Backyard Brains: Affordable neuroscience

Mouse neurons. Image via Wikimedia Commons.
Originally published in PLoS Biology.

Nerve cells, called neurons, are special cells. They interact with each other and with other tissues in part by using electrical impulses. The cool thing about these cells is that thanks to their electrical signaling, we can measure when they’re sending their messages. A neuroscientist friend of mine once poetically described as “exquisite” the ability to measure the firing of a single neuron in a finch brain. There is something special about being able to observe that usually hidden process of signaling that underlies every move you make, every thought you have, and every sensation you detect.

The very word “neuroscience” sounds expensive. Measuring the signaling of nerves? That sounds pretty fancy. But with some wires and basic neuroscience tools, anyone can give it a try, measuring the nerve signaling, for example, in an insect. Which, do you think, would be the more memorable learning experience, a full-on sensory exposure to the sights and sounds of neuron signaling, or this? 


Now, a company called Backyard Brains is really bringing the neuroscience to the people. You don’t have to use their affordable kits in your backyard, but as neuroscientist and writer Mo Costandi highlights today in an interview with Tim Marzullo, co-founder of Backyard Brains, this level of technology can become available to high-school students anywhere. In the interview, Marzullo notes that the goal is to produce kits that lower the fiscal and resource requirements for making neuroscience available to people who aren’t graduate students in neuroscience.

As part of their bringing the neuroscience to the people, the Backyard Brains scientists have created the Spiker Box kit, which lets students listen to neurons firing in a de-legged cockroach. These kits are friendly with computers, iPhones, and iPads, so students can use these devices to record and listen to the Zzzzzzztt! of a firing neuron (see video below). Electrophysiology in action, made accessible. 


An even fancier introduction to science awaits. Some proteins are especially made to change their shape in response to a light trigger. Scientists have produced animals–mostly fruit flies–that make these proteins in some neurons, where they don’t usually occur. With light-reactive proteins present in the neurons, researchers can actually make the neurons fire by giving them a shot of laser light. In other words, they can make the animals move using light. Wouldn’t it be cool if classroom students could see that kind of neuroscience in action?

Backyard Brains is on the case. They’re working on a product that will allow students to use blue light emitted from an iPad to trigger light-reactive proteins in nerves that communicate with muscle cells. Because the process involves light and organisms with introduced genes, it’s called optogenetics. That sounds even more swanky than neuroscience, but Backyard Brains is working on making it accessible.

Other Backyard Brains products include RoboRoach (you’ll have to read that one for yourself), soldering kits, and the roaches themselves

Emily Willingham

Anorexia nervosa, neurobiology, and family-based treatment

Via Wikimedia Commons
Photo credit: Sandra Mann
By Harriet Brown, DXS contributor

Back in 1978, psychoanalyst Hilde Bruch published the first popular book on anorexia nervosa. In The Golden Cage, she described anorexia as a psychological illness caused by environmental factors: sexual abuse, over-controlling parents, fears about growing up, and/or other psychodynamic factors. Bruch believed young patients needed to be separated from their families (a concept that became known as a “parentectomy”) so therapists could help them work through the root issues underlying the illness. Then, and only then, patients would choose to resume eating. If they were still alive.

Bruch’s observations dictated eating-disorders treatments for decades, treatments that led to spectacularly ineffective results. Only about 35% of people with anorexia recovered; another 20% died, of starvation or suicide; and the rest lived with some level of chronic illness for the rest of their lives.

Not a great track record, overall, and especially devastating for women, who suffer from anorexia at a rate of 10 times that of men. Luckily, we know a lot more about anorexia and other eating disorders now than we did in 1978.

