How do we know the genome sequence?

Imagine someone asked you to explain how a car works. Even if you knew nothing about cars, you could take the car apart piece by piece, inspect each piece in your hand and probably draw a pretty good diagram of how a car is put together.  You wouldn’t understand how it works, but you’d have a good start in trying to figure it out.

Now what if someone asked you to figure out how the genome works? You know it’s made of DNA, but it’s the ORDER of the nucleotides that helps to understand how the genome works (remember genes and proteins?). All the time in the news, you hear about a scientist or a doctor who looked at the sequence of the human genome and from that information could conclude possible causes of the disease or a way to target the treatment. DNA sequencing forms a cornerstone of personalized medicine, but how does this sequencing actually work? How do you take apart the genome like a car so you can start to understand how it works?

As a quick reminder – DNA is made out of four different nucleotides, A, T, G, and C, that are lined up in a specific order to make up the 3 billion nucleotides in the human genome.  DNA looks like a ladder where the rungs are made up of bases that stick to one another: A always sticking to T and G always sticking to C.  Since A always sticks to T and G always sticks to C, if you know the sequence that makes up one side of the ladder, you also know the sequence of the other side.

DNA_ladder

The first commonly used sequencing is called Sanger sequencing, named after Frederick Sanger who invented the method in 1977. Sanger sequencing takes advantage of this DNA ladder – this method breaks it in half and using glowing (fluorescent) nucleotides of different colors, this technique rebuilds the other side of the ladder one nucleotide at a time. A detector that can detect the different fluorescent colors creates an image of these colors that a program then “reads” to give the researcher the sequence of the nucleotides (see image below to see what this looks like).  These sequences are just long strings of As, Ts, Gs, and Cs that the researcher can analyze to better understand the sequence for their experiments.

sanger_sequencing

This was a revolutionary technique, and when the Human Genome Project started in 1990, Sanger Sequencing was the only technique available to scientists. However, this method can only sequence about 700 nucleotides at one time and even the most advanced machine in 2015 only runs 96 sequencing reactions at one time.  In 1990, using Sanger sequencing, scientists planned on running lots and lots of sequencing reaction at one time, and they expected this effort would take 15 years and cost $3 Billion. The first draft of the Human Genome was published in 2000 through a public effort and a parallel private effort by Celera Genomics that cost only $300 million and took only 3 years once they jumped into the ring at 2007 (why was it cheaper and fast, you ask? They developed a fast “shotgun” method and analysis techniques that sped up the process).

As you may imagine, for personalized medicine where sequencing a huge part of the genome may be necessary for every man, woman, and child, 3-15 years and $300M-$3B dollars per sequence is not feasible. Fortunately, the genome sequencing technology advanced in the 1990s to what’s called Next Generation Sequencing. There are a lot of different versions of the Next Gen Sequencing (often abbreviated as NGS), but basically all of them run thousands and thousands of sequencing reactions all at the same time. Instead of reading 700 nucleotides at one time in Sanger sequencing, NGS methods can read up to 3 billion bases in one experiments.

How does this work? Short DNA sequences are stuck to a slide and replicated over and over. This makes dots of the exact same sequence and thousands and thousands of these dots are created on one slide. Then, like Sanger sequencing, glowing nucleotides build the other side of the DNA ladder one nucleotide at a time. In this case though, the surface looks like a confetti of dots that have to be read by a sophisticated computer program to determine the millions of sequencing.

NGS

So what has this new technology allowed scientists to do? It has decreased the cost of sequencing a genome to around $1000. It has also allowed researchers to sequence large numbers of genomes to better understand the genetic differences between people, to better understand other species genomes (including the bacteria that colonize us or the viruses that infect us), and to help determineexomee the genetic changes in tumors to better detect and treat these diseases. Next Generation Sequencing allows doctors to actually use genome sequencing in the
clinic. A version of genome sequencing has been developed called “exome sequencing” that only sequences the genes.  Since genes only make up about 1-2% of the genome, NGS of the exome takes less time and money but provides lots of information about what some argue is the most important part of the genome – the part that encodes proteins.  Much of the promise of personalized medicine can be found through this revolutionary DNA sequencing technique – and with the cost getting lower and lower, there may be a day soon when you too will have your genome sequence as part of your medical record.


For more information about the history of Sequencing, check out this article “DNA Sequencing: From Bench to Bedside and Beyond” in the journal Nucleic Acids Research.

