What is that? A liquid nitrogen freezer

This is a new feature called “What is that?” where I will show a photo of something from the lab and then discuss what it is, what it does, and why scientists use it.  Every lab that I’ve ever worked in, I gave tons of tours – to my family, to other scientists, to kids and to the public!  Seeing what a real lab looks like and understanding how things work is one of the ways I use to demystify science and scientists. Think of this new series as a virtual lab tour with me as your tour guide!  I hope at some point soon to turn this feature into a short video series…but until then, enjoy learning about what “that” is!

So what are these? These are liquid nitrogen freezers.

liquidnitrogenfreezersLet’s start by talking about freezers in general. What temperature is your freezer at home? Well it needs to be cold enough to freeze things. The freezing temperature of water is 32° Fahrenheit (F) or 0° Celsius (C), so you want your freezer to at least be able to freeze water, but you also want it to preserve your food.  Part of preservation is preventing bacteria from growing since bacteria could potentially cause food poisoning when you thaw and eat the food (especially if it isn’t cooked first).  The colder the temperature, the less likely the bacteria is to be able to grow.  Also, the colder the freezer is, the less likely it is that enzymes (proteins that perform chemical reactions in cells) are active and breaking down the food’s nutrients. So the ideal freezing temperature for food is 0°F or -18°C.

In the lab, we have -20°C freezers that store reagents and look a lot like the upright freezer that my mom has in her basement to store extra food (and chill martini glasses). We also have -80°C freezers, also called ultra low freezers referring to the “ultra low” temperature.  These are better at storing proteins at a temperature that is cold enough to inactivate them. These ultra low freezers are also good for storing RNA.  RNA has a natural enemy, a protein called RNase, which is essentially a high-powered chomping Packman after the Pac-Dots dots that make up the RNA. At really cold temperatures, this RNase Packman is inactive and can’t work, keeping the RNA sample safe.

roses LN2

Creative Commons license. Original photo from Kasi Metcalfe on Flickr

As a bit of a segue, my 4 year old nephew calls me on Facetime a few times a month and always asks me to “show him some science.” One of the first things I showed him was our “Biospecimen Cryostorage” where we store the samples from our biobank, and which is what is pictured above. This room has three Liquid Nitrogen Freezers, and these are even colder that the ultra-low freezers. With liquid nitrogen (abbreviated to LN2) in the base, the whole tank is cooled to below -275°F or -170°C. If you feel like you’ve heard of liquid nitrogen before, you probably have. This is the liquid that is used at Science Centers to freeze roses and then smash them into a million pieces.  If you’ve seen any cooking show in the past 5 years, you’ve probably seen a chef use liquid nitrogen and pour it into a mix of cream and sugar to make a fast ice cream. However, in science we use liquid nitrogen as a way to quickly freeze and preserve living cells and tissue – a process overall known as cryopreservationLN2description

To better understand the photo and to really understand “what this is”, I have labeled areas above.  Each of the two tanks pictured can hold up to 40,000 individual samples.  These samples could be blood samples, tissue samples, samples of cells, etc.  In our case, these samples are stored in 2 ml (milliliter) tubes in plastics boxes in racks inside each freezer. Each box can hold 96 samples and each rack (see photo below) can hold 13 boxes (over 1200 samples). The freezers are automatically filled by tanks filled with liquid nitrogen sitting right next to each freezer.  Each freezer isn’t completely filled with liquid nitrogen for a few reasons. First, it would be really expensive but more importantly, it isn’t necessary. The temperature of liquid nitrogen is -190°C but the vapor keeps the tank colder than -170°C, which is still good enough to keep all of the proteins in these cells completely inactive.

LN2removalSamples are removed from these tanks on a regular basis and distributed to researchers.  You can see an image on the left of a rack of boxes being removed. It is important when selecting individual samples that they are not allowed to warm up and thaw.  This thawing can activate proteins that break down the samples or causes ice crystals when re-thawing that affect the integrity of a tissue sample or the viability of frozen cells, for example.

