like the hearing aids of stem cells, listening for signals heading their way.

AA: Dave and his team then set out to find the signal this particular receptor was picking up, and that’s when they discovered that it was coming from leaf cells, as opposed to the usual stem cell chatter.

DJ: Well the leaves are really out there in the environment, and they’re sensing all sorts of different environment conditions, such as light and temperature and amount of water … and the plant generally wants to tailor its growth to match the environmental conditions. For example, if there is not enough water around, if the plant keeps growing at the same rate, it’s going to run out of water and die, so, the leaf is really out there in the environment and can sense these different factors and can then send information back to the stem cells.

BS: However, and here’s the key to Dave’s work, while this receptor is designed to pick up those important signals, it barely works in the FAE-3 mutant, essentially deafening its stem cells to elite status updates about local conditions.

AA: And being unable to hear the signal to put the brakes on cell formation, a FAE-3 mutants stem cells quickly get out of control.

DJ: They tried to make too many seeds, but it’s just the number’s so high that all of those seeds are competing and they end up just almost killing each other, because there are too many mouths going after too few resources.

BS: Now, as we said, wild corn is cautious about spending too much energy on new parts the environment won’t support. Dave’s team wants corn plants to make more parts, more kernels that is, and so they had the brilliant idea of finding a middle ground; a corn plant that will make a little bit too much seed, but not so much as to threaten the plant’s ability to survive.

AA: So you’re saying they wanted to find a mutant corn plant, one with a mutation in the FAE-3 gene, but one less powerful than the FAE-3 mutation that leads fasciation.

BS: Exactly, a corn plant broken just enough.

DJ: The number of seeds is increased a little bit and somehow the plant is able to still feed them so that we can get more seeds that are productive, that are mature and viable seeds.

BS: Plant scientists like Dave, they make their living by learning from nature. By looking at how a mutant plant is abnormal, they learn a way in which to essentially muffle the signals that would otherwise limit how productive any single ear of corn can be, and this has resulted in a stunning 50 percent increase in yield in corn plants grown under controlled conditions.

DJ: The next step now is to test this in an agronomic setting in varieties that farmers grow to see if we can also get similar increases.

AA: Dave even told us that he’s excited about this work, not only because the science fascinates him, but also because he fears for the future.

DJ: I mean, the other thing that people talk about but don’t consider [inaudible 00:18:21] I think is that population growth is still going on very much. I think that the current population is 7 billion projected to go to 9 or 10 billion by the end of the century. And on top of that, and in fact, we’re almost maxed out on the amount of agricultural land that we’re using on the planet, so where is that extra food going to come from?

And, on top of that, what I’m more concerned about is that a lot of people in developing countries are naturally developing more of a rich country or a developed country lifestyle, where they eat more meat and that requires a lot more input in terms of agriculture.

BS: And that brings us full circle back to our conversation with Josef, who told us that one of his greatest concerns is not that there won’t be enough food to go around, but that demand will heavily shift towards more and more western diet.

JS: In fact, it’s already something that we’ve seen. We’ve measured this a considerable convergence in diets towards a western type of diet, so that means there is also more consumption in livestock products eggs, milk, meat and so on, which requires a lot more input on the crop side, and that certainly will add to the needs to produce more wheat, more maize, more [00:19:35]

AA: It’s then a pretty good thing that science is working hard to take agriculture to the next level. A level where understanding how plants work in general can directly impact how we will feed ourselves in coming decades.

As Dave says about this most recent discovery…

DJ: With this particular gene, I am most excited about it because it’s something we found in maize. As a plant, for the first time, it’s been discovered in any plant, so it could be broadly applicable to many different crop plants and all plants that we know.

You know, science is a process which never ends in a way, so the more we find out the more new questions we have to answer.

BS: Well, this is where we should end the story for now, but as with all the lab’s ongoing projects, we’ll be sure to keep you updated as this revolutionary research plays out.

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Episode 3: Non-modern family

From the scale of a single individual who was murdered on a snowy mountain in Europe 5,000 years ago to interactions between large groups of humans and Neanderthals who lived 100,000 years ago, genetic information holds many secrets about human history.

AA: Hello again, everyone! I’m Andrea Alfano, and I’m of course joined again by my co-host, Brian Stallard.BS: Hi, everybody! If you listened to our first two episodes, you know that on Base Pairs we like to look at the ways in which harnessing the power of genetic information has already shaped our world, and how genetic information is becoming an even more powerful tool today, as technology advances.

AA: So far, our stories have been set either in the past or the present. But today, we’re really going to straddle both—because we’re going to be talking about using DNA evidence to piece together the past.

BS: You’re talking about how we can trace DNA samples, CSI-style?

AA: That’s part of it, yeah. Except I’m not just talking about matching the DNA to a criminal, like you might have seen on Law & Order. I’m talking about forensic investigations that reach deep into humankind’s past, matching bits of DNA across thousands of years. But, our story does start out with a murder.

NOVA: “He was found in a glacier, frozen in time for 5,000 years. An ancient murder mystery. You can’t help but ask, what is his story? Secrets hidden in his genetic code. We’re rewriting the history of humankind.”

BS: Whoa… who turned on the drama? What did I just listen to?

AA: Ha! I did warn you that we’re starting with a murder. What you just heard is from the trailer for a recent TV special called “Iceman Reborn” from PBS’s NOVA series. And that mystery man goes by the name of Ötzi these days. He was named after the place where he was found—high up in the Ötzal Alps, on the border between Italy and Austria. Some tourists found him sticking out of a glacier as they were hiking up a mountain back in 1991.

BS: I remember. Ötzi was reportedly discovered by a pair of adventurers hiking those frozen peaks.

