Tag Archives: microbiology

Germ Cultivation

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I recently came upon an article in the New York Times about how people with skin disorders such as acne or eczema could be helped by a sort of topical probiotic treatment. In other words if we take bacteria from the skin of healthy people and spread them on the skin of diseased people, evidence suggests that the good bacteria will fight off the bad bacteria and the skin condition may go away.

This idea of probiotics, (using good bacteria to fight off bad bacteria) has been around for a while now, but it’s been steadily gaining popularity.

I find the whole thing fascinating for a number of reasons. I like the counter-intuitive aspect of it. I like how it looks at the problem of infection from more of a systems perspective, rather than seeing it as a single cause requiring a single remedy. And finally I like how it flies in the face of all the do-gooders who were telling us all how to live our lives in the 80’s and 90’s when I was growing up.

BactRanch

Bacteria husbandry?

It turns out (to a certain extent) it’s better to have children go out and be dirty for a bit. Visiting a farm and interacting with animals, for instance, reduces the risk of asthma. It turns out we shouldn’t take antibiotics every time we get a stomachache since it kills off our gut microbiota and could cause even nastier diseases to run rampant. And now it turns out that if you’re worried about getting a disgusting skin condition, perhaps what you should do is shake hands with as many (healthy) people as possible.

Of course it’s important not to get too carried away. A little dirt outside is okay, but living in filth is not. Just because antibiotics aren’t always the best choice doesn’t mean you should stop using them when you need them. And obviously you should wash your hands often and thoroughly to prevent the spread of diseases like MRSA and the flu.

What the researchers did in this study was put healthy bacteria into a lotion and put this on the forearms of people with eczema. There seemed to be a reduction in the disease, but there are still questions of whether the treatment will continue to work over time, or what might happen if there’s an open wound.

My personal prediction would be that a small open wound like a scratch or abrasion wouldn’t be much of a problem in this case. The bacteria used in the study (Staphylococcus hominis and Staphylococcus epidermidis) are so common that most people’s immune systems will quickly recognize the bacteria in the blood stream and destroy them before they can cause any harm. That “most people” would not include immunocompromised people like the elderly, people preparing for transplant surgery, or AIDS sufferers, however. And if someone has a skin condition, there’s a good chance that something might be off about their immune system.

Ultimately, like many science stories out there, this is cause for some cautious optimism. IF someone has a bacteria-related skin problem, and IF they don’t have some other complicating condition, then they MAY be helped by this therapy IN THE FUTURE (probably 5 years or so I would guess), ASSUMING there aren’t some unforeseen side effects.

As for most of us living outside of laboratories and going about our day to day existences, what I would say this means is that we shouldn’t worry so much about germs. Or more precisely, don’t worry so much about getting rid of them. It’s not good to douse our bodies with antibacterial soaps at every opportunity. It’s also still not a good idea to live in squalor either. Chances are, if you wash your hands regularly and don’t stink, you are clean enough.

Beyond that common sense assessment, if you want to improve your health, you might try finding someone who has healthier skin than you, and shake their hand. Or ask them to rub some lotion on you. Or maybe do none of these things. That way they won’t think you’re a creep and you may benefit from their simple proximity. Yes, it may be that if you want to be prettier, you need to hang around pretty people, which will be easier if you are already pretty. Perhaps yet another astounding example of the Matthew Effect.

How to Achieve Your Dreams

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sky-clouds-above-clouds-wallpaperThe following is a response to a question on Quora. I didn’t quite read the question correctly, but I like what I came up with as an answer. I have no definite expertise on any of this, but I have learned a few things that may be useful for somebody.

dmaicIf you’re serious about accomplishing your dreams, there are some tools that have been developed in the business world that can help. I’ve been involved with some Six Sigma projects, and I like the model of DMAIC for the most part. That is Define, Measure, Analyze, Improve, and Control. These sound boring, but they’re really not. Let’s go through them.

Define
The first step of accomplishing your dreams is to have realistic dreams. This isn’t giving up, this is building up. If you want to fly, great. I’m not going to say you can’t fly. But what exactly do you mean by flying? Is flying an airplane going to work for you? No? How about skydiving, that’s kind of like flying, or hang gliding? Do you actually want to be like a bird, or do you want to be superman?

Already, while we started off with something that seems unattainable, we now have several options that are much more attainable. One of the things that keeps you back in this step is fear. Your dream of flight is nice, but what if you don’t like it? What if it’s dangerous? What if it seems less beautiful? These what-ifs can hold you back, but they shouldn’t be ignored either. Make a list of these fears along with any other risks, because its entirely possible that you actually don’t want to accomplish this particular dream. Next to these risks, you want to list the benefits of accomplishing your dream. What will you gain from it. Why do you want to accomplish it? It could be that while your dream involves flight, what you really want is a feeling of freedom, and there might be better ways of doing this. If you think of some, great, make another list of risks and benefits for this new dream. Does it look better than what you had before? You keep at this until you have something that matches your desires and yet still fits with what can occur in reality.

If, at this point, you still don’t see how you can accomplish your dream, then look for ways to get closer to accomplishing it. If you want to be Superman, maybe look into jet packs, physical fitness, rescue work, or space travel. Depending on what it is about Superman that you most want to be, learning about these subjects might not get you there, but it will get you closer. The idea here is to bring your dream closer to reality by bringing reality closer to your dream.

