An antibody therapy for hemophilia A?

Example of an antibody. The interesting bits are purple,
as so many interesting things are.
Image credit and license info, via Wikimedia Commons.

By Jeffrey Perkel, DXS tech editor

Last night on TV I caught an ad for Humira, Abbott Laboratories’ prescription medication for a series of conditions including rheumatoid arthritis, psoriatic arthritis, and Crohn’s disease.


The ad noted that, like all drugs, this medication actually has two names, its brand name (Humira), and its generic name, adalimumab. That suffix, -mab, indicates that Humira is a monoclonal antibody, a large protein normally produced by your immune system’s B cells to recognize and eliminate proteins and pathogens that are not “self.” In particular, Humira recognizes, binds, and inactivates the protein called “tumor necrosis factor,” or TNF, which is implicated in various autoimmune disorders.


There are dozens of monoclonal antibody drugs on the market now, including the breast cancer therapeutic Herceptin (trastuzumab), Remicade (infliximab) for autoimmune disorders, and Rituxan (rituximab) for non-Hodgkin lymphoma.(*) In most cases, by binding specific proteins, either in solution or on cell surfaces, these molecules either inactivate proteins (as in the case of TNF), target the cell for death, or block inappropriate cell signaling (as in Herceptin). Other antibody designs use the antibody as a “guided missile,” targeting drug or radioisotope ”warheads” to cancerous cells. 


On Sept. 30, though, a team of Japanese researchers at Chugai Pharmaceutical, reported an example of a new kind of antibody application, and it’s pretty slick.


The paper concerns a novel treatment concept for hemophila A, an X-linked recessive bleeding disorder that affects about 1 in 10,000 men. It is caused by a lack of a clotting protein called factor VIII (FVIII), and the typical treatment is “prophylactic supplementation” of the missing protein.


There are three problems with that treatment, as the paper notes. First, FVIII is expensive. It also must be administered frequently and intravenously, which is especially difficult for pediatric patients and “negatively affects both the implementation of and adherence to the supplementation routine.” But perhaps most significantly, in about 30% of cases the body recognizes the recombinant FVIII as “non-self” or “foreign,” and develops antibodies (“inhibitors”) to inactivate it, rendering the treatment ineffective.


To circumvent that problem, the Chugai team developed what is called a “bispecific antibody” to replace FVIII. So what is a bispecific antibody?


In cartoon form, antibodies resemble the letter Y, with antigen-binding regions at the tip of either branch. In a normal antibody, those two binding regions are identical, such that each antibody can bind two copies of the same protein molecule.


A standard monoclonal antibody has two binding arms, each recognizing the same antigen (protein target).
Source: Wikipedia, http://en.wikipedia.org/wiki/Antibody

A bispecific antibody, though, has two different binding domains, one for each of two proteins, such that it can effectively act as a scaffold to bring two proteins – or the cells they are attached to – together. The only bispecific currently on the market, Trion Pharma’s Removab, acts to couple immune system T cells and macrophages to tumors.

A bispecific antibody, Trion’s Removab.
Source: Wikipedia, http://en.wikipedia.org/wiki/Bispecific_monoclonal_antibody

Chugai’s scientists developed a bispecific antibody that does something different. Their antibody, called hBS23, links two other clotting factors, FIXa and FX, thereby mimicking the function and architecture of the missing FVIII without actually administering it.

FVIII activates FX in the presence of FIXa. hBS23 is a bispecific antibody that replaces FVIII.
(c) 2012 Nature Publishing Group [Nature Medicine, doi:10.1038/nm.2942]

In test tube clotting assays, hBS23 was about 14-times less catalytically efficient than FVIII itself, yet could nevertheless induce clotting, even in cases where the plasma contained inhibitors against FVIII. (Recombinant human FVIII had no effect in those latter cases.) In a non-human primate model of hemophilia A, hBS23 prevented development of anemia and reduced internal bleeding comparable to FVIII itself.


Significantly, hBS23 lasts a long time in the primate bloodstream – with an IV half-life of 14 days and comparable subcutaneously bioavailability – yet seems unlikely to elicit inhibitory antibodies of its own. That subcutaneous activity is significant, as regular subcu administration should be more easily tolerated than an IV.

Based on the these studies, and some simulations, the authors predict that ”once weekly dosing of 1 mg per kg body weight of hBS23 would show a continuous hemostatic effect in humans.”  

Of course, that’s just a prediction. The proof of the pudding is in the eating, as they say, and only time will tell how hBS23 will fare in people. But don’t look for it on pharmacy shelves any time soon. Clinical trials take time, and further optimization of the antibody design is likely required. Still, the team is obviously upbeat about their strategy’s potential:


“A long-acting, subcutaneously injectable agent that is unaffected by the presence of inhibitors could markedly reduce the burden of care for the treatment of hemophilia A.”


For more details, you can read the report here.

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We’ve also got a partner post for you, an antibody explainer by our very own Jeanne Garbarino. Be sure to check it out! 


*Fun fact: If you’ve ever wondered about how drugs get their generic names, they are conferred by the US Adopted Names Council. The names have a kind of prefix/stem structure, linking a manufacturer-supplied but meaningless prefix (adalimu–) with a specific stem (eg, –mab) that denotes the drug class or activity. There are literally hundreds of stems, including –coxib (COX2 inhibitors), –vir (antivirals), and –stat (enzyme inhibitors); for a complete list, click here.

The Amazing Antibody and its Therapeutic Potential


NYC Campaign to alert the authorities if you see
something  suspicious.  Antibodies are like the citizens
that tell our body that something fishy is going down.

By Biology Editor, Jeanne Garbarino

There is a campaign sponsored by NYC’s Metropolitan Transit Authority (MTA) encouraging citizens to speak up if they see any activity or persons acting in a suspicious manner.  Plastered all over buses, subways, and commuter rails are posters with the following message: If you see something, say something.  This type of imagery reminds me very much of our own biological warning system programmed to, in essence, “speak up” should a suspicious character of the microscopic kind make it’s way into our bodies.  It is through our immune response that our bodies “say something” in the event of infection. 

At the very crux of the immune response are tiny proteins called antibodies, which are basically like the citizens that report any suspicious activities.  Antibodies often travel in the blood stream, and upon crossing paths with a foreign invader (bacteria, virus, etc.), an antibody will flag it down and alert the “local authorities” of the body (aka immune cells). 