AA: You can just imagine how bewildered they must have been. One moment you’re admiring the beauty of a snowy mountain range, the next, you’re standing over a frozen corpse.

BS: An accident of global warming, perhaps? He was so well-preserved that they at first thought Ötzi had died recently. But it turns out they’d stumbled upon the oldest intact mummy that anyone’s ever found.

LB: He’s got all of his parts, minus a few fingernails, but he’s got all of his internal organs.

AA: That’s Lindsay Barone. She’s an anthropologist who works over at the Cold Spring Harbor Lab’s DNA Learning Center.

LB: But, more interestingly, it appears that he was murdered. And so, trying to figure out what happened, he clearly didn’t die of natural causes, so what drove that? Why was he moving around the Alps with all of his belongings? He had an axe, he had clothing, he had a first aid kit—he had all of this stuff with him. So trying to reconstruct those movements and figure out what’s going on.

AA: Lindsay knows so much about Ötzi because apart from the South Tyrol Museum in Italy—(BS: which is near where Ötzi was found)—the DNA Learning Center is the only place in the world where you can find an official Ötzi replica.

BS: “Replica” really doesn’t do it justice. It was created by using an enormous 3D printer to make a mold, which was then filled with resin and painstakingly hand-painted. The artist even got to touch the real Ötzi to make sure he got certain textures right.

KID: I saw the process on the television up there and it looked like it took a lot of work and effort. But I think it paid off because it looks really realistic.

AA: This class is one of many that has travelled to the DNA Learning Center to learn about Ötzi.

KID: Science today is so advanced that it can just get DNA out of pretty much anything.

BS: Scientists have indeed sequenced Ötzi’s DNA, and have been able to learn quite a bit about him from it.

KID: Also they can figure out everything like his eye color and his blood type, since obviously they didn’t find much blood. They could even find if he had heart disease or if he was lactose intolerant or not.

AA: But what’s really cool is that high school students also get to learn about Ötzi themselves. For one activity, they get to sequence some of their DNA—(BS: that sequence is made up of the chemical base pairs in DNA, known by their initials, A, T, C, and G)—and compare their sequences to those of their classmates, other people from around the world, and ancient humans including Neanderthals and Ötzi.

LB: So what they’re looking for is whether or not they have the same base pairs or whether those base pairs differ. And the more base pairs the students have in common with the sequence they’re comparing to, the more similar genetically they are.

BS: It makes sense. Over time, the genome accumulates a bunch of random mutations. So if you’re only very distantly related to another person or another organism, you’ll have more differences in your sequences even if you’re looking at a gene that you share.

LB: So Ötzi is very, very similar to the modern European reference sequences. A lot of students tend to be very similar to Otzi as well.

AA: When the student compare their sequences to those of Neanderthals, though, they start to see more differences. Neanderthals and humans went their separate evolutionary ways around half a million years ago, and are considered a different species than the humans that are around today.

KID: List the differences between the Neanderthal and human skulls. I feel like their skull was bigger than the human—yeah, bigger skull. And their ribcage was a little bit bigger. But they’re actually pretty similar.

BS: At the DNA Learning Center, models of human and Neanderthal skeletons stand side by side so that you can compare their physical features. And even after a half million years apart, the similarities are striking.

KID: It may seem old to us but for the history of like humans, it’s really not that old.

AA: He’s right. Half a million years isn’t all that long in evolutionary time. In fact, humans and Neanderthals weren’t even truly apart for that entire time—since they were so similar, they could and sometimes did mate with one another. Most of us even have traces of these encounters in our DNA.

LB: Modern humans that are not of recent African origin tend to have between one and four percent of their DNA from Neanderthals. Depending on the ancestry of the student or the ancestry of the individual that is being compared to the Neanderthal, there might be a few more differences or not quite as many.

BS: Our textbooks tells us that modern humans—Homo sapiens—and Neanderthals are different species, but they’re still close enough to have offspring together. Then what makes them different species?

AA: That is a very good question.

AS: So this gets at a kind of a skeleton in the closet in evolutionary thinking.

AA: That’s Adam Siepel—(AS: professor at Cold Spring Harbor Laboratory and Chair of the Simons Center for Quantitative Biology)—and I asked him that question about modern humans and Neanderthals.

AS: We don’t really know what a species is. We could argue about whether they really could be called separate species and some people indeed argue that they should all be considered members of the same species.

BS: Wow, even people who study this stuff for a living are confused about this.

AA: It can be confusing. But, all of that seemingly chaotic gene swapping—(BS: you mean mating)—yeah, all of this mating of modern humans and Neanderthals actually helped Adam and his team discover surprising new parts of the history of humankind.

AS: We found evidence of an earlier migration out of Africa, resulting in gene flow— interbreeding—between modern humans and Neanderthals some 50,000 years before people generally think of modern humans having emigrated out of Africa at all.

BS: So modern humans started out in Africa, and eventually migrated out and explored other parts of the world—that’s the famous “out of Africa” migration. And now Adam is saying that wasn’t the first time modern humans left Africa?

AA: Yep. The famous “out of Africa” migration was about 50,000 years ago, but Adam and his team found evidence that some adventurous modern humans left way earlier than that—about 100,000 years ago. And they were able to figure it out because early modern humans and a group of Siberian Neanderthals had children together around that time

BS: What kind of evidence? Ancient bones?

AA: Yes—well, Adam’s team didn’t discover the ancient bones. They just work with genomes, and they were able to get the genome of a Siberian Neanderthal from another group of scientists. Adam’s “laboratory” is essentially a collection of desktop computers in an office, connected to some very powerful supercomputers. He does experiments by gathering genome sequences and crunching numbers to compare them and learn about them.