Measure
weight-scale-400x400-300x300How close are you to your dream today? The easiest example of this is weight loss. If you want to lose 30 pounds before next Thanksgiving, you need to monitor how you’re doing to know if the diet you are on is working or not. Even if it’s something you dread, you have to get on the scale and check, otherwise there is no point in dieting. You can get more sophisticated in this step for more benefit. You can make a graph of your progress for example and a list of all the foods you ate each day and any exercise you did. This way if there is a large dip or a peak, you can see what might have caused it. Weight loss is nicely quantitative, so measuring is easy to do.

The picture to the left links to a blog about not letting scales control your life. This is a common sentiment, and I can understand where it comes from. I think it’s a completely wrong way of thinking about things, but I understand it. If you aren’t having too much success accomplishing your dreams it can be disheartening to measure how far you’ve fallen. This is because humans aren’t robots. If you aren’t doing well in your progress, you need to either move on to the next steps (analyze and improve) or reconsider the previous step. Is loosing weight really what’s important to you? Could it be that you’re really worried about your fitness? Weight may not be the best way to measure that. If you stress eat, you might measure progress by recording times of stress and how you coped. Or maybe whatever is causing you stress is the problem. Putting serious effort into fixing that might be the best bet. You are never going to be able to levitate yourself. That’s depressing. But being able to do a pull up is close. Even Superman started with tall buildings. But whatever you’re goal you HAVE to measure your progress toward it somehow if you’re serious about accomplishing it.

For your more qualitative goals, like flying or perhaps owning your own business, you might need to make a journal dedicated to the goal. You can probably come up with many little goals and you can note your successes and your set backs in a journal as you experience them. The point is to have a record of what works and what doesn’t so you have some guidance in the next step.

Analyze and Improve
If your diet isn’t working out, change it. If you feel like you’re not getting anywhere, move. You do NOT want to be consistent if you are unhappy. A foolish consistency, as Emerson said, is the hobgoblin of little minds. Although you want to make changes that are likely to work and that aren’t too dangerous, remember it’s okay to make mistakes. You are, in fact, required to make mistakes in order to know what does not work for you. There are different kinds of writers, different kinds of digestive systems, you may, in fact, be from the planet Krypton. You can’t just follow someone else’s plan.

It is very important, however, to continue to measure your progress. You might think it’s a good idea to eat nothing but soy products in your diet, but you might find out that you actually gain weight (because, surprise, soy can be fattening!) Give it some time so you can be sure of how things changed, but if things are going worse, change your system back to how it was before if possible, or make another adjustment if its not.

houseflyI’m going to digress here for a moment to talk about house flies. If you watch a fly fly, you might notice how randomly it moves. It buzzes around your sandwich quite a bit yes, but then it takes a trip to the window and the to the lamp shade and back to your sandwich again. The actual motivations and causes for the complicated behavior of a fly is complicated, but one possible way of explaining it is as a modified random walk. A random (or drunkard’s) walk is one in which a moving object moves in a random direction for a random amount of time. The fly does just about the same thing, except it has memory, sight and smell, signals that make it prefer certain directions over others. As long as the good signals are getting stronger, the fly will keep going in the same direction, pretty much, but if there’s a bad signal that’s getting stronger or the good signals are getting weaker, it sort of tumbles in the air and flies in a new, but still mostly random direction. This is rather inefficient, but it works. If you are near a sandwich, and you get further away from it, the signal goes down. You then go in a different direction and maybe this is also leading away from the sandwich so you change directions again, and now you are going toward the sandwich again so you keep going. I should say that the fly is a bit (a LOT) more sophisticated than I’ve described here, and, while a fly does act this way somewhat, this behavior is more like how bacteria move (Howard C. Berg has written a lot of interesting work in “random walks”). The point is, that it doesn’t matter so much what you adjust, or in what way you adjust it; what does matter is how often you adjust it and how closely you monitor your situation.

If things are progressing well, don’t mess with them! But if things aren’t going anywhere, some kind of change is in order. If things are getting worse, than a change is not only a good idea, but an urgent one. Don’t let fear keep you from a better life. You might be in a situation where you don’t have a lot of options, but even if you only have two paths you can go on as Led Zeppelin says, “in the long run, there’s still time to change the road you’re on.”

Control
ControlThis step has two phases. While you’re still attaining your dream and making adjustments, you will probably find it helpful to establish some rules and guidelines. For example, jumping off a building is not an acceptable means of learning to fly. In weight loss, you might find that day to day, your weight varies by about a pound or so there’s no reason to stress about an increase unless its more than that (stress->despair->ice cream so limiting stress is also important). You may also have some go-to adjustments for when things go wrong, such as doing more exercise or taking a quiet moment to watch the birds when you’re feeling down. These guidelines that you develop on your way to your goal are the first phase of control.

The second phase of control occurs after you’ve attained your dream. So you’re successful. Now what? Well, the answer to that question is usually that you want to make sure you stay successful. A lot of the guidelines you came up with in the first phase will work in this second phase, but there may be a few things you need to do differently. If you get a job as a pilot, for example, you need to review all the safety procedures even though day-to-day you may not need to know them. You also need to keep an eye out for new technologies and if necessary train yourself on them so you don’t become obsolete. Once you lose the weight, you have to stay vigilant to keep it off, and you may have to employ different strategies as you age or go through other life changes.

