The reason why I write this blog

Just spotted this headline in a Canadian online news aggregator:

“Severe reactions to H1N1 shot: one death probed”

Then, almost at the very end of the article:

“On the issue of serious adverse reactions to the H1N1 vaccine, Butler-Jones said the rate of anaphylactic events was about 0.32 cases for every 100,000 doses of vaccine delivered - a figure that's within the norm for mass vaccination efforts.”

I just got my shot.

Do we really need two to tango?

It’s not easy finding an adequate male for reproduction. He needs to be manly, but not macho. He needs to be funny, but not immature. He needs to be romantic, but not needy. Ever wonder why we bother to go through the whole finding-a-mate dance when some species can just self-fertilize? Many animals and plants reproduce like us by outcrossing (which means two parents), but there are also a number of selfing species (meaning self-fertilizing or asexual reproduction). Oddly, when you look at the numbers, outcrossing doesn’t make a lot of sense. When selfing organisms (for example, aphids) reproduce, 100% of the offsprings can make more offsprings. When outcrossing organisms reproduce, we end up producing a variable proportion of those pesky boys (50% in the case of humans), who really are no good when it comes to having babies (except maybe for this guy). For many years, scientists have been speculating as to the evolutionary benefit of this numerical disadvantage. Recently, researchers tackled the question in a new way: by recreating evolution experimentally.

First, an important term to define: evolution. For the sake of this post, let’s use a simple definition: evolution is the change in the genetic material (genes, made from DNA) of a population of organisms from one generation to the next. Variations in the genetic material can occur in a few different ways, but a main one is mutations. Mutations can arise due to different factors: for example, a mistake can be made when the DNA is being copied during cell division, or the DNA can be damaged due to exposure to radiation or chemicals.

The study, published recently in the journal Nature, looks at a type of worm, C. elegans. Populations of this worm are composed of males and hermaphrodites, meaning this worm can reproduce both by selfing (hermaphrodites) or by outcrossing with males. The researchers were able to genetically engineer these worms to make two different populations: one that is only able to reproduce by selfing, and one that is only able to reproduce by outcrossing. This created a very valuable tool to look at how these populations deal with various evolutionary hurdles.

The researchers took both populations of worms (the selfing worms and the outcrossing worms) and exposed them to a chemical that increases the rate of mutations (a way to mimic a “sped up” evolution). They also created an environment where each population, in order to reach their food, needs to go over a worm-scale obstacle course. These two steps were important because they both impose a strong selection. Once the experiment was set-up, all the researchers did was let the worms reproduce through 50 generations and looked at which population did better.

Male readers, you’re safe! Even with all the hurdles, the outcrossing population of worms managed to maintain their fitness (or their evolutionary health) over the course of the experiment. The selfing populations of worms, however, showed a significant decline in fitness. To make sure this effect was not just a fluke, the researchers tried a different hurdle: they exposed both populations of worms to a disease-inducing bacteria. Initially, this bacteria caused an 80% mortality rate in both the outcrossing and the selfing worms. This means that the worms quickly had to learn to either avoid the bacteria or become resistant to it. This experiment confirmed what the researchers saw previously: the outcrossing population adapted rapidly to the bacteria and showed a significant increase in fitness over 40 generations, the selfing population did not manage to adapt.

This experiment may seem like a no-brainer (if we didn’t need males, they probably wouldn’t be around anymore, so they must be useful for *something*), it represents the first experimental test of the selective pressures that favor the evolution and maintenance of outcrossing. By digging into the genetics of the worms, the researchers were able to come up with two explanations for the usefulness of outcrossing. The first explanation is that outcrossing reduces the effect of harmful mutations. For example, if part of my DNA is damaged, it can be compensated for in my children if my partner’s DNA is intact. If I wasn’t mixing my DNA with someone else’s, my offspring would inevitably inherit my defective DNA, and this would weaken the population. The second reason is that in selfing organisms, mutations (good or bad) are trapped in a single genetic background. This means that a beneficial mutation can never combine with another that may have occurred in a different genetic background. Therefore, beneficial mutations can never add up or even synergize. This results in stalling evolutionary fitness.

So while it’s sometimes hard to find Mr. Dreamy, it seems like in the long run, it’s worth it.

Meet C. elegans, evolutionary tool extraordinaire

Reference: Mutation load and rapid adaptation favour outcrossing over self-fertilization. (2009) Morran LT, Parmenter MD, Phillips PC. Nature, 462(7271):350-2.