For many years, scientists have been studying antibodies and their role in the immune response, revealing many aspects surrounding their structure and function.  And through these studies, we have figured out how to use antibodies in ways that go beyond the immune system.  For instance, antibodies against human chorionic growth hormone, or hCG, are the essential ingredients in home pregnancy tests.  More recently, scientists have, in many ways, harnessed the power of antibodies for pharmaceutical uses.  A very popular example of this is the drug Remicade, which is used to treat severe autoimmune diseases like rheumatoid arthritis and Crohn’s Disease.   But, what exactly are antibodies and how do they work?

Well, I am glad I asked me that question.

As I mentioned, antibodies are proteins that we make.  Specifically, they are produced by specialized immune cells called B-cells, which are the main players during our humoral immune response.  B-cells will either secrete an antibody, which can then float around the circulatory system, or the antibody can remain attached to the outside of the B-cell.  If there is something “foreign” in our bodies, such as a virus or bacterium, antibodies will recognize and attach itself to the invader, which is scientifically referred to as an antigen.  When an antibody attaches to an antigen, it signals to our body to get rid of it.  Amazingly, each antibody can only recognize 1 antigen, which is why we need so many different types of antibodies!     

To get a better idea of how antibodies work, it is important to learn their basic structure.  Antibodies are ‘Y’ shaped proteins, and have both constant and variable regions.  The constant region is the same among all antibodies within a specific class (there are several different classes), where as the variable region is the portion of the antibody that is designed to recognize a specific antigen.      

To better explain this, consider the antibody to be a lacrosse stick.  The “stick” part is the constant region, and the mesh part is the variable region.  Now consider the lacrosse ball to be the antigen (i.e. bacterium or virus).  Only the lacrosse ball that is a triangle can fit into the lacrosse stick with the triangle-shaped mesh pocket.  The same is true for the circle.  And so on.  Once the ball fits into the mesh, meaning, once the antibody binds the antigen, a cascade of events is set off, essentially sounding the alarm.  Under normal, healthy circumstances, we take care of the antigen and the infectious agent is removed. (Note: there are different classes of antibodies and each class has it’s own “stick” part.)

A basic analology for how antibodies work.
Building off our understanding of how antibodies work, scientists have been able to develop monoclonal antibody therapy, which is the use of specific antibodies to stimulate an immune response against a disease.  For instance, we now use monoclonal antibody therapy to combat a variety of cancers by injecting cancer patients with antibodies designed to recognize specific components on the surface of tumor cells.  This helps signal to the body that it should turn on the immune response and get rid of the tumor cells. 

The list of conditions where monoclonal antibody is a potential therapy is growing, and includes a variety of autoimmune diseases and cancers, post-organ transplant therapy, human respiratory syncytial virus (RSV) infections in children, and most recently hemophilia A.  Also being explored is the use of monoclonal antibody therapy for addiction, which could essentially revolutionize how we can help people kick extremely difficult habits (i.e. cocaine or methamphetamine).

Despite the thousands of tedious and repetitive assays I’ve done using antibodies in my own laboratory, I know that I can never lose sight of how amazing these little proteins are. 

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This post is a mental appetizer for another post on monoclonal antibodies by DXS tech editor, Jeffrey Perkel. His post specifically discusses the potential use of monoclonal antibody to treat the X-linked blood disorder, hemophilia A.  Read about it here.     

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

From spiders to breast cancer: Leslie Brunetta talks candidly about her cancer diagnosis, treatment, and follow-up

According to Leslie Brunetta, she now has much more hair than she had last July.
We became aware of Leslie Brunetta because of her book, Spider Silk: Evolution and 400 Million Years of Spinning, Waiting, Snagging, and Mating, co-authored with Catherine L. Craig. Thanks to a piece Leslie wrote for the Concord Monitor (and excerpted here), we also learned that she is a breast cancer survivor. Leslie agreed to an interview about her experience, and in her emailed responses, she candidly talks about her diagnosis, treatment, and follow-up for her cancers, plural: She was diagnosed simultaneously with two types of breast cancer. 
DXS: In your Concord Monitor piece, you describe the link between an understanding of the way evolution happens and some of the advances in modern medicine. What led you to grasp the link between the two?

LB: I think, because I’m not a scientist (I’m an English major), a lot of things that scientists think are obvious strike me as revelations. I somehow had never realized that the search for what would turn out to be DNA began with trying to explain how, in line with the theory of evolution by natural selection, variation arises and traits are passed from generation to generation. As I was figuring out what each chapter in Spider Silk would be about, I tried to think about the questions non-biologists like me would still have about evolution when they got to that point in the book. By the time we got past dragline silk, I realized that we had so far fleshed out the ways that silk proteins could and have evolved at the genetic level. But that explanation probably wouldn’t answer readers’ questions about how, for example, abdominal spinnerets—which are unique to spiders—might have evolved: the evolution of silk is easier to untangle than the evolution of body parts, which is why we focused on it in the first place.

I decided I wanted to write a chapter on “evo-devo,” evolutionary developmental biology, partly because there was a cool genetic study on the development of spinnerets that showed they’ve evolved from limbs. Fortunately, my co-author, Cay Craig, and editor at Yale, Jean Thomson Black, okayed the idea, because that chapter wasn’t in the original proposal. Writing that chapter, I learned why it took so long—nearly a century—to get from Darwin and Mendel to Watson and Crick and then so long again to get to where we are today. If we non-scientists understand something scientific, it’s often how it works, not how a whole string of people over the course of decades building on each other’s work discovered how it works. I knew evolution was the accumulation of gene changes, but, until I wrote that chapter, it hadn’t occurred to me that people began to look for genes because they wanted to understand evolution.

So that was all in the spider part of my life. Then, a few months into the cancer part of my life, I was offered a test called Oncotype DX, which would look at genetic markers in my tumor cells to develop a risk profile that could help me decide whether I should have chemotherapy plus tamoxifen or just tamoxifen. The results turned out to be moot in my case because I had a number of positive lymph nodes, although it was reassuring to find out that the cancer was considered low risk for recurrence. But still—the idea that a genetic test could let some women avoid chemo without taking on extra risk, that’s huge. No one would want to go through chemo if it wasn’t necessary. So by then I was thinking, “Thank you, Darwin!”

And then, coincidentally, the presidential primary season was heating up, and there were a number of serious candidates (well, serious in the sense that they had enough backing to get into the debates) who proudly declared that they had no time for the theory of evolution. And year after year these stupid anti-evolution bills are introduced in various state legislatures. While I was lying on the couch hanging out in the days after chemo sessions, I started thinking, “So, given that you don’t give any credence to Darwin and his ideas, would you refuse on principle to take the Oncotype test or gene-based therapies like Gleevec or Herceptin if you had cancer or if someone in your family had cancer? Somehow I don’t think so.” That argument is not going to convince hard-core denialists (nothing will), but maybe the cognitive dissonance in connection with something as concrete as cancer will make some people who waver want to find out more.