AS: I’m also fascinated by the idea of using powerful statistical and mathematical and computational tools to sort of decode this hidden level of meaning in genome sequences to be able to get at these secret stories by being clever enough in the way we decode them.

BS: It’s kind of like that activity the kids were doing before at the DNALC, where they compared their sequences to those of Ötzi and Neanderthals to see where the base pairs differ. Adam’s work seems like that, but all grown up.

AA: Right, it’s a lot like that. So Adam and his team were working with this Siberian Neanderthal genome, and three other ancient genomes—two are from Neanderthals who lived in Europe, and one from another species of ancient human that was also living in Siberia. And they compared these ancient genomes with sequences gathered from modern humans with different ancestries.

AS: What we do is we build what we call genealogies—they’re sort of like family trees that are describing the relationships among these individuals across the genome.

BS: So Adam is building a family tree that goes back tens of thousands of years, but he’s only got a few family members within a giant family to work with. That sounds kind of impossible.

AA: It is pretty amazing. It’s important to keep in mind, though, that these family trees don’t show direct relationships between individuals, all of the mothers and fathers and children along the way. The individuals whose genomes Adam analyzed sort of served as representatives for large populations of humans.

BS: So it’s a tree that shows when different populations of humans separated from one another.

AA: Right. And they can tell how much time passed between these separation events by looking at the sizes of chunks of the genome that are similar between these individuals.

AS: We can use that as a clock when we try to date these ancient events. So, for example, your parents have fairly large chunks of DNA from your grandparents, right, but smaller chunks of DNA from your great grandparents and even smaller chunks of DNA from your great-great grandparents, and as you go back many, many generations, those chunks get smaller and smaller.

AA: When they compared the Siberian Neanderthal’s genome with those of modern humans from today, they saw something that really surprised them.

AS: We saw this strange pattern that we couldn’t explain, and that, to our knowledge, hadn’t been reported previously, indicating gene flow from modern humans into Neanderthals—(AA: meaning chunks of modern human DNA in the Neanderthal’s genome)—and affecting only this one Neanderthal sample, the one that was found in the Altai Mountains in Siberia

AA: And, the chunks of Neanderthal DNA that we see in the genomes of many modern humans today—

BS: Like what Lindsay was talking about earlier, how students with certain ancestry had more similarities to Neanderthals.

AA: Right, those are a lot bigger, on average, than the chunks of modern human DNA that Adam and his team found in this Siberian Neanderthal’s genome.

BS: Ohhhh, so that means that the encounter that left modern human DNA in the Neanderthal genome happened a lot earlier than the encounter we already knew about—the one that left little bits of Neanderthal DNA in our own genomes today.

AA: Yep. Since this unexpected genetic trace of modern humans showed up only in these Neanderthals who lived in Siberia, Adam and his team proposed that a group of early modern humans, who are now otherwise lost to history, left Africa a lot earlier than the previously know “out of Africa” migration 50,000 years ago. And that conclusion held up when Adam’s team put it to the mathematical test.

AS: These methods are quite intensive—some of our programs will run for two weeks or more on a computer cluster involving hundreds of compute nodes.

BS: But if we know that humans and Neanderthals had children together at least a couple of times, does that mean it happened many more times that we don’t know about?

AA: That we can’t say for sure. But we do know that those human-Neanderthal hybrid children went on to live among humans and Neanderthals and seemed to be accepted just fine in both communities.

AS: What I think is really interesting about our finding is that it suggests both of these events occurred. Human-Neanderthal hybrids were absorbed both by modern human and by Neanderthal populations. I think it’s very interesting, and in some ways it’s sort of encouraging about us all being one big happy family, maybe more so than people have recognized.

BS: A big, happy, human family. That is pretty encouraging.

AA: Right? I think so. The students at the DNALC pick up on this, too, when they realize how genetically related we all are.

LB: It’s one of those things that I think really helps clarify their position with respect to all of these people that came before them, with respect to other people that are living now, with respect to the Neanderthals and other species—you know, they get really excited about being able to make those connections for themselves.

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Episode 2: Corn controversy

The ongoing GMO labeling debate wasn’t the first agricultural controversy. In the early 1900s, it was a new and so-called “wicked” breeding technique that had everyone on edge.

BS: Hey y’all, I’m Brian.AA: And I’m Andrea. And last month for our super exciting pilot episode …

BS: Which, by the way, you really should check out if you haven’t already.

AA: You really should, because in that episode, we talked a lot about genes, research, and how all of that impacts us, the people.

BS: Today we’re gonna keep running with that theme, although, how we do so may surprise you.

AA: That’s because, and you might want to sit down before you hear this, today we’re going to talk about corn.

BS: Yup, corn. We’re serious, by the way. We’re going to all about the world changing research that came from our favorite kernel crop.

AA: But wait, don’t go just yet. There’s a really great story here, about mutants.

BS: And hybrids.

AA: About kings of the Midwest.

BS: And sweeping black blizzards.

AA: Do we have your attention now? Because we’re about to begin.

MB: It was the most evolutionary development that had occurred in corn culture since the prehistoric days of its discovery as a crop.

BS: That’s Milford Beeghly, and as a corn farmer, he made a bit of a name for himself in the late 1930’s. More about that later, but for now I just really want you to hear what he has to say.

MB: When word got around after 1906 that a number of scientists had explored the possibilities of a technique of exceedingly close inbreeding the result was a genetic explosion. Corn plants sow across upon themselves produced astounding mixtures of growth.

They yielded misshapen nubbins, occasional pod specimens, or throwbacks with every grain encased in a little husk, all its own and grotesque combinations of all that is good and bad in corn. We spoke of the dangers of close inbreeding as if it were wicked. Indeed orthodox agronomists called it ‘plant incest’.