“It’s Not About the Food”

In Bruch’s day, anorexia wasn’t the only illness attributed to faulty parenting and/or trauma. Therapists saw depression, anxiety, schizophrenia, eating disorders, and homosexuality (long considered a psychiatric “illness”) as ailments of the mind alone. Thanks to the rising field of behavioral neuroscience, we’ve begun to untangle the ways brain circuitry, neural architecture, and other biological processes contribute to these disorders. Most experts now agree that depression and anxiety can be caused by, say, neurotransmitter imbalances as much as unresolved emotional conflicts, and treat them accordingly. But the field of eating-disorders treatment has been slow to jump on the neurobiology bandwagon. When my daughter was diagnosed with anorexia in 2005, for instance, we were told to find her a therapist and try to get our daughter to eat “without being the food police,” because, as one therapist informed us, “It’s not about the food.”

Actually, it is about the food. Especially when you’re starving.

Ancel Keys’ 1950 Semi-Starvation Study tracked the effects of starvation and subsequent re-feeding on 36 healthy young men, all conscientious objectors who volunteered for the experiment. Keys was drawn to the subject during World War II, when millions in war-torn Europe – especially those in concentration camps – starved for years. One of Keys’ most interesting findings was that starvation itself, followed by re-feeding after a period of prolonged starvation, produced both physical and psychological symptoms, including depression, preoccupation with weight and body image, anxiety, and obsessions with food, eating, and cooking—all symptoms we now associate with anorexia. Re-feeding the volunteers eventuallyreversed most of the symptoms. However, this approach proved to be difficult on a psychological level, and in some ways more difficult than the starvation period. These results were a clear illustration of just how profound the effects of months of starvation were on the body and mind.

Alas, Keys’ findings were pretty much ignored by the field of eating-disorders treatment for 40-some years, until new technologies like functional magnetic resonance imaging (fMRI) and research gave new context to his work. We now know there is no single root cause for eating disorders. They’re what researchers call multi-factorial, triggered by a perfect storm of factors that probably differs for each person who develops an eating disorder. “Personality characteristics, the environment you live in, your genetic makeup—it’s like a cake recipe,” says Daniel le Grange, Ph.D., director of the Eating Disorders Program at the University of Chicago. “All the ingredients have to be there for that person to develop anorexia.”

One of those ingredients is genetics. Twenty years ago, the Price Foundation sponsored a project that collected DNA samples from thousands of people with eating disorders, their families, and control participants. That data, along with information from the 2006 Swedish Twin Study, suggests that anorexia is highly heritable. “Genes play a substantial role in liability to this illness,” says Cindy Bulik, Ph.D., a professor of psychiatry and director of the University of North Carolina’s Eating Disorders Program. And while no one has yet found a specific anorexia gene, researchers are focusing on an area of chromosome 1 that shows important gene linkages.

Certain personality traits associated with anorexia are probably heritable as well. “Anxiety, inhibition, obsessionality, and perfectionism seem to be present in families of people with an eating disorder,” explains Walter Kaye, M.D., who directs the Eating Disorders Treatment and Research Program at the University of California-San Diego. Another ingredient is neurobiology—literally, the way your brain is structured and how it works. Dr. Kaye’s team at UCSD uses fMRI technology to map blood flow in people’s brains as they think of or perform a task. In one study, Kaye and his colleagues looked at the brains of people with anorexia, people recovered from anorexia, and people who’d never had an eating disorder as they played a gambling game. Participants were asked to guess a number and were rewarded for correct guesses with money or “punished” for incorrect or no guesses by losing money.

Participants in the control group responded to wins and losses by “living in the moment,” wrote researchers: “That is, they made a guess and then moved on to the next task.” But people with anorexia, as well as people who’d recovered from anorexia, showed greater blood flow to the dorsal caudate, an area of the brain that helps link actions and their outcomes, as well as differences in their brains’ dopamine pathways. “People with anorexia nervosa do not live in the moment,” concluded Kaye. “They tend to have exaggerated and obsessive worry about the consequences of their behaviors, looking for rules when there are none, and they are overly concerned about making mistakes.” This study was the first to show altered pathways in the brain even in those recovered from anorexia, suggesting that inherent differences in the brain’s architecture and signaling systems help trigger the illness in the first place.

