Just in time for Turkey Day – the lowdown on bird flu

With Thanksgiving coming this week, it seems like a good time to talk a little bit about the impending apocalypse, delivered unto us by poultry. In other words: avian influenza.


Avian influenza (AI) is a virus with two main biological components – the hemagglutinin (which binds the virus to a host cell ) and neuraminidase (which allows it to be released from a cell ). So when you hear H5N1 – the numbers refer to specific strains of hemagglutinin and neuraminidase that vary in their pathogenicity. Wild aquatic birds (ducks, geese, gulls and shorebirds) are the natural host of avian influenza. It is very common for these birds to have one (or more) strains of AI over the course of a year – they don’t die and barely even have symptoms. “Low pathogenicity” AI strains are no big deal to aquatic birds and when they can spread to poultry, the chickens and turkeys have mild symptoms. On the other hand, “high pathogenicity” AI strains can arise from low pathogenicity strains from within domesticated poultry and are highly lethal to chickens and turkeys. The strains most likely to do this are H5 and H7 – these are the strains you hear about in the news that result in massive poultry culls. These strains can spread back to wild aquatic birds, who – if you’re a hunter or birdwatcher know – migrate across entire continents in large flocks. These strains can also spread to humans who are in direct contact with sick, high pathogenicity poultry.

SO FAR, avian flu virus has rarely (but not never) been transmitted from human to human (i.e., airborne). This is good, because the death rate of one H7N9 AI strain in China in 2013 was around 33%. Slightly worryingly,  this strain still persists there – mutating all the while. The doomsday scenario that the WHO and CDC are worried about is a high pathogenicity strain mutating such that it becomes airborne – a scenario that could put tens of millions of people at risk. I suppose a secondary doomsday scenario would be high pathogenicity AI infected ducks dropping deadly high pathogenicity AI duck turds on our heads as they fly across the country. (Did I just come up with the plot for a horror/comedy movie? I await your call, Hollywood.) The USDA is monitoring cases of high pathogenicity AI in wild North American waterfowl and they’re specifically watching an H5 strain that showed up here last year.

The internet has tons more info if you want to read more or freak yourself out. I do kind of feel like a jerk for bringing this up as we’re all headed to airports and then to our families. At least there is some “good” news – no shortage of turkey! Happy Turkey Day! (gulp)


Being a good bioinformatician


Or more accurately,  how to avoid being a bad bioinformatician. Over at the blog opiniomics (which is my new favorite name for a blog beside Nothing in Biology), Mick Watson published a lovely post: 5 ways that you may be failing as a bioinformatician.

While the premise behind this post sounds fairly negative (why not 5 practices of productive bioinformaticians?) it is extremely informative. Especially for budding bioinformaticians such as myself.

Essentially it breaks down into:

  • Keep up with the literature
  • Use appropriate software
  • Document your procedures
  • Stop reinvent the wheel

I am definitely guilty of the last bullet, and my better bioinformatics peers get on me about it all the time (“You don’t need to write your own code to collapse a 2d array into a vector/write a sorting algorithm/pick a variable without replacement. Someone has already done that.”). Which ones are you guilty of?

Well worth a read, check it out here!

What do mummy seals tell us about climate change?

Antarctica has one of the worlds driest deserts, which it turns out is perfect for preserving seals. For thousands of years. For next summer this means a new mummy movie, Seal Mummies!

But seriously, Paleontologists Paul Koch and Emily Brault from UCSC are using these mummies for something besides next summer’s blockbuster. They are looking at the long term ecological impacts of the changing climate in Antartica. What’s more, there are a TON of seal mummies just lying around. Over 500 in fact, some of them hundreds or thousands of years old. What this can tell us about the changing ecosystem is invaluable. Read about it over at Forbes.

A seal mummy on the Taylor Glacier (Picture via brookpeterson on flickr.com CC BY-ND 2.0)

A living crabeater seal in Antarctica (Image via Liam Quinn on Wikimedia Commons CC-BY 2.0)

How the squashes hitched a ride with humans

Squashes are funny, as fruits go. Even after years of selection for human consumption they have thick, hard rinds, they’re not particularly sweet — in fact, they contain bitter compounds called cucurbitacins — and their seeds don’t separate from their flesh very easily. That all suggests that the wild ancestors of butternuts and pumpkins were dispersed by large mammals, but squashes are native to the Americas, and there haven’t been many large mammals of the sort that would eat them since humans showed up there, back at the end of the last ice age. Of course, those humans since domesticated squashes, which would obviate the need for seed dispersal — and a new genetic study of wild and domesticated squash species provides support for exactly that hypothesis.