The fine print

Don’t you just hate it when you sign up for a new telephone/internet/cable plan thinking the offer is such a good deal, only to find out three months later that after the “introductory period” you are actually charged way more? You typically only make that mistake once and then learn to read the pesky fine print. In science, just like in advertising, the claims and the fine print need to be scrutinized. And typically, the bolder the claim, the more attention is paid to the fine print. For example, if I’m going around boasting that I discovered that a molecular component Y of the protein X interacts with a sub-component of the peptide Z, chances are, no one will really care enough to read about it (ah, the joys of the PhD thesis). But, if I’m going around claiming that I have a vaccine that prevents AIDS, you can be sure people will read the fine print.

In September of this year, a press conference was held to announce the results of the largest AIDS-vaccine study ever conducted. The study, funded in part by the US Army and having cost a whopping $105 million, was a “first success” in the research for an AIDS vaccine, a “yes we can” moment. However, not unlike the story about the Darwininan fossil, this press conference came before the findings were published in a peer-reviewed journal. When the paper came out in October and the fine print was read by all, the excitement dropped significantly: as it turns out, many results from the study were negative, and the positive results showed that the vaccine only protects a third of the people who got get it, and only for a short while.

The actual article presents the results from three different analyses. The first analysis looked at all the participants in the study (over 16, 000 people). For this group, the vaccine had 26% efficacy. Sounds like a good start, right? The problem is that the p value for this effect was 0.08. This means that there’s an 8% chance that this effect is just due to chance. This is quite a bit over the golden scientific standard of 5%, and should be considered not significant. The second study started with the same amount of participants (16, 000), then excluded around 4000 people because they didn’t follow the protocol exactly (for example, they didn’t get the vaccine at the correct time). Logically, the results should look better. Interestingly, they don’t. In this case, the vaccine still showed a modest protective effect, but the p value was now 0.16, meaning there’s an even bigger chance this is just a fluke. Finally, the third study looked at the initial 16, 000 people minus 7 who turned out to have been infected with HIV before the study even started. In that case, the vaccine still showed a similar effect (about 30% efficacy), but this time, the p value was under the cutoff at a less-than-impressive 0.04. Phew! Something to brag about during the press conference!

The negative, statistically insignificant results combined with a few other issues (for example, the short-term protection offered by the vaccine –only about a year) have drawn a number of criticisms not necessarily of the study, but of the bragging. As for the study itself, opinions are divided. Some see it as a glimpse of hope and an encouraging start, many see it as a weak effect, mostly not statistically significant, and possibly a waste of (a lot of) money.

With all the vaccine controversies and conspiracy theories going around these days, all I have to say is throw this new one in the mix.

Image from Scientific American

Reference: Vaccination with ALVAC and AIDSVAX to Prevent HIV-1 Infection in Thailand. (2009) Rerks-Ngarm S. et al. New Engl J Med. [Epub ahead of print]

To panic or not to panic: An interview with the swine flu (part II)

When the H1N1 story erupted in the media a little while back, I wrote a short Q and A post to give a scientific perspective on the topic. After that I really didn’t give much thought to the H1N1 flu. Since I don’t have a television at home and never listen to the radio, I live in a kind of media void. It’s glorious in there, let me tell you. Unfortunately, I was recently at a relative’s place and watched the news. I was shocked to see an endless stream of panic-inducing warnings and news about the H1N1, so the microbiologist in me decided to revive the topic here on Scientific Chick with the latest scientific information. So here you have it, a second exclusive interview with Mr. Swine Flu himself.

Scientific Chick: Mr. Flu, thanks for accepting to come back on Scientific Chick. How have you been? It seems you are gaining in strength and giving more severe illnesses.

Swine Flu: I’ve been well, thank you, but please notice that I’ve changed my name to H1N1. As you know, we are now in the regular flu season, so I am quite busy going around and infecting people. However, unfortunately for my plans to dominate the Earth, I have not been inducing an increasingly severe flu. It may seem so because with more people infected, the percentage of seriously ill patients becomes more apparent, but I’m still the same guy.

SC: How do you feel about our new H1N1 vaccine?

H1N1: I find it quite sad. You see, the vaccine is composed of my virus brothers, completely killed and inactivated. When talk of the vaccine started, I had a glimpse of hope that maybe, just maybe we could infect humans through the vaccine, but alas, that’s not possible. There is no chance a vaccine containing my dead relatives will give you flu.

SC: Surely with a vaccine so new, there is some chance of things going awry for us humans?

H1N1: I wish! It is often thought that because this vaccine is new, it is untested and unsafe. Unfortunately, because I am so similar to my seasonal cousin, the H1N1 vaccine has been produced the same way regular flu vaccines are produced every year. Health organizations (like the NIH) around the world have conducted rigorous clinical trials that show the vaccine is both safe and effective. It’s been licensed by all the governmental agencies and even though I tried to be very sneaky showing up unexpectedly like I did, no shortcuts were taken.

