Think Bomb

Wednesday, August 30, 2006

Worship at the Double Helix Altar

One of the courses I’m taking this year is Genomics, the study of the structure, content, function, and evolution of DNA. Our instructor, Barrie Robison, began the course with an interesting statement on our first day:
“You all know the central dogma of DNA correct? Everything moves from gene to protein, with RNA in between?”
We all nod in agreement.
“Well, this class is all about messing with that concept. Seriously.”

There’s a lot more to DNA than just genes, and there’s a lot more to genes than just a data spew or “blue-print” for the cell to follow. Conveniently, the book I’m reading: Monkeyluv, by Dr. Robert Sapolsky is hammering on the topic as my Genomics course. I think Dr. Saposlky and Dr. Robison would agree that there are some heavy misconceptions among the American public about DNA.
Dr. Sapolsky notes that there are two major false assumptions: the notion that biological information flows outward from the genes (“nobody tells a gene what to do”), and that genes have overbearing influence (“when the gene commands, the cell listens”). This would be to say that genes have full power over all cell functions; they are the commanders of commanders!

These two assumptions are ingrained at a young age. I recall the middle school jokes about bad genes; anything that was possibly wrong with you, you could just shrug off and blame on your genes. Whether you were depressed, chubby, or not so great at math we were all singing the same tune that I still often hear today: “it’s just my genes.”

And yet, many of us know these assumptions must be false if we take a few minutes for deductive reasoning. If genes dictate every action of the cell, then why can our environment have so much influence on our biological functions? A cell cannot know from code alone that the weather’s getting hot or cold and it’s time to acclimate, that something good has just happened and it’s time to make you happy, or that it’s morning now and time to wake up. If genes were the end all dictators, then why do we even bother with upbringing? Why would we say good parenting is key?

A good example to stress that the same genes can have different results comes from my childhood experiences with the identical Cooper twins. I remember when we were all about six Ashley and Andrea Cooper looked a lot alike although they had slightly different personalities even then. By the time high school was over, the two had shaped into completely different individuals. Andrea was smaller with a different face due to “picky eating” growing up and an insatiable love for ballet. She was shy and a bit mousey. Ashley was slightly larger (although still quite slender) with an outgoing personality that had her pursuing and enjoying a life in the spotlight as a member of the drama club.

This could not be if genes where the determinant factors! Rather, a better analogy for the cell and genes would be to say that the cellular environment is like a great, busy community. The DNA is in the central office (the nucleus) but having a constant dialogue with RNA and proteins in the cytoplasm. Recall my article from a couple weeks ago on bipolar disorder and clock genes? Circadian rhythm was maintained by a constant interaction of DNA, RNA, and proteins. Proteins can feed back into the nucleus and have either inhibitory or excitatory effects. Proteins don’t have to be made within the cell by that DNA either. Chain reactions set off by proteins in the cell membrane can effect DNA, as can some hormones, like estrogen, that move directly through cellular and nuclear membranes to act on DNA. No gene has a mind of its own; you can’t simply put a pile of DNA somewhere and expect it to grow. This is why cloning often takes hundreds of tries—the correct cytoplasmic components in the egg of the parent must be present and active before life can begin.

I don't want to discredit DNA and genes too much, there are some genes that encode very specific traits (and diseases) and genes have a great influence on all of us, but there are many ways to control gene expression. It can be done indirectly by affecting the machinery of protein production (tRNAs, ribosomes, transcription factors…), by modifying the secondary code, RNA (alternative splicing, RNA modification, RNA interference…), or directly by physically moving or binding to the DNA. The DNA is never actually modified (unless unintentionally by mutagens), but it can be moved in such a way so that a less “useful” portion is buried deeper, it can be turned "on" and "off" by proteins, and it can be enhanced or insulated.

All of these factors come together to make an organism that is far more than just the sum of all its genes. We are products of every action, and interaction, of both our genes and environment.

Sources: Robert Sapolsky (left). Monkeyluv. 2005

Tuesday, August 29, 2006

Traveling the Salmon River in Search of Evolution

For this week’s Blue Monday I interviewed Mathew Burns from Scott Nuismer’s lab. Like last week’s interviewee, Matt has been looking at a very specific case of coevolution (only a little closer to home).