Ed Yong has a nice write-up over at Phenomena:

[Squashes’] old dispersers were gone and the most likely substitutes were small rodents with diverse diets, who could have chiselled through the fruits and carried the seeds to pastures new. But Kistler found that these same animals are the most likely to be put off by the squashes’ bitter tastes. Compared to larger animals like elephants or rhinos, he found that smaller ones like mice and shrews have far more TAS2R genes, which allow them to taste bitter compounds.

Humans can’t stomach cucurbitacins either. People who’ve been unfortunate enough to swallow high levels of these chemicals have come down with a severe diarrhoeal illness called Toxic Squash Syndrome. But perhaps some ancient hunter-gatherers became skilled at finding individual squashes that produced low or tolerable levels. After eating such plants, they would have pooped the seeds out, inadvertently sowing the land with more palatable strains.

I am not personally a great fan of pumpkin pie, particularly since I tried sweet potato last Thanksgiving — but maybe this finding will make for some nice chatter over coffee after dinner. Unless you happen to have an uncle who’s into Pleistocene rewilding, anyway.


Kistler L., L.A. Newsom, T.M. Ryan, A.C. Clarke, B.D. Smith, & G.H. Perry. 2015. Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication
Proc. Nat. Acad. Sci.; published ahead of print November 16, 2015, doi: 10.1073/pnas.1516109112.

Having Dinner with Women in Science

Here at the University of Idaho (Go Vandals) we have some awesome resources in the biology department (IBEST, BCB program, BEACON to name a few).

But by far the most interesting an influential for me over the course of my graduate career has been the Randall Women in Science seminar.  It’s not that each seminar has deeply touched me because as a woman I am able to better connect with other women when they speak about any topic in science. Nor is it that each seminar happens to be exactly what I want to study/do when I grow up. But it has allowed me to talk to women have not only survived but thrived in science.

Jane Randall

Jan Randall and her gardening skills

But first, some history. The seminar series exists because of Dr. Jan Randall, who is on the faculty at San Fransisco State University. She is also an alumna of the University of Idaho’s Department of Biological Sciences (Go Vandals). She studied social structure in animals once thought to be asocial. Additionally she was (among many other things): a Fellow of the California Academy of Sciences, the Board of Directors of the Endangered Species Coalition, and Secretary of the Animal Behavior Society, and a Fellow of the Animal Behavior Society. Her website notes that she is enjoying gardening and traveling in her retirement.

In addition to all her accomplishments in science, she put an emphasis on promoting women in science. And one of her iniatives is the Randall Women in Science seminar. Since 2003, twice a year, women in science, often at the top of their respective fields, are brought to give a talk at the University of Idaho. It is an amazing opportunity as a department to bring excellent seminar speakers to the Palouse to talk about their work.

And yes, the free food and drink is wonderful.


But by far what’s more wonderful is the opportunity to sit and talk candidly with women in science who are on the other end of the career ladder. We are all just starting, working on PhDs and postdocs, while the seminar speakers are well established and completing their careers. So we have questions about how to do this science thing as a woman, some of which we make a point to ask every speaker. It occurred to me last night (at a wonderful Randall seminar dinner) that I’ll be leaving the Palouse soon, and perhaps it’s time to reflect on the answers to these questions we have asked so many influential women.


Question 1: When is a good time to have children?

This is usually the first question, as it is something all of us are thinking about. Science is EXTREMELY demanding early in your career. During your PhD we are flirting with the poverty line (dependent on your discipline/department), and having babies is expensive. Your postdoc is all about getting papers out and finding a job, which requires long hours and a fluid location, especially given it’s not likely that you’ll stay in the same town you postdoc in indefinitely. And then once you have a faculty position, the tenure clock is ticking and you have very little time to get funding and papers out the door. Financially and professionally, when in there is a good time to have a baby? What’s that you say? You can just wait till you have tenure? What about fertility?

One was a VERY successful scientist who waited till she was established (and was actually pregnant at the dinner).

Another told us how they decided to start having children during their postdoc. You’ll notice I say “they”, her husband was her co-PI and the shared child rearing 50-50.

Yet another one told us she didn’t think it was possible to have children and be successful. That she had had a number of VERY supportive partners, and made the decision to put her career first.