As you may have noticed, all these “steps” overlap, and turn back on themselves like eddies in a river. You could in fact just as easily start with Control, and then notice somethings out of whack and move to Analyze and Improve and then Measure, and then find out what exactly the problem was at the end of the whole process (Define). That’s more or less what happens when police make an arrest. Perhaps it would be better to call these phases or even aspects of goal setting, but I think if you’re looking for a way to start accomplishing your dream, defining your dream is a good place to start. If you’ve got your dream well-defined, measuring your progress is the next thing to try. Then adjusting things as needed, and finally controlling them once you have things pretty well established. They build on each other nicely that way, and besides, that’s how the business world groups them.

Note: This post used pictures from the following websites. Please visit them and consider purchasing any products they’re selling.

http://www.jeesukkim.net/velocity/

http://www.sixsigmadaily.com/what-is-dmaic/

http://blogcritics.org/how-heavy-does-your-scale-weigh-on-you/

http://www.qpm.ca/Pests/House-Fly-How-to-Kill-Exterminate-Get-Rid-Eliminate-Pest-Control.html

http://www.mwultd.co.uk/services/part-exchange/control/

Review of The Windup Girl

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Image from http://bit.ly/9zOK9t

It’s a dilemma we all face to one extent or another: we like technology, but we hate what it does to the environment. We like driving, but not oil spills. We like electricity but we don’t like to think about what ecosystems are being damaged to produce it. You’ve got solar cells? Great, what are they made of? Is that recyclable? We are in the process of resolving this conflict, but we’re not there yet. Let’s say the fossil fuels we rely on finally go out. Let’s say all the things environmentalists have been warning us about actually happen. What’s next? How would people cope?

The Windup Girl, by Paolo Bacigalupi, takes place in a different world. A world that is born after the world as we know it ends. The primary sources of energy are metal springs wound by hand or by the use of elephantine beasts of labor, and the methane produced when burning the refuse from men and beasts alike. The main police force is the Environment  Ministry,  who patrol the city in their white uniforms, ruthlessly burning or destroying anything that might pollute resources too much, or release plague into the populace. The only edible plants that survive are genetically modified to resist such plagues and even then have to be closely monitored. The “white shirts” are at constant odds with businesses, who often hire mercenaries to protect their cargo from destructions when bribes to corrupt white shirt officers don’t work. And then there are the people who are genetically modifying the crops. Called gene rippers, they are loathed by all because they are the source of the plagues that threaten the populace, but tolerated because without them, there would be nothing to eat.

From this short description, you can already get an idea of the vast amount of world building that Bacigalupi did for this book, and his characters are as complex as the world they inhabit.

Anderson Lake is a gene-ripper who has a cover job as the overseer of a massive kink spring factory. The factory is huge, with giant elephant beast turning giant cranks in giant baths of algae. Helping him out with the logistics of this operation, and with bribing the necessary officials is Hock Seng (pronounced hock sahn), an Chinese refugee from the genocidal massacres that had taken place in Malaysia several years before. Hock Seng’s entire family was killed during the tumult there , and he had barely made it out alive. So now, even as he pretends to do Anderson’s bidding, he is secretly making plans to steal enough money to establish himself as a merchant in a country where he won’t be persecuted.

The book starts as Lake finds a bizarre fruit in a market that seems to be immune to plague. Realizing that this means there must be another Gene-ripper around, and that this gene-ripper must have access to other sources of genetic information, Lake quickly makes meetings with important business leaders in order to leverage himself into getting access to the gene pool. One of these meetings takes place in a brothel where a beautiful looking Japanese girl, with skin eerily white and smooth, serves Lake. She moves in stops and starts, identifying her as a genetically modified or “new” person. She is Emiko, the wind-up girl.  She is lower than a slave in the brothel, only allowed to exist because of the bribes paid to white shirts. She is mocked, ridiculed and despised by almost everyone she comes into contact with. But Lake is intrigued by her, and he tells Emiko of a village of wind-ups to the North where Emiko might be accepted. This gives Emiko hope for the first time in years.

Finally there are Jaidee and Kanya. Jaidee is the captain of a squadron of white shirts. He started out as a Muay Thai boxing champion and carries his fighting spirit into his job. When there is a ship full of suspicious cargo, he doesn’t bother trying to sort through it, he burns it all. Even while most of the Environment Ministry are despised by the people for their corruption and meddling, Jaidee is well-liked because of his pure motives. But his exuberance has cost a lot of powerful businessmen, and they are going to try to make him pay for it.

Kanya is Jaidee’s first officer, and where Jaidee is boisterous, Kanya is quiet. She rarely ever smiles. She seems at first to be a relatively minor character, but she has many secrets, and after a series of catastrophes, she becomes one of the most important characters in the book.

The Windup Girl is science fiction written as epic fantasy. If you’re ready for it, the plot is intricate and engrossing, but if you aren’t, it can also be complicated and confusing.  There are also several sections depicting gory scenes, and there are two rape scenes that I find disturbing. These scenes aren’t gratuitous. They are important to show the arcs of the characters, but you should know this isn’t a book of chaste kisses on gleaming spacecraft or anything. This is a gritty depiction of an all too possible future, a future that you could argue is already taking place in some developing countries.