BS: Hmm, plant incest. Sounds real bad, right? You definitely wouldn’t want a mouthful of incestuous corn, and yet.

AA: This is where you’re gonna tell me that I’ve been eating wicked corn all my life, isn’t it? I know how these things go.

BS: Well, it wouldn’t do to jump to conclusions. That’s why we asked Dr. Rob Martienssen to help us tell the story.

RS: The notion that plant breeding is somehow unnatural has been around for hundreds of years.

AA: Rob is a pioneering plant scientist here at the lab.

RS: I’m a plant biologist, plant geneticist, not an economic historian or anything, so I’m not an expert.

AA: But just by the virtue of being in his profession for over 25 years, he’s picked up a story or two. By the way, Rob is a Fellow of the Royal Society and an HHMI investigator in addition to being a CSHL professor.

RS: The medieval church castigated plant breeders and animal breeders for tinkering with God’s work. Thought that, you know, breeding is like a bad thing. So, there’s a long history to this.

BS: The man’s an encyclopedia of fun science facts, but we set out to talk with Rob about those scientists that farmer Beeghly spoke of earlier. The men who unwittingly turned corn so darn wicked by 1906.

AA: You just like saying that, don’t you?

BS: Yeah I kinda do. But it didn’t take all that long for this incestuous corn to shake of its bad reputation. This wicked technique actually gave rise to modern agriculture thanks to the innovative mind of one of Cold Spring Harbor Laboratory’s first scientists, a plant geneticist named George Shull.

AA: Shull was a true pioneer in his field. Actually, everyone from the field of genetics was kind of a pioneer at that time.

RS: Yeah, so I think it’s important to keep George Shull in context with his time. This was done in 1906 to 1908 and genetics itself had only just been rediscovered in 1900.

AA: Rob’s talking about the rediscovery of a paper by Gregor Mendel, the Austrian monk. In the mid 1800’s he uncovered the basic laws of genetic inheritance by breeding pea plants.

BS: When Shull was first appointed to the Carnegie Institution’s Station for Experimental Evolution …

AA: Basically just a main lab building, now our library.

BS: In 1904, word of Mendel’s work had only just resurfaced.

AA: So, inspired by the Monk and others, Shull got to work.

But breeding a plant with itself is a pretty strange thing to do. How does that even work?

BS: Well, some plants, like corn, are hermaphrodites, they have both male and female reproductive parts. In the case of corn, the top of the plant has a tassel that contains the plant’s sperm, the pollen, and the plant’s ovaries are the kernels.

AA: So I’ve been eating wicked ovaries?

BS: Hah, yeah, well I mean, yes you’ve been eating ovaries. You’ll see that this corn really wasn’t wicked at all, just bear with me.

Shull noticed as he was breeding corn plants with themselves, taking pollen from the tassels and using it to fertilize the flowers of the same plant, he noticed that this did result in some …

MB: Grotesque combinations of all that is good and bad in corn.

BS: That’s the best way to put it. Thanks Milford.

The products of this corn incest were usually weaklings. They had some good features, but they were less healthy, less fit overall. Shull was the first to notice this phenomenon, which is a really important one in plant breeding.

AA: I have to admit, though, forcing corn to propagate with itself and saying the results are weird … that doesn’t exactly sound like science.

BS: Well, Shull was extremely meticulous about his work, painstakingly recording everything his crops did. He would walk through his fields looking for star corn plants, the ones with really desirable traits like big juicy kernels and lots of them. Those were the ones that he would breed with themselves in the hopes of intensifying those good traits.

AA: But you said these crops wound up being weaklings, how can that be?

BS: When Shull was going through his fields and picking prime plants he was choosing them based on the features he could see, but there were lots of things that he couldn’t see, and those are still crucial to a plant’s survival. For example, the kernels on one plant might be extra luscious, but the same plant may not be putting enough effort into growing strong roots.

AA: Oh, so when Shull bred the plant with itself to intensify the good traits, he accidentally ended up bringing out the bad traits too.

BS: Exactly. Breeding plants with themselves basically ensures the next generation will boast not only the good traits you desire, but also the bad and ugly that come with it, in varied intensities from cob to cob.

AA: So some plants would have the size or shape that Shull desired but also wound up being particularly vulnerable to insects or disease.

BS: But Shull noticed another very important feature of those strange corn plants.

RS: So the inbreds suffered from depression, which means they look bad, right? But, if you select rare individuals each generation of inbreeding, you can effectively remove, select against some of those deleterious qualities. And if you do that enough, you will eventually get something that’s stable enough that can be propagated more or less intact every generation.

AA: It makes sense. If you only planted the seeds from better looking plants every year that helps to tip the scales toward the good traits in the population. It would take generations, but eventually, this could create a smaller gene pool that pretty much guarantees that the crop has certain desirable traits.

BS: Mm-hmm (affirmative). These corn plants were more reliable, but this wasn’t Shull’s big innovation. He still needed a way to get around the fact that when you breed a plant with itself it becomes weaker overall, even if it consistently has a good trait or two.

AA: Yeah, big juicy kernels won’t do a farmer much good if the plants are so sensitive to disease that half of them die before harvest.

BS: So, one day, Shull started a new experiment, one that was so wildly successful that it completely changed the course of agriculture. He decided to take two separate groups of these weaklings …

AA: Whose good traits he had honed through breeding with themselves …

BS: And tried breeding the two different groups with each other.

RS: In a very deliberate way, the hybrids were not only higher yielding, but they were also very uniform and really perfect for agriculture.

BS: Weak plus weak somehow added up to very strong. These hybrids had a certain vigor to them that was virtually impossible to achieve by breeding plants with themselves. Shull suspected that this was because hybrid seeds were getting only the best traits from their parents. He called this phenomenon heterosis, but today it’s commonly known by a more intuitive name: hybrid vigor.