Here is an amusing short video about how Next Generation Sequencing works described by the most interesting pathologist in the world.

Journal Club: The Microbiome Autism Connection

As I’ve mentioned in other posts, scientists have to read about and understand the current scientific literature. Lots of the time this is done alone, at your desk in the office or the lab, for hours and hours so that you can really understand whatever topic it is that you’re studying. But one of my favorite ways to share scientific papers is through a weekly meeting with the whole lab called a Journal Club. Although my husband laughs about this kind of nerdy science “club” (akin to his amusement about scientific societies), it’s a great way to discuss a particular topic and dive deep into a discussion about how the researchers got their results and came to their conclusions. This is the first of many Journal Clubs where we will do an abbreviated version of what we would discuss in a typical journal club in the lab. 

Paper TItle:  Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children

Authors: Dae-Wook Kang , Jin Gyoon Park ,Zehra Esra Ilhan, Garrick Wallstrom, Joshua LaBaer, James B. Adams, Rosa Krajmalnik-Brown
Full disclosure, Dr. LaBaer is the Director of the center I previously worked in at the Biodesign Institute at ASU. Drs. Park and Wallstrom worked in offices down the hall from me and Dr. Krajmalnik-Brown was in another center at the Biodesign Institute.

Journal: PLOS One (PLOS stands for “Public Library of Science”). In case you want to read the whole article, it can be downloaded (for free) here

Background/Introduction: Before this paper was published, scientists knew that many children with autism also had gastrointestinal (GI) issues suggesting that there may be a connection between the two. There have been some studies looking at antibiotic treatment (which could change the gut microbiome) before 3 years of age and how this might be connected with autism.  There have also been studies connecting the gut microbiome and the brain. So there was evidence that the gut microbiome and autism may be related in some way.

When this paper was written, scientists also knew about the microbiome and how changes in the bacteria (all 1,000,000,000,000,000 of them) that are in the gut are found in patients with many different diseases – from C. diff infection to obesity to depression.

Goal of this paper: Look closely at the changes in the gut microbiome of children with autism to better understand how these two might be related.

Methods/what did they do?: Bacteria in fecal samples is considered representative of bacteria in the gut microbiome. Therefore, the researchers collected fecal samples from children both with (20 children) and without (20 children) autism.  The samples from patients without autism were used as a “control” to compare to the autistic samples. The researchers also asked the children (or their parents) questions to help determine the level of GI issues, the severity of their autism, and their environmental factors like their diet. The researchers isolated bacterial DNA from each of these fecal samples and then sequenced the DNA to determine what types of bacteria are in the gut.

autism microbiome diversity

A figure from the paper comparing the phylogenetic diversity (PD) of the bacteria in autistic versus non-autistic children. you can see that the red boxes (for autistic children) are lower than the blue boxes (for non-autistic children) indicating a lower microbiome diversity.

Results: Through sequence analysis and other statistical methods, the authors found that children who did not have autism have a more diverse microbiome compared to autistic children.  If there is higher diversity, it means that the gut contains more different types of bacteria, and lower diversity means a smaller variety of bacteria in the gut. They also found that in the autistic patients with a greater diversity in their microbiome, their autism was generally less severe. They also did not find any correlation between age, gender or diet with these microbiome changes.

The scientists also looked at what specific genus and species of bacteria were more represented in non-autistic versus autistic children. Specifically the bacteria from genus Veillonellacaea, Provetella, and Coprococcus  are less abundant in autistic children.

Discussion/Significance: What does this all mean?  The researchers did find a correlation between decreased gut microbiome diversity and autism. It should be clarified that just because GI problems are often found in autistic children and the severity of the GI issues correlates with the severity of autism, this does not necessary mean that GI issues cause autism or vice versa.  That still needs to be determined. Also because the diversity of bacteria in autistic children is low, it is not clear if this is a cause of autism or an effect of a child having autism.  However, this paper does provide a “stepping stone” to better understand what is happening in the gut of autistic children and may help define a target for diagnosing autism (by looking at the decreased diversity in the gut as a diagnostic test) or treatment (perhaps through fecal transplant).