So why should you read it if it’s so depressing? First off, I wouldn’t call it depressing. I would say illuminating and even uplifting to an extent. The book illustrates an important point about the conflict between technology and nature: there is no real conflict. Technology comes from us, and we are part of nature. Nature changes all the time, and like all creatures, we must adapt or perish. We can now control larger and larger areas of nature. As part of nature, we have to adjust to this. We can’t eliminate technology, but we can’t be reckless with it either. We’re grabbing the steering wheel of the Earth-mobile. If we don’t pay attention, this could go very badly.

This isn’t the only theme of the book,  and I’m not sure if the author would even agree completely with my interpretation. You don’t have to agree with the theme to like the book, though. The characters carry the story. They are all flawed people trying to do the right thing even while they end up fighting against one another. Anderson Lake is my least favorite of the point of view characters, but even though he can be arrogant and inconsiderate, even cruel, he has a discernible arc, and his motives are understandable.  All of the characters, Anderson included, had numerous moments where I was rooting for them.

http://paolobacigalupi.blogspot.com/

On the negative side, there were some ends that were a bit too loose at the end of the book. Particularly for Hock Seng. He was the biggest underdog in the story and his fate was a bit too unclear for my taste. Although some things made sense after thinking about them for a while, the ending initially felt a little too abrupt too. I wasn’t sure about the arc of all the characters. Once I figured out how everything tied togethera couple days after finishing the book, I was struck at how moving it all was. As I figured out, there is an emotional theme along with the semi-political one. To paraphrase Jaidee…Cities don’t matter. Plans don’t matter. In the end, what matters is people.

There were some moments as I was reading to the book that I didn’t like it much at all, mostly because some of the scenes with Emiko were a bit hard to get through, and because it took a while to get a grasp on the plot, but by the end of the book, it was a 7/10, and after I reflected on it, it reached 8/10. (This is a pretty high score. For comparison, the Lord of the Rings movie series gets an 8/10 from me).  I bought the book after attending a panel at The Southern Festival of books where Bacigalupi was a guest. He does an incredible amount of research for his books and seems to look deeper into things than most people. After reading this book, I want to meet him again so I can be properly impressed.

How to Make a Mutant: Transgenesis

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(this creature does not exist)

Even though at some level, we’ve been making mutants for hundreds, even thousands of years through selective breeding and agriculture, these aren’t the kind of mutants we think of. We usually expect something bizarre and alarming that happens almost immediately. Like the Incredible Hulk turning green, or turtles becoming sentient, bipedal, and proficient in martial arts. We get a little closer to that sort of thing with environment sensitive genes.

Biologists usually first learn about these genes in bacteria, with the lac-operon system. The lac-operon system is an arrangement of proteins and DNA that essentially lets bacteria adapt to their environment. Bacteria like to eat sugar, and they survive the best on glucose, the simplest of the sugars. If glucose isn’t available, they can eat other sugars, like galactose or lactose, but that requires more machinery and the bacteria don’t want to rev up those machines until they know they have to. How the lac-operon transcription system works involves the use of two proteins, one that blocks the expression of the lactose-eating gene lac-x and one that amps up the expression. When lactose is present, the blocker protein can’t work, and the amp-up protein only binds if there isn’t any glucose. So with this system, a bacterium can shift to eating different sugars like a car shift gears.  This is something of a simplification of the process, but the upshot is that while the bacterium’s DNA remains the same, it’s expression is altered significantly by the environment.

Similar situations occur in more complex animals. Researchers often make use of temperature sensitive genes in fruitflies to create flies that are genetically identical to a control group, but have a protein that works differently due to being exposed to higher temperatures while forming inside the egg. In nature, this happens with many cold blooded animals whose sex is determined by the temperature where their eggs are kept.

These environmental affects control the expression of genes, and not necessarily the genes themselves, still, this isn’t as trivial as it may seem. The well-known statistic that our genes are 96% similar to chimpanzees’ is only true when we don’t count the so-called junk DNA that doesn’t seem to directly code for anything. But while this DNA doesn’t seem to make anything, recent evidence has shown that it may have an effect on how things are made or when they’re made. In other words the obvious difference between us and other animals may have more to do with how our genes are expressed rather than what genes we have in the first place.

”]Scientists can also insert known genes into the genomes of animals to create transgenic creatures. For example the gene that produces the fluorescent protein GFP in jelly fish can be inserted into the DNA of bacteria using electroporation, a technique where a electric field is used to create pores in the cell membrane of bacteria, which allows foreign DNA to enter. This can also be done through abruptly increasing the temperature, which forces the bacteria to open pores in their membranes to adapt to the situation.

Bacteria will incorporate DNA into their genome, and as long as the new DNA doesn’t interfere with their ability to survive and reproduce, the bacteria will quickly grow in number, providing a way of naturally increasing the amount of foreign DNA available. Scientists can then use  enzymes to cut out the gene that they want from the bacteria and insert it into the genome of a more complicated organism through several methods

Lab workers can insert DNA directly into the nucleus of a stem cell, for example, or simply allow the cell to take in the DNA on its own. Alternatively, scientist might use a virus that has had all its DNA replaced with the foreign DNA so that it can be injected into the cell without direct human supervision.