One other speaker told us how she had had her first child during her PhD and the department wrote her off, and didn’t think she would finish. But she (this is a theme among the success stories) decided that she had to be more efficient with her time. She could only work from 9-5 so she did nothing during those hours EXCEPT work. No reading the paper, no socializing, no talking. Like a Jedi master, she focused on the tasks at hand so she could do more with the hours she had available.

You must have the efficiency and mind control of a jedi

You must have the efficiency and mind control of a jedi.

What struck me the most is how each woman had a different strategy. There is not really good answer to this question. So the overall pattern was “This science thing is important to me. How can I make my life work within its confines?”.

Question 2: Have you felt discriminated against as a woman in science?

Surprisingly most people said no to this question. But there were some exceptions:

One scientist told us how she had tried to report a professor in her department for sexual harassment. He had propositioned his graduate student and threatened to kick her out of the program if his advances were rebuffed. The student went to our seminar speaker, who promptly approached the dean. The dean told her it wasn’t an issue, and she handed in her resignation the moment she found another job. This was the most extreme example, and we had a long discussion about how to avoid departments where the good old boys club still reigns supreme.

Another scientist told us she had only once felt discrimination. She had an established lab, a few successful graduates, a number of grants, and an impressive publication record. She is inarguably at the top of her field. But when she went for a job interview (a lateral move, she already had an established lab) she was told that she was too timid and the chair of the department doubted Women_in_Science3whether she would be able to run a research lab of her own. She laughed and left.

And another told us how she had been told that she couldn’t have an extra year on her tenure clock because she was having twins. So she jumped over the chair, the dean of science and the dean of the college and went to the president of the university and asked for the extra year so that she could spend time with her children. She was one of the first women granted this extension.

Question 3: How do you deal with the two body problem?

Most of our speakers have a spouse outside of science. But there were a few that faced the difficulty of balancing two careers.

One speaker gave us the whole love story of her marriage with her husband. They worked together, both with respect to their family and with their research. I have seen this work in a number of situations and find it admirable but difficult to achieve.

Another, both her and her husband were in the same field. They applied for the same jobs. He got a job, and she was a spousal hire. The department chair thanks her husband almost daily for bringing her to their department.


We all face these questions and concerns, especially early in our career. What has amazed me is how much variety there has been in answers. How differently each of these women have tackled these very fundament and challenging problems. It has been inspiring, not knowing that it will be easy, but knowing that we can figure it out, as many have before us. And that there are places/ways for us to succeed in this academic realm.


The War over Wood

The title of this post isn’t something clever I came up with, but rather what the locals have named the conflict over protecting trees and biodiversity in the Amazon rain forest.Self proclaimed “Guardians of the Forest” (local rubber tappers, read about them here) are defending the forest that gives them their livelihood. And they are defending it against not massive scale deforestation, but rather the selective logging of high value wood by what essentially are criminal entities.

In an excellent post over at NPR, Lourdes Garcia-Navarro describes a day on the front lines. What is remarkable is how insightful and dedicated these local people are to conserving their forest, rather than giving in to the desire to cash in on its value.
“Rubber tapper Helenílson Felix stands near the stump of a tree that was felled by illegal logging. The tappers explained that this is how deforestation begins: The forest is thinned of its biodiversity, picked apart tree by tree.”


And it appears that despite putting up a strong effort, they are losing the fight.

One of three illegal logging camps dismantled and set on fire by Elizeu Berçacola and his crew.


When and how to use comedy in your science presentations

Over at Science Careers a self proclaimed scientist/comedian Adam Ruben discusses why he used humor in science.

“Blah blah citric acid cycle blah blah succinic dehydrogenase blah blah DOONESBURY CARTOON blah blah pyruvate.”

More importantly, he discusses when he stopped.

“My adviser never outright said so, but I knew what he was thinking: You had time to make the goat picture, but you didn’t have time to improve the actual science? I wanted to explain that, in the same way that people who are full can still eat dessert and claim it’s destined for “a different stomach,” science-improving and goat-Photoshopping were not mutually exclusive activities, but I didn’t think it would bolster my cause.”

He also ends on a somewhat sobering note:

“Just don’t use humor in grant applications. There’s no need—scientific funding is already a joke.”

Worth thinking about for sure!

Read more of his column Experimental Errors!