AA: Still, if this hybrid vigor thing sounds too good to be true, it sort of is.

RS: Well a really important implication of hybrid vigor, which was immediately realized by people who were commercializing it, was that the hybrid corn, although it was wonderful in the field in the year that you planted it, if you were to collect seed from those plants and try to reproduce the same vigor in the next generation, it didn’t work. And the reason was because the genes get shuffled up again in the process of sexual reproduction. So, you can’t maintain the hybrid, you have to re-make it every year.

BS: Feed farmers wouldn’t dare set aside land just to raise inbred lines. It’s just not something most can afford, but they could afford to buy new seed every year.

RS: And that was the foundation for the hybrid seed industry because, thanks to Shull’s investigations, they knew that if they had inbreds that they could maintain and just cross them every year, then they’d be able to sell that hybrid seed every year to the farms.

AA: It was still over a decade after Shull’s work that this industry even truly saw its beginnings with a man named Henry Wallace.

He was selling hybridized seeds straight out of the back of his pickup truck for another 10 years before his company, Pioneer Hybrid, really took off.

BS: And remember Milford Beeghly? This is really where he comes into the picture. Beeghly was one of Wallace’s first customers, and in the 1930’s he even started selling his own seed.

MB: Let me introduce myself, I’m Milford Beeghly of Beeghly Best Hybrids. I just happen to be in the neighborhood and thought I’d drop in. Better order your corn now from your local dealer.

BS: That commercial was one of Beeghly’s first attempts at really getting the public’s attention, but just as Wallace did, he struggled a lot with suspicions of hybrid corn.

AA: Filmmaker Monteiths McCollum spent 7 years digging up stories and sound bytes about his grandfather, Milford Beeghly, and many of these clips show how even the tassling corn, the practice that made crossing corn possible, was viewed as ludicrous.

MB: I put it on … in the field back away from the road so people couldn’t see it very well, because whenever you detassel female rows … people had never seen that before, and they would think, “That guy’s kind of gone off his rocker a little bit.”

BS: Monteiths was kind enough to share these audio gems with us, but the culmination of his work can be seen in the award-winning film ‘Hybrid’. Visit our blog for more information.

MB: It was kind of a discouraging endeavor, but yet I had confidence that hybrid seed was the wave of the future.

AA: What I find most interesting about Beeghly is that he was a very educated man, a graduate of Iowa State College and AIMS, he was not only familiar with Shull’s work, he understood it well.

BS: His shame then was not that he questioned his own practices, but more so that he was diverging from tradition, something that the corn belt is heavily steeped in, even today.

AA: But those practices that pioneers like Beeghly and Wallace went out on a limb for, now they are tradition.

RS: Enormous fields, yeah. And every summer teenagers are employed by companies like Pioneer Hybrid to go and tear the tassels, the male flowers, off of the corn plants to make sure that they’re fertilized by the other parent of the hybrid, so it forces hybrid pollination. That’s still practiced today, not that different from how it was in the 1920’s.

BS: You have to admit, it’s a pretty big headscratcher. In 1930, the Beeghly hybrid seed corn company was nothing more than a few corn fields hidden away from narrowing eyes, but by 1950 Milford was known as the king of corn in the Midwest. No, I’m not exaggerating.

AA: And Wallace? His pioneering seed company is actually still around today, reincarnated as Dupont Pioneer, an international entity that rakes in an estimated 6 billion dollars in revenue every year.

BS: So, what happened? As the saying goes, desperate times call for desperate measures.

FDR: I shall never forget field after field of corn, stunted, earless, stripped of leaves, for what the sun left, the grasshoppers took.

BS: That’s president Franklin Delano Roosevelt, who, in 1936, visited the corn belt when it was experiencing a massive drought. The region would soon become part of what history calls ‘The Dust Bowl’, complete with massive clouds of whipped uprooted soil.

AA: See, corn and wheat crops had been literally holding the Great Plains together. With these plants withering by the acre, the soil of these farms was suddenly at the mercy of the wind. And by 1934, an estimated 350 million tons of dusty land tumbled through the Midwest skies.

BS: Many people fled from the sun scorched lands and dusty black blizzards, but as FDR put it during his fireside chat …

FDR: No cracked earth, no blistering sun, no burning wind, no grasshoppers are a permanent match for the indomitable American farmers who have carried on through desperate days and inspire us with their self-reliance, their tenacity and their courage.

BS: Sure enough, those farmers did weather the drought, dust storms, and even the Great Depression that struck during the same years.

Most untouched were the hybrid corn farmers, who, with seed bred for drought resistance, were able to press on where the skeptics had failed.

AA: The switch also just made sense to farmers who were now far more skittish about investing in a field.

RS: So, you know, when people were planting more sort of heirloom varieties of corn, from year to year they couldn’t guarantee getting the same thing. When the hybrids came along, because they were deconstructed every year in exactly the same way, they were very reproducible, and I think that helped things like crop insurance and all of these economic factors that were really important at the time.

AA: This unsung agricultural revolution also resulted in a stunning spike in corn yield. With the acceptance of hybrid seed alongside improvements in crop husbandry, the number of bushels per acre your average corn farmer can obtain has increased by nearly 8 fold since Shull made his first cross over a hundred years ago.

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Episode 1: From phages to faces

A lot has changed since DNA research first began, but the field has been filled with remarkable stories from the start. The first episode of Base Pairs tells two stories—one from each end of the timeline.

AA: Welcome to the first episode of Base Pairs, a new podcast from Cold Spring Harbor Laboratory. I’m Andrea Alfano, and my co-host Brian Stallard and I—we aren’t scientists. But we do get to spend quite a bit of time talking to scientists around the Lab.

