Proteins as tools for research

I’m gonna talk a little bit about the new project I’m taking on (which I was going to start working on this past week, but a nasty cold set me back a bit, so I haven’t actually done anything with it yet. I’m almost fully recovered though!).

Basically this new project is testing a super cool tool, and that tool hinges on the fact that proteins can do things based on their shape. What we’re doing is shining light at proteins to make them change shape and do something we want. And because we control when the light goes on and off, we can control the precise moment that this protein starts doing its job, and the precise moment when it stops. Which is pretty useful for studying how things work and interact in a cell! Also this concept has actually been around and used for awhile, and I’m just testing the tool being used in a slightly new way. And I didn’t develop or create it, I’m just testing it in a slightly new application to see if it works in our frogs.

Okay, so why are proteins so amazing? Proteins are what actually do most things in your cells (and outside them). They do this by generating chemical environments that facilitate certain reactions, they bind molecules to recognize them or change what they’re doing, and they provide structure and support and sometimes elasticity or shape.

A quick refresher for people who don’t know/remember: proteins are made up of amino acids. Each amino acid has a certain shape and certain chemical properties (some are acidic, some are basic, some are hydrophobic, some are hydrophilic, some are big and take up a lot of space, some are tiny and can tuck into small pockets, some are very flexible, and others are very rigid and are locked at certain angles). The protein is sort of like a string of beads, where the amino acids are the beads. This string then gets arranged to form a dense ball in a certain shape, and this shape (along with the locations of the amino acids within it) determine the protein’s function. That shape can determine whether or not the protein can bind other things (imagine puzzle pieces fitting together), and how well it can bind those things.

But these shapes aren’t static. They can be changed by other proteins or molecules binding. They can also be changed by the chemical environment (because it changes how the amino acids interact with each other and their surroundings), which is influenced by electromagnetic forces such as light as well. Basically, certain wavelengths of light can change certain proteins’ shapes. And this can cause all sorts of things to happen depending on what the protein is.

For an example, this is what a tool called optogenetics does. My project isn’t optogenetics exactly (I’m working with different proteins to do a different thing in the cell, but this is something you may have heard of on the news, and it’s really cool).

First a quick neuroscience lesson. Neurons can send electrical signals, and what starts these electrical signals is ions (which have a charge) moving into or out of the neuron. This happens when ion channels (they’re proteins that act as tunnels with gates that allow certain ions through when open) change shape to cause a pore to form. Two common examples of what could cause this shape change in neural ion channels is a molecule (termed a ligand) binding or by a voltage change. Below is a great image demonstrating how a voltage-gated ion channel works:

[Source]

But green algae and some bacteria also have ion channels that can be induced to change shape with certain wavelengths of light (actually some of your retinal cells can change shape in response to light, which is how you see! They’re called rhodopsins, but they aren’t ion channels and cause the light signal to be sent in a slightly different way).

That means that now you have a protein in one species that you can shine light on and cause it to allow the flow of ions. And you have neurons which “turn on” and “turn off” in response to ion flow. And with some genetic techniques that have been around for decades, we can actually cause these algal and bacterial proteins to be expressed in specific neurons in the lab! Which means you have precise control over when a certain group of neurons turn on or off! Below is a video of that in action. Note that when the blue light comes on, the mouse begins to run around the edges, which is very different from its behavior before and after.

Now this may seem a little creepy and over the top from just that video. But it’s not like we’re just around the corner from mind control. But it does allow us to study the neural circuits in lab animals. Because trying to study how all the billions of neurons in your brain work to coordinate movements and thoughts is incredibly difficult. Being able to turn on a specific group of neurons can begin to tell us which behaviors different ones are involved in, and therefore will help people piece together how they’re interconnected.

This tool has also been discussed in the treatment of diseases such as Parkinson’s. One issue in Parkinson’s is that you lose a certain group of neurons, but we know from other treatments (deep brain stimulation) that keeping the remaining neurons firing helps in managing the disease. So if you could implant a light to periodically turn on the neurons on the appropriate time, it could be therapeutic. The hard part is actually getting the proteins to be expressed (while we’re very good at genetic manipulations in research animals, gene therapy for humans isn’t quite here for the masses yet).

If you want to hear a little more (and put much more eloquently, haha), watch this Ted talk about optogenetics!

So that’s a popular example of how we can use proteins to precisely control a certain cellular function in order to study how something works! Which is basically what my project is doing, except we’re using light to control the production of proteins instead of using it to turn neurons on and off. But both are tools based off the fact that proteins have functions that are related to their shape, and we can use things like light to control the shape of certain proteins. Yay for biological tools! And yay for proteins!

