Saturday, June 29, 2013

Story Behind the Paper*: Bif-TRFLP

One type of post that I plan to regularly put on my blog is the "Story Behind the Paper" series, where I talk about what motivated the research in my papers and tells the paper's backstory. In an aggregation of firsts, this first installment will be talking about my first ever first-author paper, "Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities." (Published in the Journal Anaerobe v. 19 (2013) pg. 62-69)


Background


I study the gut communities of infants. There are a couple of nice things about infants that make them an important and useful model. First of all, who doesn't like babies? They are cute! No one wants them to get sick, and studying their gut microbes can help us understand how to prevent and treat gastrointestinal (and possibly other) diseases.

Happy baby
See! Look how cute!
By Weird Beard (Happy) [CC-BY-2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons
Premature infants in particular can have lots of problems, including the very nasty necrotizing enterocolitis. It is thought that a large cause of these types of diseases is an imbalance in the gut community. If there is not enough good (or at least neutral) bacteria in their guts this leaves a spot open for bad bacteria to grow. If we put lots of good bacteria in, the good bugs (metaphorically) eat all the food and sleep in all the beds and there is no room for bad bacteria. This is the concept behind probiotics.

One thing that has held back probiotics as a field is that is is hard to know which effects are caused by which factors. There are a lot of variables, lots of things going on in the gut. Everything you eat introduces new bacteria to the environment and new things for bacteria to eat. Different species of bacteria have "favorite foods" that they like to eat, so what you choose to eat can have a big impact on what type of bacteria can grow in your gut. How can you tell when an effect you are seeing is caused by something different from what you are measuring?

Babies are nice because early on, they mostly eat one thing... breast milk! Many health organizations recommend exclusive breast feeding for at least the first several months of life. This gets rid of one variable that confounds studies on adults. (You usually have to pay adults pretty well to control everything they eat if you want to study them. How much would you charge someone for them to be able to tell you everything you could eat for weeks on end? Tell me in the comments... The economist in me would really like to know!)

If you want to study gut bugs, it usually means you need to collect poop. (There are studies that take pieces of the intestine and other similar methods, but they are much harder to do.) Another nice thing about babies is that most parents are already collecting the their baby's poop by using diapers, and are happy to make a few bucks off of letting us take some.

Now to my paper.


One thing the lab I am in works on a lot is trying to figure out what the gut community of babies consists of. The bacteria my paper studies are the most abundant member of the gut community in most infants, and are considered "good bacteria." They are called "bifidobacteria."

Bifidobacteria as seen in a microscope.


There has been a very important methodological development in biology recently called next-generation sequencing (NGS) that can provide us with data on the microbes in an environment.


The original type of Next-Generation Data
http://memory-alpha.org/en/wiki/Data
It does this by sequencing (finding out the what the order of the A's T's G's and C's is) DNA that is extracted from the microbes in the environment and counting the numbers of DNA snippets that match the sequences of different types of microbes. This has been revolutionary and has enabled us to study things we couldn't before. One limitation of the method (at the moment) is that it can only tell us what is there at a coarse taxonomic level. I'll try to explain this by using an analogy to a more familiar environment... your neighborhood! NGS would tell us how many dogs there were in a neighborhood, but it wouldn't tell us whether they were wolves or dachshunds or chihuahuas or St. Bernards. It could definitely distinguish a cockroach from a human from a shark from a bird though. The problem is that sometimes we really care whether gut bacteria are "wolves" or "chihuahuas." You would probably care about that if you were going to move into a neighborhood, right?

My neighborhood, certified shark free since 1954.
http://www.housing.ucdavis.edu/housing/apartments_orchard_solano.asp

Since what we care about in babies is bifidobacteria, I (together with lots of help from lab members) designed and validated a method that will tell us what species of bifidobacteria are in a baby, since NGS won't do that right now. Since different species of bifidobacteria have different genes that do different things, this will let us test lots of different hypotheses about why bifidobacteria are so common in infant guts, what they do in that environment, and what health effects they have. The method involves taking the DNA from the bacteria in the environment and cutting it with special DNA-cutting enzymes called restriction endonucleases. The enzymes cut the DNA from different species of bifidobacteria in different places, which lets us quickly and cheaply tell them apart from each other by looking at the sizes of the pieces.