BS: When you sit down and talk with a scientist, you get to hear about all of the stuff that academic journals usually leave out: stories of the remarkable lengths scientists go to make discoveries, the way they felt when they first saw an important result, the relationships they formed through their scientific endeavors, the sparks that ignited their curiosity…

AA: This podcast is a way for us to share these stories with you. Some of them will be about recent discoveries, some will be historical…

BS: …some will reveal insights about the brain or the body while others will delve into ideas for protecting our planet.

AA: But they will all be rooted in one magical family of molecules: nucleic acids, the molecules that make life possible.

BS: Nucleic acid is what the N-A in DNA stands for.

AA: And DNA… well that’s the blueprint for life! It’s how cells know what proteins to make, what structures to form, which cells go where.

BS: All of this is dictated by that essential little molecule. But curiously enough, even a year before James Watson and Francis Crick announced their discovery of the double helix, scientists were still arguing about whether DNA was in-fact the incredible blueprint we now know it is.

AA: In the early 1950s, there was a clear divide among experts. On one side were the scientists who saw DNA for what it was: this seemingly modest molecule that somehow wields the power to pass information from one generation to next.

BS: Then there was the other camp: experts who looked at DNA- this large yet simple molecule that’s essentially just the same four ‘letters,’ or bases, strung together, and thought, “there’s no way! it’s too simple!”

AA: This latter group even went as far as to call DNA the “stupid molecule.” They argued that proteins, which have incredibly complex structures, were the master molecules behind genetics.

BS: “Stupid molecule!” That’s pretty harsh. You’d expect such polar groups to be at each other’s throats–

AA: But apparently most academics at the time were just thrilled to be part of a new and exciting field.

FS: The idea that you could understand Gregor Mendel’s wonderful data at the level of a molecule was—entrancing.

AA: That’s Frank Stahl,

FS: Professor of biology emeritus at the University of Oregon.

AA: He’s the Stahl in the famous Meselson-Stahl experiment you may remember from your high school biology textbook – which was a major contribution to understanding how DNA replicates.

BS: and he’s talking about Mendel… the “father of Genetics,” Mendel – the guy who used peas to show the world that heredity followed strict rules.

BS: In 1952, Frank was just a wide-eyed graduate student newly arrived at Cold Spring Harbor Laboratory.

FS: I said, “Well, my boss wanted to get rid of me for the summer so he shipped me down here!”

AA: That’s what Frank told people anyway. His thesis advisor had actually sent him to work in the kitchen at the Lab, but he was quickly enamored with the science that was going on… (music cut in) not to mention the party life.

FS: Hey, I don’t remember an awful lot about that summer, I’ll have to tell you, because it was a pretty wild summer. But I do remember that I was convinced that I had to work in that field.

BS: [Laughs] This is kind of hard to believe, really. Scientific greats gallivanting around the harbor by night, making world-changing discoveries by day – even while still nursing their hangovers.

FS: Uhhh, let’s not go any further with that.

AA: (in phone call recording) That’s fair!

AA: Still, Frank does remember that there was cause for celebration that summer. Remember that big debate we mentioned earlier? Protein vs. DNA? Someone had all but settled it.

FS: People there were talking about the experiment. People were pleased, impressed, and considered it real progress.

AA: He’s talking about the famous experiment conducted by Al Hershey and Martha Chase – one of the final nails in the coffin for the theory that protein carried genetic information.

BS: So what was this experiment? Put simply, the researchers put a bunch of bacteria in a blender… and what came out was strong evidence that DNA carried the blueprints for life.

AA: Isn’t that a bit TOO simple?

BS: Sure, but that was kind of the beauty of this experiment. Modern scientists have come to call it Hershey Heaven if you have an experiment that not only works, but you can do every day.

AA: Let’s maybe break it down a little more.

BS: Alright, let’s!

AA: Alright, listeners, meet the bacteriophage – a type of virus that turns bacteria into its own personal factories.

BS: Today, we know that these little critters physically inject DNA into their victims, hijacking the bacteria’s machinery to produce more phages.

AA: Phages are what scientists call bacteriophages for short – viruses that make a living by infecting bacteria. Anyway, phages have to take over bacteria because, like other viruses, they aren’t exactly living. They’re just a protein shell with DNA inside, and that’s it. They don’t have the rest of the stuff they need to reproduce, so they sneak into bacteria and steal theirs.

BS: It’s like if Skynet had to enslave humans to make more terminators. Like that.

AA: Uh… Sure? But back in the 1950s, it wasn’t clear how exactly phages hijacked their victims. All experts knew was that this little virus –

BS: It looks a lot like a turkey baster with robotic legs –

AA: Ok, they knew this turkey baster would latch onto the outside of a bacteria cell and a little later, dozens of new phages could be found within.

BS: Frank—like Jim Watson before him—wound up taking a course on phages during his summer at the Lab, and he quickly learned why they were ideal for study.

FS: Phages could multiply, mutate, segregate their genes, genetically recombine—they could do everything, it seemed, that higher organisms could do when it came to the transmission of hereditary material.

BS: And, as we mentioned before, they are also made of just protein and DNA. No other organism yet discovered was so perfectly designed to settle the genetic molecule debate.

AA: Hershey and Chase were also well aware of this, and that’s why they chose to work with these simple phage viruses. They designed two tags—one to mark the phages’ protein and the other for their DNA.

AA: They theorized that if one of those molecular tags also wound up inside the bacteria… that would indicate which molecule was providing the blueprint for the new phage babies.

BS: Still, there was one hitch to this plan: parent phages latch securely onto outside of their bacterial victims, which means some tags were present outside of the bacteria. But Hershey and Chase were only interested in what wound up INSIDE. So the scientists designed an elegant solution. They used a blender.