Food Is Medicine

Some of the best news to come out of research on anorexia is a new therapy aimed at kids and teens. Family-based treatment (FBT), also known as the Maudsley approach, was developed at the Maudsley Hospital in London by Ivan Eisler and Christopher Dare, family therapists who watched nurses on the inpatient eating-disorders unit get patients to eat by sitting with them, talking to them, rubbing their backs, and supporting them. Eisler and Dare wondered how that kind of effective encouragement could be used outside the hospital.

Their observations led them to develop family-based treatment, or FBT, a three-phase treatment for teens and young adults that sidesteps the debate on etiology and focuses instead on recovery. “FBT is agnostic on cause,” says Dr. Le Grange. During phase one, families (usually parents) take charge of a child’s eating, with a goal of fully restoring weight (rather than get to the “90 percent of ideal body weight” many programs use as a benchmark). In phase two, families gradually transfer responsibility for eating back to the teen. Phase three addresses other problems or issues related to normal adolescent development, if there are any.

FBT is a pragmatic approach that recognizes that while people with anorexia are in the throes of acute malnourishment, they can’t choose to eat. And that represents one of the biggest shifts in thinking about eating disorders. The DSM-IV, the most recent “bible” of psychiatric treatment, lists as the first symptom of anorexia “a refusal to maintain body weight at or above a minimally normal weight for age and height.” That notion of refusal is key to how anorexia has been seen, and treated, in the past: as a refusal to eat or gain weight. An acting out. A choice. Which makes sense within the psychodynamic model of cause.

But it doesn’t jibe with the research, which suggests that anorexia is more of an inability to eat than a refusal. Forty-five years ago, Aryeh Routtenberg, then (and still) a professor of psychology at Northwestern University, discovered that when he gave rats only brief daily access to food but let them run as much as they wanted on wheels, they would gradually eat less and less, and run more and more. In fact, they would run without eating until they died, a paradigm Routtenberg called activity-based anorexia (ABA). Rats with ABA seemed to be in the grip of a profound physiological imbalance, one that overrode the normal biological imperatives of hunger and self-preservation. ABA in rats suggests that however it starts, once the cycle of restricting and/or compulsive exercising passes a certain threshold, it takes on a life of its own. Self-starvation is no longer (if it ever was) a choice, but a compulsion to the death.

That’s part of the thinking in FBT. Food is the best medicine for people with anorexia, but they can’t choose to eat. They need someone else to make that choice for them. Therapists don’t sit at the table with patients, but parents do. And parents love and know their children. Like the nurses at the Maudsley Hospital, they find ways to get kids to eat. In a sense, what parents do is outshout the anorexia “voice” many sufferers report hearing, a voice in their heads that tells them not to eat and berates them when they do. Parents take the responsibility for making the choice to eat away from the sufferer, who may insist she’s choosing not to eat but who, underneath the illness, is terrified and hungry.

The best aspect of FBT is that it works. Not for everyone, but for the majority of kids and teens. Several randomized controlled studies of FBT and “treatment as usual” (talk therapy without pressure to eat) show recovery rates of 80 to 90 percent with FBT—a huge improvement over previous recovery rates. A study at the University of Chicago is looking at adapting the treatment for young adults; early results are promising.

The most challenging aspect of FBT is that it’s hard to find. Relatively few therapists in the U.S. are trained in the approach. When our daughter got sick, my husband and I couldn’t find a local FBT therapist. So we cobbled together a team that included our pediatrician, a therapist, and lots of friends who supported our family through the grueling work of re-feeding our daughter. Today she’s a healthy college student with friends, a boyfriend, career goals, and a good relationship with us.

A few years ago, Dr. Le Grange and his research partner, Dr. James Lock of Stanford, created a training institute that certifies a handful of FBT therapists each year. (For a list of FBT providers, visit the Maudsley Parents website.) It’s a start. But therapists are notoriously slow to adopt new treatments, and FBT is no exception. Some therapists find FBT controversial because it upends the conventional view of eating disorders and treatments. Some cling to the psychodynamic view of eating disorders despite the lack of evidence. Still, many in the field have at least heard of FBT and Kaye’s neurobiological findings, even if they don’t believe in them yet.

