A Blog for Brooke and Andy
geek stuff
Primer: Neurotransmission
Aug 20th
These posts, tagged “Primer,” are posted for two reasons: 1). to help me get better at teaching non-scientists about science-related topics; and 2). to help non-scientists learn more about things they otherwise would not. So, while I realize most people won’t read these, I’m going to write them anyway, partially for my own benefit, but mostly for yours.
As I’ve mentioned…oh…countless times, I became interested in my chosen field primarily because of a class titled “Psychopharmacology,” offered by the Psychology Department at Truman. As the name suggests, the class primarily focused on how drugs modify an individual’s mental state, whether it’s an illicit drug that changes the way you act (e.g. methamphetamine), or one that’s used to help you cope as you carry out your day (e.g. diazepam [Valium]).
Back in June, I posted about Pharmacology, the study of how a drug acts within an organism. One thing I discussed, but did not elaborate on, was that many drugs function at receptors, and the modification of these receptors is what gives you the desired effect of said drug. However, in order to understand how these receptors actually do something to your body, you need to understand the basics of how neurotransmission works.
Basically, neurotransmission is a signal sent between two specialized cells called neurons. These cells make up a large portion of the brain (i.e. there are other cell types, including astroglia and microglia) and provide all the processing power you need to carry on with whatever task you wish. Therefore, if you want to modify something about that task, these are important cells to consider and/or target with a drug. Neurons take advantage of channels in their membranes that allow selective transfer of ions like sodium, potassium, chloride and calcium. When these ions cross the membrane from outside the neuron to the inside (or vice versa), an electrical charge is produced. These channels open and close selectively to allow certain things through, and keep other things out. For example, sodium channels in neurons typically allow sodium into the cell, while potassium channels tend to allow potassium to leave the cell.
Many of the receptors that drugs are targeted toward are channels, or the drug-targeted receptors somehow affect the ability of channels to open or close. Therefore, if you can target your drug toward a specific channel, you can keep it open longer, or close it sooner, allowing you to affect whether a neuron is able to continue propagating its signal.
So, the electrical signal caused by transfer of ions across a neuron’s cell membrane (or “action potential“) travels down the neuron, from end to end. On one end is the “cell body” (or “soma”) and on the other end is the “axon terminal.” The electrical signal always goes from the cell body to the axon terminal. The cell body is covered in “dendrites,” outcroppings of the cell that receive a signal from another neuron’s axon terminal. Therefore, typically, (1) a signal will start at the dendrites; (2) travel down the axon; (3) trigger a set of events in the axon terminal resulting in (4) the release of a neurotransmitter that (5) crosses the synapse until it reaches another dendrite and (1) starts the process over again.
What happens between the axon and the dendrite can best be described by this image, stolen from Wikipedia:
Neurotransmitters are packaged in “vesicles” that are directed to release their contents into the synaptic cleft where they travel across the cleft to the opposing dendrite, setting off a similar cascade in the next neuron. There are also “reuptake transporters” in the cleft to help remove excess neurotransmitter, so you don’t have that opposing neuron continuing to fire too long.
Examples of neurotransmitters include dopamine, adrenaline (epinephrine), acetylcholine, nicotine and serotonin.
Now, you probably recognize a few of those neurotransmitters, right? For example, you probably know that serotonin happens to be very important to your mood. If you don’t have serotonin, you tend to get depressed. So what can you do to help combat this deficiency? Try taking an SSRI (selective serotonin reuptake inhibitor). That drug targets the “reuptake transporter” in the cleft, allowing the serotonin you’re already making to stay in the cleft longer, helping to activate those neurons to keep your mood a bit happier.
You’d use an SSRI to help serotonin to reach its target neuronal receptors, thereby allowing for increased signal propagation through neurons. But what if you want to limit propagation of signals, for example, in the case of an epileptic seizure when neurons are firing uncontrollably? You can use a depressant like carbamazepine. This drug targets channels and modifies them in such a way that the electrical signal (“action potential“) being sent down the axon is limited, or “depressed.” It prevents the signal from continuing and, therefore, less (or no) neurotransmitter is released into the synapse. That same drug can be used to help treat the manic symptoms of bipolar disorder, as well.