DXS: You mention having been diagnosed with two different forms of cancer, one in each breast. Can you say what each kind was and, if possible, how they differed?

LB: Yes, I unfortunately turned out to be an “interesting” case. This is one arena where, if you possibly can, you want to avoid being interesting. At first it seemed that I had a tiny lesion that was an invasive ductal carcinoma (IDC) and that I would “just” need a lumpectomy and radiation. Luckily for me, the doctor reading my mammogram is known as an eagle eye, and she saw a few things that—given the positive finding from the biopsy—concerned her. She recommended an MRI. In fact, even though I switched to another hospital for my surgery, she sent emails there saying I should have an MRI. That turned up “concerning” spots in both breasts, which led to more biopsies, which revealed multiple tiny cancerous lesions. The only reasonable option was then a double mastectomy.

The lesions in the right breast were IDCs. About 70% of breast cancers are diagnosed as IDCs. Those cancers start with the cells lining the milk ducts. The ones in the left breast were invasive lobular carcinomas (ILCs), which start in the lobules at the end of the milk ducts. Only about 10% of breast cancers are ILCs.

Oncologists hate lobular cancer. Unlike ductal cancers, which form as clumps of cells, lobular cancers form as single-file ribbons of cells. The tissue around ductal cancer cells reacts to those cells, which is why someone may feel a lump—she’s (or he’s) not feeling the cancer itself but the inflammation of the tissue around it. And because the cells clump, they show up more readily on mammograms. Not so lobular cancers. They mostly don’t give rise to lumps and they’re hard to spot on mammograms. They snake their way through tissue for quite a while without bothering anything.

In my case, this explains why last spring felt like an unremitting downhill slide. Every time someone looked deeper, they found something worse. It turned out that on my left side, the lobular side, I had multiple positive lymph nodes, which was why I needed not just chemo but also radiation (which usually isn’t given after a mastectomy). That was the side that didn’t even show up much on the mammogram. On the right side, the ductal side, which provoked the initial suspicions, my nodes were clear. I want to write about this soon, because I want to find out more about it. I’ve only recently gotten to the place emotionally where I think I can deal with reading the research papers as opposed to more general information. By the way, the resource that most helped us better understand what my doctors were talking about was Dr. Susan Love’s Breast Book.  It was invaluable as we made our way through this process, although it turned out that I had very few decisions to make because there was usually only one good option.   

DXS: As part of your treatment, you had a double mastectomy. One of our goals with this interview is to tell women what some of these experiences with treatment are like. If you’re comfortable doing so, could you tell us a little bit about what a double mastectomy entails and what you do after one in practical terms?

LB: A mastectomy is a strange operation. In a way, it’s more of an emotional and psychological experience than a physical experience. My surgeon, who was fantastic, is a man, and when we discussed the need for the mastectomies he said that I would be surprised at how little pain would be involved and how quick the healing would be. Even though I trusted him a lot by then, my reaction was pretty much, “Like you would know, right?” But he did know. When you think about it, it’s fairly non-invasive surgery. Unless the cancer has spread to the surrounding area, which doesn’t happen very often now due to early detection, no muscle or bone is removed. (Until relatively recently, surgeons removed the major muscle in the chest wall, and sometimes even bone, because they believed it would cut the risk of recurrence. That meant that many women lost function in their arm and also experienced back problems.) None of your organs are touched. They don’t go into your abdominal cavity. Also, until recently, they removed a whole clump of underarm lymph nodes when they did lumpectomies or mastectomies. Now they usually remove just a “sentinel node,” because they know that it will give them a fairly reliable indicator of whether the cancer has spread to the other nodes. That also makes the surgery less traumatic than it used to be.

I opted not to have reconstruction. Reconstruction is a good choice for many women, but I didn’t see many benefits for me and I didn’t like the idea of a more complicated surgery. My surgery was only about two hours. I don’t remember any pain at all afterwards, and my husband says I never complained of any. I was in the hospital for just one night. By the next day, I was on ibuprofen only. The bandages came off two days after the surgery.

That’s shocking, to see your breasts gone and replaced by thin red lines, no matter how well you’ve prepared yourself. It made the cancer seem much more real in some way than it had seemed before. In comparison, the physical recovery from the surgery was fairly minor because I had no infections or complications. There were drains in place for about 10 days to collect serum, which would otherwise collect under the skin, and my husband dealt with emptying them twice a day and measuring the amount. I had to sleep on my back, propped up, because of where the drains were placed, high up on my sides, and I never really got used to that. It was a real relief to have the drains removed.

My surgeon told me to start doing stretching exercises with my arms right away, and that’s really important. I got my full range of motion back within a couple of months. But even though I had my surgery last March, I’ve noticed lately that if I don’t stretch fully, like in yoga, things tighten up. That may be because of the radiation, though, because it’s only on my left side. Things are never quite the same as they were before the surgery, though. Because I did have to have the axillary nodes out on my left side, my lymph system is disrupted. I haven’t had any real problems with lymphedema yet, and I may never, but in the early months I noticed that my hands would swell if I’d been walking around a lot, and I’d have to elevate them to get them to drain back. That rarely happens now. But I’ve been told I need to wear a compression sleeve if I fly because the change in air pressure can cause lymph to collect. Also, I’m supposed to protect my hands and arms from cuts as much as possible. It seems to me that small nicks on my fingers take longer to heal than they used to. So even though most of the time it seems like it’s all over, I guess in those purely mechanical ways it’s never over. It’s not just that you no longer have breasts, it’s also that nerves and lymph channels and bits of tissue are also missing or moved around.

The bigger question is how one deals with now lacking breasts. I’ve decided not to wear prostheses. I can get away with it because I was small breasted, I dress in relatively loose clothes anyway, and I’ve gained confidence over time that no one notices or cares and I care less now if they do notice. But getting that self-confidence took quite a while. Obviously, it has an effect on my sex life, but we have a strong bond and it’s just become a piece of that bond. The biggest thing is that it’s always a bit of a shock when I catch sight of myself naked in a mirror because it’s a reminder that I’ve had cancer and there’s no getting around the fact that that sucks.    

DXS: My mother-in-law completed radiation and chemo for breast cancer last year, and if I remember correctly, she had to go frequently for a period of weeks for radiation. Was that you experience? Can you describe for our readers what the time investment was like and what the process was like?