Change comes slowly. But it comes.

* * *

Harriet Brown teaches magazine journalism at the S.I. Newhouse School of Public Communications in Syracuse, New York. Her latest book is Brave Girl Eating: A Family’s Struggle with Anorexia (William Morrow, 2010).

be there for that person to develop anorexia.”

One of those ingredients is genetics. Twenty years ago, the Price Foundation sponsored a project that collected DNA samples from thousands of people with eating disorders, their families, and control participants. That data, along with information from the 2006 Swedish Twin Study, suggests that anorexia is highly heritable. “Genes play a substantial role in liability to this illness,” says Cindy Bulik, Ph.D., a professor of psychiatry and director of the University of North Carolina’s Eating Disorders Program. And while no one has yet found a specific anorexia gene, researchers are focusing on an area of chromosome 1 that shows important gene linkages.
Certain personality traits associated with anorexia are probably heritable as well. “Anxiety, inhibition, obsessionality, and perfectionism seem to be present in families of people with an eating disorder,” explains Walter Kaye, M.D., who directs the Eating Disorders Treatment and Research Program at the University of California-San Diego. Another ingredient is neurobiology—literally, the way your brain is structured and how it works. Dr. Kaye’s team at UCSD uses fMRI technology to map blood flow in people’s brains as they think of or perform a task. In one study, Kaye and his colleagues looked at the brains of people with anorexia, people recovered from anorexia, and people who’d never had an eating disorder as they played a gambling game. Participants were asked to guess a number and were rewarded for correct guesses with money or “punished” for incorrect or no guesses by losing money.
Participants in the control group responded to wins and losses by “living in the moment,” wrote researchers: “That is, they made a guess and then moved on to the next task.” But people with anorexia, as well as people who’d recovered from anorexia, showed greater blood flow to the dorsal caudate, an area of the brain that helps link actions and their outcomes, as well as differences in their brains’ dopamine pathways. “People with anorexia nervosa do not live in the moment,” concluded Kaye. “They tend to have exaggerated and obsessive worry about the consequences of their behaviors, looking for rules when there are none, and they are overly concerned about making mistakes.” This study was the first to show altered pathways in the brain even in those recovered from anorexia, suggesting that inherent differences in the brain’s architecture and signaling systems help trigger the illness in the first place.
Food Is Medicine
Some of the best news to come out of research on anorexia is a new therapy aimed at kids and teens. Family-based treatment (FBT), also known as the Maudsley approach, was developed at the Maudsley Hospital in London by Ivan Eisler and Christopher Dare, family therapists who watched nurses on the inpatient eating-disorders unit get patients to eat by sitting with them, talking to them, rubbing their backs, and supporting them. Eisler and Dare wondered how that kind of effective encouragement could be used outside the hospital.
Their observations led them to develop family-based treatment, or FBT, a three-phase treatment for teens and young adults that sidesteps the debate on etiology and focuses instead on recovery. “FBT is agnostic on cause,” says Dr. Le Grange. During phase one, families (usually parents) take charge of a child’s eating, with a goal of fully restoring weight (rather than get to the “90 percent of ideal body weight” many programs use as a benchmark). In phase two, families gradually transfer responsibility for eating back to the teen. Phase three addresses other problems or issues related to normal adolescent development, if there are any.