(blender sounds)

AA: Normally when I think of lab equipment, I envision fancy microscopes, test tubes, super-specialized machines that I have know idea what they could even possibly do. But that’s not what this was.

BS: That’s right. Hershey and Chase dumped all their hard work into a metal Waring blender—hardly different that your standard kitchen blender—and hit the power button.

BS: But they weren’t making a smoothie. The blending dislodged and separated the phage shells from the infected bacteria. When they then looked inside these bacteria, they saw a whole lot of DNA tag and hardly any protein tag. It was really compelling evidence that DNA was the blueprint a phage factory needs.

AA: Hershey and Chase published their work in April of 1952, just before the start of the summer phage course. Perfect opportunity to party, you’d think. But unlike the rest of the Lab, that just wasn’t their style.

(ocean sounds)

FS: He spent his summers sailing on Lake Superior, I think.

BS: that’s Frank again, remembering Hershey.

FS: In that way, he escaped the summer crowds, got genuine rest away from the laboratory, because when he was at the Cold Spring Harbor, he was a compulsive worker. He worked two sessions each day: he worked from early morning ‘til lunch, then he went home and took a nap, then he came back and worked on into the night, day after day.

BS: This is not to say that you can’t be fun-loving to do great research. Plenty of other scientific greats have been known as the life of the party.

AA: Still, many will argue that it was Hershey’s reserved nature and penchant for detail that helped him craft such an elegant experiment. And as for Martha Chase, she shared this understated nature.

FS: She was a rather shy person, reticent, not easy to converse with [BS: Kind of like Hershey in that regard?] Indeed, but a nice person.

BS: And I know what you’re all wondering: “what about that third celebrity? The blender that changed the field of genetics as we know it!” Well according to biologist Gerry Rubin, somehow even it eschewed the limelight.

GR: When I was in Ray Gesteland’s lab I needed a blender. And he said to go to the shed and look if there are any blenders there. And I actually came back with this little metal blender. And he said, oh, my god. This is the blender from the Hershey-Chase experiment! For the next four years this blender sat on Ray Gesteland’s desk with his pencils in it as his pencil holder, and then finally I guess it went to the museum.

AA: The blender is indeed in CSHL’s Archives now. Hershey and Chase may not have been the type to boast about their work, but CSHL is certainly proud to have them in its history.

BS: It’s been about 65 years since the Hershey-Chase experiment—65 years since the big question in biology was “how in the world is genetic information passed from generation to generation?” And now, scientists are able to take basic scientific insights about genetic inheritance and answer really specific questions like, ‘how did these two boys from Utah inherit a severely disabling disorder that no one else in the family has?’

AA: As you might suspect, we didn’t pull that last question completely out of nowhere. We know someone who asked it—and amazingly, was able to answer it.

GL: My name is Gholson Lyon, I work here at the Lab, Cold Spring Harbor Laboratory, I’m on faculty here in genetics—and yes, I am a child and adolescent and adult psychiatrist.

AA: That’s our friend Gholson, and he’s spent the last decade not only investigating harmful mutations, but also getting to know the people who are affected by them.

GL: Many people that are doing genetics research… they’ve never really interacted longitudinally… with patients—you know, people that have real disease.

BS: Real patients, like a pair of disabled brothers–

AA: Ryker and Daxton, 15 and 13 respectively

BS: —who Gholson had the pleasure of meeting back in 2006.

(cut to recording of Gholson with patients)

GL: All right Heyyyy Ryker how are you?

(Dax makes noise)

GL: Can I see your palm like that for me?

JL: Flip your hand over… oh! Look at that!

(JL/Daxton/Ryker: Wooooow!)

AA: And something about them – well a lot of things, actually ¬– caught Gholson’s attention right away.

GL: These boys have very severe intellectual disabilities, trouble walking, their gait is a little bit off, cramping in their muscles, very odd facial features, problems with their ears, hyperactive…

BS: All tell-tale signs of one or many genetic disorders. Just… no one was sure which.

JL: Can you pick that up for mom? Hand it to mom?

(Child succeeds this time with a pleased sound)

JL: That’s better than he normally does it.

AA: That’s Jalene Lee, Ryker and Daxton’s mother, and she’s a pretty incredible person.

JL: I was introduced to Dr Lyon through Alan Rope, he works at the University of Utah through their genetic department and felt like we would be good candidates to sort of push forward with genetics testing.

GL: Do they ever lock their legs when they walk at all? Or is this about how they always walk?

JL: It’s pretty average.

(walking sounds in the park)

AA: They would plan meetings – sometimes in an office, sometimes at a park, and Gholson would just… get to know them… all the time taking notes and video.

GL: And neither one of them has ever said a word, right?

JL: Ummm, Daxton does some voice inflection – kind of imitates words. And Ryker, about the only thing he can say is “mom.”

(cuts back to interview)

JL: I mean, their personalities are different because they are two different children, but their disabilities themselves—it was kind ok one of those things where we said, “ok, so there is definitely some sort of genetic basis.” And we just sort of proceeded from there.

BS: Ok sooo everybody’s got 46 chromosomes… that’s 23 pairs?

AA: 23 for us humans, anyway.

BS: Right. But there’s one pair in particular that really separates us guys and gals. They’re often called the “sex chromosomes”

GL: In males, you have both an X chromosome and a Y chromosome and in females you have two X chromosomes.

And in boys of course, of course they only have one X chromosome so there’s only one X chromosome being expressed. In women, they have this thing called dosage compensation where one of the X chromosomes is randomly inactivated.

BS: Basically, the genome is protecting itself. You know, “compensating” because too much X chromosome can kill a cell.