What is that? Liquid nitrogen freezers and a filler tank
What does it do? Keeps biospecimens or other samples at really low temperatures
Why do scientists use the? To keep samples well preserved and viable so that they work better for their experiments.

For more “What is That?”, click here.

What are vaccines and how do they work?

Vaccines are a hot topic. Vaccines bring up lots of discussion, lots of false information, and a vitriolic passion rarely seen in matters of science and pseudoscience. I’m going to start my discussion about vaccines by explaining what they are and what they do. My second post will address some of the false information and controversy (with an added bonus of bringing in my lovely sister’s fabulous point of view as a mom of two!) My final post will answer a question I was asked about whether or not vaccinations are needed after a stem cell transplant.

Let’s talk about what immunizations do and how they do it.  Vaccines (aka immunizations) use biological agents to induce an immune response that protects you from that disease. The immunization itself could contain a weakened version of the disease-causing agent (like an inactivated poliovirus to vaccinate against polio), a non-human version of the disease (such as the cowpox virus to vaccinate against smallpox) or a small part of the disease-causing agent (for example, the toxin or a protein on the surface of the disease-causing agent).  The vaccine is injected into the body, but it isn’t strong enough or functional so it doesn’t cause the disease, but the body attacks the vaccine’s biological agent using immune cells and develops a “memory” of this infection.  This memory is made up of both antibodies and immune cells.  Antibodies are shaped like the letter Y and the top part of the Y functions like a puzzle piece that fits together with a complementary piece on the infectious agent (called an antigen).  When the anitbody encounters a matching puzzle piece it will bind to the infectious agent and kill it quickly before it can cause disease. Therefore, the effectiveness of a vaccines depends on how good the vaccine is at making a puzzle piece fits the antigen puzzle piece on the infectious agent.
antibodySo let’s have an example.  The flu vaccine contains small proteins from several flu strains that, when injected, stimulate the immune system to create antibodies against those flu strains.  When a person encounters the flu,for example because their neighbor has the flu and sneezed on them, the antibodies and immune memory that were created by the vaccination will attack and neutralize the flu virus before it can infect the cells and make you sick.  If the flu vaccine didn’t contain proteins that create puzzle piece antigens that bind to the most common flu strain in a particular year, the flu shot is less effective and more people will get the flu.

Vaccines have done amazing things.  They have eradicated smallpox, a deadly disease that had been around for over 12,000 years and killed 30-35% of people who were infected.  Eradicating this disease saves the lives of over 5 million people each year who would have been infected and died otherwise.  Polio, another crippling disease, has nearly been eradicated with only a few hundred cases in 2012 compared to over 350,000 in 1988. Common childhood diseases like measles and whooping cough have also been decreased considerable, saving millions of lives each year through vaccines.  They are truly a modern medical miracle!

Why is water so interesting? Featuring Olympic Gold Medalist Misty Hyman

MistyandCathy

Misty (left) and me getting ready to swim

In this two part series, I partner with my friend, Olympic Gold Medalist Misty Hyman, winner of the women’s 200 meter butterfly in the 2000 Australian games.  Misty currently coaches private lessons, leads swim clinics, and gives motivational speeches around the world.  Misty was also recently named the senior assistant coach for the Arizona State University swim team. In her spare time, Misty extends her passion for swimming into the community as a spokesperson for FitPHX and encouraging everyone to learn how to swim.

I met Misty five years ago in Valley Leadership as members of Class 32 (Best Class Ever!!) We became fast friends, even though you may not expect a scientist and a swimmer to have much in common.  To be honest, I’m not much of a swimmer, though I do love my pool and my technique improves every lesson I take with Misty.  Misty, on the other hand, is quite a scientist. Part of her swimming success came from a careful, scientific analysis of every aspect of her stroke. As we were talking one evening, we starting thinking about what we could discuss together on my blog.  What cool things in science would also be interesting to a swimmer? My first thought – WATER!