So, all of these principles are taken into account (as well as countless others…) when looking for drug targets, and when doctors are prescribing medications. This is why you can have so many complications when you are prescribed a cocktail of medications, especially when you get older. If you are taking, say, 10 different medications per day, prescribed by different doctors, it is easy for at least one of those drugs to counteract the effects of another. There are many factors to consider when prescribing or taking these kinds of medications, as they have effects all over the body. One simple example is methamphetamine. This drug targets that reuptake transporter, much like an SSRI does, but it (1) does so for a class of neurotransmitters called catecholamines, and (2) reverses the transporter, rather than blocks it. The class of catecholamines include dopamine and adrenaline. So, if you take methamphetamine, you will be increasing the amount of dopamine and adrenaline in your body, not just your brain. Your heart races because of the adrenaline, and the psychological effects occur because of the dopamine (including its addictive qualities).
In summary, neurotransmission is pretty complicated, but its basics are understandable. The take-home concepts are:
- Neurons are responsible for “processing” in your brain, and they use electrical and chemical signals to communicate with each other
- Many drugs that affect your psychology target the ability of neurotransmitters to “continue the signal” from neuron to neuron
- Some drugs affect more than one aspect of neurotransmission, and in more than one location
“Print” Lives?
Aug 10th
I’ve had magazine subscriptions of various types for years now, beginning with Boy’s Life (the Boy Scout magazine…) and various computer game mags, and then eventually to Popular Science and Consumer Reports. However, in recent years, there have been a number of news stories discussing “The Death of Print Media,” including magazines and newspapers, primarily. This is mostly due to the Internet and its ability to get you the same information much, much faster than a weekly or monthly periodical can, and cheaper as well.
Recently, however, certain magazines have begun to toy with digital versions of their material. These are magazines that have either dropped in subscribers to a substantial degree, or have already folded for a variety of reasons. For example, while TIME Magazine is apparently weathering the storm, Newsweek just got hammered by a drop in subscribers to the point where they were looking for a buyer. Gourmet Magazine shipped its final issue at the end of 2009. On the gaming side, Electronic Gaming Monthly was shuttered at the beginning of 2009.
Some magazines have gotten around this problem by increasing the quality of their material. Edge Magazine, a gaming periodical in Europe, has proven to be successful by starting to use thicker, glossy paper, raising the perceived value of their product over their competitors. The magazine just looks good sitting on your table, with its larger paper and glossy images. It’s the kind of thing you want to keep on your coffee table, as opposed to other magazines that are constantly including more and more ads and thinner, newspaper-like print. They also limit the number of individual magazines they produce, only making enough to send to subscribers (all over the world…) and keep a limited number on news stands. This helps keep their costs down, rather than making more magazines than the public will buy.
Alternatively, some of the aforementioned publications are going digital…and in a big way. The advent of the iPad has allowed Newsweek and Sports Illustrated (amongst others) to get weekly content to readers on-the-go very cheaply, effectively replicating web-based content in a magazine-oriented format. You can turn the pages as you would with a book, but now making a touch-based gesture on your iPad screen. The images are very colorful, print easy-to-read, and perhaps most important of all, they can now include hyperlinks and video content that you can’t with a regular magazine. Recently, it was also announced that Gourmet Magazine was relaunching as Gourmet Live, also releasing on iPad (announcement video below).
Similarly, Electronic Gaming Monthly was bought out by the guy that started the magazine in the first place back in the 90s and relaunched in both print and digital formats. For a demo, click this link and it will take you to a freely available copy of the magazine (pictured above) so you can see what it looks and feels like (and you should “Experience in Full Screen”). While you may not be interested in video games in the least, at least you’ll get an idea of what is possible through digital distribution of magazines. EGM also has an iPad version, but this particular example is representative of what you can experience in any web browser.
So, is “print dead?” Probably not, but it’s definitely evolving. Everything I’ve heard suggests that print journalism majors are finding it difficult to get jobs once they graduate from college, as many newspapers and magazines are scaling back, if not shutting their doors. The primary hurdle appears to be advertising, as very, very few companies have been able to make it with their large-scale operations solely on the advertising revenues of web-based content. The New York Times tried unsuccessfully to require subscriptions on portions of their website years ago (and they’re trying again in 2011), but our culture tends to shun pay-for content on the internet, at least with regards to news. There are just so many blogs available, or other free sites, that get you the same information for no money at all.
Personally, I’m on board with a model like Edge or EGM is using, one where they produce magazines in limited quantity for the people that want it, but otherwise provide digital versions for those that don’t care either way. Honestly, I still read everything on blogs and only go to the “primary source” sites when linked there. I like the way EGM has set up their content, but I think I’d rather have an iPad or some other similar device for that purpose, rather than use my heavier and more unwieldy laptop (imagine sitting in bed and reading…would you rather hold your laptop or your iPad?).