Optogenetics Experiment in Mouse (Source: MIT)

One of the most dramatic examples of transgenic research involves the use of a protein called channel rhodopsin. This protein is related to the protein that detects light in the cells of our eyes. When the gene that produces the protein is introduced into the neurons of a mouse, and a light of a certain color is show on the neuron through LEDs or  fiberoptic cable implanted in the mouse’s skull, it can cause the neurons to fire, directly affecting the behavior of the mouse. Not only that, but the channel rhodopsin can be altered to respond differently to different types of light so that blue light might cause a neuron to fire, while orange light might cause it to stop firing. This system has opened up an entirely new field of biology called optogenetics and researchers are currently finding ways to use the techniques to help sufferers of all sorts of brain diseases from Parkinson’s to Alzheimer’s.

So real mutants might not fly or shoot laser beams out of their eyes, but in many ways they’re even cooler than that.

How to Make a Mutant: Mutagens

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http://bit.ly/p2fCgl

The term “mutant” gets bandied about quite a bit in popular culture. It can mean some freakishly deformed animal or person, or, more recently someone with magical, almost god-like powers (if you think that the X-men stories are completely scientifically accurate, then you have a disturbingly unrealistic understanding of the universe). But the reality is that mutants are all around us. The word comes from the Latin mutantem which means to change. In some sense, then, we are all mutants, as our genes are naturally a mix between the genes of our parents and therefore are always changing. Usually though, by “mutant” we mean some organism that has had their DNA altered by artificial means. Even this more focused definition still applies to an astounding number of the things we look at every day.

There are basically two ways of making a mutant: using a mutagen, or specifically targeting  an organism’s genome. We’ll talk about mutagens first. A mutagen can be anything from nuclear radiation to insecticide. Anything that’s a labeled carcinogen is also mutagen, as cancer is perhaps the most common form of mutation. Since cancer happens naturally, it’s perhaps a little  incorrect to put  it under the heading of “mutation,” but as some unfortunate people are intimately aware, cancer can be caused by man made materials, so it does fit.

Before we get too ahead of ourselves, we should first go over how a mutagen might make a mutant. The way it works is this: every living thing starts out as a single cell. How this cell behaves is determined by the genetic information in the DNA of the cell. This behavior includes how it divides, what structures it makes, whether it moves around, how it connects to other cells, you name it. If this cell is exposed to a mutagen, then this DNA might be altered. For instance, if the cell is subjected to ionizing radiation,  subatomic particles will scour through all the material of the cell including DNA, knocking electrons and possibly even whole atoms off the molecules that make up each material. If the intensity of the radiation is low enough, most cells can repair this damage, but some damage might be too severe to repair, or might be missed by the repairing processes, and if this happens to DNA, a mutant can result.

Ionizing radiation, as you might imagine, is a rather ruthless mutagen. It’s a bit like trying to hit the bull’s-eye of a target with a shotgun. You might get lucky and hit the area you want, but even in the best case scenario you’re going to have collateral damage. So while this type of mutagen is the most commonly found in nature, it isn’t something you want to use to find a beneficial mutation.

A slightly more nuanced approach is to inject material that looks like a section of DNA into the originating cell while it’s dividing. This approach only affects the DNA, and so you don’t have to worry about killing the cell outright, but it’s still random and so it could cause changes that an organism won’t be able to survive. There is a more sophisticated version of this involving actual foreign DNA, but we’ll get to that in the next post.

One of the mutagens most commonly used in labs is a chemical called EMS (Ethyl MethaneSulfonate). This chemical will affect the DNA of a cell by affecting  only a single nucleotide base pair. This allows much more of the mutants to divide and develop fully into adult organisms.

All these methods will produce mutants, and this is far from a complete list, but scientists usually have a specific mutant in mind. For example, a scientist might be interested in muscle growth and wants to find an animal mutant that will mimic a known human disease.

http://bit.ly/pLanTO

The first step for this is to find the right animal model. Animal models are used in many kinds of research genetic and otherwise. A human model wears fashions or tries different products so that we can see how they supposed look or work in an idealized environment. In a similar way, an animal model is given different ailments so that scientists can see how the animal responds to different treatments and other situations, with the hope that a human might have the same result. Humans are not all that different from other animals, as even Aristotle was aware, (We should venture on the study of every kind of animal without distaste; for each and all will reveal to us something natural and something beautiful. -Parts of Animals I.645a21)  but certain animals are better for studying different systems. If you want to study the higher functions of the brain, for instance, you probably want to work with mice, or chimpanzees. If you are interested in the steps involved with development from a single cell to an embryo, however, you might use zebrafish, as zebrafish embryos are transparent, allowing you to see many processes hidden in other animals.

One thing that is common for most animal models is that they tend to have faster life cycles, and produce more young. If you are a graduate student hoping to get your PhD in two years, you don’t want to have to wait ten months for an animal to get born, just to find out it doesn’t have the right genetic make up and you have to start all over again. In lectures, scientists often talk about how expensive each animal is. In other words, how much grant money goes into studying each individual animal. If a study is supposed to follow the entire lifespan of a rat, then it’s going to take four to seven years, and so that rat is going to be very expensive. If a scientist does a similar study with a fly, on the other hand, it will only take a few months and therefore be only a fraction of the cost. Also, while there maybe eight to twelve rats born from a mother, which is a good number in comparison to a chimpanzee, there still may not be enough chances for the pups (baby rats) to have the right genetic make up. If one of the pups needed for the study dies, it can be devastating, while if a fruit fly dies, there might be forty other flies to take its place. This is one reason why fruit flies are used often in genetic studies.