I remember the first time I really learned about water was in my freshman year of college in my intro to chemistry class. I was amazed that an entire chapter was devoted to the physical properties of water.  I knew that water was incredibly common: 71% of the planet is covered in water and humans are 65% water.  There are 100,000,000,000,000,000,000,000,000,000,000 molecules of water in an Olympic-sized swimming pool.  So what makes this incredibly common, important and useful substance so freaking cool and worth devoting an entire textbook chapter to?

water_polarity

By OpenStax College [CC BY 3.0 ], via Wikimedia Commons

Lets start with the molecular structure. Water is made up of one oxygen (O) and two hydrogen (H) molecules, which is why the abbreviation for water is H2O (two Hs and one O).  The oxygen is connected to each of the hydrogens by covalent (permanent) bonds. Because of the way that the electrons within the oxygen and hydrogen atoms are distributed, the oxygen is slightly more positively charged and the hydrogens are slightly negatively charged.  This essentially makes water a weak magnet.  In chemistry, we call that “polar“. This polarity is the reason that water has so many unique properties, but I’m only going to talk about one that directly relate to swimming: surface tension. To learn more about water polarity, check out this fabulous TedEd talk.

water-strider-691039_1280

A great example of surface tension thanks to Pixabay

Surface tension is best described by examples:  filling a glass of water over the top, rain beading on your windshield, or bugs walking on the water of the pool.  The water doesn’t spill out of the glass, the rain doesn’t turn in sheets and the bugs don’t fall under the water and die because of surface tension. More accurately, these things happen because the polar (aka slightly magnetic) water molecules are attracted to one another and stay together.  Or to be even more scientific –  the water inside the glass or raindrop or pool is surrounded by other water molecules that can move around each other.The water molecules at the top of the water glass or pool or raindrop don’t have water molecules above them, so they are pulled inwards toward the other water,  creating surface tension.

Interestingly, surface tension directly relates to swimming.  Just take a look at this amazing photo of the effects of surface tension on the 2012 Olympic 200 meter backstroke winner Tyler Clary.  He eventually does leave the water – but he will need to use energy and force to break the surface tension at the top of the water.  This is why swimmers can swim faster underwater than on the top of the water – they aren’t fighting surface tension (plus there are other physics “things” in play like less less drag and less energy wasted with splashing underwater).

Misty’s Message: Although she would LOVE to encourage everyone to just stay underwater, that’s not realistic because we don’t have gills. However, most kinds of tension – including “surface tension” – should be avoided at all costs especially while swimming. Instead of focusing on the reality that you have to break the surface tension in order to breathe, focus on reducing drag because “not being streamlined – that’s a drag.”

Does the media sensationalize terrible science? Oh, yes.

The other day, I was drinking a glass of wine with a friend of mine, and she mentioned a story that she recently read in Scientific American called “Changing Our DNA Through Mind Control.”  She was excited to tell me how scientists had found that decreasing your stress can actually change your DNA! This was fascinating!  She was excited!  I was excited!  But being the scientist that I am, I wanted to understand what, how and why, so I needed more information. To gather this information, I looked at the original scientific article in the journal Cancer. (see here for my post on what a scientific article looks like).

om

Thank you Wikipedia for the image

The researchers had taken breast cancer patients and split them into two groups – one group went to mindful  meditation classes and the second group did not.  The scientists then took a sample of their DNA isolated from the patient’s blood and tested the length of their chromosome’s telomeres. To remind you, all people have 23 pairs of chromosomes in each and every cell. Telomeres are found at the ends of the chromosomes and protect the chromosomes from being damaged (essentially eaten away at from the ends by DNA-chomping proteins inside the cell).  A common comparison is to think of telomeres like the plastic bits at the end of shoelaces. The shorter the telomeres (or the shorter the plastic bit), the closer the chromosome (or the shoelace) is to being damaged.   In this study, the researchers found that the telomeres in cancer patients who went to meditation were longer than the patients that didn’t . Because of this, their DNA was better protected.  How incredible!