I think a lot of people value the content they get from magazines and newspapers, as the journalists that write them get access to news and information they otherwise can’t. Bloggers generally don’t have correspondents in Afghanistan, so they rely on organizations like NPR and the Associated Press to gather the news, and bloggers just put their own spin on it and spread it as well. We still need primary news sources to survive this transition from “old media” to “new media!”
Primer: Mass Spectrometry
Jul 26th
These posts, tagged “Primer,” are posted for two reasons: 1). to help me get better at teaching non-scientists about science-related topics; and 2). to help non-scientists learn more about things they otherwise would not. So, while I realize most people won’t read these, I’m going to write them anyway, partially for my own benefit, but mostly for yours.
My postdoctoral fellowship here at the University of Iowa still involves research on the mechanisms by which Parkinson’s disease progresses, much like my research at Saint Louis University, but I’m employing different techniques. In an effort to explain those techniques, I’m going to try outlining them here, as it’s a technique that’s “tossed around” on shows like “CSI:” on an almost weekly basis.
Mass Spectrometry is a technology developed over 100 years ago and has been employed by researchers for much of that time. The high cost of procuring one of these instruments (easily in the $10,000s, if not approaching $100,000+) makes them somewhat difficult to find in the undergraduate setting, and sometimes difficult to find in graduate schools. Larger institutions, such as the University of Iowa, will have a few of them, but more than likely, you’ll have to share the instrument with quite a few others, not-so-patiently waiting their turn.
The instrument I’m using is called an LCMS-IT-TOF, pictured above. The acronym stands for “liquid chromatography mass spectrometer – ion trap – time of flight.” Each section of the acronym represents a distinct component of the mass spectrometer: there are different components that can be inserted to achieve similar analytical results in a different fashion. Some components are better for some types of analyses, while other components are better for others.
But, in keeping this relatively simple, I won’t go into it each part. Feel free to check out the Wikipedia article on the subject if you really want to know more about it, but basically, a mass spectrometer is divided into three primary components:
- A source
- A mass analyzer
- A detector
The “source” effectively destroys whatever you’re wanting to look at. There are a variety of different sources one can have in their configuration (e.g. MALDI, ESI, ACPI, etc.) In my case, let’s say you have a protein you want to investigate. The mass analyzer can look at it, but the nature of the type of data it provides makes it much easier to break the protein up into smaller bits first. Therefore, the source breaks up your relatively large molecule of interest (such as the protein in our example) into smaller, more manageable pieces. As with many other things, taking things in “baby steps” is much easier to deal with.
The “mass analyzer” is necessary to help with sorting of all those small, manageable pieces. Think of this process like a box of cereal (I know, right?). Specifically, Frosted Mini-Wheats. When you open the box, you’ll notice that there are mostly fully-formed Mini-Wheats at the top of the box. As you continue on toward the bottom, you’ll start seeing some smaller pieces, some that may have split in half, for example. And at the bottom of the box, you’ll see all the individual wheat fibers and sugar frosting. The same premise holds for a mass analyzer. All those pieces of protein broken up by the source are in different sizes, and the mass analyzer helps sort them out in such a way that the small pieces, medium pieces, and the large pieces are all separated. As with the source, there are many different types of mass analyzers (e.g. TOF, IT, Quadrupole, etc.) used to carry out this work, depending on what you’re looking at.
The “detector” is the piece that really gives us the information we want. After those bits of sample are sorted, they each hit the detector one at a time and the detector tells us what the mass is, typically by actually reading the electrical charge of the sample. Typically, the source (sometimes referred to as an “ionization source”) introduces a charge to each piece of the sample, allowing for the detector to…um…detect them. :-)
So, how is my work fitting into this? Our lab is interested in how a particular molecule, 3,4-dihydroxyphenylaldehyde (DOPAL) may be involved in Parkinson’s disease. DOPAL is a metabolite of dopamine, the neurotransmitter necessary in order for you to make voluntary movements. When you run out of dopamine (or the cells that produce it, in the region of the brain where you need it), you get Parkinson’s disease. Dopamine is present in those cells, which therefore means DOPAL is present, too. DOPAL is an aldehyde, which means, on a chemical level, it can bind with other molecules relatively easily. What we want to know is whether DOPAL may bind to proteins within those cells. This may matter because cells tend to function in certain ways, and if their individual parts (e.g. DNA, organelles, proteins, etc.) get modified somehow, they won’t work properly and, subsequently, the cell will kill itself to prevent further damage to surrounding cells and tissues.
We want to see whether DOPAL binds to any proteins. If we can find proteins that DOPAL binds to, and if we know what those proteins do inside a cell, then we may be able to a). protect them against DOPAL’s binding, or b). develop drug targets toward those proteins to help prevent them from causing death of the cell.