Quick correction: I said what I’m doing is a bit different than optogenetics, which is actually incorrect. It falls under the heading of the term optogenetics. I had just only ever heard the term be used to specifically describe the method of using genetics to express light-sensitive ion channels, specifically. I wasn’t aware that it is used more generally to refer to using genetics to express any exogenous* protein you can manipulate with light.

*exogenous means non-native to the tissue/cell/organism. basically that the protein you’re expressing is not normally found there. Also just a reminder that if I ever use a term that makes you go, “wait, what the heck does that mean?” feel free to aks! Especially if googling isn’t helpful because 1) sometimes the use of a term in a specific sub-field is different than the common definition and 2) I use words wrong all the time, so it’s entirely possible I misused it. As in the case of optogenetics!

Misogyny, Racism, and the importance of diversity in STEM

I actually have a fun, new project, but I’m gonna save that for next week’s post (it’s based on changing protein’s shape with light!)

But today I’m gonna instead highlight a couple of great articles pointing out misogyny and racism in STEM and why diversity is important. There are several articles, but they’re all great and talking about a very important problem that not only hurts the individual women and people of color (and LGBTQ people, more on that specifically at a later date) in science, but hurts all of science, and by extension all of society that’s missing out on the amazing research and progress that those people could be contributing if their time and energy weren’t taken up with dealing with discrimination.

First of all, it’s amazing (in a deeply disappointing way) that there are still people who believe discrimination doesn’t happen in the sciences. But it absolutely does. And the fact that it isn’t believed and isn’t taken seriously, is a huge part of why it’s so hard to combat. Because nowadays, we don’t have departments actively excluding women, and I’ve never been explicitly told that I shouldn’t be in science. But the methods by which we exclude women (and people of color, though that article focuses on gender), are much subtler and more insidious, making it easy to write off differences in female enrollment or accomplishment or matriculation rates as just being due to “personal choice,” or (even worse) “fundamental differences between men and women” (the day you show me a study demonstrating differences between men and women where all environmental and societal factors have been controlled for is the day I’ll start considering any conclusions based on this premise). Here’s another article about misogyny in the sciences.

Okay, I’m sad that I even have to bring up this point, but some people may ask, “Well, so what? Maybe women aren’t as good at/as interested in/necessary in sciences.” But science is fundamentally creative and therefore thrives off of diversity. We can’t have scientific progress without diversity of thought. Sticking to the same old ideas (and people) is detrimental to progress. The larger the pool of scientists (and specifically the pool of backgrounds and thought patterns and experiences), the better off we all will be. Because sometimes you need someone thinking a little differently (sometimes questioning ideas we’ve taken for granted for decades) to move forward or find something new.

Finally, I want to leave you with two things. The first is a great little list calling into question the idea that academia should or is best as it is, and instead encouraging a more “gentle academic” which I think addresses some of the issues I have found with grad school and academia and are important to strive for to create a scientific culture more open to new, better ideas (by the way, this comes from herfirstfeeblemovements.tumblr.com but tumblr makes it very difficult for me to post a link to this):

“towards a gentle academic

  1. be up front and honest about the things you do not know
  2. acknowledge the intrinsic value of others’ knowledge bases, even if they do not seem important to you from your institutional context
  3. do not feign mastery where you have none
  4. respect the gaps in others’ knowledge bases
  5. be generous, not only with others
  6. but also with yourself
  7. you overwork yourself at the risk of legitimizing a culture of overwork
  8. privilege voices and perspectives that have historically been left out of the academy
  9. nothing is ever neutral or apolitical
  10. support the progress of other scholars
  11. collaboration over competition”

And the second thing is this great post from warmheartedradfem.tumblr.com “10 Black Scientists You Should Know” (via gender-and-science.tumblr.com which is an excellent blog I highly recommend!). If you follow that link, there are pictures and blurbs of the scientists, but below is just a list of the names and their field (how many of them have you heard of? And how many could you say something about them or their work? I’ll admit I’d only heard of 3, and 30% is a pretty abysmal rate):

1. Ernest Everett Just – developmental biologist (fertilization and cell division)
2. Patricia Bath – opthamologist (cataract treatment)
3. Marie Maynard Daly – biochemist (cholesterol and sugar in disease)
4. David Harold Blackwell – statistician (game theory)
5. Neil deGrasse Tyson – astrophysicist (and science educator)
6. Percy Julian  – chemist (synthetic progesterone and cortisone)
7. Mae Jemison – astronaut (and chemical engineer and doctor and dancer!)
8. Charles H. Turner – animal behaviorist (insect perception, memory, and learning)
9. James West – engineer (invented technology still used in most microphones)
10. George Washington Carver – botanist (invented hundreds of uses for soybeans, peanuts, and sweet potatoes)

Open Access Science

One of the reasons I started this blog was because I think it’s important for scientific research to be accessible to everyone. This sounds simple, but actually requires several things:

  1. Research results need to be easily accessed by the public.
  2. How the research was conducted needs to be accessible.
  3. The public needs to be able to understand it.