Pumpkin Beer 101

By Lisa Cohen and Peter Cohen

It’s fall, and many tasty options for pumpkin beers are available on tap and in bottles. If you don’t like sweet beers, no problem. Pumpkin beers come in all flavors and types, dark, spicy, light, hoppy. Some examples include: Dogfishhead’s Punkin Ale, Southern Tier’s Warlock and Pumking, and  Ninkasi’s Imperial Pumpkin Sleigh’r. We would like to shout out to our neighborhood favorites in Florida: Intracoastal Brewing Company (Melbourne, FL) for Pumpkin Ain’t Easy and Hourglass Brewery (Orlando, FL) for Stupid Pumpkin Face.

We were wondering, what are pumpkin beers? It seems that there are more options for pumpkin beers these days compared with the past. Like many scientists, we’re fascinated by beer. We thought we’d explore with you all what beer is, then look at where pumpkin flavoring comes from.

History of beer

Reports of fermented alcoholic beverages date back over 9000 years evidenced from chemical analysis of jars found in Neolithic Jiahu, Henan, China. European breweries are famous for their history of beer, Bohemian monks in what is now known as the Czech Republic cultivated yeast and methods for brewing beer for hundreds of years, passing down secrets from one generation of monks to the next. Each monastery was known for their own special flavors and can still be visited today.

Today, it’s pretty easy for anyone to make their own beer. If you’re considering making your own, there are many books and references on the topic (some listed at the end). People are getting creative! Brewmasters with small craft beer businesses are popping up everywhere with some tasty beers. In 2014, craft brewers reported an 18% increase in volume and another increase by 16% already in 2015. There is a market for unique and flavorful craft beers, and pumpkin beers are no exception.  While the craft beer industry is on the rise, overall beer consumption has decreased.

Beer Styles

Beer comes in many styles and flavors. Just like a good wine, we don’t want to make the mistake of ordering a palate-wrecking IPA before a pilsner to pair with our tres leches dessert.

Lagers are stored for long times at cold temperatures with bottom-fermenting yeast cultures. The result is a clean and crisp taste with with a smooth finish. Lagers can be anywhere from light to dark, usually low in alcohol content.  A pilsner is a light and hoppy version of a lager. Hotter than Helles from Cigar City, Baba Black Lager from Uinta are a few of our favorite lagers, along with the pilsner Mama’s Little Yella Pills from Oskar Blues.

Ales are produced quickly using a top fermenting yeast at warm temperatures. The result is sweeter with higher alcohol content. The bitterness from hops can be used to balance the sweet malty backbone. Ales come in many forms: brown, pale, scotch, golden, each with a variety of bitterness, sweetness, alcohol content. A variety of flavors can be imparted with different hops, delivery, malts, yeasts, water, and culture parameters. The possibilities are endless.

What is fermentation?

“Beer” with us, there’s some chemistry. Ethanol fermentation is the conversion of sugar into ethanol and carbon dioxide. Behold, the chemical structure of simple carbohydrates, e.g. glucose (C6H12O6):

Sugar comes in many forms, including being stuck together with glycosidic bonds over and over in long chains of cellulose and starch (n = number of repeating units):


Many researchers are coming up with ways to break down cellulose, which plant cell walls are made of, into sugar for various downstream uses. The most common polysaccharide used for beer comes from the barley plant, which is malted (wetted, grown and dried), breaking down into simpler fermentable components (glucose-maltose-maltodextrins). Proteins are broken down during the malting process. Then, when the malted barley is boiled and reduced down into a thick syrup that looks like molasses, it contains tons of simple sugars. The degree of malting and drying can impart wonderful flavor to the final beer product.

We need lots of glucose to make beer. Now, we need to break down the glucose into alcohol. This is the part where we conveniently call upon our friends, the yeast microorganisms.

The 10-step process of glycolysis, where glucose gets broken down into pyruvate for energy production (in the presence of oxygen) or ethanol (absence of oxygen), takes place in all living cells including our own. We could do each step individually in separate vials in a lab, but yeast organisms are way more efficient and happy to perform this service for us under the right conditions. Each step of glycolysis requires a different enzyme, conveniently manufactured by the yeast. All steps are shown below. It looks complicated, but really isn’t. Just think of it as a series of atomic rearrangements where each arrow is facilitated by a different enzyme protein. All of these molecules are present in certain concentrations, moving around in the syrup solution with the yeast, running into each other at a certain temperature, volume, and pressure. For every molecule of glucose, two molecules of pyruvate get produced:

If there were to be oxygen present, the microorganisms would continue respiration to create chemical energy, ATP. But, when there is no oxygen, pyruvate is decarboxylated by the pyruvate decarboxylase enzyme towards the final end-product of ethanol. Therefore, it is really, really important that no oxygen is present during the beer-making process. That is why fermentation must take place in sealed off containers.