LB: I went for radiation 5 days a week for about 7 weeks. Three days a week, I’d usually be in and out of the hospital within 45 minutes. One day a week, I met with the radiology oncologist and a nurse to debrief, which was also a form of emotional therapy for me. And one day a week, they laid on a chair massage, and the nurse/massage therapist who gave the massage was great to talk to, so that was more therapy. Radiation was easy compared to chemo. Some people experience skin burning and fatigue, but I was lucky that I didn’t experience either. Because I’m a freelancer, the time investment wasn’t a burden for me. I’m also lucky living where I live, because I could walk to the hospital. It was a pleasant 3-mile round-trip walk, and I think the walking helped me a lot physically and mentally.
DXS: And now to the chemo. My interest in interviewing you about your experience began with a reference you made on Twitter to “chemo brain,” and of course, after reading your evolution-medical advances piece. Can you tell us a little about what the process of receiving chemotherapy is like? How long does it take? How frequently (I know this varies, but your experience)?
LB: Because of my age (I was considered young, which was always nice to hear) and state of general good health, my oncologist put me on a dose-dense AC-T schedule. This meant going for treatment every two weeks over the course of 16 weeks—8 treatment sessions. At the first 4 sessions, I was given Adriamycin and Cytoxan (AC), and the last 4 sessions I was given Taxol (T). The idea behind giving multiple drugs and giving them frequently is that they all attack cancer cells in different ways and—it goes back to evolution—by attacking them frequently and hard on different fronts, you’re trying to avoid selecting for a population that’s resistant to one or more of the drugs. They can give the drugs every two weeks to a lot of patients now because they’ve got drugs to boost the production of white blood cells, which the cancer drugs suppress. After most chemo sessions, I went back the next day for a shot of one of these drugs, Neulasta.

The chemo clinic was, bizarrely, a very relaxing place. The nurses who work there were fantastic, and the nurse assigned to me, Kathy, was always interesting to talk with. She had a great sense of humor, and she was also interested in the science behind everything we were doing, so if I ever had questions she didn’t have ready answers for, she’d find out for me. A lot of patients were there at the same time, but we each had a private space. You’d sit in a big reclining chair. They had TVs and DVDs, but I usually used it as an opportunity to read. My husband sat through the first session with me, and a close friend who had chemo for breast cancer 15 years ago sat through a few other sessions, but once I got used to it, I was comfortable being there alone. Because of the nurses, it never felt lonely.

I’d arrive and settle in. Kathy would take blood for testing red and white blood counts and, I think, liver function and some other things, and she’d insert a needle and start a saline drip while we waited for the results. I’ve always had large veins, so I opted to have the drugs administered through my arm rather than having a port implanted in my chest. Over the course of three to four hours, she’d change the IV bags. Some of the bags were drugs to protect against nausea, so I’d start to feel kind of fuzzy—I don’t think I retained a whole lot of what I read there! The Adriamycin was bright orange; they call it the Red Devil, because it can chew up your veins—sometimes it felt like it was burning but Kathy could stop that by slowing the drip. Otherwise, it was fairly uneventful. I’d have snacks and usually ate lunch while still hooked up.

I was lucky I never had any reactions to any of the drugs, so actually getting the chemo was a surprisingly pleasant experience just because of the atmosphere. On the one hand, you’re aware of all these people around you struggling with cancer and you know things aren’t going well for some of them, so it’s heartbreaking, and also makes you consider, sometimes fearfully, your own future no matter how well you’re trying to brace yourself up. But at the same time, the people working there are so positive, but not in a Pollyannaish-false way, that they helped me as I tried to stay positive. The social worker stopped in with each patient every session, and she was fantastic—I could talk out any problems or fears I had with her, and that helped a huge amount.

DXS: Would you be able to run us through a timeline of the physical effects of chemotherapy after an infusion? How long does it take before it hits hardest? My mother-in-law told me that her biggest craving, when she could eat, was for carb-heavy foods like mashed potatoes and for soups, like vegetable soup. What was your experience with that?

LB: My biggest fear when I first learned I would need chemo was nausea. My oncologist told us that they had nausea so well controlled that over the past few years, she had only had one or two patients who had experienced it. As with the surgeon’s prediction about mastectomy pain, this turned out to be true: I never had even a single moment of nausea.

But there were all sorts of other effects. For the first few days after a session, the most salient effects were actually from the mix of drugs I took to stave off nausea. I generally felt pretty fuzzy, but not necessarily sleepy—part of the mix was steroids, so you’re a little hyped. There’s no way I’d feel safe driving on those days, for example. I’d sleep well the first three nights because I took Ativan, which has an anti-nausea effect. But except for those days, my sleep was really disrupted. Partly that’s because, I’m guessing, the chemo hits certain cells in your brain and partly it’s because you get thrown into chemical menopause, so there were a lot of night hot flashes. Even though I’d already started into menopause, this chemo menopause was a lot more intense and included all the symptoms regularly associated with menopause.

By the end of the first session, I was feeling pretty joyful because it was much less bad than I had thought it would be. By the second week in the two-week cycle, I felt relatively normal. But even though it never got awful, the effects started to accumulate. My hair started to fall out the morning I was going to an award ceremony for Spider Silk. It was ok at the ceremony, but we shaved it off that night. I decided not to wear a wig. First, it was the summer, and it would have been hot. Second, I usually have close to a buzz cut, and I can’t imagine anyone would make a wig that would look anything like my hair. My kids’ attitude was that everyone would know something was wrong anyway, so I should just be bald, and that helped a lot. But it’s hard to see in people’s eyes multiple times a day their realization that you’re in a pretty bad place. Also, it’s not just your head hair that goes. So do your eyebrows, your eyelashes, your pubic hair, and most of the tiny hairs all over your skin. And as your skin cells are affected by the chemo (the chemo hits all fast-reproducing cells), your skin itself gets more sensitive and then is not protected by those tiny hairs. I remember a lot of itching. And strange things like my head sticking to my yoga mat and my reading glasses sticking to the side of my head instead of sliding over my ears.

I never lost my appetite, but I did have food cravings during the AC cycles. I wanted sushi and seaweed salad, of all things. And steak. My sense of taste went dull, so I also wanted things that tasted strong and had crunch. I stopped drinking coffee and alcohol, partly because of the sleep issues but partly because it didn’t taste very good anyway. I drank loads of water on the advice of the oncologist, the nurses, and my acupuncturist, and I think that helped a lot.

During the second cycle, I developed a fever. That was scary. I was warned that if I ever developed a fever, I should call the oncologist immediately, no matter the time of day or day of week. The problem is that your immune response is knocked down by the chemo, so what would normally be a small bacterial infection has the potential to rage out of control. I was lucky. We figured out that the source of infection was a hemorrhoid—the Adriamycin was beginning to chew into my digestive tract, a well-known side effect. (Having to pay constant attention to yet another usually private part of the body just seemed totally unfair by this point.) Oral antibiotics took care of it, which was great because I avoided having to go into the hospital and all the risks entailed with getting heavy-duty IV antibiotic treatment. And we were also able to keep on schedule with the chemo regimen, which is what you hope for.