FBT is a pragmatic approach that recognizes that while people with anorexia are in the throes of acute malnourishment, they can’t choose to eat. And that represents one of the biggest shifts in thinking about eating disorders. The DSM-IV, the most recent “bible” of psychiatric treatment, lists as the first symptom of anorexia “a refusal to maintain body weight at or above a minimally normal weight for age and height.” That notion of refusal is key to how anorexia has been seen, and treated, in the past: as a refusal to eat or gain weight. An acting out. A choice. Which makes sense within the psychodynamic model of cause.
But it doesn’t jibe with the research, which suggests that anorexia is more of an inability to eat than a refusal. Forty-five years ago, Aryeh Routtenberg, then (and still) a professor of psychology at Northwestern University, discovered that when he gave rats only brief daily access to food but let them run as much as they wanted on wheels, they would gradually eat less and less, and run more and more. In fact, they would run without eating until they died, a paradigm Routtenberg called activity-based anorexia (ABA). Rats with ABA seemed to be in the grip of a profound physiological imbalance, one that overrode the normal biological imperatives of hunger and self-preservation. ABA in rats suggests that however it starts, once the cycle of restricting and/or compulsive exercising passes a certain threshold, it takes on a life of its own. Self-starvation is no longer (if it ever was) a choice, but a compulsion to the death.
That’s part of the thinking in FBT. Food is the best medicine for people with anorexia, but they can’t choose to eat. They need someone else to make that choice for them. Therapists don’t sit at the table with patients, but parents do. And parents love and know their children. Like the nurses at the Maudsley Hospital, they find ways to get kids to eat. In a sense, what parents do is outshout the anorexia “voice” many sufferers report hearing, a voice in their heads that tells them not to eat and berates them when they do. Parents take the responsibility for making the choice to eat away from the sufferer, who may insist she’s choosing not to eat but who, underneath the illness, is terrified and hungry.
The best aspect of FBT is that it works. Not for everyone, but for the majority of kids and teens. Several randomized controlled studies of FBT and “treatment as usual” (talk therapy without pressure to eat) show recovery rates of 80 to 90 percent with FBT—a huge improvement over previous recovery rates. A study at the University of Chicago is looking at adapting the treatment for young adults; early results are promising.
The most challenging aspect of FBT is that it’s hard to find. Relatively few therapists in the U.S. are trained in the approach. When our daughter got sick, my husband and I couldn’t find a local FBT therapist. So we cobbled together a team that included our pediatrician, a therapist, and lots of friends who supported our family through the grueling work of re-feeding our daughter. Today she’s a healthy college student with friends, a boyfriend, career goals, and a good relationship with us.
A few years ago, Dr. Le Grange and his research partner, Dr. James Lock of Stanford, created a training institute that certifies a handful of FBT therapists each year. (For a list of FBT providers, visit the Maudsley Parents website.) It’s a start. But therapists are notoriously slow to adopt new treatments, and FBT is no exception. Some therapists find FBT controversial because it upends the conventional view of eating disorders and treatments. Some cling to the psychodynamic view of eating disorders despite the lack of evidence. Still, many in the field have at least heard of FBT and Kaye’s neurobiological findings, even if they don’t believe in them yet.
Change comes slowly. But it comes.
* * *
Harriet Brown teaches magazine journalism at the S.I. Newhouse School of Public Communications in Syracuse, New York. Her latest book is Brave Girl Eating: A Family’s Struggle with Anorexia (William Morrow, 2010).