What has been done since? This paper was published in 2013.  So what has changed since the paper was published?  Do we know whether or not changes in the gut microbiome cause autism or not?  Unfortunately, this is still unclear.  However, if these microbiome changes are a cause of the neurological changes in autism, then one would want to do a clinical trial to test what happens to autism symptoms when the microbiome has been altered.  This could be done in a number ways including diet modulations, prebiotics, probiotics, synbiotics, postbiotics, antibiotics, fecal transplantation, and activated charcoal.  Researchers have started this process by holding a meeting that included patients and their families to figure out how this type of trial could be designed (for more details, check out this journal article).

For more information about the microbiome/autism connection, check out Autism Speaks. To read more Journal Clubs, visit the archives here.

Five Ways for You to Participate in Science – Citizen Science

Bunsen_burner

The Bunsen burner I didn’t have. Thanks Wikipedia for the image

I had a chemistry set growing up.  It was small with tiny white bottles holding dry chemicals that sat perfectly on the four tiny shelves of an orange plastic rack.  My dad would let me use the workbench in the basement to do experiments – entirely unsupervised!! You might expect that I did really interesting chemical reactions, and this formative experience helped me to develop into the curious scientist that I am today. Completely wrong.  I remember following the instructions, mixing the chemicals, and then getting stuck because I didn’t have a Bunsen burner.  So many chemical reactions rely on heat, and the green candle stuck to the white plastic top of an aerosol hairspray can wasn’t going to cut it.

My main options for doing science as a kid revolved my failed chemistry experiments, my tiny microscope and slides, and a butterfly net that never netted a single butterfly (not for lack for trying).  However, today with computers (that’s right – no computer growing up – that’s how old I am!) there are hundreds if not thousands of ways for people to get involved in science, without having to invest in a Bunsen burner. This citizen science movement, relies on amateur or nonprofessional scientists crowd-sourcing scientific experiments. I’m talking large scale experiments run by grant-funded university-based scientists that have the possibility of really affecting how we understand the world around us. One example you may have heard about is the now defunct Search for Extraterrestrial Intelligence (SETI) which used people sitting at their computers to analyze radio waves looking for patterns that may be signed of extraterrestrial intelligence. They didn’t find anything, but it doesn’t mean that they wouldn’t have if the program had continued!

Here are five ways that you can become involved in science from where you’re sitting right now!

americangut1. American Gut: Learn about yours (or your dog’s) microbiome

For $99 and a sample of your poop, you will become a participant in the American Gut project. After providing a sample, the scientists will sequence the bacterial DNA to identify all of the bacterial genomes that are present in your gut.  This study already has over 4,000 participants and aims to better understand all of the bacteria that covers and is inside your body – called your microbiome – and to see how the microbiome differs or is similar between different people or between healthy people versus those who may be sick. The famous food writer Michael Pollan wrote about his experience participating this the American Gut project in the New York Times.  They are also looking at dogs and how microbiota are shared with family members, including our pets!

2. Foldit: solve puzzles for sciencefoldit

Puzzles can be infuriating, but at least they have a point to them when you get involved in the Foldit project.  Proteins are the building blocks of life.  Made out of long strings of amino acids, these strings are intricately folded in your cells to make specific 3D shapes that allow them to do their job (like break down glucose to make energy for the cell).  Foldit has you fold structures of selected proteins using tools provided in the game or ones that you create yourself.  These solutions help scientists to better predict how proteins may fold and work in nature.  Over 240,000 people have registered and 57,000 participants were credited in a 2010 publication in Nature for their help in understanding protein structure.  Read more about some of the results here.

3. EyeWire: Mapping the BrainEyeWire-Logo

The FAQs on the EyeWire website are fascinating because as they tell you that there are an estimated 84 billion neurons in the brain, they also insist that we can help map them and their connections. After a brief, easy training, you’re off the the races, working with other people to map the 3D images of neurons in the rat retina.  You win points, there are competitions, and a “happy hour” every Friday night. The goal is to help neuroscientists better understand how neurons connect to one another (the connectome).

4. Personal Genome Project: Understanding pgpyour DNA

The goal of the Personal Genome Project is to create a public database of health, genome and trait data that researchers can then use to better understand how your DNA affects your traits and your health. This project recruits subjects through their website and asks detailed medical and health questions.  Although they aren’t currently collecting samples for DNA sequencing because of lack of funding, they have already sequenced the genomes of over 3,500 participants. The ultimate goal is having public information on over 100,000 people for scientists to use.

mindcrowd5. MindCrowd: Studying memory to understand Alzheimer’s Disease

Alzheimer’s Disease is a disease of the brain and one of the first and most apparently symptoms is memory loss.  MindCrowd wants to start understanding Alzheimer’s disease by first understanding the differences in memory in the normal human brain.  It’s a quick 10 minute test – I took it and it was fun!  They are recruiting an ambitious 1 million people to take this test so that they have a huge set of data to understand normal memory.