After that, I became even more careful about avoiding infection, so I avoided public places even more than I had been. I’m very close to a couple of toddlers, and I couldn’t see them for weeks because they were in one of those toddler constant-viral stages, and I really missed them.

The Taxol seems to be much less harsh than the AC regimen, so a lot of these side effects started to ease off a bit by the second 8 weeks, which was certainly a relief.

I was lucky that I didn’t really have mouth sores or some of the other side effects. Some of this is, I think, just because besides the cancer I don’t have any other health issues. Some of it is because my husband took over everything and I don’t have a regular job, so I had the luxury of concentrating on doing what my body needed. I tried to walk every day, and I slept when I needed to, ate when and what I needed to, and went to yoga class when my immune system was ok. I also went to acupuncture every week. I know the science is iffy on that, but I think it helped me with the side effects, even if it was the placebo effect at work (I’m a big fan of the placebo effect). We also both had extraordinary emotional support from many friends and knew we could call lots of people if we needed anything. That’s huge when you’re in this kind of situation.

Currently, I’m still dealing with some minor joint pains, mostly in my wrists and feet. I wasn’t expecting this problem, but my oncologist says it’s not uncommon: they think it’s because your immune system has to re-find its proper level of function, and it can go into overdrive and set up inflammation in the joints. That’s gradually easing off, though.

Most people don’t have it as easy as I did in terms of the medical, financial, and emotional resources I had to draw on. I’m very mindful of that and very grateful.

DXS: You say that you had “few terrible side effects” and a “very cushy home situation.” I’m sure any woman would like to at least be able to experience the latter while dealing with a full-body chemical attack. What were some factors that made it “cushy” that women might be able to talk to their families or caregivers about replicating for them?

LB: As I’ve said, some of it is just circumstance. For example, my kids were old enough to be pretty self-sufficient and old enough to understand what was going on, which meant both that they needed very little from me in terms of care and also that they were less scared than they might have been if they were younger. My husband happens to be both very competent (more competent than I am) around the house and very giving. I live in Cambridge, MA, where I could actually make choices about where I wanted to be treated at each phase and know I’d get excellent, humane care and where none of the facilities I went to was more than about 20 minutes away.

Some things that women might have some control over and that their families might help nudge them toward:

  • Find doctors you trust. Ask a lot of questions and make sure you understand the answers. But don’t get hung up on survival or recurrence statistics. There’s no way to know for sure what your individual outcome will be. Go for the treatment that you and your doctors believe will give you the best chance, and then assume as much as possible that your outcome will be good.
  • Make sure you talk regularly with a social worker or other therapist who specializes in dealing with breast cancer patients. If you have fears or worries that you don’t want to talk to your partner or family about, here’s where you’ll get lots of help.
  • Find compatible friends who have also had cancer to talk to. I had friends who showed me their mastectomy scars, who showed me their reconstructions, who told me about their experiences with chemo and radiation, who told me about what life after treatment was like (is still like decades later…). And none of them told me, “You should…” They all just told me what was hard for them and what worked for them and let me figure out what worked for me. Brilliant.
  • Try to get some exercise even if you don’t feel like it. It was often when I felt least like moving around that a short walk made me feel remarkably better. But I would forget that, so my husband would remind me. Ask someone to walk with you if you’re feeling weak. Getting your circulation going seems to help the body process the chemo drugs and the waste products they create. For the same reason, drink lots of water.
  • Watch funny movies together. Laughter makes a huge difference.
  • Pamper yourself as much as possible. Let people take care of you and help as much as they’re willing. But don’t be afraid to say no to anything that you don’t want or that’s too much.

Family members and caregivers should also take care of themselves by making some time for themselves and talking to social workers or therapists if they feel the need. It’s a big, awful string of events for everyone involved, not just the patient.

DXS: In the midst of all of this, you seem to have written a fascinating book about spiders and their webs. Were you able to work while undergoing your treatments? Were there times that were better than others for attending to work? Could work be a sort of occupational therapy, when it was possible for you to do it, to keep you engaged?

LB: The book had been published about 6 months before my diagnosis. The whole cancer thing really interfered not with the writing, but with my efforts to publicize it. I had started to build toward a series of readings and had to abandon that effort. I had also started a proposal for a new book and had to put that aside. I had one radio interview in the middle of chemo, which was kind of daunting but I knew I couldn’t pass up the opportunity, and when I listen to it now, I can hear my voice sounds kind of shaky. It went well, but I was exhausted afterwards. Also invigorated, though—it made me feel like I hadn’t disappeared into the cancer. I had two streams of writing going on, both of which were therapeutic. I sent email updates about the cancer treatment to a group of friends—that was definitely psychological therapy. I also tried to keep the Spider Silk blog up to date by summarizing related research papers and other spider silk news—that was intellectual therapy. I just worked on them when I felt I wanted to. The second week of every cycle my head was usually reasonably clear.

I don’t really know whether I have chemo brain. I notice a lot of names-and-other-proper-nouns drop. But whether that’s from the chemo per se, or from the hormone changes associated with the chemically induced menopause, or just from emotional overload and intellectual distraction, I don’t know. I find that I’m thinking more clearly week by week.

DXS: What is the plan for your continued follow-up? How long will it last, what is the frequency of visits, sorts of tests, etc.?

LB: I’m on tamoxifen and I’ll be on that for probably two years and then either stay on that or go onto an aromatase inhibitor [Ed. note: these drugs block production of estrogen and are used for estrogen-sensitive cancers.] for another three years. I’ll see one of the cancer doctors every three months for at least a year, I think. They’ll ask me questions and do a physical exam and take blood samples to test for tumor markers. At some point the visits go to every six months.

For self-care, I’m exercising more, trying to lose some weight, and eating even better than I was before.

DXS: Last…if you’re comfortable detailing it…what led to your diagnosis in the first place?