Two fruitflies contributing to research -http://bit.ly/oy62XW

Let’s look into how to make a fruit fly mutant. The procedure is typically to subject fertile, male flies to a mutagen (EMS for example) for a period of time, and then allow them to reproduce with normal female flies. Some degree of care must be taken to ensure that the female flies are virgins, so that there isn’t any chance of another fly’s genetic material getting involved. Thankfully virgin females are paler and a black dot is visible on their abdomens. They are therefore distinguishable from older females, which don’t have the black dot, and males, which have darker coloring and a reddish structure at the ends of their abdomens. To examine these features, a researcher can take flies and subject them to CO2 gas, which knocks them out. They can then manipulate them using tweezers and a low magnification microscope. The virgin female flies are sequestered in a separate vial with a mutagen-treated male and allowed to mate. The female will lay mutant eggs, which will eventually become mutant larvae, and then mutant flies. Depending on what trait a researcher is looking for, they will analyze either the larvae or the flies for altered behavior or health.

Wild banana -http://bit.ly/l1jut6

This method  of producing mutants has been around for decades. You might think that they are science fiction things, but if you walk into any sophisticated biology lab and talk to somebody there, you’ll find that mutants are not only studied a lot, but they are almost taken for granted.  Furthermore if you take away the use of mutagen, this kind of directed evolution has been around for ages.Without human intervention bananas are, fat, green, cumbersome things that are difficult to work with. By cultivating the trees that produced the tastiest, easiest to eat fruits, however, humans managed to breed the trees to produce the banana we know and love today, a fruit that fits so nicely in the hand, and opens so easily it seems like it was designed for us. It seems that way because we designed it.

This also has happened with animals. Geneticist Dmitri Belyaev managed to domesticate foxes, by breeding the ones that were the most tame. The breeding program was successful, but oddly the tame foxes began to look an awful lot like dogs.  Belyaev’s research suggests that many of the same genes that control physical attributes, also control behavioral ones. Just as he domesticated foxes within his life time, wolves must have at one time been domesticated by early humans. In other words, when you look at a dog, you’re probably looking at a mutant wolf.

Reading Your Blueprint: Karyotyping

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DNA is  what makes us who we are. It identifies us. The government uses it to control us. Well, that last one isn’t quite true…yet. Still most of us, even those of us who should know better, treat DNA as if it were magical fairy dust that wizards in lab coats use to answer questions. But the only difference between the wizards and you is some knowledge and equipment. This blog will help with the knowledge part.

There are three main ways to use DNA to tell something about an individual: Karyotyping, DNA fingerprinting, and Genome sequencing. I’ll go over Karyotyping in this post and tackle the other methods later.  Karyotyping is basically looking at the chromosomes of a cell as it’s dividing. Cells divide to make new cells, but in order to make sure each new cell has everything it needs, everything has to be copied, including the genetic information. Unless the cell is a bacterium (or an archeum), it will keep its genetic information in a sort of ball of denser material called a nucleus. Most of the time this ball is all we see of the cell’s DNA, but if we add a dye and watch the cell divide, we can see several strange, threadlike structures, or bodies, that are colored by the dye. These “colored bodies” are the chromosomes, named after the Greek “chromo” for colored and “soma” for body. A chromosome is actually DNA wound up around proteins and then wound up again and again until it becomes a tight tangled mess, similar to what happens if you twist a coiled telephone cord.

As you look at  chromosomes under a microscope, in other words, you are actually looking almost directly at DNA.  Normally the chromosomes are haphazardly arranged around the nucleus of the cell, but after taking a picture of them, you can rearrange them so that they’re aligned the same way and in order from largest to smallest. This is a Karyotype.

Usually a lab worker who wants to karyotype a person’s blood, will look at some white blood cells, which are easier to work with for a variety of reasons, and wait for themto start dividing. Then, he or she will use a drug such as colchicine or vinblastin to stop the cell from dividing completely. This allows the technician to look at all the chromosomes under the microscope and analyze them using dyes that bind to different genes. The lab worker or another scientist or technician can then compare the karyotype of one individual to another to see what differences they are in where the dye shows up.

The drugs used to stop the cells from dividing have interesting histories. Colchicine started out as the active ingredient in an herbal remedy extracted from autumn crocuses to treat gout and inflammatory arthritis. Crocus extract was used as such as far back as 1500 BCE though it was only isolated from crocus extract in the late 1800’s. Colchicine is still used to treat severe cases of gout today, however, the difference between an effective dose and a toxic one is rather small, so takers of the drug have to be careful.

Chromosomes of a cell. Vinblastin or colchicine used to keep them from separating.

Vinblastin also comes from a plant extract, this time from the madagascar periwinkle plant. The plant was originally crushed into a tea, and researchers noted that people who drank the tea had a lower white blood cell count, leading researchers to look into the active ingredient as a possible treatment for diseases that affect white blood cells.

White blood cells are primarily responsible for the body’s immune response, which causes inflammation, the primary complaint of gout and arthritis sufferers. These cells also  affect a number of diseases, including cancer. White blood cells use microtubules to initiate movement, and all cells use microtubules to separate chromosomes as they divide. Cochicine and vinblastin both inhibit the production of microtubules, which is why the drugs are useful in karyotyping as well as a number of other diseases.

