Save the Bananas!

Interesting facts: All commercial bananas in the US/Europe/Canada (really all imported bananas) are all decended from one banana grown on the estate of the Duke and Duchess of Devonshire (Chatsworth House).

They are all clonal, which makes them particularly susceptible to a coevolving disease.

Such as Panama Disease, which is now killing off bananas in the thousands.

What’s more, this has happened before… and may result in there being no bananas left on our grocery shelves.

Read more about it over at the BBC.

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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)

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!

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(almost as cool as Microbes on Mars)

 

Friday Coffee Break, Easter/April Fools edition

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?

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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The beef I have with The Paleo Diet

I’ve heard a lot about “The Paleo Diet” lately and every time a popular news source (say NPR or ABC or Fox News or New York Times) does a piece, I cringe a little bit. For those of you who have never heard of the Paleo Diet (from Wikipedia):

The paleolithic diet…is a modern nutritional plan based on the presumed ancient diet of wild plants and animals that various hominid species habitually consumed during the Paleolithic era—a period of about 2.5 million years duration that ended around 10,000 years ago with the development of agriculture.

So that’s the basic idea – people restricting their diet to things that we ate before modern agriculture. I don’t really have a problem with the diet, per se – removing highly processed foods and increasing your activity level is a good idea for almost anyone. But the rationale that always accompanies the diet – that’s where the cringe comes in.
The rationale goes like this (again from Wikipedia):

Paleolithic nutrition is based on the premise that modern humans are genetically adapted to the diet of their Paleolithic ancestors and that human genetics have scarcely changed since the dawn of agriculture, and therefore that an ideal diet for human health and well-being is one that resembles this ancestral diet.

I can break this rationale down into three assumptions/statements:
1. Evolution acts to optimize health.
2. Evolution adapted us to eat a specific diet.
3. Therefore, today, we should eat that diet to optimize our health.

As an evolutionary biologist, I think there are logical and scientific flaws to each of these statements.

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