LB: My breast cancer was uncovered by my annual mammogram. I’ve worried about cancer, as I suppose most people do. But I never really worried about breast cancer. My mother has 10 sisters and neither she nor any of them ever had breast cancer. I have about 20 older female cousins—I was 50 when I was diagnosed last year–and as far as I know none of them have had breast cancer. I took birth control pills for less than a year decades ago. Never smoked. Light drinker. Not overweight. Light exerciser. I breastfed both kids, although not for a full year. Never took replacement hormones. Never worked in a dangerous environment. Never had suspicious mammograms before. So on paper, I was at very low risk as far as I can figure out. After I finished intensive treatment, I was tested for BRCA1 and BRCA2 (because mutations there are associated with cancer in both breasts) and no mutations were found. Unless or until some new genetic markers are found and one of them applies to me, I think we’ll never know why I got breast cancer, other than the fact that I’ve lived long enough to get cancer. There was no lump. Even between the suspicious mammogram and ultrasound and the biopsy, none of the doctors examining me could feel a lump or anything irregular. It was a year ago this week that I got the news that the first biopsy was positive. In some ways, because I feel really good now, it’s hard to believe that this year ever happened. But in other ways, the shock of it is still with me and with the whole family. Things are good for now, though, and although I feel very unlucky that this happened in the first place, I feel extremely lucky with the medical care I received and the support I got from family and friends and especially my husband.
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Leslie Brunetta’s articles and essays have appeared in the New York Times, Technology Review, and the Sewanee Review as well as on NPR and elsewhere. She is co-author, with Catherine L. Craig, of Spider Silk: Evolution and 400 Million Years of Spinning, Waiting, Snagging, and Mating (Yale University Press).

Pregnancy 101: The science behind the wand of destiny


You hold a stick in your hands, one that you’ve just peed on. It foretells a future of sorts, for you. But the magic behind that stick is really all about a biochemical sandwich and a scientific test named ELISA.

By Jeanne Garbarino, DXS Editor

OH MY GOD OH MY GOD OH MY GOD OH MY GOD OH MY GOD OH MY GOD

Over and over again, that was all I could say.  At the same time, I heard my husband on the other side of the bathroom door, in a very panicked voice asking, “Why are you saying oh my god? WHAY ARE YOU SAYING OH MY GOD?!?!” 

Though, he really knew why.

The events immediately preceding our synchronous freak out session involved unwrapping a small plastic wand, removing its lilac cap, and subsequently inserting its absorbent tip into my stream of pee. Yes, folks, we are talking about the wand of destiny that is the pregnancy test.

Shortly after that lucky sperm cell unites with the prized product of the ovulatory process, theegg, a woman will immediately begin to experience changes required for growing another human inside of her body. One of the first detectable signs of pregnancy is a surge in a hormone called human chorionic gonadotropin or hCG. 

Once the fertilized egg finds a cozy resting place in the wall of the uterus (a process termed implantation), the production of hCG is significantly ramped up. On average, implantation usually takes about 8-10 days for normal, healthy pregnancies[1]. It is around this point on the baby growing timeline that home pregnancy tests can begin to detect the increased presence of hCG.

Chronologically speaking, we have sex, a sperm cell fertilizes an egg cell, said fertilized egg implants into uterus, our bodies up the production of hCG, and we pee on a stick to find out if all of these things really happened. But, exactly how do these little wands of destiny work?

The technology harnessed within the pregnancy test involves a biochemical assay called a “Sandwich ELISA” (ELISA = enzyme-linked immunoabsorbant assay, more on the “sandwich” part in a bit).  The general function of an ELISA is to detect (and sometimes quantify) the presence of a substance in a liquid. In the case of a home pregnancy test, the substance is hCG and the liquid part is our urine. 
Once pee is applied to the pregnancy test, it travels along the absorbent fibers, reaching defined areas that are coated with molecules, called “capture” antibodies, specifically designed to capture hCG. To help you visualize antibody science, picture a lacrosse stick, except the mesh pocket can only fit one specific type of ball:

Now, back to the sandwich part. On a home pregnancy test, there are three separate zones containing capture antibodies. Using their sharp wit and radical humor, scientists came up with “sandwich” to describe this sort of ELISA as they felt it was analogous to two slices of bread surrounding some delicious filling. Hilarious, right?

Ok, now that you’ve calmed down from laughing so hard, let us get back to the science. The first “slice of bread” is called the reaction zone, the “sandwich filling” is called the test zone, and the “last slice of bread” is called the control zone (see figure 2). Each of these zones is coated with capture antibodies, but differ from each other in how they work. 

The antibodies on the reaction zone will capture only hCG and will detach from the strip upon exposure to urine. The test zone also contains capture antibodies that can only bind hCG, except they are securely attached to the absorbent strip, plus, there is an added dye. The control zone contains a general antibody (a lacrosse stick that will fit any ball) plus a dye, and serves to let the frantic user know that the test is functional. 

Not pregnant

Pregnant
As urine travels up the absorbent strip, it takes with it the reaction zone antibodies. If the urine is obtained from a pregnant woman, the reaction zone antibodies will be bound to hCG molecules found in the pee. When the pee solution reaches the test zone, there are two possible outcomes. If you are pregnant, the hCG/reaction zone antibody complexes will stick to the test zone antibodies and cause the dye to release (sometimes in a little “+” formation). If you are not pregnant, the reaction zone antibodies will just pass on through without saying hello.

The test culminates at the control zone, which is lined with general capture antibodies. Going back to picturing antibodies as lacrosse sticks, you will see that only the shape and size of the mesh pocket varies; the stick part is always the same. The general capture antibodies on the control zone will recognize and bind to the “stick” part of the reaction zone antibodies, and release a dye while doing so. This is how we know that the test worked correctly. 

Biochemically speaking, the home pregnancy test is nothing but a soggy antibody sandwich that smells of urine. From a family planning standpoint, however, this technology can impact us in ways beyond belief. But, aside from the potential for the “are you pregnant” window to induce one into a hyperventilated state, the process happening within that handheld chemistry lab is actually quite impressive. In a matter of minutes, we can know if it is ok to go out and party with friends, or if it would be a better choice to stay in and begin to nest – all from the comfort of our own bathrooms. Three cheers for science!
For a cool animation showing how a pregnancy test works, go here. Visit WomensHealth.gov for more information about pregnancy tests.  Planned Parenthood offers scientifically accurate information about women’s reproductive health. For blogs, check out this list on Babble, and this list on BlogHer.      


[1]Wilcox AJ, Baird DD, Weinberg CR. Time of implantation of the conceptus and loss of pregnancy. N Engl J Med. (1999) Jun 10;340(23):1796-9.


Towards better drug development, fewer side effects?

You may have had the experience: A medication you and a friend both take causes terrible side effects in you, but your friend experiences none. (The running joke in our house is, if a drug has a side-effect, we’ve had it.) How does that happen, and why would a drug that’s meant to, say, stabilize insulin levels, produce terrible gastrointestinal side effects, too? A combination of techy-tech scientific approaches might help answer those questions for you — and lead to some solutions.