Biology Explainer: The big 4 building blocks of life–carbohydrates, fats, proteins, and nucleic acids

The short version
  • The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
  • Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
  • Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
  • Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.                                                                                                      
  • The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.

                                                  

Big Molecules with Small Building Blocks

The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.

We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
Carbohydrates

You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.

When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.

Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.

The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.

Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.

On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.

The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!

If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.

The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?

If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.

In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.

Sugar and Fuel

A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.

Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.

Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.

Polysaccharides: Fuel and Form

Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.

Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.

Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.

Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.

The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.

Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.

The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.

That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.

These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.

Lipids: The Fatty Trifecta

Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.

Fats: the Good, the Bad, the Neutral

Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?

Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows.  Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.

Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.

Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.

Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.

The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.

You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.

In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.

A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.

Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.

Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.

Phospholipids: An Abundant Fat

You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.

Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.

There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.

Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.

The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.

Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.

Steroids: Here to Pump You Up?

Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.

But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.

Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.

Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.

Proteins

As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.

Levels of Structure

Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.

For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.

This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.

Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.

The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.

In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.

A Plethora of Purposes

What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.

As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.

Nucleic Acids

How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.

Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.

DNA vs. RNA: A Matter of Structure

DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.

So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.

RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.

DNA vs. RNA: Function Wars

An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.

These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.

RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.


 By Emily Willingham, DXS managing editor 
This material originally appeared in similar form in Emily Willingham’s Complete Idiot’s Guide to College Biology

Sesame Street helps unlock the secrets to the brain during children’s learning

By Tara Haelle, Health Editor
[This post appeared previously at Red Wine and Apple Sauce.]

Looking to let go of a little “mommy guilt” for using the television now and then to give yourself a breather? There may be plenty of evidence that leaving children to watch too much television is a bad idea, but there is something to the idea that educational TV is, well, educational. We have the brain scans to prove it!

A study published in PLOS Biology used functional MRI scans to check out the brains of 26 children and 20 adults while they watched 20 minutes of Sesame Street. The actual purpose of the study wasn’t to find out if Sesame Street was educational per se. Rather, it was to observe the neural processes in the brain while a child is learning “naturalistically” and then see whether what they saw could predict how well the children would perform on standardized IQ tests.

Often, participants in studies receive fMRI scans while they are doing some sort of task that is supposed to simulate learning and/or stimulate certain neural processes. For example, a study subject might be asked to put together a three-dimensional puzzle on a computer (so their head remains still enough for the scan) to see how the brain interprets spatial relations.

However, these sorts of oversimplified “lab” tasks are not always representative of real-world activities, so it’s not clear whether what the researchers see on the brain images during these tasks is necessarily indicative of what REAL-life spatial relations thinking looks like. Are the neural processes seen in an fMRI scan while putting together blocks on a computer screen the same as what’s seen in the brain while a person builds a treehouse?

In this study, the researchers found a partial answer to exactly that kind of question, and the answer is no.

The children in study, ranging in age from 4 to 11 and all typically developing, watched the same 20-minute montage of short clips with Big Bird, Cookie Monster, the Count, Oscar and the rest of the gang teaching numbers and letters, shapes and colors, planets and countries, and so on. Meanwhile, the fMRI was taking a snapshot of their brain every two seconds.

The fMRI (which uses a giant magnet, not radiation, to peek into the brain) works by dividing the brain into a 3-D grid so that it can measure the intensity of the brain signals in each little section (about 40,000 of them, called voxels). The researchers collected a total of 609 images of each participant’s brain, which they could then use to map out the neural processes of the participants while they were watching.

They also had the children (23 of them), in a separate fMRI scanning period, perform a one of those lab-only fMRI tasks. In this case, the kids matched isolated pairs of faces, numbers, words and shapes on the computer (they pressed a button if the two images shown matched) while the fMRI images of their brains were created.

Finally, the children (19 of them) took IQ tests that primarily tested their math and verbal skills. Then the researchers analyzed the maps of neural processes in the children and their comparisons with the adults.

They found a couple of interesting things. First, the kids whose neural “maps” were most similar to the adults also performed the best on the IQ tests. This means kids’ brain structure matures in a predictable way, which the researchers called “neural maturity.”

“Broadly speaking, the children showed group-level similarity to adults in cortical regions associated with vision (occipital cortex), auditory processing (lateral temporal cortex), language (frontal and temporal cortex), visuo-spatial processing and calculation (intraparietal cortex), and several other functions,” the authors wrote.

The fMRI scan on the left represents correlations in neural activity between children and adults, in the middle between children and other children, and on the right between adults and other adults. Such neural maps, says University of Rochester cognitive scientist Jessica Cantlon, reveal how the brain’€™s neural structure develops along predictable pathways as we mature.

Second, the brain maps created during the Sesame Street viewing accurately predicted how the children performed on the IQ tests. Kids who did better on the verbal tasks showed more mature neural patterns in a part of the brain that handles speech and language, called the Broca area. Meanwhile, the kids whose math scores were highest had more neural maturity in a part of the brain that processes numbers, called intraparietal sulcus.