As one travels up the Salmon River, one can find moths from the genus Greya and their host, the flowering Heuchera grossulariifolia plant. Like the Yucca moths and Joshua tree, these two species are in a constant evolutionary arms race. Unlike the previously mentioned species though, there is not a distinct group of plant to go with their distinct moth population. Instead, there is a convenient gradient of coevolution that can be seen as one travels up the Salmon.

Imagine yourself on hike along the beautiful Salmon River. As you travel, you will begin to see plants with thicker stems and hairs along with corresponding moths with longer ovipositors.

Why does this occur and what genetic mechanisms are at play here? That is what Matt and the Nuismer lab is trying to discover. One interest is how polyploidy (multiple chromosome sets) shapes the host range of their predatory insects. Unlike us, plants can pass on multiple chromosome sets to their offspring. Even the most minor chromosomal duplication in humans produces disastrous effects (for example, three copies of chromosome 21 produces Down Syndrome). Additional chromosome sets are not always a problem in plants though, so long as they are inherited in even numbers so they may be separated evenly during gamete formation. Polyploidy, along with other types of gene flow and selection, shape the population of Greyas and their flowers along the river.

The Nuismer team hopes to develop and test mathematical models of the gene flow occurring in this Salmon River area, including models that helps explain the geological structure that shapes and is shaped by these host-parasite interactions. These models could hopefully be applied to more widespread populations and useful in predicting possible evolutionary outcomes in the future.

Source: the Nuismer lab web site,

Friday, August 25, 2006

Good Taste is Sometimes a Pain

As I sliced my onion for an omlete the other day, I became curious as to why they make your eyes water and sting. The cutting of onions results in the rupturing of the cells within the onion. This disrupts the cell structure, allowing enzymes to come in contact with sulfides also found in the cells. The enzymes break the sulfides down into smaller compounds of sulfenic acid. These exist in a gaseous state at room temperature, allowing them to reach your eyes. Some of these compounds react with water in the eye, forming some sulfuric acid which stings and burns!

So if you're cutting onions, stand back a bit and don't rub your eyes, it'll only get worse.

Image source:

Wednesday, August 23, 2006

Facts, Theory, and Bunk

I know a lot of scientists and science majors read this blog so I don’t often write about some of the more basic aspects of science. One of my goals though is to make this blog fun and understandable even for the unscientific crowd. So today, I thought I’d talk a little bit about science itself and how it’s done.

Right now I am a teaching assistant in the biology 102—“Biology and Society” for non-science majors. For me, the lectures are a welcome break between biological chemistry and organic chemistry on Mondays, Wednesdays, and Fridays. For many the students, it will be their only venture into the scientific realm during their college career.

Margaret Ricci, the instructor for the course, is personable and fun and presents science in a way that’s entertaining and understandable for all listeners. She remembers to take things from the viewpoint of a non-science major, something many of us scientists forget how to do!

Today she went over some of the most basic concepts in science—facts, theory, and bunk. She started the lecture off with a real skeptics view saying that facts are, to a degree, overrated. Everything in science is built brick by brick, through careful observation and experimentation. Each fact is like a brick, but this building has no pan and often bricks must be reexamined and re-laid.

“That’s why they call it research,” says Margaret, “because you have to go it again and again and again.”
(“Also know as job security for us scientists,” she jests.)

As the bricks, facts are a little cheaper, but theories are the foundation onto which whole new towers can be built. We’re not talking about the kind of theories you have at four in the mornin’ after a few margaritas, she emphasized. That is the colloquial meaning of theory. In a scientific community, the theory must be solid before more bricks are laid. That means a great number of observations are tied together by the theory, it makes predictions that can be tested, and it is supported by accumulated evidence. A theory is not easily toppled, but it does happen. Earth quakes and shakes are no stranger to science!