SC: At least most formulations of the vaccine contain thimerosal, so if we don’t catch you, you’ll at least have the consolation that we’ll suffer from mercury poisoning and all the associated conditions.

H1N1: Well, that would be nice, but you are grossly exaggerating. While it is tempting to blame thimerosal (a mercury-derived preservative) for a number of conditions, there is just no scientific evidence for any sort of suggestion that thimerosal is unsafe. Since the hypothesis that thimerosal causes autism broke out many years ago, scientists have been working very hard to prove or disprove that link. Interestingly, some of the best, largest, most well-controlled and unbiaised clinical studies came out of this controversy, all concluding that there is no link. The irony is that there is more mercury in a can of tuna than in any vaccine.

SC: So really, if I wanted to give up vaccines for fear of thimerosal, I’d also have to give up ahi tuna tacos? That’s just not a possibility. What about adjuvants in vaccines? How do you feel about those?

H1N1: I like adjuvants, because since they boost your immune response to the vaccine, less inactivated virus is needed per dose, which means less deaths in my family. That being said, whether you receive a vaccine with or without an adjuvant depends on where you live. In the USA, no adjuvants will be used. In Canada and some European countries, the vaccines contain adjuvants. Adjuvants are not new, and they also have a good safety track record. I hear a lot of concerns about squalene being used as an adjuvant, but you find squalene in olive oil.

SC: I hear a lot of discussions about Guillain-Barré Syndrome. Should we worry?

H1N1: Guillain-Barré Syndrome (GBS) occurs when your body’s immune system turns against its own nerve cells, and this leads to paralysis. If caught early enough, it can be reversed. And yes, vaccines are among the many risk factor for GBS, at a rate of about one in a million. Guess what else is a risk factor for GBS? Me! The nasty ol’ flu. Pick your odds.

SC: Are you hiding in my tasty pork tenderloin and bacon?

H1N1: No. You can only catch me through coughing or sneezing droplets from someone who is already infected, or through touching something contaminated and then letting your hands get to your face before they get to a sink to be washed.

SC: Should I wear a mask if I want to avoid you?

H1N1: Also a no. The Public Health Agency of Canada doesn’t recommend wearing surgical masks to avoid catching me. While this may sound counter-intuitive, there is actually scientific evidence that shows that this is not an effective way to prevent flu transmission in the general public. People tend to use the masks incorrectly, contaminate themselves when putting the mask on or taking it off, and increase their risk of infection by trapping me near their mouth. That would really make it too easy for me.

SC: H1N1, thank you. While it was lovely having you, I hope this was the last time.

H1N1: Thank you. Did you want to come closer? I have a secret for you…

This plush H1N1 virus is safe to cuddle with!

References:
Autism and vaccination-the current evidence. (2009) Miller L, Reynolds J. J Spec Pediatr Nurs. 14(3):166-72.

A Novel Influenza A (H1N1) Vaccine in Various Age Groups. (2009) Zhu FC et al. N Engl J Med. Oct 21.

The H1N1 flu pandemic. What you need to know. (2009)
Mayo Clin Womens Healthsource. (11):4-5.

The Centre for Disease Control and Prevention – www.cdc.gov Public Health Agency of Canada – www.publichealth.gc.ca

A new kind of mind control

Remember subliminal messages? Those images supposedly flashing too quick for your mind to register, but still managing to convince you to drink more soft drinks, eat more fries, buy a luxury car? While those days may not be over yet, new forms of mind control (albeit more biological than psychological) are emerging thanks to the tiniest of creatures, the bacteria.

A friend of mine, Cal, recently alerted me to an interesting article about optogenetics. If you’re not familiar with the word, that’s because it’s very new, and it essentially means playing with light and genetics at the same time. It’s all the rage in neuroscience right now and articles such as the one I’ll be describing in this post are popping up every week.

It all starts with a tiny little pump called halorhodopsin found in bacteria. This pump sits at the surface of cells and pumps chloride ions from outside the cell to the inside (table salt is sodium chloride - same chloride). Cells use chloride for different reasons, but this pump can be especially relevant for brain cells (called neurons). Neurons pass information to one another through electric currents. And it just so happens that chloride ions are charged negatively. That means that if many chloride ions accumulate inside a neuron, the cell becomes increasingly charged negatively, making it harder to reach the positive threshold it needs to pass currents to other neurons.