But the researchers’ other finding was that those areas of neural maturity seen during Sesame Street viewing — the ones that matched up with the children’s scores on the IQ test — were not seen during the fMRI task of matching faces, numbers, words and shapes. Basically, the “let’s try to simulate what learning looks like in the brain” task designed specifically for fMRI scans didn’t help much. But the more naturalistic, organic learning that takes places while watching Sesame Street did work.

Researchers now know they can use activities like viewing educational TV to scan children’s brains and learn more about how they learn — and it’s more accurate and helpful than invented computer tasks. It’s possible this technology and research could be applied to understanding better what’s going on with certain learning disabilities.

But a nice additional finding is that, hey, Sesame Street really IS educational! Of course, my son’s favorite show is a different PBS production — Dinosaur Train (which I admit I enjoy too) — so I also feel a better that little D spends a half hour or two, several days a week, learning from Buddy the Tyrannosaurus Rex, Tiny the Pteranodon, Mr. Conductor and Dr. Scott the Paleontologist about dinosaurs, carnivores, herbivores and how to test a hypothesis. All aboard!

Tiptoe through the thalamus…

This is how people looked at the brain in 1673. Things have changed.
Sketch by Thomas Bartholin, 1616-1680. 
Image via Wikimedia Commons. Public domain in USA.
In early October, the Allen Institute for Brain Science dropped a metric buttload of brain data into the public domain.
Founded by Microsoft co-founder Paul Allen, the Allen Institute for Brain Science is, not surprisingly, interested in, um, the brain. Specifically, according to the Institute’s web site, its mission is
“to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through integration of experiments modeling and theory.”
Towards that end, researchers at the Allen Institute have been mapping gene expression patterns in the human and mouse brains, as well as neural connectivity in the mouse brain. Why? Well, because as a general rule, science requires a control. If scientists are ever to understand the brain – how we think, how we learn, how we remember things, and how all those processes get scrambled during disease or trauma – they first must understand what a typical baseline brain looks like. The Allen Institute is doing the heavy lifting of mapping out these datasets, one brain slice at a time.
In particular, they are mapping the gene expression and neural connectivity of every part of the brain, so that researchers can identify difference between regions, as well as the physical links that tie them together. Differences in gene expression patterns may reveal, for instance, that seemingly related regions actually have different functions, while connectivity, or brain “wiring,” could shed light on how the brain works. 
I’m a technology nut, so I’m less interested in the answers to these questions than in how we arrive at them. And thanks to the Allen Institute, I (and you) can view these data from the luxury of my very own laptop, no special equipment required. (To be clear, you can’t view the data from my laptop. You’d need my computer, and you can’t have it.) You don’t even need to be a brainiac (I couldn’t help myself) to do it.
Here’s how. Point your browser to http://www.brain-map.org/. From there, choose a dataset – say, “Mouse Connectivity.” This is a dataset of images created by injecting fluorescent tracer molecules into the brains of mice, waiting some period of time, then sacrificing the mice, cutting their brains into thin slices — picture an extremely advanced deli slicer — and taking pictures of each one to see where the tracer material went. The result is a massive collection of images, collected by injecting hundreds of mice, preparing thousands of brain slices, and represents gigabytes upon gigabytes of data, which Allen Institute researchers have then reconstructed into a kind of virtual 3D brain.
In the parlance of neuroscientists, this dataset represents a first-pass attempt at a “connectome” – a brain-wide map of neural connections. But it’s definitely not the last; the connectome is vast beyond reckoning. According to one estimate,
Each human brain contains an estimated 100 billion neurons connected through 100 thousand miles of axons and between a hundred trillion to one quadrillion synaptic connections (there are only an estimated 100–400 billion stars in the Milky Way galaxy).
Efforts are currently underway to map the connectome at a number of levels, from the relatively coarse resolution of diffusion MRI to the subcellular level of electron microscopy. That’s a story for another day, but if you’re interested in this topic, I highly recommend Sebastian Seung’s eminently readable 2012 book, Connectome: How the Brain’s Wiring Makes Us Who We Are.