How does mass spectrometry fit into this equation? Back to our early example of a protein being introduced into a mass spectrometer. The instrument will tell us how much a protein weighs on a molecular level. We also know how much a single molecule of DOPAL weighs. We can, thus, use a mass spectrometer to see whether the mass of a protein increases when DOPAL is present. If that occurs, we can show that DOPAL has bound to the protein. We can also get information as to where on the protein DOPAL bound, or how much DOPAL bound to the protein, and so on.
In the image above (upper left), you can see some vertical lines we refer to as “peaks.” Each peak represents a single mass of a given protein or molecule. You can then take that peak and “fragment” it into smaller peaks. You can do this multiple times (e.g. MS, MS2, MS3 and so on…). Fragmentation patterns give you an idea as to what makes up a complex molecule. For example, if you went from MS to MS2 and had a loss of 18, you could say that you lost a water molecule during fragmentation (O=16, H=1…H2O=18). In the case of DOPAL, we would see an increase in mass (and a shift of the peak) of 151, depending on how DOPAL bound to our protein of interest.
So, basically, that’s what I’m doing in the lab. There’s quite a bit more to the story than this, but I think I’ve simplified the concepts to a mostly understandable level.
Probably not, though. :-)
Primer: Pharmacology
Jun 30th
These posts, tagged “Primer,” are posted for two reasons: 1). to help me get better at teaching non-scientists about science-related topics; and 2). to help non-scientists learn more about things they otherwise would not. So, while I realize most people won’t read these, I’m going to write them anyway, partially for my own benefit, but mostly for yours.
Whenever my parents had to try and explain what I was getting my Ph.D. in to their friends or my extended family, the common response would be: “he’s going to be a Pharmacist?” Whenever I’d be asked the question, I’d typically respond with a “sigh” and then continue to say: “The difference is that a Pharmacist sells drugs, and a Pharmacologist makes drugs.” Of course, that’s a simplified definition, but was typically good enough for my purposes.
In actuality, that isn’t completely accurate. The Dictionary.com definition reads as follows
pharmacology -noun
the science dealing with the preparation, uses, and especially the effects of drugs.
The Wikipedia article on Pharmacology is also pretty useful, and goes into much greater depth than I prefer to here. To summarize more broadly, Pharmacology is the study of how drugs work in an organism. This definition encompasses how a drug gets produced, how it gets into your body, where it goes once it’s in your body, what effect it has once it reaches its destination, and how it ultimately gets out of your body.
According to Goodman & Gilman’s The Pharmacological Basis of Therapeutics (11 ed), the study of Pharmacology can be subdivided into a few different categories, both dependent upon one another.
When a drug enters the body, the body begins immediately to work on the drug: absorption, distribution, metabolism (biotransformation), and elimination. These are the processes of pharmacokinetics. The drug also acts on the body, an interaction to which the concept of a drug receptor is key, since the receptor is responsible for the selectivity of drug action and for the quantitative relationship between drug and effect. The mechanisms of drug action are the processes of pharmacodynamics. The time course of therapeutic drug action in the body can be understood in terms of pharmacokinetics and pharmacodynamics.
So, the study of pharmacokinetics looks at how a drug moves through your body (“pharma” for drug; “kinetic” for movement). It is important to understand these principles when developing or prescribing a drug. For example, in the case of sleeping medication, you want the drug to act rapidly in your body so that you fall asleep, however you also want the drug’s effects to last for enough time to keep you asleep…but wear off in time for you to get up the next day. The study of a drug’s pharmacokinetic properties will help develop treatment regimens that those other doctors (read: M.D.s) can use to prescribe medications accordingly, for whatever the situation calls for.
Pharmacodynamics, on the other hand, looks at how a drug works once it reaches its destination in the body. Some drugs work primarily in the brain, some in the heart, some in the lungs, and so on. Many drugs have their function by binding to a receptor on the outside of a cell (example: diazepam [Valium]), perhaps a receptor that is responsible for “exciting” the cell or “depressing” the cell (i.e. increasing a cell’s function or decreasing a cell’s function). Perhaps Drug A will bind more effectively to that receptor, giving you a more efficient response. However, maybe Drug B isn’t quite as efficient in eliciting a response. Along that paradigm, while Drug A may be more efficient, perhaps the desired function by you and your doctor is a more delayed, longer lasting effect, and Drug B could fit that bill (typically, you want anti-anxiety medications to last throughout the day, for example…not just for a few hours).