This is a randomly selected list based on what I’m interested in and things that I’ve participate in, but you can find a much longer list of projects you can participate in on the Scientific American website or through Wikipedia.  Also, if you’re interested in learning more about the kind of science that people are doing in their own homes, the NY Times wrote an interesting article: Home Labs on the Rise for the Fun of Science.  If decide to try one out, share which one in the comments and what you think!

Can your body contain DNA that isn’t yours? Yes! Chimerism

There was a House episode (Season 3 Episode 2 Cane an Abel) about a young boy who was convinced that he was being probed by aliens.  Though a series of very House-like (aka “unrealistic”) medical twists and turns, House’s team finds cells clumped together in different parts of this boy’s body, including his brain, that are functioning abnormally and causing his various systems.  From sequencing the DNA from those cells, House’s team finds that those cells have different DNA than the boy’s.  In the fictional world of House, the doctors were able to quickly create a probe for the foreign DNA, find all the cells that were different and remove them (House does brain surgery!!) also removing the symptoms including the alien hallucinations. This episode is so wildly out of the realm of current medical ability and practice – so much so that I participated in a “Science Fiction TV Dinner”  all about the science and “science” found in this episode. You can watch highlight from this discussion, which included Dr. Kenneth Ramos from University of Arizona Center for Precision Medicine, below or listen to the whole podcast here.

Science Fiction TV Dinner: House M.D. from Science & the Imagination on Vimeo.

However, what I found most interesting about this episode was the fact that the boy had TWO DIFFERENT genomes in his body. Can this actually happen in real life?  If so, how??

chimera

“Chimera d’arezzo, fi, 04” by I, Sailko. Licensed under CC BY-SA 3.0 via Wikimedia Commons

The answer is yes, and it’s called a chimera or chimerism. In mythology, a chimera is a terrifying hybrid animal that’s a lion, with a goat head coming out of it’s back and a tail with a snakes head on the end. It may be clear that I’m a scientist since I’m sitting here wondering whether all three heads eat and if so, do they all connect to the same or different stomachs. But I digress…  In genetics, a chimera is an organism composed of two distinct sets of cells with two different sets of DNA. As you may remember from other discussions on this blog, DNA is the genetic material that provides the blueprint to make an organism.  DNA is also what is passed along to offspring, so that a child has 50% of the DNA from one parent and 50% of the DNA from the other (more about hereditary here). This is also why paternity tests work – if the child has 0% of DNA from the father, it’s clear that he isn’t the father,

So how in the world can a person have two different sets of DNA?  Especially since all people start off as one fertilized egg with one set of DNA instructions?  There are a few ways:

  • Organ transplants or stem cell transplants.  That organ or cells (more about stem cell transplants here) come from another person who has entirely different DNA from the transplant recipient.  So when a person gets an organ transplant, they become a chimera.  This is also true, at least temporarily, for people who have blood transfusions.
  • Are you a mother or a person who a mother gave birth to?  In that case, you might also be a chimera.  This is called fetomaternal microchimerism.  Mothers usually have a few cells identical to their children that stay in their body long term. This is often caused by immune cells being transferred back and forth between the mother and the placenta during development.   Even 22% of adults were found to still have blood cells from their mother! These cells are really difficult to find – in part because there usually isn’t any reason to look for them – but easier if the mother has a boy because then the chimeric cells contain a Y chromosome whereas the mother’s cells do not.
  • In vitro fertilization (IVF) also has the possibility of resulting in chimeric adults.  Since IVF often implants multiple fertilized eggs into the mother, there is an increased possibility of two fertilized eggs fusing – resulting in one developing human developing into an adult with two sets of DNA.
chimericperson

Illustration of a chimeric person from and awesome article about chimeras from the EMBO journal