The easiest thing you can do with karyotyping, after determining species, is determining sex. A normal human being has 23 pairs of chromosomes and sex is determined from the 23rd pair. Genetic females have two longer chromosomes, called “X” chromosomes here, while for genetic males one of the chromosomes is shorter and called a “Y” chromosome. Sometimes a person might have two or more X chromosomes along with a Y chromosome in a condition called Klinefelter’s syndrome. There are also a number of other possibilities, such as XXX or even XXXY. All these scenarios usually result in learning disabilities, and regardless of how many X chromosomes there are, if there is a Y chromosome the person will be physically male. These situations where there are more than two sex chromosomes are examples of aneuploidy.

Karyotype of a normal male. From biology.iupui.edu

The word “aneuploid” comes from four Greek words mashed together: “an-” for not, “eu” for good,”ploos” for fold, and “oidis,” which means form or type. So all together you have “not good fold type,” a set of chromosomes that is not correctly paired. This sort of situation can occur in other chromosomes as well, such as in the case of Down syndrome, the second most common inherited  form of mental retardation, where there is an extra copy of chromosome 21.

In biological terms, “-ploid” refers to how many complete sets of chromosomes there are. The normal number of copies for a set of chromosomes is two, so most cells are called diploid. Sperm and eggs only have half the normal amount of chromosomes, so they are haploid. Plants and some other organisms can have more than two sets of chromosomes, making them polyploid. While polyploidy can occur in human fetuses, it never results in birth. In fact no vertebrate animal can be polyploid.

A normal x chromosome on left, fragile x on right.

Fragile X is the most common inherited form of mental retardation, and while it is not a aneuploidy disorder, diagnosticians can also identify it using a karyotype. In fragile X one of the x chromosomes looks thinner in an area that has a long string of the same DNA sequence. Because of this repeated sequence, a protein required for normal development can’t be produced properly and the neurons of the brain cannot form the proper connections as a result.

Diagnosticians can tell that someone has Fragile X from the way a certain area of a chromosome is affected naturally, however they can also tell other genetic attributes by how the chromosome is affected by the dye they use. Giemsa, the most common dye used for karyotyping, will concentrate in different bands on the chromosome, which you can see in the picture of the normal male karyotype above. By comparing where these bands show up between different karyotypes, researchers can begin to find abnormalities and differences that may have something to do with how a person looks, acts, or feels.

Other labeling techniques have also been used to get more information from chromosomes. Especially exciting is the work done on telomeres, which can be labeled using a protein attached to a fluorescent marker. These are the ends of the chromosomes, which are made up of repeating patterns of DNA that act like the aglets of shoelaces, keeping the chromosome from shortening prematurely. Telomeres have been found to be  linked with the aging process. Although the telomeres will shorten and lengthen throughout life, various stresses can cause them to shorten more than usual. It seems the older we are, the shorter our telomeres get. If we can figure out how to lessen the shortening process, we may find a cure for aging itself.

TELOMERES cap the ends of chromosomes. Image: WIKIMEDIA COMMONS/NATIONAL HUMAN GENOME RESEARCH (user GIAC38)

Suggestions? Corrections? Questions? Observations? I’m trying to cover a lot of ground here without letting things get too complicated, so I’m bound to make some mistakes. Please feel free to comment on this post or email me at zorknot (at) gmail.com about what I’ve written.

Immunohistochemistry

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Diagram of how an atomic force microscope works

So there’s this amazing protein you want to study, and it might very well change the world, but you have a problem: how do you study the protein when its too small for even a microscope to see?

There have been a number of solutions to this problem over the years, many of which are still being used. You could, for instance, study the protein’s effects by adding controlled amounts of it to a sample, or you could keep an organism from producing the protein  through surgery, drugs, or geneticsand see what what happens when it isn’t there. More directly, the obvious solution is to get a better microscope. What do I mean by a “better” microscope? Well, although there are some drawbacks, there are some microscopes that can give much higher resolution and/or provide added information about what you’re looking at.

One example of this is an atomic force microscope. How this works is that a small needle on a cantilever connected to a computer is dragged across what you want to look at. The computer then measures all the bumps that the needle encounters and gives a visual representation on the screen. As you might suspect this method has a number of drawbacks, (the cantilever is fragile, samples have to be specially prepared, etc) but it is possible to identify single atoms using this method.

Another type of microscope that can help you find a protein is an electron microscope. The idea here is to use electrons instead of photons to look at a sample. There are a number of drawbacks to this idea as well, for one thing, samples usually have to be “fixed” with a chemical such as Osmium tetroxide  and this can sometimes change the way things in a sample look. However, here the drawback can also be a good thing. What “fixed” means in this case, is that the molecules are attached to the things around them, and so aren’t going to move around all over the place like they would normally. If you want to see stuff moving around, you’re out of luck, but often you want to see where something is at a particular time and you don’t really want it to be free to wander.

There is another benefit to using electron microscopes. Parts of a sample will be darker depending on how electron dense they are after they’ve been fixed.  the electrons that the microscope uses to scan the sample will bounce off of that part of the sample, causing there to be a dark region. It isn’t always easy to tell which molecules will be more electron dense than others, but there are ways of making it easier. For one thing, if you have a molecule that you know is electron dense that you also know will form a bond with the protein you are looking for, you can add that to your sample and then you can compare the dark regions in the treated sample to how an untreated sample looks. The dark regions that appear in the treated sample but not in the untreated will most likely be your protein.