One of the most important elements she hit on today was credibility. Before something can make it to the fact phase of becoming a “brick,” it’s got to go through the “factory.” The outcome of an experiment must be measurable. I had some trouble with this one in my last experiment because although certainly relevant, opsin scoring is not quantitative or linear. Many professors who heard my talk on opsin expression we acing for a good, linear graph of the outcome, something I could not provide!

In addition to a measurable outcome, the experiment needs “replication,” a large “n.” This means multiples runs or a large population of subjects. An experiment also needs controls, a group that is comparable to the experimental group. Ideally there is only one variable being tested: randomization, placeboes, and blind experimentation help reduce the chances of interference by confounding variables. A critical thinker needs to ask: “is this relevant to what could really be happening?” For example, when performing an experiment in vitro (test tube work), a lot of questions arise about whether this is relevant to what could actually be happening in the tissues of a living organism where so many inter and intra cellular mechanisms are at play. Consider last Wednesday’s article no bipolar disorder and depression (Yes, even my articles must be taken with a grain of salt!). Researchers found that lithium in vitro affected certain cellular clock components. Is this how it works in the living organism? Possibly.

Finally the experiment must be replicatable by others and proven multiple times. This brings up another item to consider about last weeks article and, as Margaret pointed out, pretty much ALL newsworthy articles, is that they’re usually preliminary studies. I took my story straight from the newest research, but there have not yet been follow-up studies. Will the clock version of how lithium works to stop bipolar disorder be disproven? We don’t know, and we may never know, because by then many would no longer consider the subject news!

In any case, I am glad to be a part of a class that teaches non-science majors one of the most important aspects of science: critical thinking and a skeptic eye!

Image source: (confused man)

Tuesday, August 22, 2006

A Precarious Partnership

In the hot desert regions of southwestern California and Arizona it seems that life has few options in its struggle to endure. Organisms are forced to make strange and intimate partnerships, one of the most interesting being the Joshua tree (Yucca brevifolia) and its sole pollinator: the yucca moth. The tree must trade "seeds for seeds" as the yucca moths are not only its pollinator, but its parasite as well.

For this Blue Monday, I interviewed Jeremy Yoder from Olle Pellmyr's lab. He and others have studied thoroughly this strange pairing of yucca and yucca moth as it may provide insight into elements of how co-evolution and ecological partnerships work.

Here is a little more on how their relationship works:
The moth pollinates the tree as it lays its eggs into its flowers. On the up side, the tree is fertilized and those seeds that survive may create the next generation. On the down, the moth larvae must eat the seeds to provide new pollinators for the next generation.

This seems like a very precarious relationship. After all, what stops the moth from simply overdoing it and laying far too many eggs, killing off the Joshua trees and later yucca moths all together?

The answer is natural selection. Not just any natural selection either, but selection that is mediated by the Joshua tree itself! With-in the fruit of the Joshua tree is a mechanism that destroys over-egged fruit. The tree can sense when the partnership is being abused by a trigger deep within the fruit. When the eggs or ovipositor of the moth delve too deeply, the fruit is aborted, rejected by the Joshua tree. The Joshua tree misses an opportunity for seeding in this way, but it also eliminates over-egg laying genotypes by destroying the eggs of the abusive moth as well.

This puts the yucca moth and Joshua tree in a constant state of co-evolution that makes for some fairly noticeable morphological differences over evolutionary time. Interestingly, the trees and their corresponding moths have marked differences from region to region as dictated by their interactions with one another. Jeremy has found that trees and their moths in two slightly separated regions have taken separate approaches to the partnership. In the westernmost regions, the trees have a bottle shaped pistil to their flowers for the long ovipositors of their moths, while in the Eastern regions the pistils are more jug-shaped to accommodate smaller yucca moths.

Using genetic analysis, Jeremy and the Pellmyr lab hope to discover if these changes are truly due to inheritance and natural selection among these close knit species or not. It is projects like these that allow us to witness evolution in action and magnifies the delicate, fascinating interactions of organisms in their environments.

Source: The Pellmyr lab web site:

Friday, August 18, 2006

Blackberry Summer Cake!