Now to talk a bit about each of these:

  1. With modern technology, that means it needs to be online and it needs to not be behind a pay wall. For those who aren’t familiar with the term “pay wall,” it’s basically when a publisher requires you pay some amount of money (often as much as $50) to read an article. In practice, nobody gets single articles, and instead universities and large research groups will buy subscriptions to databases that have access to articles from a variety of publishers, but these can cost thousands of dollars a year and so are only available to people affiliated with universities and research groups.
  2. Research is only as good as the way in which it was done. Due to publications requiring increasingly extensive data to be considered acceptable but simultaneously placing increased restrictions on article length, “materials and methods” sections (which is where this information is located) is increasingly being reduced or relegated to “supplemental materials,” which is published online only and often buried slightly.
  3. This is one of my most important and most difficult parts. If people don’t understand, then they don’t actually have access to the information. The problem is that the complex terminology really does serve a purpose. Much of the language we use in science has very specific definitions that make it difficult to communicate as efficiently and effectively without it. And I don’t actually think that should change among scientists. But it absolutely needs to for communication with the public. You shouldn’t need a college degree to understand the research being done with your money (because most research is funded by government grants). And I think the solution to this needs to be better simplified communication by the researchers themselves. Science media could serve this purpose, but it can’t possibly account for all the research being published every day.

I was recently shown this website: http://labscribbles.com/. Dr. Rachel Harding is publishing what she’s doing and her data in real time, which I think is awesome! That is what I wish this blog could be. I love that Dr. Harding is not only using her blog to make her data accessible to the research community, but to the broader public as well. And it’s useful to get feedback in real time (which comments and emails allow when you publish what you’re doing) because it can keep you from spending months doing research based on a faulty premise or incorrect technique. So why am I not publishing my data? Why am I being secretive about what exactly I’m doing?

I’m in my first year and have no publications. That means I have at least 4 more years, and in that time I need to publish in a respectable journal. You’ve probably heard the term “publish or perish.” And it is absolutely true. It is extremely difficult (and not advised) to get your PhD without publishing on your work. The number of publications you have is one of the major numbers that gets looked at for hiring. If I were to graduate with no publications, I would have an extremely difficult time finding a job. Because publication is viewed as verification that you have done work worth reading.

But many journals will not publish any data that’s been published before (which seems like it makes sense at first because you shouldn’t just copy what you’ve done before to make it look like you’ve done more than you have), but that includes things that have been published online. Which means if I put out my data on this blog, it may be incredibly difficult for me to publish on it, which could seriously hurt my future. And I’m nowhere near established or experienced enough for my career to survive that.

Another big problem with publishing data online is “scooping.” This is when another lab publishes on your research before you. Journals will only publish new research (which is one of the reasons we have a big replication problem). So if another lab already published experiments similar to mine, I won’t be able to publish my own. In actuality, two labs typically aren’t doing exactly the same thing, so the lab that publishes later probably will still get a publication, but it will be in a “lesser” journal (journals are ranked by how good they are; I have plenty of complaints about that if you want to hear them). So how does this happen? Usually it just happens that labs pursue the same questions by accident because they’re both interested in similar topics (which means making your research public is actually great because it means you could see what other people were working on and work with them or go in a slightly different direction!) But occasionally you get people who specifically try to scoop someone. I’ve heard numerous stories of labs that send grad students to scope out posters and talks in order to steal ideas and then try to finish the project first and beat them to publication. Which is a waste of everyone’s time and money, but because all that matters is publications, people have incentive to cheat like that.

So I’m not in a place in my career where I can feel secure putting my data out there. Dr. Harding already has her PhD, a post doc position, and several publications. And because most scientists would love if research were more open access, her blog could even be used as a selling point for hiring committees. But I’m just not there yet. And as much as I agree that the publication and research access system is deeply broken, I’m not yet in a position where I can afford to not work within it.

Fortunately the vast majority of researchers agree that data should be more open access, so this will hopefully change in the future. And of course, when I do get a publication (still working on the getting data part though, so it could be awhile), I will definitely let you know and provide explanations so you can understand what my data actually mean, because that’s the most important part.

As always, if you have any questions about anything, let me know!

Animals in Research

First of all, sorry about the lack of posting last week! I totally forgot and kept meaning to make it up this week and it just didn’t happen, whoops.

But this week I want to talk a little bit about animal use in research because this week I was the frog person.

