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Genetic Auditing

by Hird

For those of you who don’t dabble* in genetics, we’re in the midst of a major revolution. New technologies have literally transformed the questions we can ask and the data we can gather. It is currently possible (although not always advisable) to collect hundreds of gigabases (that’s 10^11) of data in a single run of a “high-throughput sequencer” (HTS). As a reference, I think there were 10^5 bases in my entire master’s thesis which, let me do the math, means one run on a HTS is equivalent to 1,000,000 of my theses?!?! Although that makes me a little queasy, it’s obvious and amazing progress.

Anyway – what can we do with these awesome new technologies? Coghlan et al. have found novel use, published in a recent PLoS Genetics.

"Bear Bile Crystals". One of the samples genetically audited for illegal and harmful components. From Figure 1 of Coghlan et al. (2012).

Traditional Chinese medicines (TCMs) have been used to remedy maladies for thousands of years. The popularity of TCM as a primary, secondary or supplementary medical practice has grown to the point where it is a multi-million dollar industry. TCMs rely heavily on plant and animal components – some of which can come from highly endangered (and thus illegally acquired) species or be harmful to the user. However, determining exactly what’s in a pill or powder isn’t as easy as reading the label.

HTS to the rescue!

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Friday Coffee Break

by Hird

coffee ( again)
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 Noah: A chain of events: Human hunting –> extirpation of large megafauna –> Australia’s wet rainforests become dry savannah.
Exploring sediment cores for past evidence of big herbivores, researchers found that the arrival of humans coincided with the loss of a menagerie of magnificent beasts, from giant kangaroos to fearsome marsupial lions and monster birds to Komodo dragon-like reptiles. The decline of this megafauna ultimately led to ecological changes that may have caused Australia’s rainforest to become savannah.
From Devin: A new independent overview of Peerage of Science appears in Trends in Ecology and Evolution:
PoS has the ambitious aim to enhance peer-review quality, save time for authors, reviewers and editors, and money for publishers. It is designed to be an open community, but reviews can only be written by scientists who have already published a peer-reviewed scientific paper. Manuscripts are submitted through the PoS web application, which allows peers to sign up for reviewing and subsequently automatically coordinates a four-stage peer-review process.
Also from Devin:  A short video describing a plant-bird mutualism from TEDEducation.

And from Sarah: A National Trust in the UK finds: Nature is good for you!
The trust argues, as have other bodies in previous years, that the growing dissociation of children from the natural world and internment in the “cotton wool culture” of indoor parental guidance impairs their capacity to learn through experience.

The Amazing Stinkbird

by Hird

The hoatzin is an amazing bird. Look at it:

It’s awesome. The hoatzin is the only bird in the family Opisthocomidae and its taxonomic position amongst other birds is unresolved. It’s a weak flier and it smells bad (think cow manure) and both of these traits are due to the awesomest thing about the hoatzin: it’s a foregut fermenter.

The hoatzin has an enlarged crop for the purpose of fermentation (see figure below). A “crop” is an anatomical structure in throat of some animals (including most birds) that primarily stores food. In the hoatzin, however, it does much, much more. Foregut fermentation is a digestive strategy where microbes living in or before the stomach break down vegetation for their host. Microbes are required by foregut fermenters because only the microbes are capable of breaking down the cell wall of plants, a barrier that confines most of the nutrients found in plant cells. The hoatzin is the only bird to use foregut fermentation and is the smallest known foregut fermenter. It’s a weak flier because of the anatomical accommodations the enlarged crop requires. And it stinks because fermentation is an odoriferous process. (The bright side to being the Stinkbird is that the hoatzin is not eaten by humans and this probably contributes to the fact it is NOT endangered!)

Figure 1 from Godoy-Vitorino (2008); "Bacterial community in the crop of the Hoatzin, a Neotropical folivorous flying bird"

Figure 1 from Godoy-Vitorino (2008); "Bacterial community in the crop of the Hoatzin, a Neotropical folivorous flying bird"

And this brings us to today’s paper. Previous work from the Dominguez-Bello research group has characterized the crop microbiota (and by that I mean, sequenced the DNA of and taxonomically identified the bacterial species present). The goal of the current study was to compare the microbiota at a population level. Godoy-Vitorino et al. (2012) sampled three birds at two populations in Venezuela roughly 500km apart (6 birds total). At each site, they performed vegetation surveys (to identify potential food sources) and recorded about 30 hours of hoatzin foraging behavior. To compare the microbial communities, Godoy-Vitorino et al. used a PhyloChip – a microarray specifically for identifying bacterial species in a complex sample.

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“Let’s stay together.” – Al Green

by Hird

Some of the biggest questions in evolutionary biology deal with the origin of life. For example, if I go back one generation, I find my parents. Two generations, my grandparents. Ten generations are human beings who may or may not have looked like me. Five hundred thousand are, oh, I don’t know. Maybe a bipedal hominid? Anyway, if we continue going backward like this, we inevitably get to time zero and encounter some big-time questions that can really cause a brain to cramp up.

One of these major questions that can cause someone to drool on their shirt in amazement of evolution is the transition of life from unicellular, sovereign entities to cooperative multicellular organisms. A recent paper by Ratcliff et al. (2012) from the University of Minnesota posits that the first step towards multicellular organisms is cellular clustering; they then proceed to evolve clustering in unicellular yeast and ask questions about the clusters.

RECIPE FOR EVOLVING MULTICELLULAR CLUSTERS FROM UNICELLULAR YEAST

Premise: Bigger things settle in solution faster than smaller things.

(Oversimplified) Materials: Unicellular yeast (Saccharomyces cerevisiae), test tubes, solution that the yeast can eat, time

Step 1: Suspend unicellular yeast in solution in a test tube.

Step 2: Wait 45 minutes.

Step 3: Transfer the cells at the bottom of the tube to a new tube with fresh solution.

Step 4: Return to Step 2 60 times.

Step 5: Look in microscope. Continue reading →

My gut microbiota made me do it!

by Hird

Our bodies are teeming with bacteria: for every one human cell in your body, there are at least 10 microbial cells. That’s about 100,000,000,000,000 microbes – what are they all doing?

The communities of microorganisms that live on or in a particular host are called the microbiota, and are responsible for a lot of physiological and biochemical functions. It’s probably no surprise that the gut microbiota digest complex molecules we’ve eaten and they keep pathogens from colonizing our bodies (most of the time). They synthesize vitamins and amino acids that we can’t make ourselves. Recent studies have shown that variation in gut microbiota are associated with obesity, diabetes, normal brain development and insulin signaling (which has a downstream affects on body size and developmental rate). But there’s one effect that variation in microbiota can have on their host that is particularly fascinating to me: they can influence host mate choice.

In 1989, Diane Dodd reared fruit flies (Drosophila pseudoobscura) from a common stock on two different food sources: starch and maltose. She found that after multiple generations of isolation on their separate substrates, starch-flies preferred to mate with starch-flies and maltose-flies preferred to mate with maltose-flies. The result was robust and repeatable, but the reason why and its mechanism were unknown.

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