It’s no secret I love lab technology. I’m a technophile. A geek. I call my web site “Biotechnically Speaking.” So when I saw this paper in the September issue of Nature Biotechnology, well, I just had to write about it.

The paper is entitled, “Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.” If you read that and your eyes glazed over, don’t worry –- the article is way more interesting than its title. 

Those trees on the right are called SPADE trees. They map cellular responses to different  stimuli in a collection of human blood cells. Credit: (c) 2012 Nature America [Nat Biotechnol, 30:858--67, 2012]
Here’s the basic idea: The current methods drug developers use to screen potential drug compounds –- typically a blend of high-throughput imaging and biochemical assays – aren’t perfect. If they were, drugs wouldn’t fail late in development. Stanford immunologist Garry Nolan and his team, led by postdoc Bernd Bodenmiller (who now runs his own lab in Zurich), figured part of that problem stems from the fact that most early drug testing is done on immortalized cell lines, rather than “normal” human cells. Furthermore, the tests that are run on those cells aren’t as comprehensive as they could be, meaning potential collateral effects of the compounds might be missed. Nolan wanted to show that flow cytometry, a cell-analysis technique frequently used in immunology labs, can help reduce that failure rate by measuring drug impacts more holistically. 


Nolan is a flow cytometry master. As he told me in 2010, he’s been using the technique for more than three decades, and even used a machine now housed in the Smithsonian.


In flow cytometry, researchers treat cells with reagents called antibodies, which are immune system proteins that recognize and bind to specific proteins on cell surfaces. Each type of cell has a unique collection of these proteins, and by studying those collections, it is possible to differentiate and count the different populations.


Suppose researchers wanted to know how many T cells of a specific type were present in a patient’s blood. They might treat those cells with antibodies that recognize a protein known as CD3 to pick those out. By adding additional antibodies, they can then select different T-cell subpopulations, such as CD4-positive helper T cells and CD8-positive cytotoxic T cells, both of which help you mount immune responses.


Cells of the immune system
Source: http://stemcells.nih.gov/info/scireport/chapter6.asp
In a basic flow cytometry experiment, each antibody is labeled with a unique fluorescent dye –- the antibody targeting CD3 might be red, say, and the CD4 antibody, green. The cells stream past a laser, one by one. The laser (or lasers –- there can be as many as seven) excites the dye molecules decorating the cell surface, causing them to fluoresce. Detectors capture that light and give a count of how many total cells were measured and the types of cells. The result is a kind of catalog of the cell population. For immune cells, for example, that could be the number of T cells, B cells (which, among other things, help you “remember” previous invaders), and macrophages (the big cells that chomp up invaders and infected cells). By comparing the cellular catalogs that result under different conditions, researchers gain insight into development, disease, and the impact of drugs, among other things.


But here’s the problem: Fluorescent dyes aren’t lasers, producing light of exactly one particular color. They absorb and emit light over a range of colors, called a spectrum. And those spectra can overlap, such that when a researcher thinks she’s counting CD4 T cells, she may actually be counting some macrophages. That overlap leads to all sorts of experimental optimization issues. An exceptionally talented flow cytometrist can assemble panels of perhaps 12 or so dyes, but it might take months to get everything just right.


That’s where the mass cytometry comes in. Commercialized by DVS Sciences, mass cytometry is essentially the love-chid of flow cytometry and mass spectrometry, combining the one-cell-at-a-time analysis of the former with the atomic precision of the latter. Mass spectrometry identifies molecules based on the ratio of their mass to their charge. In DVS’ CyTOF mass cytometer, a flowing stream of cells is analyzed not by shining a laser on them, but by nuking them in superhot plasma. The nuking reduces the cell to its atomic components, which the CyTOF then measures.

Specifically, the CyTOF looks for heavy atoms called lanthanides, elements found in the first of the two bottom rows of the periodic table, like gadolinium, neodymium, and europium. These elements never naturally occur in biological systems and so make useful cellular labels. More to the point, the mass spectrometer is specific enough that these signals basically don’t overlap. The instrument will never confuse gadolinium for neodymium, for instance. Researchers simply tag their antibodies with lanthanides rather than fluorophores, and voila! Instant antibody panel, no (or little) optimization required.

Periodic Table of Cupcakes, with lanthanides in hot pink frosting.
Source: http://www.buzzfeed.com/jpmoore/the-periodic-table-of-cupcakes
Now back to the paper. Nolan (who sits on DVS Sciences’ Scientific Advisory Board) and Bodenmiller wanted to see if mass cytometry could provide the sort of high-density, high-throughput cellular profiling that is required for drug development. The team took blood cells from eight donors, treated them with more than two dozen different drugs over a range of concentrations, added a dozen stimuli to which blood cells can be exposed in the body, and essentially asked, for each of the pathways we want to study, in each kind of cell in these patients’ blood, what did the drug do?


To figure that out, they used a panel of 31 lanthanides –- 10 to sort out the cell types they were looking at in each sample, 14 to monitor cellular signaling pathways, and 7 to identify each sample.


I love that last part, about identifying the samples. The numbers in this experiment are kind of staggering: 12 stimuli x 8 doses x 14 cell types x 14 intracellular markers per drug, times 27 drugs, is more than half-a-million pieces of data. To make life easier on themselves, the researchers pooled samples 96 at a time in individual tubes, adding a “barcode” to uniquely identify each one. That barcode (called a “mass-tag cellular barcode,” or MCB) is essentially a 7-bit binary number made of lanthanides rather than ones and zeroes: one sample would have none of the 7 reserved markers (0000000); one sample would have one marker (0000001); another would have another (0000010); and so on. Seven lanthanides produce 128 possible combinations, so it’s no sweat to pool 96. They simply mix those samples in a single tube and let the computer sort everything out later.


This graphic summarizes a boatload of data on cell signaling pathways impacted by different drugs.
Credit: (c) 2012 Nature America [Nat Biotechnol, 30:858--67, 2012]
When all was said and done, the team was able to draw some conclusions about drug specificity, person-to-person variation, cell signaling, and more. Basically, and not surprisingly, some of the drugs they looked at are less specific than originally thought -– that is, they affect their intended targets, but other pathways as well. That goes a long way towards explaining side effects. But more to the point, they proved that their approach may be used to drive drug-screening experiments.


And I get to write about it. 

Leaky gut and wonky immune response might be double whammy leading to inflammatory bowel disease (in mice)

A case of ulcerative colitis, a form of inflammatory bowel disease.
Photo via Wikimedia Commons. Credit: Samir.

