Category Archives: genetics

Roller derby is like giant hug with every girl on the track: swapping microbes due to contact

by cej9f

Often I think we as scientist do a really good job of convincing ourselves that our work is important. However, our research rarely makes a big enough splash that a study is widely accepted by everyone as awesome. Trust me, I have recently tried to excitedly explain to a non scientist at a party why finding the recessive mutation behind disliking cilantro was sooooo cool. It didn’t work…

But this study is so cool that it has already blown up the blogosphere. So much so that I was considering posting on an awesome new review by two of my favorite researchers out of the UK (if you haven’t read this yet you should. Also check out Britt Koskella’s blog… it’s pretty awesome). But being a roller derby skater myself (Rolling Hills Derby Dames), I decided I couldn’t let such an awesome study go by without posting about it.

At the moment, the field of microbial ecology is going from big to huge. This is partially due to the inexpensive availability of genome data making it possible to asses the frequency and species of microbes within all sorts of environments. It could also be due to the immediate applicability to human health, as the composition of the microbiome has been linked to obesity, bacterial vaginosis and potentially irritable bowel syndrome.

These communities vary across different parts of the body and individuals, and change over time. And although we know quite a bit about how pathogens can be passed from person to person due to contact, not much is known about the effect contact has on the microbiome.

Lots of contact. Photo Credits to Scott Butner

Lots of contact.
Photo Credits to Scott Butner

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One of these moths is not like the other … but does that matter to Joshua trees?

by Yoder
A Joshua tree flower, up close.

A Joshua tree flower, up close.

A huge diversity of flowering plants rely on animals to carry pollen from one flower to another, ensuring healthy, more genetically diverse offpsring. These animal-pollinated species are in a somewhat unique position, from an evolutionary perspective: they can become reproductively isolated, and to form new species, as a result of evolutionary or ecological change in an entirely different species.

Evolutionary biologists have had good reason to think that pollinators often play a role in the formation of new plant species since at least the middle of the 20th century, when Verne Grant observed that animal-pollinated plant species are more likely to differ in their floral characteristics than plants that move pollen around via wind. More recently, biologists have gone as far as to dissect the genetic basis of traits that determine which pollinator species are attracted to a flower—and thus, which flowers can trade pollen.

However, while it’s very well established that pollinators can maintain isolation between plant populations, we have much less evidence that interactions with pollinators help to create that isolation in the first place. One likely candidate for such pollinator-mediated speciation is Joshua tree, the iconic plant of the Mojave Desert.

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Friday Coffee Break, Easter/April Fools edition

by yoderjb

black coffee with chocolate easter eggs

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

To get this weeks coffee break started, Amy brings us a post about the Paleo diet.  A new book by Marlene Zuk aims to show that the Paleo diet is a misinterpretation of evolution.

Jeremy takes the time this week to wonder about the effect on sea level if all the ships in the ocean were removed.  Alternatively, XKCD also wondered what would happen if you removed all the sponges.

Sarah stumbled upon this gem of a PDF book which will hopefully prove useful as she transitions from student to post doc.  She also brings up the potentially scary idea that you may not own your own DNA.  At least if the current patent situation remains upheld.  What happens if a company can own a 15-base pair fragment of DNA?

CJ continues the discussion on DNA with an article on the recent sequencing of the HeLa genome and the continued controversy regarding the ownership and publication of an individuals genome.  We continue to venture on into a strange new world with these issues.

Which came first: The obese chicken or its obese microbiota?

by Hird

Historically, medical research has focused on pathogenic bacteria when trying to understand the relationship between human health and microorganisms. This makes intuitive sense – since pathogens make us sick – but our bodies host way more nonpathogenic bacteria than pathogens and they function in keeping us healthy. Our gastrointestinal tract has trillions of bacteria in it and much recent work has been trying to understand these complex communities. Mice are a common model for understanding human gut microbes and health. Enter Obie, the obese mouse (Figure 1, left) and Lenny, the lean mouse (right).

Figure 1: Obie and Lenny

Obie and Lenny are genetically different at a locus in their genomes that codes for leptin – a hormone that inhibits appetite. Mice that can’t make this hormone become very hungry and morbidly obese. These two mice also differ in the composition of their gut microbiota – obese individuals (both mice and human) have different amounts of the main bacterial phyla in their gut and as a result, are able to more efficiently extract calories from food. In other words, if you give both of them the exact same amount of food, Obie is going to get more calories from it than Lenny, contributing to Obie’s weight problem. In humans, where the status of our “leptin locus” is not normally known and probably not as straightforward as the case of Obie and Lenny– it’s been hard to tell whether this shift in gut microbiota is the CAUSE of obesity or the EFFECT of obesity. That brings me to today’s paper: a short communication in The ISME Journal (that’s open access!) by Fei and Zhao that addresses this exact problem.

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Natural History in the -omics era

by Hird

This post is a guest contribution by Michael Harvey, graduate student in Robb Brumfield‘s lab at the Museum of Natural Science at Louisiana State University. Mike studies avian evolution, phylogenomics, and Neotropical ornithology. 

Blackwater river…approximate Bayesian computation…dawn song…genomic islands…wing chord…target DNA enrichment…

My life as an evolutionary biologist straddles two worlds. I study the comparative phylogeography of Amazonian birds, and on the one hand my research involves laboratory and computational methods that push the limits of new technologies and analytical techniques, and on the other, expeditions to the tropics that are nearly indistinguishable from the natural history work conducted by Victorian era biologists. I am a PhD student at Louisiana State University, and for most of the year my work is in the lab and at my desk. For several months of the year, however, my work is general ornithological collecting expeditions to the Amazon Basin.