Let’s talk about this last option a bit more because this is what House and Co. blamed as the cause of the child’s chimerism, but also because this is really interesting medically and socially.  There have been several noteworthy stories about  women who, for different reasons, were found to be chimeras.  Lydia Fairchild was looking for child support after a divorce, but when DNA tests to prove paternity were requested, it was found that the father was the father, but Lydia wasn’t the mother.  After numerous traumatic events, including being accusing of trying to commit fraud to obtain benefits and having the birth of her third child observed (to prove that she was that child’s mother, even though genetically it didn’t appear that the child was), Lydia was lucky.  Her lawyer heard about Karen Keegan, a women in need of a kidney transplant several years earlier, but when testing her three sons for compatibility, the tests indicated that only one was hers.  Only by looking at other cells in her body were doctors able to determine that her body contained two sets of DNA – one set was passed on to two of her boys and the other set was passed on the other.  Fortunately for Lydia, this discovery prompted DNA testing of members of Lydia’s extended family as well as other parts of Lydia’s body.  This testing showed that Lydia’s cervical cells matched her childrens’ and she was able to obtain child support. The media LOVED this. Just an example of the titles for news articles about Lydia and Karen:

However, besides the obvious media hype, chimerism has practical and legal implications. For example, in 2005, a cyclist Tyler Hamilton was charged with blood doping because they found another person’s blood mixed with his own.  He blamed this on chimerism (New York Times article here) where he had chimeric blood cells that had different DNA than the rest of his body.  He lost his case 2-1, but it brings up an interesting idea.  If everyone knows about chimerism – either through the popular media or TV shows like House – then this could lead to the “reverse CSI effect” where the jury is so aware of the possibility of chimerism that they discard all mismatched DNA evidence blaming it on chimerism.

Besides how strange this all seems, what’s even stranger is that more people are probably chimeras that scientists even realize. The only reason we know that Karen Keegan and Lydia Fairchild are chimeras is because scientists were forced to look at them more closely.  For the rest of us, we likely won’t need a transplant or have alien-probing hallucinations that induce scientists to look at many different parts in our body to see if the DNA is different.  And if more of us are chimeras, what does that mean? This is still something scientists will have to figure out.

Want to hear more about this amazing phenonemon? Check out  or this great article from the EMBO journalNPR’s RadioLab story Mix and Match featuring Karen Keegan’s story.

Book Club – A Short History of Nearly Everything

short

Thanks to Amazon for the image

A Short History of Nearly Everything by Bill Bryson is a brilliant book. Bill Bryson is known for his travel writing and humorous writing style, but it this book he focuses his talents on explaining science. He starts at the beginning looking at the advent of our universe to understanding atoms and quarks to delving into our planet to the beginnings of life itself.  In particular, he has a chapter called “Cells” that provides one of the best descriptions of cell biology written for the public that I have ever read.  A few chapters later in “The Stuff of Life” he describes DNA and genetics in an equally accessible way.  This is one of the few popular science books that I would unreservedly suggest to anyone from ages 15 to 115.

The book won numerous, well-deserved awards including the 2004  Aventis Prize for best general science book and the 2005 EU Descartes Prize for science communication.  Please feel free to continue the conversation once you read the book by commenting below or by Asking me a Question.

For more Book Club books, click here.

What is a cell? Based on a conversation with my husband

I was at an awesome brewery in Flagstaff over the weekend (shout out to Historic Brewing Company) with my husband.  Over a beer and homemade chips, we start discussing science.  Now, don’t imagine that just because I’m a scientist that I insist on talking about it all the time.  Most of the time we’re talking about our dogs or work or school or this blog.  This weekend, the science discussion actually started by taking about grading curves and how they are sometimes fair and sometimes not, and they sometimes measure student’s performance and sometime the teacher’s (sophomore year physics – I’m referring to you!).  From here, the discussion gets a bit fuzzy, but we eventually starting discussing cells and start arguing about the difference between eukaryotic and prokaryotic cells.

Before I get into the details of the argument, let’s talk about what a cell is. Cells are the lego blocks of all living organisms.  Cells contain the genetic material and can divide and replicate into new cells (in a process called the cell cycle).  If you take any part of an organism and zoom in, you will see cells. Cells don’t all look or function the same – as you may imagine because cells in your body do different thing than cells in a plant or cells in a fungus or a bacterial cell. And even different cells in your body look and function differently. Blood cells are round and flow through blood vessels.  Blood vessels are made out of multiple layers of cells surround by muscle cells to help contract and expand the vessels to move the blood. Muscle cells are different depending on where in your body they are located. For example, heart muscle cells look and function different than muscle cells found in your bicep. Nerve cells (called neurons) in the brain often have lots of branching so that they can connect to other nerve cells to transmit signals .  And just to clarify, I know I said that you could zoom into ALL parts of your body and see cells, however there are exceptions to everything.  For example, hair and nails are make out of a hard, tough protein called keratin and not cells.