How unbelievable. Unbelievable for a few reasons:

  1. The researchers looked at the length of telomeres over a three month time span.  Telomeres shorten over a lifetime, so I wouldn’t expect to see a significant change over 3 months (whether sick, well, stressed, or not stressed).
  2. Because of this reasoning, I looked carefully at the data they presented in the paper.  None of it was statistically significant.  There is a trend that showed that patients that did not go to meditation were slightly, on average, a tiny bit lower than patients that went to mediation, but nothing that convinces me that what they are seeing is real,  In fact, even the paper’s authors said that if they wanted to have enough patients to get to statistical significance in the results, they would need to do a bigger study with more than double the number of participants.
  3. As a final nail in the coffin, in the psychological analysis comparing the mood of the meditating versus non-meditating patients, the researchers didn’t notice a change in stress or mood scores.  So even if there was a change in the DNA (which there isn’t), since their mood doesn’t change, a decrease in stress cannot be the cause of the telomere/DNA changes.
I’m not saying that mood doesn’t have the ability to affect your DNA – maybe it does.  I just don’t think that they showed it in this study.
chocolate

Thank you Wikipedia for the image

But I don’t want to harp on these researchers or this study. In fact, here’s another interesting example. A science journalist, Dr. John Bohannon, recently wrote a scientific article based on an actual study that they did studying people’s diet and how chocolate contributed to their weight loss. They found that eating chocolate once a day significantly increased weight loss!  The data was real, they published the results, and the media picked it up like wildfire.  It was published by news media around the world!!! Only problem – the conclusions they they drew were crap, and Dr. Bohannon published them with the intention of baiting the media.  In this case, there were too few participants, so they found something that was “statistically significant” in this group of people but wouldn’t necessarily pan out if there was a full, well-designed study. John Bohannon wrote a great blog post about this whole experiment and why this is the case.

So what’s the message here?  I think the first is that the media often looks for science that can create a striking, head-turning headline.  The problem is that when the conclusion is so cool, journalists don’t always read the original article or evaluate the data to make sure that this cool headline is supported by evidence in the publication.  To be fair, journalists may assume that since other scientists already reviewed the paper for scientific accuracy (a process called “peer review”) that it will be good to go.  But just because a stranger hands you a drink in a bar and says its okay, should you just believe them that it doesn’t contain Roofies?  I also don’t want to imply that all science journalism falls into this trap, but with ever shortening deadlines and competition for the “hot headline,” I can only imagine how appealing it is to take shortcuts.

To conclude, I actually have a problem in writing this post in that I don’t have a solution for you, my reader.  Unlike the friend I was having drinks with, you may not have a scientist at your beck and call to vet all news stories for scientific accuracy.  And as much as I hope that this blog is helping you to obtain your own PhD in biology, you won’t have all the tools you need to evaluate scientific articles on your own.  So maybe I will leave you with a tried an true saying “Don’t believe everything you read” or maybe “If it sounds too good to be true…” it might be.

I’m not the only person who has written about this topic.  If you’re interesting in reading more, check out this article from NPR, numerous articles from Ben Goldacre about how science is misrepresented in the media compiled on Bad Science, and a different point of view, an article published in Salon about how just because someone is a scientist doesn’t mean that they are an expert (especially if they are on Fox News).

Do you want to ask a question?

Often, when people find out that I’m a scientist, the first thing they do is ask me a question.  It may be about their family member who has cancer or about something they recently read in the news that was scientifically related. I’ve gotten questions about a drug they were recently (or about to be) prescribed or about what it’s like to be a scientist.  I’ve been asked to look up statistics about a disease or to talk to their child or grandchild about my career.  Since my Mom has the opportunity daily to ask me all of her scientific questions, I want to give you the opportunity too.  On my new “Ask A Question” page, you or your child or grandchild can send me a question.  I will respond personally (as soon as I can!!) and maybe even use your question to prompt a blog post.

Looking forward to hearing from you!

How does a gene make a protein? Introducing RNA!