Since there are so many summer birthdays in my friends circle, I thought it would be fun to make a cake for this Fridays Science of Yum! Thanks to all those b-days, I've perfected a really quick and easy cake recipe: blackberry summer cake.

Simply take any of your favorite chocolate cake box mixes (this usually requires three eggs, some water, and some vegetable oil in addition)

A couple boxes of Jiffy white cake frosting

A jar of blackberry preserves, preferably whole fruit or sugar free.

Make the cake up in two round cake pans, as directed by the box.
Once the cakes have cooled, place the first layer on a serving plate and frost. Add a thin layer of blackberry preserves for the middle. Plop the second layer on, frost, and add more preserves on top. Let chill in refrigerator for at least a couple hours. It tastes so good!

One of the things that makes this cake possible is the old process of canning. Canning, made popular in the early 1800's, is a simple yet genius way of preventing bacterial contamination and preserving foods. The food stuff, blackberries in our case, are boiled in the can or jar to kill off all the bacteria. Next the jar is sealed air tight, to disable entry of any new pathogens. This seal can be a bit of a trick at times, if you're not exactly the most muscular person (like myself!). A good way to relieve some of the pressure and allow for easier opening of the jars is by smacking the edges of the lid from the top with a spoon.

Wednesday, August 16, 2006

Resetting the Clock on Bipolar Disorder

I was flipping through an old issue of Science (Feb. 2006, so not that old) when I happened upon an article with relevance to bipolar disorder. Since I've know a few people with this condition, I was immediately taken by it.

Bipolar disorder is characterized by episodes of mania followed by a long depressive lull. The patient will often feel euphoric and very active during manic periods, usually going with little sleep, working tirelessly on projects, and talking often to themselves or others. Some argue that manic depressive disorder should not be treated, because the ideas that individuals touch upon during the manic phase are sometimes novel or useful. This phase usually only lasts a couple weeks though, and many feel it is not worth the months of depression that follow. In high contrast to the flitting, rapid speech of the manic phase, the patient will often speak more slowly during a depressive episode. The depressive phase is draining; the patient often feels worthless and unmotivated (Carlson, 533-534).

There are a few highly effective treatments of this disorder though, the most widely known being lithium carbonate. More specifically, it is the lithium in the mixture that is thought to be the active ingredient. Lithium is most effective when administered during the manic phase. It immediately brings the person back to a normal state of functioning and prevents the depressive lull that would normally follow the mania. The mental side effects of the drug are pretty much nonexistent; it does not impair cognitive functions or regular emotional responses to life. A patient on lithium, for example, can still feel depths of sadness or happiness appropriate to a situation, but does experience the prolonged, excessive mania or the months of depression that he or she may otherwise feel. Unfortunately, there are side effects for the body with prolonged use of lithium. Lithium carbonate is not always easy for the body to process! If the patient’s blood lithium levels are not carefully monitored, the individual could develop hand tremors, excessive thirst and urine production, and possible weight gain (Carlson, 535). Carbamazepine and other drugs have been developed in the hopes of producing similar effects to lithium, but without any of the related toxicity problems. Finding better drugs has been a difficult process though, because how lithium works and what cellular pathways it works on are not yet known! I recall reading just last semester in my physiological psychology text that researchers “…have not yet discovered the pharmacological effects of lithium that are responsible for its ability to eliminate mania.”(Carlson, 536).

This is where that article in Science magazine comes in! It appears that the lithium-sensitive component has been found, at least in vitro. According to Yin et al., the nuclear receptor Rev-erba is directly effected by lithium and activity of glycogen synthase kinase 3 (GSK3) is effected as well. GSK3 is the enzyme responsible for regulating circadian rhythm in several model organisms. Cellular circadian rhythms are maintained by interconnected transcriptional feedback of clock genes involved in multiple negative and positive feedback loops.