I’ve mentioned before, but our lab uses frogs as a model organism, meaning we study frog neurons in order to better understand basic mechanisms of neuron development. And this actually tells us a lot about how neurons develop in humans because a lot of the basics have been highly conserved through evolution. But of course frogs are much easier to study in a lab (not to mention the serious ethical problems with trying to learn the same things from humans).

But yes, that means we have to keep and use frogs. And since I was the frog person this week (we rotate weeks so everyone is the frog person about every month or two), that meant it was my responsibility to get frog embryos.

Since we study neurons during early embryonic development, we actually only do research on embryos, not adult frogs. But in order to conduct our experiments reliably and reproducibly, we need to know exactly how old they are. That means we need to control exactly when the eggs are fertilized.

And this is that week’s frog person’s job. The night before we need embryos, we inject the frog with hormone to prime them for ovulation. About 16 hours later, we “squeeze” the frog to induce egg laying (we call it “squeezing,” but really it’s massaging the ovary, which simulates the male frog mounting the female). Then to fertilize, we put a piece of teste into the dish with the eggs and pull it apart to release the sperm, then shock the eggs with water (normally they’re in a salt solution) to induce them to fertilize. Now we know exactly when the eggs were fertilized and can accurately perform developmental experiments!

Which all sounds fine in the abstract, but what I’ve learned is that I hate having to handle them. I just feel bad because all they want to do is hang out in their tanks. They don’t like being picked up and they don’t like being injected and they don’t like the noises and vibrations that come with moving them.

Have you ever had to trim a cat’s claws? Even if it’s better for them in the long run, they’re usually not happy. And it just feels bad to have to hold them there when they want to just go sleep in the sun in peace.

And dealing with the frogs is a lot like that. Even though this research is absolutely important to understand how we develop a functional nervous system, which has implications for diseases and disorders that affect millions of people and which could be used to improve the lives of billions of people in the future, you just feel bad.

But that’s part of the price of doing research like this. Because there really is no better way to learn what we’re learning. Computer simulations can only ever have predictive value, and observations can only ever be correlative. To actually learn causal information about what happens in a living organism, we have to perform experiments in living systems.

And the rules that govern whether or not certain animal research is allowed are actually quite comprehensive and effective.

First of all, there’s economic incentive to be frugal in regard to animal use. Animals are expensive to house and care for. Our frogs have a tank system that is far better than what almost all aquatic animal pet owners have. They are fed on a very regular schedule by trained animal technicians. There is a team of vets who oversee our animals and whom we can contact if we notice any problems (our animals are watched much more carefully than most pets). All of this is expensive, so it encourages researchers to be thoughtful about how many animals they really need for an experiment. Additionally, all research funded by the NIH (National Institute of Health), which almost every research lab in the country has at least some funding from, has their own standards of care that include that you use as few animals as possible while still maintaining the integrity of the study.

And all animal protocols must be written up and approved by a board at each institution called the Institutional Animal Care and Use Committee (IACUC). They must approve all animal research protocols and they take into account things like (a) is animal use necessary to answer this question or can it be answered another way? (b) are your protocols humane? (you must operate under the assumption that any procedure that would cause pain in a human would cause pain in the animal) (c) is your research necessary enough to justify the use of animals?

This all scales with type of animal as well. For instance, there are very few restrictions regarding what types of things you can do with fruit flies. However primate research is exceedingly difficult to get approval for and requires extensive restrictions and considerations. Mice are more in-between; there are many procedures you’re allowed to perform but they must often be done under anesthesia and with painkillers and antibiotics to minimize the harm to the animal.

Of course for almost every biological study, the animal must be euthanized in the end. This is often because the data you want to gather requires tissue samples or requires you to extract certain material from the cells or requires you to verify that your procedure did what you thought it had. And even here, all animal euthanasia must be performed twice, with two different approved methods, to ensure that no animal suffers excessively (which is far more strict and humane than common practice in agriculture and hunting).

In the end, animal research has clearly improved our lives by so much. And while there are certainly horror stories from throughout history, there is extensive regulation to ensure that animals are well taken care of and dealt with humanely and ethically.

So even though I feel bad every time I have to inject a frog, I know that the research we do justifies it and necessitates it. But this is something people working in research have to decide for themselves, and for me, personally, it is worth being able to research neural development.

Note: I’m no longer gonna put “Sci-Friday” at the beginning of posts since once-a-week seems to be a pretty manageable posting frequency (usually), so my idea of science updates on fridays and other posts interspersed during the week was a little too ambitious. And sometimes research goes slower than usual (last week studying for an exam wiped out the second half of the week for me, so I didn’t actually get much research done), so this way I can alternate research updates with other things.