Genes are pieces of DNA that code for a protein.  That sounds great…but how does it do this? DNA is made out of nucleotides (A, T, C, and G) and proteins are made out of amino acids.  To “crack the code” and transform the DNA code into the protein code, you need an intermediary.  That’s a molecule called RNA!  messenger RNA  (or mRNA, for short) to be precise, because it is the message that communicates the information from the DNA to the protein.

Let’s revisit our car blueprint analogy to discuss the role of mRNA.  If DNA is the blueprint for the steering wheel, and the protein is the steering wheel, mRNA is the person in the middle who reads the blueprint and builds the steering wheel.

gene_mRNA_protein

So let’s see how this actually works.  The first step is to understand what RNA is actually made out of. DNA stands for DeoxyriboNucleic Acid and RNA stands for RiboNucleic Acid, and if they sound like they are related, you are correct. Here are the three main differences

  1. DNA is double-stranded and RNA is single stranded (see the photo here)
  2. DNA is made from A, T, C, and G and RNA uses A, (standing for uracil), C, and G
  3. In DNA, A always matches with T, whereas with RNA, A always matched with U

Because they are made up of similar components, the cell can copy the code from the DNA into the single-stranded mRNA molecule.  Also because these two molecules are related, this process is call transcription – like what you would do when copying the words in a book from one place (DNA) to another (mRNA).

The mRNA is then what codes for the protein.  It does this just like you would expect any code to – using a key.  In this case, each set of 3 nucleotides codes for an amino acid.  The cells have machinery (called a ribosome) that “reads” the mRNA strand.  The combination of “ATG” always tells the ribosome to START making a protein.  It then reads the three digit code, adding the appropriate amino acids along the way, until it reads one of the three codons that tells the ribosome to STOP making protein.  At this point, the protein can fold up to make the 3D structure so it will function.  Because this process takes nucleotides and codes them into amino acids (a totally different molecule), this process is called translation.  Just like translating a book from English into French, this process translates mRNA into a protein.

translation

 

Wow what a lot to take in! This process from DNA (the gene) to mRNA to protein is called the “central dogma” of molecular biology.  This process was originally described in 1956 by Francis Crick (the same guy who along with Watson discovered the structure of DNA).  Why is it called this? Probably because when it was described, they realized that this was a fundamental process for all life.  It’s also important for us to know for so many reasons.  If you know that DNA codes for RNA which codes for protein, any changes in this process can result in a protein that isn’t quite right.  What if you have change the code of the DNA?  This will change the protein!  What if you change the amount of the mRNA? You will change the amount of protein!  And what can this do?  Cause problems in your cell that cause disease!

transcription-translation

What is a blog?

One of my puppies, Indy, hanging out with us outside today

One of my puppies, Indy, hanging out with us outside today

I had high hopes today of writing many great and interesting things about genetics. But instead, I spent the day outside watching my puppies chase lizards, playing cards and enjoying the weather.  And if you are in New England (like my family is), I’m so sorry.  You should have spent spring break with me.

Speaking of my family, my family has been reading this blog since I started it.  This includes my Mom, who wants to comment on every post, but doesn’t want to post her name. I end up learning a lot from her and others non-blog-posted feedback, and the first thing I realized is that a lot of people don’t know what a blog is!!  Since my target audience is my mom and other people who may not read a lot of other blogs, I thought I’d take a moment to just describe a blog.

All of my journals from years and years of on and off writing

All of my journals from years and years of on and off writing

Blog is short for weblog.  Essentially any person who wants to talk about anything can start a blog online.  You could think of it as a public journal or an online method to express some type of viewpoint or convey certain information or even as a method to sell a product or idea. Usually blogs have a specific focus.  In my case, I have three main things I hope to accomplish with this blog:

  • Talk about science in a way that everyone can understand
  • Provide interesting books and links to websites that you can read to learn even more!
  • Tell stories about my journey and the lives of scientists so that when you hear the word “scientist”, you don’t first think of describing us as “mad” or imagine a photo of Einstein.