Initiated by signals from the hypothalamus, transcription factors BMAL1 and CLOCK activate the clock genes (Per1, Per2, Cry1, and Cry2), creating the corresponding PER and CRY proteins. These proteins form dimmers in the cytosol and return to the nucleus to inhibit there own transcription. It is GSK3 that directs the length of this process by degrading PER in the cytosol, lengthening the time before negative feedback begins. Another feedback loop involved in circadian rhythm includes Rev-erba. Rev-erba's primary target is the Bmal1 gene, which is active during the night phase of circadian rhythm. Like PER and CRY, Rev-erba inhibits its own transcription, so too much of the protein can lead to over inhibition, while too little may effect expression of Bmal1.

This study reveals that bipolar disorder is probably more a disorder of circadian rhythm than anything else, and traditional anti-depressants such as MAO inhibitors are not likely to help in the long run. It also provides possible hypothesizes for the cause of bipolar disorder; could it be that patients have an inability to degrade all of the Rev-erba protein, leading to ill-maintained oscillation of clock genes? Could it be some other mutation in the circadian pathway? Another exciting aspect of this research is that understanding the biological pathways behind the disorder will allow for development of better drugs, which act directly on target enzymes or genes, with reduced side effects.

Here is a link to the article:

Sources: Carlson. Physiolgy of Behavior. 2003
Yin et al. "Nuclear Receptor Rev-erba is a Critical Lithium-Sensitive Component of the Circadian Clock." Science pg 1002. 17 feb 2006
Images: (masks) (brain clock)

Tuesday, August 15, 2006

Forbidden Love:
Tamias ruficaudus
and Tamias amoenus

This Blue Monday I had the pleasure of interviewing my former lab TA, Masters student Sarah Hird. Sarah is working in Jack Sullivan’s lab, investigating a cute-n-cuddly (although admittedly sometimes rabies ridden) Idaho favorite: chipmunks. She is mainly examining two species; red tailed (Tamias ruficaudus) and yellow pine (Tamias amoenus) chipmunks as well as their four subspecies that appear in overlapping species boundaries in Idaho and Montana.

Traditionally, species were thought to be discrete with no possible interbreeding. It appears though, in the case of these chipmunks, that species lines have been burred. These “loose chipmunks” show genetic markers that do not line up with the traditional measure of speciation in chipmunks: the penis bone. The penis bone may sound like an odd morphological difference to look for, but primates are actually a rare variety of mammal in that we do not have penis bones. Like most mammals, chipmunks do and they differ in shape and size from species to species.

Sarah is working with new methods of phylogenetic analysis (the estimation of evolutionary trees) to identify the relatedness of these species and subspecies. Primarily, she is utilizing analysis of microsatellite DNA. Microsatellites are sequences of tandem repeating base pairs that are non-functional, and therefore can show more variation between individuals and help determine relatedness. Microsatellites are also commonly used in forensics, to figure out “who done it.” She is looking into mitochondrial DNA as well, which can be an indicator of maternal inheritance. These techniques are important not only to solving the chipmunk mystery, but also help pioneer new techniques for developing phylogenetic trees.

On the Sullivan lab web sit, they write that phylogenetic analysis "has become the cornerstone of evolutionary biology," as it is a more precise method of measuring relatedness, available right in the genetic code.

So will these novel techniques have poor Linnaeus spinning in his grave? Probably not, as biology is a science as changing and adapting as the organisms it seeks to understand. The old Linnaean classification system was the best they could do at the time, but with new technology and the blooming science of genomics we can have a better understanding of organism classification, their evolutionary development, and their relationship to each other.

The Drink!
: Sarah is enjoying a Bloody Marry which consists of 2 shots vodka in tomato juice, 3 drops Tabasco, 1/2tsp Worcestershire, pepper, lime slices and green olives or celery sticks.


Friday, August 11, 2006

Pizza Heaven!

For this Friday’s Science of Yum, my friends and I enjoyed a traditional college favorite: beer and pizza. Although this may sound bland, pizza is more delicious, healthy, and (depending on the toppings you get) can be less expensive than any commercial carry out.

For homemade pizza, you'll need:
2 cups hot water
1 and 1/2 packages quick rise yeast
1 tsp sugar
2 tsp salt
Italian seasonings
1/4+ cup vegetable oil
2 cups wheat flour
2 1/2 cups white flour
Any other toppings you like

Dump warm water into a large bowl. Gently stir in the sugar and yeast. Let stand for ten minutes.

