Tag Archives: evolution

How to Make a Mutant: Transgenesis

(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

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.

Flagella and Philosophy

Most bacteria, including E. Coli bacteria, which cause food poisoning, move around by using flagella. Under the microscope, flagella look like kinked up hairs sticking out of the cell and undulating rapidly. If you remember high school biology you might already know, or think you know all about flagella. They’re those hairl-like  things that cells whip back and forth to move forward right?

Not exactly. There are basically two kinds of flagella, the ones that bacteria have, and the ones that eukaryotic cells have. The eukaryotic ones do in fact whip back and forth. The bacterial ones, however, actually propel the cells they’re attached to by corkscrewing through the fluid. As I went over in a previous post, the situation bacteria are presented with isn’t the same as a submarine in a ocean. It’s more like a submarine in a large silo filled with vibrating pebbles. Drag is a huge deal. Bacteria need a powerful technique to move around and a corkscrew type action works rather well.

When you use a corkscrew on a wine bottle you basically turn it around in a circle as it progresses into the cork. So here’s a question: how does a bacterium do that? The flagellum has to be attached to the cell with a buttload of strength to pull the cell along, but at the same time it has to be able spin around like a drill bit. If you look at all the different components of the flagellum (pictured below) you can see that the structure is pretty complicated. WTF? Aren’t bacteria supposed to be primitive organisms?

Well, yes and no. You see, the thing that’s easy to forget about evolution is that every thing that’s around has been evolving for just as long as everything else. It’s just that while our cells were busy trying to figure out how to differentiate and work together to get to places where there was better food and water and such, bacteria were hunkering down and learning to live in the environments they found themselves in. They’re just as good at being bacteria as our cells are at being part of a larger organism. Still, the flagellum is so mind-bogglingly complicated and yet robust in its implementation, that it has from time to time been used to prove or disprove the non-existence of God.

The argument runs something like this: “We and the organisms of Earth have to have been created by a God,” say creationists, “because the bacterial flagella is so complicated that it could not possibly have been formed by chance, any more than a hurricane could blow through a ship yard and create an aircraft carrier.”

“But,” say non-creationists, “each protein that makes up the structure of a flagellum looks similar to proteins used in other, less complicated bacterial structures. Furthermore the flagellum of E. coli is only one variant of many, indicating that one Doesn’t it make sense that flagella might have come from mutations that put the proteins together in ways that were somewhat beneficial? If even one bacterium survived a trying situation better than its neighbors, it would quickly begin to dominate. And evolution of bacteria has been directly observed in nature and in the lab. At the very least that seems more plausible than everything getting poofed into existence through some unknown process by a magical man in the sky.”

You can probably tell which side I favor.

Something that you start to notice if you study biology is how complicated and diverse proteins are. Proteins aren’t just little specks that bump into each other in random ways. Each protein has a different shape and different areas that have different properties that interact with other proteins in different ways depending on environmental factors. It’s an imperfect analogy, but you could almost say proteins have personalities. Almost like people, proteins will work together, compete with each other, and even find things in their environment and use them to accomplish a “goal.” A protein may be stuck in a bad position, for example, and it may come into contact with another protein that likes to pry things apart, and then they will help each other out.

So it’s not exactly the same situation as a hurricane picking up a bunch of aircraft carrier parts and arranging them into a complete aircraft carrier. Its more like a bunch of people who don’t know how to make an aircraft carrier getting a steady supply of parts and enough time and resources to try things out. Eventually, given enough time, people in that situation will eventually make something like an aircraft carrier. Though they’d probably start out making houses, cars, and a number of other things out of the parts before hand. In fact you could look at the current real-life production of an aircraft carrier as an example of evolution. Evolution is simply the effect of variation subjected to some environmental pressure. There were many different types of ship before the aircraft carrier came about. For one thing, there had to be aircrafts in order for there to be any use for one. Humans wanted a place to put planes on the ocean and the aircraft carrier fulfilled that purpose

In a similar way, proteins just want to be in equilibrium, and so they will often use things like enzymes to make equilibrium easier to achieve.

If you are doubtful of any of this, you need only see a video of how a flagellum is formed in a bacteria. The formation of a flagellum is a marvelous and awe-inspiring dance and it happens hundreds of times a second in a single organism ALL THE TIME. You don’t need religion for miracles. You just have to look around.