shapesofcells

Thanks to Wikipedia and http://upload.wikimedia.org/wikipedia/commons/e/e5/414_Skeletal_Smooth_Cardiac.jpg

Even though cells may look different and function differently, all cells have a few things in common:

  1. All cells are surrounded by a membrane, often called the plasma membrane, that is typically made up of fats (called lipids) and proteins.  You can think of this as a plastic bag that can hold stuff inside of it.
  2. The stuff inside this cell membrane includes cytoplasm – you can think of this as a jello inside the plastic bag made up of lots of proteins.
  3. Inside all cells is the genetic material (DNA) that is required to make and replicate the cell and for the cell to function.

Even though different types of cells have different shapes and different functions, there are two main types of cells:

  1. Prokaryotic cells – these are cells that do not have membrane bound structures inside the cell membrane (floating around in the jello-like cytoplasm).
  2. Eukaryotic cells – these cells have membrane bound structures called organelles. We’ll discuss specific organelles in future posts, but some organelles that you may already be familiar with are the nucleus, which is another membrane-bound structure that contains the DNA, or mitochondria, which are the energy-producers of the cell, or chloroplasts, which are the organelle that converts sunlight into energy in plants.
kindsofcells

Thanks to Wikipedia for the images

So, if a cell has a nucleus, it’s eukaryotic and if not, it’s prokaryotic. And this is where the argument started.  My husband insisted that eukaryotic cells are defined by the fact that they are only found in multi-cellular organisms.  Multi-cellular refers to any organism that’s made up of more than one cell – like humans who have about 100 trillion cells, redwood trees, spiders, birds, seaweed, whales, algae, mushrooms, etc.  Although it is true that eukaryotic cells are mostly found in multi-cellular organisms, protists are single-celled and contain a nucleus – making them eukaryotic. Conversely, most prokaryotes are single cells – like bacteria and plankton.  However, some of these single-celled prokaryotes can stick together and work together as a community in a slimy biofilm that is very similar to being multi-cellular.

Why in the world does this matter? Why did I spend any of my energy on a Friday night (and a bit on Saturday when we rekindled the discussion) even discussing this point?  It’s because definitions matter and understanding the details matter – especially in science. But that ultimately isn’t the point of this post – it’s about cells.  Without cells, life as we know it wouldn’t exist.  Without an understanding of cells and how they work, we can’t understand what it means when they dysfunction and cause disease in humans.

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).

How do you find a biomarker? A needle in the haystack.

biomarker_useBiomarkers are biological substances that can be measured to indicate some state of disease.  They can be used to detect a disease early, diagnose a disease, track the progression of the disease, predict how quickly a disease will progress, determine what the best treatment is for the disease, or monitor whether or not a treatment is working. Biomarkers have the potential to do so much, and identifying biomarkers for different steps in the health/disease continuum would help doctors to provide each individual with targeted, precision healthcare.  Biomarkers have the potential to save billions of healthcare dollars by helping prevent disease, by treating disease early (when it’s usually less expensive to treat), or by targeting treatments and avoid giving a treatment that won’t be effective.

spotthedifferencesWith all this potential, you would expect doctors to be using data from biomarkers to guide every single healthcare decision – but this isn’t the case quite yet.  First scientists have to find these biomarkers – a process often referred to as biomarker discovery.  I like to compare finding a biomaker to those “spot the differences” games where you have to look at two images and circle what is different in one picture compared to the other.  This is exactly what scientists do when finding a biomarker, except instead of comparing pictures, they are comparing patients.  And it’s not an easy game of “spot the differences” it’s complicated: the pictures are small and there are tons of details.