Knowing principles of pharmacokinetics can help you maximize how much drug gets to the site of action. Knowing principles of pharmacodynamics can help maximize how much of an effect the drug has once it’s there. Both of these concepts are essential to effective drug design and usage.
As a brief (yet related) aside, I first became interested in the subject when taking a class on Psychopharmacology in the Psychology department at Truman State. It was very interesting to learn about how different drugs affect your brain to result in different effects. For example, a drug like diazepam (Valium) is a drug that’s intended to function as an anxiolytic and sedative. The basis of its function, however, is that it works on specific receptors that effectively “depress” neurons, limiting their firing ability. It turns out that function is also quite useful to help prevent seizures, a disorder where neurons fire more often than they should. So, some drugs that are intended for one purpose can be useful in another, but you need some understanding of how that drug works before you can begin to apply it to another situation.
So, in short, pharmacology refers to the study of how drugs work and, therefore, a pharmacologist works on such things. I should point out that pharmacists do play an important role in the development of drugs, as well. Merck and Pfizer employ both Pharmacologists (Ph.D.) and Pharmacists (Pharm.D.), amongst a wide variety of others.
But, they’re quite different in their training.
The Next Big Thing
Jun 23rd
The Electronic Entertainment Expo (E3) was held last week in Los Angeles. It is always interesting for me to watch the coverage in the gaming media during that week, looking at live blogs about the different press conferences (Microsoft, Nintendo and Sony, primarily), and gathering everyone’s opinions about the proverbial “future of gaming.” Essentially, E3 is the time where most consumers hear about what games or platforms will be available for the holidays, or shortly thereafter. All the major media outlets tend to cover it in order to tell their viewers what they’ll be buying for themselves or their kids this Christmas.
You may have read in the news about Microsoft’s Kinect, or Sony’s Move. Both of these systems are attempts at cashing in on some of Nintendo’s motion control success that the Wii had. Microsoft focused a bit too much on Kinect, while Sony did a little better job of showing some games that the wider audience would want to play. No pricing has been announced for Kinect, but $150 seems to be the prevailing wisdom, plus the cost of the console. The Move will cost $120 or so to get started, but an additional $60 per person in order to get the “full motion control effect.”
While Microsoft and Sony were duking it out over motion control, Nintendo went a different direction: the Nintendo 3DS. I kinda wanted to post something about it last week, but I wanted to hear more analysis from the weekly podcasts I frequent, as they were able to get some “hands on” experience with it. To quote Jeremy Parish over at 1up:
Then I actually got to use the 3DS, and… wow. It works. It doesn’t strain my eyes at all, yet I can absolutely see the depth. I’m not exaggerating that the realization that my poor eyesight won’t shut me out of the next generation of portable gaming was the single happiest moment I’ve ever had at a gaming industry event.
To get a sense of what the 3DS can do, check out this YouTube video. This video does NOT take place on a 3DS, but demonstrates the kind of visuals and gameplay it should be able to handle when it comes out in 2011.
Nintendo will have a tough time demonstrating the 3D technology in TV commercials as very few TVs actually display 3D images. The tech is rumored to work by having two LCD screens overlapping, where the top one is shifted slightly such that one eye sees the top one and the other eye sees the bottom, allowing for stereoscopic 3D without the need for glasses.
That last bit is why this technology will be the new hottness next year, and why this thing will sell like hotcakes. You don’t need 3D glasses. And it’ll probably sell for close to $200, making it affordable 3D, as opposed to needing a multi-$1000 TV and 3D shutter glasses that sell for a few hundred dollars each (like Sony was demonstrating). This product marks the first time real, working, 3D images will be available to consumers (no, the Virtual Boy doesn’t count).
The Nintendo 3DS even has two cameras on the outside, allowing you to take 3D pictures.
Also, Nintendo was demonstrating some 3D movie trailers on the 3DS as well, suggesting that the device will have the ability to play movies. So, your kids that loved “How To Train A Dragon” or “Shrek 3D”…they’ll be able to watch it in 3D, and you won’t have to spend that much money to make it happen.
So, for the average consumer, the 3DS is a pretty big deal. The Nintendo DS has sold 130 million units, making it the most successful console ever. Parents buy them for their kids for Christmas without even thinking about it. It’s a way to entertain the kids at home and in the car without requiring you to give up your TV. If it sells for less than $200, it will still be a no-brainer. But, the fact that it has true 3D without the need for glasses will get the average consumer that doesn’t have kids to sit up and take notice.
I’ll be first in line when it releases in Spring 2011 (projected release time frame).