Other types of chloride pumps already exist in your brain cells, but almost nobody makes a fuss about those. So how is halorhodopsin different? This is where the “opto” from “optogenetics” comes in. This particular pump is activated by light. This means that if neurons have this special pump, you can control whether they are active or not just by flashing a light onto them.

In a recent paper published in PNAS, the researchers genetically engineered zebrafish so that their brain cells expressed the special light-activated chloride pump. The researchers then recorded the electrical signals generated by the brain cells (they look like spikes, much like what you would see on an EEG). I don’t know if you can imagine what kind of feat that represents, but I’d like to make a motion to modernize the saying “like finding a needle in a haystack” to “like poking an electrode into a brain cell of a live fish”. Once they knew what the signals looked like in normal conditions, they shone the light on the fish*, and amazingly, all the brain cells went quiet. It worked! The light activated the pump, negatively charged chloride ions accumulated in the cells and made it too difficult to reach the spiking threshold.

The black lines are the current spikes that normally occur when brain cells transmit information. The yellow section is when the researchers shone the light: no more spikes.

Now a fish doesn’t have that many brain cells to start with, and since it spends most of its life moving it’s pretty safe to assume that a large portion of the fish’s brainpower is devoted to swimming. The researchers thought they had a pretty cool tool to test this, and so they did. They put a bunch of genetically-engineered zebrafish in a dish, watched them swim around for a bit, and then shone a light on them*. Sure enough, the fish stopped moving and lost coordination. I realize we’re talking about lousy, bottom-of-the-food-chain fish here, but think about it: *that’s* mind control.

The article continues to great lengths, going into details about what specific part of the brain controls the swimming behavior and describing control experiments that confirm that this isn’t a fluke (i.e. the fish aren’t just spooked by the light). All things considered, it’s a very elegant example of how to use optogenetics to better understand the brain. And the relevance of these advances lies in the increased understanding of not only the brain but also diseases of the brain. Recently, these new techniques used in animal research gave us important insights into Parkinson’s disease.

What about using these tools as ways not only to understand disease, but also to treat them? What if we made our own brain cells express this special pump so we could use light to activate or inhibit different areas of our brains? While this may seem like science fiction right now, don’t be so sure. I attended a talk on optogenetics recently, and the researcher firmly believed that this emerging field of neuroscience would eventually cure blindness. In the meantime, let’s see if you can think of all the ethical questions this would raise…

* For these experiments, the researchers used fish in the larvae stage. The skin of the fish at that point is transparent, and this allows the light to reach the brain cells.

This little zebrafish is doing his best to contribute to science.

Reference: Optical control of zebrafish behavior with halorhodopsin. (2009) Arrenberg, A.B., Del Bene, F., Baier, H. Proc Natl Acad Sci USA, 106(42):17968-73.

Yet another reason for a good night's sleep

How much do you sleep at night?

If you’re like most of the people I know, the answer is “not enough”. There’s a reason Starbucks coffee shops are popping up literally meters away from one another. Everybody has a reason to be sleep-deprived: new kid, big job, World of Warcraft, etc. So what if we’re cutting the night short a few hours? Other than the need for an overpriced coffee (or two, or three), it should be just fine, right?

Maybe not, if you believe the latest research on sleep and Alzheimer’s disease.

Alzheimer’s disease, a debilitating form of memory loss and cognitive decline, is the most common form of dementia. It is thought to be caused at least in part by amyloid beta (A-beta), a peptide (short protein). Your brain cells (neurons) normally make some A-beta. The problem that arises with Alzheimer’s disease is that neurons make too much A-beta, and these molecules aggregate together in chunks. It’s those A-beta chunks that are toxic, and their formation is concentration-dependent, which means the more A-beta you have floating around, the higher the probability of toxic chunks forming.

The recent article published in the journal Science looks at levels of A-beta in the brains of normal mice and in the brains of a mouse model of Alzheimer’s disease. The researchers studied the mice when they were 3 months of age, so well before big deposits and chunks of A-beta start occurring.

The interesting finding of this study is that the levels of A-beta in the brains of both types of mice were significantly correlated with the amount of time they spent awake. More time spent awake lead to more A-beta. Because the control, normal mice also exhibited this relationship, it means that it is not linked to the disease. It’s just a normal fluctuation of A-beta levels linked to the sleep-wake cycle. To be certain this link was relevant for human physiology, they also tested this in healthy humans and, sure enough, they observed the same correlation.

Not surprisingly, when the researchers proceeded to sleep-deprive the mice, they showed an even larger increase in A-beta levels. This increase was also observed when the mice were given a drug that promotes wakefulness (don’t extrapolate this to coffee just yet… But maybe keep it in mind…). The study also points out that the Alzheimer mice who are sleep-deprived showed much greater numbers of A-beta chunks (the toxic stuff) compared with non sleep-deprived mice.