My favorite blogs are as diverse as they are addicting.  Some have to do with science, like I f**king love science or Pharyngula.  Some are associated with major online news magazines like Future Tense.  While others are mommyblogs like dooce that are a hilarious view of life with kids, but with a philanthropic edge. Because there are over 150 million blogs out there, everyone creates their blog a little differently and posts different things.  It’s like having 150 million different magazines at your fingertips (with varying levels of quality and content).

Now that you know what a blog is, what do you do about them?  If you find a blog that you like, you can bookmark the URL and check it out every once in a while to read whatever new things they have posted.  Many blogs are also linked to Facebook or Twitter pages.  You can follow this blog’s Facebook page here or my Twitter feed here.  Whenever I post something on this blog, it will automatically be posted to both Facebook and Twitter, and then you can click on the link to go and read the new post.  Or you can join the mailing list (look to the right side of the screen – there should be a place to sign up), which will email you whenever I post something new.

However you find this blog, I just hope you enjoy it and learn something.  And please don’t be afraid to post a comment or question! That’s what I’m doing this for!

 

What is DNA?

There’s so much to know about science and biology that requires background information.  This may be tedious to read, but it’s essential to understanding so much of how things work (or don’t, in the case of disease).  Many of my posts will provide this kind of background, and they will also be archived in the “Background Info” menu for future reference.  If this is old hat to you, that’s okay!  If not, please read and learn – it’s worth taking the time so that future posts make more sense.

So probably everyone knows what DNA is. Right?  It’s talked about on the news all of the time.  Maybe vaguely it’s defined in your head as “the building block of life”.  Maybe you know about the double helix (more on that soon!!).  Maybe you’ve even isolated DNA as part of a science fair experiment.  But really, WHAT IS IT?

dna double helixI remember the first time I learned what DNA was in a biology class.  The biology book’s fourth chapter was entitled “Marcomolecules” and one of these molecules was DNA.  It was confusing.  All the different macromolecules were introduced all at one time.  I had no idea how they were related to one another or why I was learning about them.  And why were they called macro?  That implied big, and I knew for a fact that DNA was small (because it has to fit in a cell!) So let’s break down what DNA really is, in a way that I hope is far less confusing than my first biology book.

DNA is the genetic code that makes up all of human life – or any life on earth (yes, your DNA is made up of the same parts as angler fish DNA or tulip DNA) .  A lot of times, people compare it to a blueprint, where the DNA provides the instructions to make whatever organism it is supposed to create.  This is essentially true.  DNA itself is made up of individual parts called nucleotides.  There are four nucleotides – each containing a different base:GCAT

  • Adenine (A)
  • Thymine (T)
  • Guanine (G)
  • Cytosine (C)

These are often abbreviated using the single letter listed above – A, T, G or C.  These bases are each associated with a sugar and a phosphate, which forms what is commonly referred to as the “backbone” of DNA.  Look at the picture above to see what this looks like.  DNA looks like a ladder – the sugar and phosphate forms the sides of the ladder (the light blue in the picture) and the bases form the rungs.  What’s really neat and interesting is that these bases don’t pair up randomly.  Adenine always pairs up the Thymine and Guanine always pairs up the Cytosine. Want to know why?  Well, it’s because of the shape of the bases.  Take a look at the pictures above. A and T have two places where they can bind to each other and G and C have three.  If you tried to get an A to bind to a C, it wouldn’t work because the C would have an empty binding spot hanging out there.

replicationSo why in the world is this important at all?  Well, think of this – because we know this rule, if we know the sequence of As, Ts, Gs and Cs of one strand of the DNA ladder, we also know sequence of the other strand.  This means that when DNA copies itself (what scientists call replication), two copies of the DNA can be made relatively easily: the ladder unzips and each separate side of the ladder functions as a template to make two exact copies of the DNA.  This process happens 10,000 trillion times in your lifetime.

There are so many interesting things about DNA and how it works – all will be discussed in future posts.  But in case you want more information right now, I have compiled interesting DNA references can be found here.