This is when the real magic that makes the pizza crust delicious happens! Yeast is a single celled organism, actually part of the fungi kingdom like mushrooms and mold. Saccharomyces cerevisiae is the most commonly used yeast in baking and brewing. Each brand of yeast sellers you see in the supermarket owns their own strain which they have bred to be what they feel is a superior yeast. As the bowl sits seemingly peaceful on your countertop, the yeast is busily eating the sugar and making its characteristic byproducts, alcohol and carbon dioxide:
C6H12O6 (glucose) →2C2H5OH + 2CO2

Letting the yeast sit for ten minutes allows it to live and reproduce for a bit, because when you add the next ingredient, salt, some of the yeast will die. After the salt add the Italian seasonings, then the flour. Stir in as much as you can, then begin kneading the dough. The kneading of the dough makes it more elastic because of the properties of the gluten protein in the wheat. It is this stretchy gluten material that captures the carbon dioxide of the yeast in bubbles, giving the dough and more spongy texture. The dough still needs time to maximize this yeast-gluten interaction, so let it rise for 30 min. This may also be a good time to start preheating your oven to 425 degrees.

Once the yeast has had some time to work its magic, you're ready to lay the dough onto two pizza pans (since we didn't have pizza pans, we used cookie sheets, which works just as well!).

Pour some vegetable oil onto the center of each pan. Divide the dough into two even balls, and place over oil in center of pans. Starting from the center, knead the dough out to the edges, making certain that there is always enough oil under the dough to coat the pan. Oil up the top of the dough as well. Bake this dough for 11-15 minutes, until you begin to see a slight browning of the crust. Now, if you’re brewing, you’re very interested in keeping the alcohol byproduct, but as we are making pizza crust, we simply allow the alcohol to evaporate when we bake the dough. It's the CO2 we're really interested in, and you'll see your dough get nice and thick from it as it bakes.

Take out the dough and add your sauce, cheese, and toppings. These can be chosen according to your preference, we used a pre-shredded pizza cheese mix, but cheddar, mozzarella, or provolone will do (just please don't use American cheese!). We added salami, olives, tomatoes, and eggplant as toppings.

Once the toppings are on, let them cook for 10-14 minutes, until there is a slight browning of the cheese. Now it’s ready to serve! We decided to give a full celebration of yeast's amazing abilities by including a round of brewskis!

Here’s a photo of the pizzas, which were delicious:

Since I had extra tomato and eggplant, we sliced them, let them soak in the left over juice from the olive can and threw on some Italian seasonings. It made a real tasty addition to the meal:

Sources: Wikipedia
Image (yeast):

Wednesday, August 09, 2006

My Research on the Sonic Hedgehog Gene Mutation in Zebrafish!

Yesterday I had the wonderful opportunity to share my research with fellow scientists at the INBRE conference in Coeur d'Alene. My poster can be seen above (sorry you can't make out much more than the title) and I'd like to share with you all the juicy details about hedgehog genes and zebrafish today!

My entire summer thus far has been spent researching hedgehog (Hh) genes in zebrafish (Danio Rerio). Despite the name, hedgehog genes have little to do with hedgehogs, other than that they, like all vertebrates, possess them too. Hedgehog genes produce hedgehog proteins that play an important role in regulating the development of many cell types. They were so named for the mutation that led to their discovery; a mutation that would create a spiky, hedgehog appearance in fruit flies. In vertebrates, hedgehog proteins are known to play an important role in signaling from the midline of the developing organism, allowing it to maintain body symmetry as it grows, as apposed to a cycloptic look. Some studies have been done on their role in limb and trunk development, but my interest this summer has been the eye.

At some point in their evolutionary history, zebrafish had their genome duplicated and now have two versions of the hedgehog gene; one called sonic hedgehog and the other tiggy-winkle hedgehog (proof that smart-assed scientists get published too). This fact has some pretty sweet implications to research. Scientists have produced a sonic hedgehog knock-out mutant (called syu), which completely lacks the sonic hedgehog gene but retains tiggy-winkle. A complete absence of all hedgehog protein signaling would kill the embryo too soon, but allowing one hedgehog gene to remain while the other is absent will give us an opportunity to examine the effects of reduced hedgehog protein signaling on the development of the retina.