If you come to Scientific Chick for relevant findings, this one is for you. The study essentially implies that optimizing sleep time could potentially inhibit the formation of chunks of toxic A-beta and slow the progression of Alzheimer’s disease.

We all know that Alzheimer’s disease is terrible, and that sleeping in is glorious. Let’s just put two and two together, shall we? Easier said than done, I know…

Mr. Minou gave up on caloric restriction but approves of this new approach to ward off age-related diseases.

Reference : Amyloid-{beta} dynamics are regulated by orexin and the sleep-wake cycle. (2009) Kang JE, Lim MM, Bateman RJ, Lee JJ, Smyth LP, Cirrito JR, Fujiki N, Nishino S, Holtzman DM. Science Sep 24. [Epub ahead of print]

Yet another reason to exercise

Last weekend I went for a bike ride and when I reached the bottom of the big hill leading to UBC, I noticed quite a bit of activity going on. I didn't pay too much attention at first, but once I was booting up the hill, I was passed by several senior citizens on top-notch bicycles and I started getting curious. I asked a person who seemed to volunteer for the event what was going on. As it turns out, I was cycling right in the middle of the BC Seniors Games. Now for those of you who might not know me, my thesis research has to do with aging and the brain and nothing warms my heart like witnessing older adults and seniors exercising. I had just hit the jackpot!

The reason I'm so enthralled to see seniors exercise is because it is the single best thing they can do to preserve their brains. Today's paper highlights recent research done in California that shows just that.

First, a bit of background. You have a gene called APOE (mice also have it). It comes in 3 flavors, and each person only has one of the three: APOE2 (not important for today’s article), APOE3 and APOE4. If you got lucky and scored the APOE3 kind, all is well. If you happen to be in the 20-25% of the population who has the APOE4 kind, you may be in trouble: APOE4 is a known risk factor for Alzheimer's disease. Does it mean you'll for sure get Alzheimer’s disease? No, but you are 10 to 30 times more at risk of developing Alzheimer's disease if you carry the APOE4 gene.

In this paper, researchers compared old APOE3 (normal) and APOE4 (at risk for dementia) mice. In general, aged APOE4 mice experience cognitive decline faster and earlier than APOE3 mice. The researchers were interested in studying whether exercise (running on a mouse wheel!) had any effect on this cognitive decline.

The researchers used cognitive tasks that rely on a part of the brain that's important for memory, the hippocampus. One of the tasks, called place recognition, involves putting a mouse in an arena with two objects. The mouse is then removed from the arena, one object is moved, and the mouse is put back in the arena. Presumably, a normal mouse will then spend more time exploring the object in the new location. For this task, the aged APOE4 mice were initially impaired compared with the APOE3 mice. This means that during the second trial of the task, they tended to explore both objects for similar amounts of time, instead of spending more time on the object at the new location. This result suggests that the APOE4 were unable to remember the initial object locations well. The good news? Mice who exercised did significantly better at this task. Interestingly, this was valid for both APOE3 and APOE4 mice. Even more interestingly, exercise improved the scores of both types of mice for all the tasks that tested the hippocampus.

What's going on in the brains of these exercising mice? It is thought that exercise increases the levels of a protein called BDNF (for Brain-Derived Neurotrophic Factor). BDNF regulates many important functions in the brain, including the making of new neurons and the making of new connections between neurons, and these effects are thought to be important for memory.

Regular readers of Scientific Chick know not to get too excited when I report about animal studies. Well, I'm happy to add that the results that were observed in those mice were also observed in humans. In fact, there are countless human studies out there that confirm that physical activity is a powerful way to improve and maintain your cognitive abilities.

When I try to urge certain people to exercise (you know who you are), I almost always hear the same excuse: “Well, my uncle so-and-so never got off his couch and he lived to be 100!” In some cases, heredity can be on your side, that's true. But genetics can be quite the lottery, and it's important to keep in mind that several forms of cognitive decline, including the most common form of Alzheimer's (called “sporadic” in scientific lingo) are not hereditary.

So to all my older readers out there, I'll see you on the road at next year's BC Seniors Games. And if you're not ready for cycling, there's always the cribbage category.

Winners from this year's BC Seniors Games, cycling event. This could be you!

Reference: Exercise improves cognition and hippocampal plasticity in APOE epsilon4 mice. (2009) Nichol K, Deeny SP, Seif J, Camaclang K, Cotman CW. Alzheimers Dement. 5(4):287-94.