Next-generation sequencing methods are constantly improving, and might shortly make doing this unnecessary for lots of purposes, but the lab I am in didn't want to wait for that improvement to answer some important questions. We are using this technique as a part of several other studies now.

If you'll indulge me in some inside baseball of science, I want to note that we ended up submitting this paper twice, to two different journals. The first submission was rejected for reasons that (in my opinion, from my communications with the editor) had less to do with the scientific validity of the paper, and were more about it not being "important" enough for that particular journal to publish. This first journal (which is in the same prestige "tier" as Anaerobe) has the right to do that of course, but it slowed down the publication of the paper. We made some very minor changes (emphasizing how the method is complementary to NGS approaches) and resubmitted to Anaerobe. Anaerobe accepted the paper directly after hearing from the peer-reviewers, who had "no substantive comments" (we didn't need to make any changes). Several of my co-authors on the paper commented that that had never happened to them in their publishing careers, to have a paper accepted with no revisions (and they have a combined 40+ years of publishing under their belts.)

I say this not to out of indignation or a need to be publicly vindicated (since everyone usually thinks their papers are good and should be accepted), but to point out the somewhat capricious nature of scientific publishing. It makes me appreciate the PLoS One model of publishing everything technically sound regardless of perceived importance even more. For those of you who want to read my paper, Anaerobe has a pay wall, so unless you have a subscription (or are part of an organization that does) you may have some trouble. Another point for open access publishing. Here is a PubMed link.


*Note- Hat tip to Jonathan Eisen for the idea of a "Story Behind the Paper" series.



Wednesday, June 26, 2013

Book Review: Guns, Germs, and Steel

Guns Germs and Steel by Jared Diamond




Okay, so it's been around for a while, but I just recently finished reading it. This book seeks to answer the question "Why did some nations/cultures survive and conquer, while others failed and disappeared." Dr. Diamond narrows the reasons down to three main developments that enable some nations/cultures to beat out others. These developments lend the book its title:
  • The development of firearms
  • Immunity to diseases, particularly ones found among groups living in higher population densities
  • The ability to make steel, useful for weapons and other purposes
But this only gets us one step down. Why did some nations/cultures develop guns and steel and resistance to diseases they could then pass to others who weren't resistant? The author traces the chain of causality down to the basic structure of the Earth, with different parts having different types and numbers of useful plants and animal species depending on the lay of the land. The meat of this book is taking the reader on that journey with heaps of well-explained evidence along the way. As an ecologist working on symbiotic bacterial species, I appreciate his survey of "macrobial" species that influenced human evolution. As someone whose work involves looking at the evolution of human milk across the world, I liked the anthropological information he gave as well. And a book that ties the fate of nations in to microbes... well that's just right up my alley.

This book makes my list because not only is it interesting, it also makes some important points. I know of some fundamentalist religious and political groups that try to justify institutionalized racism by saying that God favors one group of people over others, and cite as evidence the history of specific groups being conquered by others. They say that a nation's/culture's current economic state is evidence of some blessing or punishment given by God for past obedience or disobedience. This book gives readers the scientific ammunition to support a (to me) less odious explanation of how the world ended up the way it is. The idea that one race of people is somehow (genetically?) superior to another can be fought with information about the evolutionary history of the area they live in.

Overall, this is one of my better reads from the last few years. I give it 5/5 Petri dishes!