In previous studies, the rate of retinal mitosis was found to be reduced in syu mutants. In about half of the mutants, no cell differentiation occurred in the retina. In the half that did undergo differentiation, the spread of red and rod opsin (the receptor that reacts to various wavelengths of light) expression was very limited.

I had an opportunity this summer to look into the expression of other photoreceptor specific genes in syu mutants, including blue opsin and the transducins (the g-protein coupled to the opsin).

To study these mutants, fish must first be bred and sorted, which I have made a nifty diagram of below:

Since full mutants don’t live past 75 hours post fertilization (hpf), two zebrafish heterozygous for the mutation must be bred and the mutants are sorted out later by morphological differences. You can really see the difference below, at 50 hpf right after I dechorionate them (decorionate = pop open the eggs).

The embryos are fixed (killed and preserved) at 70 hpf, because this is an optimal time to look at photoreceptor development. Next, I used in situ hybridization to detect gene expression. In situ hybridization involves attaching complimentary RNA probe to messenger RNA (the first product of gene expression). We make the probes using E. coli bacteria, then extract the probe and introduce it into the tissue of the fixed embryo. Once exposed to the probe, the tissues have been prepared in such a way that will allow them to take up the probe and hybridize it to their mRNA. The next step involves attaching an antibody to that, then a dye is added that reacts with the antibody and produces purple coloration wherever gene expression is taking place. Below is a series of photos of the magnified eyes of mutant and control zebrafish. All the purple splotches and dots are where gene expression of our target genes is occurring. As you can see, the mutants had extremely reduced expression of these genes.

For each probe, I've tested 1 to 2 clutches of embryos. I hope to collect more embryos and produce additional data for statistical purposes. After that, I hope to look at how we can recover these lost photoreceptor cells by adding certain chemicals like retinoic acid or exogenous hedgehog proteins. This is exciting research because diseases that affect photoreceptor cells, such as macular degeneration, are a leading cause of blindness in the elderly population. Understanding how photoreceptors form by studying zebrafish may provide insight for future medical applications.

Monday, August 07, 2006

While I'm here in Coeur d'Alene, I thought it would be fun to interview my mother, Randi Lustig, a long time Coeur d'Alene resident and epidemiologist at the local health department. Epidemiology is the study of the causes, distribution, and control of diseases in populations. The health department and epidemiologists are an essential part of any community as they seek to mitigate the spread of disease and ensure a healthy population.

In Idaho, there are over 60 reportable diseases, most of which are communicable and present a considerable public health concern. Some of those diseases include Chlamydia, a common STD, West Nile Virus, Hepatitis A and other food borne diseases, Pertussis (whooping cough), and Meningitis. The work of an epidemiologist is as variable as the people they treat and the diseases they encounter. It combines a bit of sleuth skill to find out who’s at risk, the care of a nurse when dealing with patients face to face, and sometimes a commander-like role is called for to get a handle on potential epidemics.

For example, rabies is a concern in Coeur d'Alene as it is spread by our large bat and dog populations here. Finding the sources of the disease usually involves sending out the heads of infected animals for examination.
"When heads roll, we pack 'em," says my mom of this curious aspect of her work life.

Although some diseases are dealt with only a few people (or bats or dogs for that matter) at a time, others require a more wide scale effort for control. A case if Tuberculosis (TB), one of the deadliest diseases today, caused a recent scare at one of the local high schools. The health department's nurses had to test over 1300 individuals for exposure to the bacterium. The methods behind the TB test are intreguing; a fluid tiberculin solution is injected into a small bubble under the arm of the skin (only millimeters wide, nothing too squimish!). After a few days, the body's immune response will indicate whether that person has encountered the diseases before. If they are having a secondary immune response, the body will quickly recognize the particles in the solution and begin to inflame the small bubble more than a primary immune response, which takes longer to react, would. Depending on how much the bubble has grown, nurses can identify whether the person should have further testing of is not of conern.