AA: And Gholson knew that when one X is carrying a harmful mutation, that X is more likely to be turned off.

BS: It’s a lot like a second line of defense that guys just don’t have, since instead of having two X chromosomes, we have an X and a Y.

GL: In this family, with the mother, we—we speculated that because this was in the two boys that it might be on the X chromosome

AA: Gholson ended up doing something called an GL: X chromosome skewing analysis AA: which is essentially a blood test of the mother that shows which copy of the X got shut off.

BS: In a typical woman, you’d expect to see a 50:50 ratio. And yet, when Gholson tested the Lee family, a rare 99:1 ratio turned up in Jalene.

AA: It seemed that for some reason, her cells were strongly favoring one X over the other.

GL: We still don’t know which of the genes, which of the chromosomes was being expressed, um, but we kind of assume that because it’s 99 percent that probably the skewing was favoring the copy that does not have the mutation on it. So we ended up conjecturing that maybe that this was an X chromosome linked disorder between the two boys

BS: And that’s it, right? He looked at the X and found what was wrong?

AA: Well, not exactly.

GL: So, we ended up doing whole genome sequencing in that family because I wanted to make sure that we didn’t miss something that was not on the X chromosome.

AA: Basically, the odds were that there was something wrong on the X. But that didn’t rule out the possibility of troublesome mutations on the other 22 chromosomes.

BS: What did they find?

AA: TAF1.

BS: That’s T-A-F and the number 1?

AA: Exactly. Ryker and Daxton both had the same mutation in this gene called TAF1 which was right where Gholson expected it to be.

BS: On the X.

AA: And, it was the only meaningful mutation shared between these two brothers.

BS: But wait… you’re saying that a mutation in this one gene hinders development in the brain, the body… everything?

AA: Yeah, TAF1 influences how cells read information in the rest of the genome, and so any trouble with it can cause a cascade of problems. Think about it like a traffic accident.

BS: So, a mutation of a less important gene would sort of be like a fender bender on a side street. It could slow some things down, but you’re probably getting to work on time.

AA: Right. But a mutation in TAF1 could be like a major collision on a highway.

BS: Everyone’s going to be late.

AA: Or, in Ryker and Daxton’s case, that means global developmental delay.

BS: And that’s it, isn’t it? Now we can say for sure what’s causing this disease.

AA: Not quite. The problem was that Gholson only had the case of the Lee brothers to work with.

BS: And in science, a sample size of just two… that doesn’t cut it.

AA: So, he started searching

GL: Going to mini conferences…putting up posters…giving talks…I would meet with other medical geneticists and I would show them the pictures of the boys and ask them if they had seen anything like this before.

BS: In the end, and we’re talking about years of searching here, Gholson and his colleagues identified a whopping 14 cases world-wide

AA: It’s amazing that’s all they found.

BS: But you’ve got to remember… this is but one mutation in the estimated 20,000 or-so protein-coding genes humans have.

AA: And it’s important to note: this is a diagnosis, not a cure. It isn’t going to solve Ryker and Daxton’s problems, and it’s not even going to solve all of Jalene’s problems.

JL: When I say “They have global developmental delay and TAF1 gene mutation” people look at me and go, “well, what the hell does that mean?”

BS: I recently spoke with Jalene, and she made me realize that the fact that her boys’ syndrome is undefined… it makes getting help all the more difficult.

JL: You know, Down syndrome families get to discuss certain things and autism families deal with certain things and they’re able to bounce ideas off of each other and to be honest I feel kind of alone in my situation, because nobody exactly understand what it is that we’re going through… and it’s almost as if they’re not even accepted without some sort of a name.

BS: Jalene even resorted to calling her boys’ disease RykDax, a combination of their names, Ryker and Daxton.

JL: We’ll get people that are like, “can I ask you what they have?”—“I don’t know.” And they look at me funny almost like I don’t even care to know, type of scenario…And from there it just kind of stuck that they have “RykDax disease.” And, you know, people kind of settle down and are like “oh, ok!” Like that makes sense. And I don’t know why it makes sense but… it’s fine and that’s just kind of how we’ve dealt.

AA: That’s how they’ve dealt, but now that impromptu name may become an official part of medical texts across the world.

GL: You know… you and I have talked about trying to name this syndrome after the two boys so, in the current paper we have down that we’re thinking about calling it RykDax Syndrome — (spells it out)

JL: Absolutely. Yes.

AA: The thing is, while a name might seem pretty arbitrary, it gives people a way to come together and talk about the disease for the first time.

GL: What I’m hoping is that the families will now start to communicate with each other more through maybe social media like Facebook and maybe they’ll begin to get a better idea of the natural course of the illness.

BS: And that’s an important point. Gholson and his colleagues kept the Lee family in the loop even as they went on to discover other cases of RykDax. And learning about these patients has given Jalene some peace of mind about Ryker and Daxton’s futures.

JL: We’re ready to go. In whatever direction life takes us, whether something to do with this disease that they have affects it or not, you know, our path is there and we just need to move forward and while we still have them maybe we can help someone else.

BS: It’s a forward-looking perspective, Jalene’s. And it’s one that Gholson hopes other families will share.

AA: Every test, every grain of knowledge, is just another step towards a better future for those affected by this disease.

GL: This is just a small piece of the puzzle. You know, there’s so much more that needs to be done in terms of trying to figure out if there’s anything that we can do to help the children.

JL: The long—super long—story is that I’m happy that the boys are here and that we are able to help.

BS: Well, that’s it! Our first episode, done.

JL: Sorry for my little rant (laughing).

FS: Well I think I’ve told it all. Thanks. Bye bye.

GL: Thank you very much for having me on this podcast.

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