File:Agar plate with colonies.jpgFile:Agar plate with colonies.jpgFile:Agar plate with colonies.jpgFile:Agar plate with colonies.jpgFile:Agar plate with colonies.jpg

Tuesday, June 25, 2013

On the Automation of Data Analysis

I spent the day analyzing data today. I rigged up some Excel spreadsheets to do what I wanted them to do, but it wasn't pretty. I swear by Darwin's ample beard that once I am done with the paper I am trying desperately to get out quickly, and will thus have some time, I will write some Python code to automate the whole process I just did and spit me out my results.

Darwin's Ample Beard. I wonder what he would've though about a wonderful math-doing machine that can keep track of and analyze all the morphometric data about finches you can throw at it.

I know enough about Python (thanks to the Software Carpentry course I took) that I can envision exactly what I want my code to do. (If a cell in this column is blank, fill it in with the contents of the cell above it; Add a new column with labels depending on the value of another column; Delete all rows with a number less than this value in this column; etc.) It is just a matter of sitting down and learning the syntax and functions, which is an investment that will definitely pay off over time, but requires a lump cost up front. (Relevent XKCD) This particular data flow is something I can see the lab I am in spending an hour on every month for at least the next 5 years, which according to the XKCD chart means I can spend up to two days writing code to automate it before it becomes no longer worth it. Challenge accepted! As soon as I finish this paper, I promise...

Saturday, June 22, 2013

Why I Decided to Write a Blog

I'm a busy guy. I enjoy my life, and have a good number of hobbies I like doing. Why would I take the time to write a blog, when there are no guarantees anyone would want to read it?

Well,  I'm glad I asked. It started with a paper I read in a scientific journal about social media in the sciences by an acquaintance of mine from a neighboring lab at UC Davis, where I study/work (I never did decide which description is more accurate to describe grad school in the sciences, where you get a stipend for learning about and doing science). Holly Bik wrote this great paper in PLoS Biology (a very respected scientific journal) which included a part about blogging which got me thinking about the benefits of having my own blog. I later attended an event put on by her and others about social media and the sciences. I was persuaded that it would be good for me even if few people ended up reading what I wrote.

One factor that convinced me was that it might help my writing skillz. Another is that potential future employers could get to know who I am by blogstalking me, which would tell them more than a formal resume/CV ever could. I have been in a position to hire/advise about hiring people before, and when deciding between the otherwise qualified candidates I know I would have liked to be able to see who someone really is by reading a blog they write before making a decision.

Another reason is that I think this is a better forum for my thoughts than what I had been using: Facebook. I was getting tired of writing thoughtful Facebook posts that probably just annoyed half my friends who don't care about science/my research/my views and just want to see pictures of my pets or laugh at funny memes I share. (I must admit to feeling similarly about some of my friends' posts who are just into different things than I am.) I would put effort into writing a post that I thought was insightful and would inspire debate and get one measly like. Then I would post a picture of a tree or something and get thirty likes and 10 comments. (Not that there is anything wrong with the tree, or that likes are a good measure of something's worth... but still!) This is probably my fault for expecting too much of the medium and not using it appropriately. I figure writing a blog will be a way to separate my personal and professional lives a little more. Through a blog I can reach people who care about the things I do more easily, and include people besides Facebook friends from high school, who may just want to hear about my major life events.

Seriously, this tree is one of my more popular Facebook posts, beating out my analysis of the Supreme Court decision regarding patenting human genes-- getting 7 times as many combined likes and comments. I guess it is a pretty tree though.

I am on Twitter as well (@zactlewis), but I feel that 140 characters and shared links aren't my cup of tea. I like it for some purposes (its great for keeping up on microbial ecology and finding papers) but I worry I am not communicating very clearly on it.

The last reason is that I feel my blog can be a public good. Other people can benefit from my work in reading and sifting through the amount of information that I do (I am a news/info junkie-- just ask my wife) and maybe have to do less of it when I share things they might find valuable. I know I use other blogs this way. I will probably talk about some of my own research after it is published, and telling "the story behind the paper" can be useful for other people who end up being interested in my research.

So here I am. Welcome to my thoughts. Enjoy your stay.