A two-hit punch in the gut might explain why some people find themselves alone among their closest relatives in having inflammatory bowel disease (IBD). The double gut punches come in the form of a compromised intestinal wall coupled with a poorly behaved immune system, say Emory researchers, whose work using mice was published in the journal Immunity. IBDs include ulcerative colitis and Crohn’s disease, the latter of which is slightly more common in women.

An inflamed gut is the key feature of IBD, which affects about 600,000 people in the United States each year. Typical symptoms include bloody diarrhea, fever, and cramps, which can come and go with bouts of severe inflammation punctuating relatively calm periods. The going explanation for these disorders is a wonky immune system, but some breach of the barrier that keeps your gut contents in their place is also implicated. Researchers also have identified a link between bouts of gastroenteritis–known around my house as “throw-up” illnesses–and development of IBD. What’s remained unclear is how people who have these so-called “leaky guts” don’t develop a disease like Crohn’s when a close family member with a leaky gut does.

These hints in humans led the Emory investigators to examine the interaction of a compromised gut and the immune system in mice. The mice in the study had ‘leaky’ gut walls because they lacked a protein that usually ties cells together into water-tight sheets. Without these proteins sealing up the intestinal lining, bacteria and other components can make their way their deeper into the intestinal wall, triggering chronic inflammation.

The thing is, these mice with their leaky guts don’t develop colitis spontaneously, a situation, the investigators hypothesized, that  reflects families full of people with leaky guts but rarely IBD.  Permeable intestines alone aren’t enough. Some other dysfunction related to the immune system, they figured, must pile onto that leakiness and bring on the inflammatory disorder.

If you’re an immunologist–which I am not–an obvious choice for investigation is a class of immune cells called T cells. These cells come in a dizzying array of types, but one way to narrow them down relies on a protein that some but not all of them make. Pulling out the T cells that make this protein, says Timothy Denning, PhD, a mucosal immunologist at Emory and study author, is “the simplest way” to start examining the immune system involvement because these cells play a ton of roles in balancing different immune responses. So, they first collected the T cells carrying this protein from the mouse intestines.

“There are good and bad” versions of T cells carrying these identifier molecules, though, says Denning, so the next step was to find the “good” ones that might be protecting mice in spite of their sieve-like intestinal linings. To achieve that goal required some fancier lab moves. “We stimulated the cells and looked at the cytokines (immune signaling molecules) they make,” explains Charles Parkos, MD, PhD, an experimental pathologist and mucosal immunologist at Emory and also a paper author. “We found that the cells in the mice that were better protected predominantly secreted TGF-beta, a prototypic marker for ‘good’ cells.”

One of the things T cells do with TGF-beta is to talk to B cells, another class of immune cell. B cells take responsibility for remembering what’s attacked you in the past and marshaling forces if it attacks again. Also, when B cells are stimulated, explains Parkos, one way they respond is to release proteins–antibodies–that target the offending invaders. In the gut, the kind of antibody the B cells make in response to the TGF-beta message is immunoglobulin A, or IgA. This antibody “keeps bacteria in check,” says Denning, and also probably “broadly neutralizes lots of different microorganisms” in the intestines, adds Parkos.

The Emory-based team found that when the leaky-gut mice also had an IgA deficiency, they became more open to the types of immune cells that cause gut inflammation. The animals also were far more susceptible to colitis triggered by a chemical treatment in the lab and had much worse disease. Without the IgA, the mice couldn’t dampen inflammation triggered by bacteria slipping through the intestinal breaches. The results of this two-step physiological fail, in mice, at least: severe inflammatory  gut disease.

Denning cautions that these results in mice don’t suggest a rush to TGF-beta or IgA treatment for inflammatory diseases. “TGF-beta has many effects and on many different cell types, and too much is not a good thing because it’s known to play a role in fibrosis and cancer,” says Denning. “If your child had IBD, the last thing you’d want to do is to give TGF-beta.” Much more work has to be done, he adds, for a better understanding of the implications of these results before anyone starts talking about therapies. Parkos agrees. “To our knowledge, administration of TGF-beta is not a viable therapy.”

The same applies for IgA, Denning says. “We couldn’t just take any old B cells and get them to make IgA and put it in and hope that it would do something,” he says. The reason, he explains, is because B cells make many different types of IgA molecules specific to foreign invaders they encounter, a process that happens on the spot, not in a lab dish. “We need to understand much more about the basic mechanisms, but we do believe that these pathways would be critical to induce in people who are more susceptible to IBD, such as first-degree relatives.”

Some research groups are conducting trials to treat IBDs with helminth worms–intestinal parasites–on the hypothesis that their presence would induce a balance in the immune system and tamp down an overactive inflammatory response. The balance in this case is supposed to be between two competing aspects of the immune system, called Th1 and Th2. But one issue in these intestinal inflammatory disorders, says Denning, is that Crohn’s is linked to Th1 hyperactivity while ulcerative colitis is associated with Th2.

Yet the worms appear to show some beneficial effects in both disorders, in spite of the different involvement of Th1 and Th2. The TGF-beta signaling effect on IgA that the Emory group identified operates by a third component, tentatively identified as Th3. Both Denning and Parkos are intrigued by the possibility that the presence of helminths might trigger this pathway, rather than influencing Th1 or Th2, explaining why worm treatment has sometimes proved useful for both Crohn’s and ulcerative colitis.

As for why IBD arises, the researchers hope their findings answer some questions. “There are different camps in the IBD community,” says Parkos. “Some say immune system, some say barrier, others say genetics or environment.” What they have with their results, he says, is evidence showing that a leak alone is not enough and that a wonky immune system alone is not enough. But the double-whammy of a leaky gut and an absence of immune protection “dramatically increase susceptibility to disease, and that helps explain why diseases are so complicated,” he says.

The use of parasitic worms for these inflammatory diseases arose from the concept of the hygiene hypothesis, the idea that we’re too clean in the modern developed world, leading to an immune imbalance that can include chronic inflammation and autoimmune disorders. Asked about any links between the hygiene hypothesis and this pathway to IBD they identified in mice, Denning says, “It’s not obviously all about the parasites. That’s just one key thing–it’s probably an exposure to a lot of different types of things in your gut and airways.” He describes the immune system as being a thermostat that registers a specific set-point early on based on these exposures. This set-point, he says, is lower in people who grow up in developed countries like the United States and leads to a “trigger-happy immune system that is ready to fire much more easily.”

That doesn’t mean that a worm infection or just being dirty will prevent your developing IBD. That said, these immunologists both have the same general advice for parents regarding their children. “Being too clean is not a good thing,” they agree. As immunologists, he adds, “We feel exactly the opposite. Go play in the dirt.”

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.
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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).