How confocal microscopy works

This trick also works with fluorescent and confocal microscopes. These microscopes shoot  beams of light at a constant, controlled frequency on the sample, causing some molecules to fluoresce, emitting light at a slightly different frequency. Confocal microscopes have the added benefit of being able to control where exactly the lasers focus so that it can show not only where something is in terms of up, down, left, and right, but also where it is in terms of depth. Once again, if you know a molecule is fluorescent and that it binds to the protein you’re looking for, you can add it to your sample and then check it out in the fluorescent microscope to find your protein. That’s great, but how do you find a fluorescent molecule to bind to your protein?

Diagram of antibody production

Well, your body has a ready-made system for finding molecules that will bind to proteins that has been tested over millions of years of trial and error. The immune system. If a virus or a bacterium enters your body and starts causing problems, your immune cells will start producing antibodies for the proteins that are present on the surface of the intruder, so that if it shows up again, it will be dealt with before it can cause any damage. Antibodies are large (by protein standards), y-shaped molecules produced by white blood cells. There are binding sites at the ends of the smaller arms of the y that bind to specific parts of a molecule. The binding sites act as a sort of lock, where the key is the part of the molecule the antibody binds to. There are a huge number of different binding sites that are available due to the genetic information encoding the antibodies getting shuffled and mutated all the time. When a cell in the body gets stressed, it sends out a signal that a white blood cell(a macrophage to be specific ) can respond to. This white blood cell then invites another cell (a T-cell) to take a look.  This T-cell will then go out and talk to another cell (a B-cell), which has a catalog of antibodies available for production that the T-cell can peruse by seeing if the peptide, or protein part, that’s in the stuff the macrophage ate, is also in the B-cell. If any antibodies from the B-cell  bind to something in the T-cell saw in the macrophage, then the B-cell knows to produce more of that kind of antibody. After that, wherever an antibody encounters its target, it triggers a response from other white blood cells.

Sometimes a cell might be stressed, but the antibodies will bind to something that isn’t the cause. Molecules, from peanuts, pet hair, pollen or just about anything might happen to be present in greater quantities than the thing that’s really causing the problem. This is how allergies happen.

That’s the bad news. The good news is that because antibodies can be found for almost any kind of molecule around, scientist can used lab animals to produce antibodies to the proteins they want to study. Furthermore, by manipulating the genetics of the animal, they can cause each antibody to be attached to a fluorescent molecule. The antibodies can be stored in a vial in a freezer and transported cold to labs all over the world. All a scientist needs to do then, is bathe whatever he or she is studying in a dilution of the antibodies, and then look at the sample with a fluorescent microscope. Wherever the sample fluoresces, that’s where the protein is.

This process is called immunohistochemistry. Immuno- because it deals with antibodies from an immune response, histo- from the Greek for tissue, and chemistry because it deals with the binding of molecules.

Antibody production diagram is from A Positron Named Priscilla: Scientific Discovery at the Frontier (1994) National Academy of Sciences (NAS) ( http://www.nap.edu/openbook.php?record_id=2110&page=69 ) all other images from wikipedia.

Myxobacteria are Awesome

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Swarming myxobacteria
Image pulled from http://bit.ly/m51q1q

I am writing this post because myxobacteria are awesome, and I think more people should know about them.

You could go through your entire life without ever hearing about myxobacteria. Pretty much everything you need to know about microorganisms in general is that there are things moving around that are so small you can’t see them, sometimes they can help with things like digestion and pollution cleanup, and sometimes they can cause diseases such as salmonella, so you should really make sure to wash your hands, cook your food and  pasteurize things.

Everything beyond that is a detail that you can probably overlook without any serious repercussions.

But what’s the fun in that?

As with just about any facet of science, if you look into microbiology you soon find yourself falling through a magnificent and intimidating rabbit hole of information. It helps to have a specific thing to latch on to to make sense of everything.

Myxococcus fulvus fruiting body
image pulled from http://myxobacteria.ahc.umn.edu/whataremyxos2.html

Even focusing on myxobacteria gives you a lot to take in though. The picture above shows how they move around in swarms or wolf packs. The colors indicate the direction each cell is moving in. For instance, all the cells that are colored orange are traveling to the right. Why do they do this? How do they do this? They don’t have any flagella or cilia (not in the classic sense anyway) They release slime,( myxobacteria comes from the greek myxo for slime after all), but how does that help? I’ll say more about myxo movement in a later post, but there’s more.When food is scarce, myxobacteria start lumping together in visible fruiting bodies, about a millimeter tall,  like in the picture on the right. These fruiting bodies will eventually release bacterial cells with thicker cell walls that act as spores, eventually budding and making more myxobacteria, which then repeat the process.

Well, okay, that’s your basic fungus, right? But the weird thing here is that these are all still bacteria. They don’t even have nuclei! How do they show such complicated behavior?   How do they know enough to organize themselves into a heap to release spores? How is it that the spore cells look so different from the other cells?

Scientists know the answers to many of these questions, but others are still still a mystery. As you go through some of the explanations, you start to notice these strange correlations between how bacteria sense things and how social networks and mobs of people form and behave. You start to wonder about how some professions get more specialized and whether businesses and franchises are fruiting bodies. It’s eerie. And if these dumb bacteria act this way, is it possible that we act in similar ways because we’re in a similar environment? What can we take from that? Are we too much like bacteria, or not enough? What does this say about free will?

Deep, huh?

Like I said, Myxobacteria are awesome.