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Friday Coffee Break, Spring Break Style

by yoderjb

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

beachcoffee

To get things started, CJ found a depressing study (depending on your perspective anyway) about how your attitude can affect your health.  It’s not what you would expect a study to find, but there are additional conflicting studies so take it as you will.  However, she follows it up with another article about how the privatization of space flight has a long way to go before we can all reach for the stars.

From Amy, a new variant in the African-American Y-chromosome leads to the speculation on how long ago the common ancestor of modern humans existed and/or whether there was potential interbreeding between Neanderthals and modern humans.

To follow that up, Jeremy found an interesting video that shows a morphing of the faces of human ancestry.

From Sarah, a rather fun blog post on Scientific American on how one individual looked for answers to questions and found lots of information, but failed to answer the original question.

Finally, to return to the spring break theme, the CDC reports in its weekly grand rounds about multi-drug resistant gonorrhea.

Herd Immunity

by yoderjb

vaccination

Over the past several years there has been a growing trend of parents that are terrified of vaccinating their kids citing reasons such as the debunked link to autism or that it just isn’t “natural.”   A healthcare blog run by several infectious disease doctors called Controversies in Hospital Infection Prevention has run frequent stories reporting on the declining vaccination rates as well as problems that ensue because of that, most recently about the whooping cough epidemic in Washington and wondering why Jenny McCarthy has so much influence on national views on vaccinations.

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More than just a metaphor, Wright’s Adaptive Landscape provides inspiration

by devindrown

Review of The Adaptive Landscape in Evolutionary Biology edited by Erik Svensson and Ryan Calsbeek

adaptive_landscape_book_coverHave you ever wished you could go back in time to be present at a particular historical event? The 1932 International Congress of Genetics sounds perfect, right? There R. A. Fisher, J. B. S. Haldane, and Sewall Wright all presented papers of their recent research. If you’re a student of population genetics, you probably recognize these names as some of the founders of the field. At this meeting, Wright was asked to condense some of his more technical mathematical framework into a form that was more widely accessible to the audience of biologists. The result was his conceptualization of the Adaptive Landscape where an analogy is made between the fitness of an individual or population and the varied topographic landscape (pictured on the cover of the book). Wright used this metaphor to describe aspects evolutionary dynamics of populations.

The editors of a recent book, The Adaptive Landscape in Evolutionary Biology, gathered together contributions from evolutionary biologists, ecologists, and philosophers to demonstrate the impact that the Adaptive Landscape has had on the field of biology. This book embraces an 80 year old metaphor created by one of the founders of the modern synthesis to explore the breadth and depth of research generated in evolutionary biology. Unlike a recent book addressing aspects of the modern synthesis, Evolution: The Extendend Synthesis (Pigliucci and Müller, 2010) which called for a revolution, Svensson and Calsbeek have assembled authors that explore the innovations and contributions that build upon the fundamental ideas of population genetics and seek to grow the field. Early in this book, Pigliucci asks about the utility of the Adaptive Landscape metaphors, even titling his chapter with the question, “what are they good for?” I think the rest of the book provides a more than sufficient answer to his question.

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C is for colostrum; C is for cool

by Hird

Colostrum |cuh-laas-trum| (noun): the first secretion from the mammary glands after giving birth, rich in antibodies 

The amount of research happening right now on microbes and human health is enormous. Think multi-hundred-million dollar, international-collaboration enormous. I’m sure the interest has been building for a long time, but the game changer I’m aware of is Ley et al. (2005), which showed that bacterial communities in obese mice were statistically similar to those from other obese mice and statistically different from normal-weight mice. Turnbaugh et al. (2006) showed that the shift that occurs from normal to obese* microbial communities favors microbes that are more efficient at extracting energy from a given amount of food. I’ll repeat that part: obese individuals extract more calories from a given piece of food than normal-weight individuals extract. The obese individuals have lower bacterial diversity, a trait that has also been linked to allergies. The childhood obesity epidemic is of particular concern to us all – up to a third of American children are obese and the detrimental health effects of this disease are well documented. Having a well-functioning gut microbiota may be a key to healthy weight.

That brings me to today’s topic: human breast milk (which I’ll refer to as HBM for the rest of the post). Cabrera-Rubio et al. (2012) analyzed the bacterial composition of HBM from 18 women at three time points over 6 months. The mothers in the study varied in weight and delivery method. The researchers were basically exploring what factors influence the microbial composition in breast milk, with an emphasis on weight of the mother. They used next-generation sequencing to produce a library of sequences that were analyzed for what specific bacteria were found in each sample and how the samples relate to one another as whole communities.

I couldn’t bring myself to Google image search “human breast milk” so instead I searched “babies”. Note1: there were over a billion hits (click the image to see the little text above it). Note2: the third “Related Searches” term was “black babies” which made me think – why ARE all the Google babies the same color? Curious.

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Friday Coffee Break, Turkish style!

by yoderjb

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

From Jeremy and Noah:

Apparently this particular link is so impressive it gets two recommendations!  ”OneZoom is committed to heightening awareness about the diversity of life on earth, its evolutionary history and the threats of extinction. This website allows you to explore the tree of life in a completely new way.”

From Sarah:

The quintessential list of items every graduate student should have (at least something similar in each category).  And also, in this story on NPR global warming could have a very detrimental effect on one particular species of  lizard the Tautara as egg temperature determines gender.

From Devin:

Australian scientists respond to massive government budget cuts for funding here and also here.

From Amy:

The evolution of drug resistent strains of gonorrhea or how the clap came back.

And finally from Jon:

Healthcare is very slow to adopt new technology but the flood of mobile technology might help make trips to the doctors office less painful with real time updates on when the doctor is available and to help patients check in.