Back to the Allen Institute datasets. When you click on ‘Mouse Connectivity’, the site presents you with an index of injection sites, 47 in all. Let’s click on “visual areas.” The next page that comes up is a list of datasets that include that region. For the sake of this example, let’s click on the first entry in that list, “Primary visual area,” experiment #100141219.

The resulting page contains 140 fluorescent images of brain tissue slices in shades of orange and green. Click one to see it enlarged. Orange areas are non-fluorescent – they didn’t take up the tracer, meaning they are not physically connected to the injection site. On the bottom of the window is a series of navigation tools – you can tiptoe through the thalamus if you’d like, simply by moving these sliders left-right, up-down, and front-back. Just like a real neuroscientist!
 

This is your brain (well, a mouse brain) on rAAV (a fluorescent tracer).
(Source)

You can also zoom in to the cellular level. Here’s a close-up of a densely fluorescent area of the mouse brain — you can actually see individual neurons in this view. 
 

This is a closeup of your brain on rAAV. (Again, if you were a mouse)
(Source)

Another option is to download the Allen Institute’s free Brain Explorer software, a standalone program that lets you view these data offline. With Brain Explorer you can “step” through the brain slice by slice, rotate it, highlight regions. It’s way cool, even if (like me) you don’t know very much about brain anatomy.
Here’s a screenshot from the application, showing gene expression data in the center of the brain.
 

Screenshot of the Allen Institute’s Brain Explorer software

If you’re interested in how the amazing researchers at the Allen Institute are doing this work, they lay it out for you in a nice series of white papers (here’s the one on the mouse connectivity mapping project). I recommend you take a look!
 
The opinions expressed in this post do not necessarily reflect or conflict with those of the DXS editorial team or contributors.

You – Yes, You – Are an Astronomer

On January 7, 1610 (402 years ago today!), Galileo first identified three moons of Jupiter, the first satellites ever observed orbiting another planet. He later found a fourth, and today those moons — Io, Europa, Ganymede, and Callisto — are known as the Galilean moons in his honor. Galileo was able to do this because he used a telescope to observe: every new way to see reveals something new to be seen.

You can buy a telescope that’s more or less equivalent to Galileo’s ‘scope here for a very low price. (It’s actually much better, in my opinion, since the housing is made of plastic instead of cardboard! Also, you don’t have to grind your own lenses.) I don’t endorse most products, but I’ll happily plug this one: it’s a non-profit group whose aim is to get people looking at the skies, and I’ve used these ‘scopes in my astronomy classes. What was a specialist’s tool in 1610 is something available for everyone today; you can even see the four Galilean moons of Jupiter with a decent pair of binoculars.

I spent the holidays with my family in Iowa: my parents live in a very very very small town, without much light pollution. It was clear at night several days, and so we went out in the backyard to see what we could see. With my parents’ binoculars, we managed to see all four Galilean moons, and over three nights of viewing, saw how their positions changed as they orbit Jupiter. We were doing astronomy in the backyard: no specialized equipment, no special training, no observatory needed. Even in a city, you can still see the brighter planets (Jupiter is the third-brightest object in the night sky, after the Moon and Venus), and if your city is like mine, amateur astronomy groups are around that set up public nights to show you the sights.

You don’t need to be a trained professional to be an astronomer. You don’t need a huge telescope. You just need to look up. You can learn to read the night sky, identify planets, look for interesting nebulae and stars. If the sky is clear tonight, you can go outside and see Jupiter after sundown, and if you have binoculars or a small telescope, all four Galilean moons will even be visible. Jupiter is high above the horizon, and the brightest object other than the Moon tonight. Go look, and when you’re done, call yourself an astronomer. I’ll back you up.

(This post originally appeared at Galileo’s Pendulum.)