Let’s imagine a scenario that a scientist might face when wanting to find a biomarker for the early detection of pancreatic cancer.   Cancer is caused by mutations in the DNA, so you decide to look for DNA mutations as your biomarker for pancreatic cancer. So how do you “spot the differences” to find DNA biomarkers for pancreatic cancer?  First, you will need patient samples – maybe tissue or blood samples from a biobank that already has samples from patients with pancreatic cancer.  If samples aren’t already available, you will have to initiate a study partnering with doctors to collect samples from pancreatic cancer patients for you.  You will also need the second “picture” to compare the pancreatic cancer “picture” to.  This second picture will be samples from people who don’t have pancreatic cancer (scientists usually call this group the “control” group).  Then you have to “look” at the two groups’ DNA so you can find those differences.  This “looking” is often done by some genomics method like sequencing the DNA. This is where a lot of the complication comes in because if you look at all of the DNA, you will be comparing 3 billion individual nucleotides (the A, T, G, and Cs we’ve discussed in earlier posts) from each patient to each of the controls.  Even if you just look at the DNA that makes proteins, you’re still comparing 30 million nucleotides per patient.  And you can’t just compare one patient to one control!  Each of us is genetically different by ~1%, so you need to compare many patients to many controls to make sure that you find DNA that is involved in the disease and not just the ~1% that is already different between individuals.  But wait, we’re not done yet!  The biomarkers that you identify have to be validated – or double checked – to make sure that these differences just weren’t found by mistake.  And before biomarkers can be used in the clinic, they need to be approved by the Food and Drug Administration (FDA)

biomarker_discovery

From http://www.pfizer.ie/personalized_med.cfm


Whew… that was a lot of work! And so many people were involved: lead scientists who directed the project and got the money to fund it, researchers who do most of the work, computer people who are experts at crunching all of the data, and maybe even engineers to help run the equipment. Finding the biomarker needle in the biological haystack is difficult and takes time, money, and lots of people.  This is one of the reasons why there are only 20 FDA approved biomarkers for cancer (data from 2014).  But just because it’s difficult, doesn’t mean it’s impossible.  Furthermore, this effort is necessary to improve healthcare and decrease healthcare costs in the future.  It just might take a bit more time than we’d all like.

If you want to read more about the challenges and some of the solutions to biomarker discovery in cancer, take a look at this scientific article.  Or read about some successes from right in our backyard at Arizona State University on identifying biomarkers for the early detection of ovarian cancer and breast cancer.

 

How and why do cells divide? The cell cycle!

You started off as one cell: one tiny little zygote containing a full set of DNA (23 pairs of chromosomes).  As an adult human being, you are now made up of over 37 trillion cells. This means that that one cell  divided to make two cells, each of those cells divided to make 4 cells, those 4 cells divided to make 8 cells and on and on until the 37 trillion cells that make up you today. Even now, your body makes around 60 billion cells each day to create new skin cells, intestine cells, hair cells and and nail cells. When you cut yourself, the body needs to make new cells to heal.  And if your cells divide out of control, this can cause cancer and if they stop diving this causes of aging. So understanding how cells divide is super important!

The cell cycle, which is the process of one cell and one set of DNA turing into two cells with two sets of DNA.  There are three main parts of the cell cycle:

1.  To make two cells from one, you can imagine that a few important things need to happen.  First, you need the cell to grow to get bigger and to accumulate enough nutrients to support two cells.  Second, you need to replicate the DNA so that when the cell divides, each “daughter” cell gets one copy of the DNA. These two things happen in the interphase part of the cell cycle.  Interphase is separated into 3 parts

  • Gap 1 (usually just called G1 phase) where the cell grows
  • Synthesis (usually just called S phase) where the DNA is copied so that two complete copies of DNA are now in the cell
  • Gap 2 (usually just called G2) where the cell grows some more

Metaphase

The chromosomes (shown in blue) condense and line up before being pulled into two cells by microtubules (shown in green)
By Roy van Heesbeen (Roy) [Public domain], via Wikimedia Commons 

2. Once the cell has copied the DNA and grown big enough to split into two cells, the cell undergoes mitosis.  Mitosis is when the copied chromosomes are separated into two different cells.  Remember that if you took all the DNA in a cell and stretched it out from end to end that it would be 6-10 feet long? Since this DNA is already replicated by the time the cell gets to mitosis, there are 92 chromosomes (two copies of the two pairs of 23 chromosomes) and 12-20 feet of DNA that needs to be organized and sorted into two separate cells.  How does the cell make this nearly impossible sounding task happen?  First, when each chromosome makes a copy of itself, it stays connected to the orignal (kind of like if there were little protein magnets holding them together). mitosis Second, when the chromosomes are ready to separate into different cells they “condense”, getting much, much smaller (see the blue DNA in the photo above).  Third, there are mechanisms in the cell that make the chromosomes line up.  So what you end up with are all of the chromosomes in tight little bundles lined up in a row.  At that point, the cell creates “ropes” out of a protein called microtubules that pull the copied chromosomes apart into the two separate cells.

cytokinesis3.  Finally, now that the DNA is separated into the two new cells, these cells have to officially split into two in a process called cytokinesis.  You can imagine this is like pulling a drawstring closed to pinch the space between the two cells until they have completely split apart.