1300 is impressive, but far from the health department’s max load. After 9/11, the Center for Disease Control started a national stock pile system that would allow shipping of antibiotics, IV, and other important materials to outbreak sites in 12 hours. In June the Coeur d'Alene health department ran an exersise to see if they could potentially provide anti-anthrax biotics to the entire district population, and, "yes," my mom says, "it's doable."

The Drink!: My mom's always been a big fan of red wine and one of her current favorites is Sata Ema Merlot, which she is enjoying on her back porch.

Image source:

Thursday, August 03, 2006

Field Trip into the Mind

Last week I had the pleasure of visiting Dr. Mark DeSantis’s lab to examine actual preserved human brains with my fellow Research Experience for Undergraduates participants. Dr. DeSantis was kind enough to provide a tour of the structures and functions of some of the readily viewable portions.

Most of the brains were cut right down the middle, in a way that would divide the left and right sides of your face exactly. This cut also divides the left and right cerebral hemispheres exactly, although the cerebellum, being less symmetrical, is cut mid-lobe. Cutting the brain in this fashion is called a midsagittal cut; its popularity is no surprise as it exposes some interesting structures.

Unfortunately, my images were too small to label myself, but there is an excellent labeled midsagittal diagram in Carlson’s Physiology of Behavior, my text for physiological psychology. It is pictured below so you can follow along as anatomical structures are mentioned. If you would like to see a larger image, here is a link to the University of Texas’s posting of that same diagram.

Looking at a midsaggital cut, the thing that seems to pop out right off is the corpus callosum. The corpus callosum is a brain favorite of Dr. Terry Armstrong whose work is mentioned in previous blog entries. He theorizes that a large posterior region of the corpus callosum (called the splenium) may be found in more sensitive individuals as its fibers project and help connect portions of the limbic system (among other things), while a large anterior region (called the rostrum) could be linked with greater reasoning capacity as it projects to the frontal lobes of the right and left cerebral hemispheres.

"You deserve a man with both," he joked with me, "one who's smart and sensitive."
I can imagine it now—-a futuristic dating service with full CAT scan included. Find your true love for only five thousand bucks! Who knows? I imagine anatomical structures alone will never provide full insight into the personalities or overall intelligence of an individual, though.

In addition to the corpus callosum, you can also see much of the limbic system when viewing the brain midsagittally. Our anatomy guide, Dr. DeSantis, pointed out all of the visible parts for us. The limbic system is fascinating to me because it is so fundamental yet still mysterious.

Again, Carlson and the University of Texas provide us with a great figure:

Here is the link to that same figure.

You can see the amygdala, often called the “seat of emotion,” which is known to be involved with aggression and fear. The hippocampus, the elongated structure snugged right up to the amygdala, is essential for laying down memories, especially episodic memory. The hippocampus receives input from subcortical regions via the fornix, also shown. Not much is known about the function of the mammillary bodies, which receive input from the hippocampus through the fornix, although they too appear to be involved in memory. Not labeled is nucleus accumbens, which plays a role in pleasure and our internal reward system. The olfactory bulb, which extends from the limbic region to right over the nasal passage, is responsible for our sense of smell. Many theorize that the olfactory’s close connection to the brain’s memory and emotional centers are what make smells such a potent source for flashbacks, recall, and those sentimental feelings. Some texts also include the hypothalamus as part of the limbic system. The hypothalamus is a fascinating character itself, regulating important autonomic and homeostatic functions like hunger, thirst, arousal, and heart rate by releasing hormones. The thalamus, which can be seen in the first diagram, is like the brain’s routing station, receiving and relaying signals to various parts of the brain. Before I dive into too much detail though, I’d like to save discussion of related areas like the septum, ventral tegmental area, and the basal ganglia for a later date. As for tonight, I hope you’ve enjoyed our field trip inside the mind!

Eternal links: Check out the anatomy of Einstein's brain at

Neil Carlson. Physiology of Behavior, Eighth Edition. 2004