Carbon dioxide (CO2) comes off as a by-product along with acetaldehyde, which is then reduced and rearranged by the yeast’s alcohol dehydrogenase enzyme to produce – here’s the big moment – ethanol!

The term “alcohol” is really just a hydroxyl group stuck to a carbon molecule. Ethanol is not to be confused with other alcohols, such as isopropanol (rubbing alcohol).

Microbial fermentation

We love our little domesticated yeast microbes. And they love us. We use these microorganisms for their enzymes, feeding them the glucose from the malted barley syrup. They produce ethanol and flavor, and in exchange we keep them alive in culture for the next batch. We select for batches that are tasty and throw away the batches that don’t work. Micrograph of yeast from a microbiology course lab notebook (2 um scale bar):

Yeast microorganisms aid in common fermentation methods including mead (fermented honey), sake (fermented rice), cider (fermented apples), and beer (barley or wheat fermented with yeast). Whereas cider takes advantage of natural endogenous microbes originating from within the fruit to break down the sugar into ethanol, mead, sake, and beer introduce yeast organisms purposefully cultured to aid in fermentation.

High-throughput DNA sequencing technology is recently allowing us to examine the evolutionary relationship of yeast microbes. Along the way, on the road to domestication, we have been positively selecting for genes in these microorganisms. This has resulted in functional differences between species. In a study of the domesticated fungal species used for sake (rice) fermentation, Gibbons et al. 2012 from the Rokas lab at Vanderbilt University studied Aspergillus sp. in sake, demonstrating that genes associated with flavor and carbohydrate metabolism have been selected for. In addition, production of chemicals that are toxic to humans have been down-regulated.

The Saaz and Frohberg yeast strains used for beer fermentation have been shown to be two separate lineages originating from Bohemia and Germany, respectively. Studies have recently shown that they were domesticated then diverged several different times. They belong to the species, Saccharomyces pastorianus syn. S. carlsbergensiswhich is a hybrid between the common yeast, S. cerevisiae and the cold-tolerant S. eubayanus. The differences between them include temperature tolerance, flavor chemicals and fermentation rates, with Saaz strain producing considerably lower alcohol (~4.5% abv) than the Fohberg strain (~6.5% abv) at 22degC fermentation temperature.

How does beer get its pumpkin flavor?

In short, the pumpkin flavor in beer (usually) comes from actual pumpkins. The meaty squash vegetable is cooked and added along with the malted barley syrup to the fermentation process, allowing the yeast to feast upon the pumpkin in addition to the malted barley. Since the pumpkin is a plant, it contains complex carbohydrates just like the barley. This feeds the yeast more sugar and the flavor molecules from the pumpkin stick around. We did not have a bountiful harvest of pumpkins this year, unfortunately. So, this does not explain why there have been more options for pumpkin beers available in stores than in years past. The reason for the increase in options is likely because of the creativeness of the craft beer industry. You can use canned pumpkin, or pumpkin bread, or even just the spices themselves. Pumpkin beers come in many varieties from bourbon barrel aged stouts that taste like pumpkin pie, to light ales, and even lagers.

That’s it! Hope you enjoyed this exploration. We sure did. :)

Additional References

Yet another example of how microbiology is important

When people say they have gut feelings, they usually mean that they are going on instinct.

However, it turns out that your instinct, or behavior, could actually be coming from your gut. Microbes that is.


Over at Scientific American, an excellent article summarizes a study by Rebecca Knickmeyer on just that.

She followed a group of developing infants to determine if their guts really are altering their behavior.

Check it out!


(almost as cool as Microbes on Mars)


Biology is Has a Public Relations Problem

Here on NiB we often mention the problems that science is having with public perception. From controversies over biological collections, to finding extra terrestrial life in the octopus , to more basics like teaching evolution and vaccinations.

We as a group have trouble relating to the public what we do and why we do it. And it truly is a shame.

In response a recent post on Yale Climate Connections made a desperate call for scientists to do just that. 

The article also introduces “Grad Slam“. Started in the University of California system, it asks graduate students to take years of academic toil and work and to present it free of jargon or technical lingo. In just three short minutes. It’s like a Ted talk, an exit seminar and an elevator speech had a love child. Check it out below, and consider throwing one of your own.