If this sounds like a complicated process, you’re right.  It is.  But it happens flawlessly 10,000 trillion times in a lifetime.  Part of the reason why this is a flawless process is because the cell puts checkpoints into the process.  It’s like when your bank calls you because they observed a strange transaction on your credit card and they put your card on hold.  If the cell sees something strange happening when the cell is trying to undergo cell division, it puts a hold on the whole process until it gets fixed.  We’ll discuss this a lot more in the future because when the cell cycle isn’t running flawlessly and these checkpoints aren’t working, this contributes to causing cancer and other diseases.

What happens when there are too many chromosomes?

Twenty three.  That’s how many pairs of chromosomes each of us has.  They are numbered from 1 to 22 with two sex chromosomes – two Xs if you are female and one X and one Y if you are male.  One of each pair comes from each parent. This number of chromosomes provides a balance.  Two copies of every chromosome and two copies of every gene.

(As an aside – if you’re thinking about this carefully, you’ll realize that you actually do not have two copies of every gene.  If you’re male, then each gene on your X chromosome and Y chromosome only have one copy each.  And if you’re female, one copy of your X chromosome in every cell becomes inactivated (the inactivated copy is called a Barr Body, in case you were wondering), so technically only the genes on the active copy are being made into proteins.  However, this is NOT the point of this blog post!)

trisomy21So what if instead of two copies of every chromosome, you have three copies of a chromosome?  This is called a trisomy – “tri” meaning that there are “three” of one chromosome.  Examples of this include Trisomy 21 (three copies of chromosome 21), which causes Down Syndrome and Trisomy 18 (three copies of chromosome 18), which causes Edwards Syndrome.

There are also cases when you may have only one copy of a chromosome or two copies of a chromosome (when you’re only suppose to have one copy).  Great examples of this are when you have more (or less) copies of the sex chromosomes:

  • Only one X chromosome causes Turner syndrome, where the girls are usually shorter than average, have delayed or absent puberty, and may be infertile.
  • XXY causese Klinefelter Syndrome, and these boys are taller than average, may have delayed or absent puberty and are often infertile
  • Triple X (XXX) and XYY Syndrome, on the other are found in girls (XXX) and boys (XYY) and may cause them to be taller than average, but generally have no birth defects and no fertility problems.

The two big questions you may be asking yourself now are:

  1. Why would extra copies (or too few copies) of a chromosome have effects on a person’s development or behavior?
  2. How does this happen, anyway?’
Three copies of a chromosome mean that there are three copies of each gene, which can make 50% more protein

Three copies of a chromosome mean that there are three copies of each gene, which can make 50% more protein

Well, as you know, the DNA on chromosomes codes for proteins and these proteins have functions in the cells.  If you have three copies of a gene, you will likely make 50% more protein.  In the case of Down Syndrome, you will make more protein for all 310 genes on chromosome 21 including some genes that are involved in neuronal function.

As for how this happens…we haven’t talked a lot about how babies are made. I won’t get into how my Mom described it (though it does involve love and laying down very, very close to a man), but scientifically speaking, the egg and the sperm each have one copy of each chromosome (22 chromosomes plus one sex chromosome).  These fuse during fertilization to create a fertilized egg (called a zygote) with all 22 pairs of chromosomes plus the two sex chromosomes.  If, by accident, an egg or a sperm ends up with an EXTRA chromosome (though a process called nondisjunction, in case you were wondering), when it fuses to create the zygote, the zygote will have 23 pairs of chromosomes plus one extra.

nondisjunction

When an egg or sperm is created, the chromosomes need to separate into individual cells so that only one copy of each chromosome is in each egg or sperm cell.  This is a process called meiosis. If this doesn’t happen correctly (nondisjunction), an egg or sperm can end up with more or less chromosomes.

Why don’t we have people walking around with all different combinations of different numbers of chromosomes?  Mostly it’s because in most cases the zygote doesn’t survive if you add or take away chromosomes.  The cells of the zygote do not divide or develop properly to create a human. It’s only in the cases where the zygote can divide and create a fully developed person (albeit a person who may have developmental or physical changes), that people with different numbers of chromosomes exist.