Archive

Archive for October, 2014

Awesome depiction of bioluminescence across all the kingdoms of life

October 29, 2014 Leave a comment

Could resist posting this one too, thanks again to Elanor Lutz from tabletopwhale.com

Love how she lays out the different organisms, colors, and even some structures! Super cool!!!

A visual compendium of glowing creatures

Encompasses even more than just bioluminescence, link here

She sells these as posters, get one for your lab today!

Incredible illustration of breathing in mammals, avians, and bugs

October 27, 2014 Leave a comment

Thanks to Elanor Lutz of tabletopwhale.com

A super cool, and scientifically accurate illustration of gas exchange in three representative organisms.

Ever wonder what the difference is between Ale vs. Lager yeast?

October 22, 2014 2 comments

Despite being a yeast researcher, and supposedly having a pretty good handle on yeast genetics, I have always struggled to fully understand what the underlying genetic differences are between ale and lager yeasts. Thanks to a great article by Martha Harbison from Popsci, and research done by Libkind et al, I have finally figured it out!

Generally ales are fermented warmer with”top fermenting” yeast, and produce more fruity esters as a result. Lagers tend to be fermented cooler with “bottom fermenting” yeast, and produce more “reductive” or sulfur characters.

Ale vs. Larger

This description, while great for brewers was always unsatisfactory to me as someone with an interest in genetics and taxonomy. This was further complicated by the interchangeable use of S. calsbergensis and S. pastorianus. Top fermenting yeast are generally just plain old Saccharomyces cerevisiae. Bottom fermenting yeasts are generally more variable and have allotetraploid chromosomes, i.e. 4 chromosomes made up of mixed up bits and pieces of different yeast genomes.

So, where the hell did lager yeast S. pastorianus come from? And why did it only show up in the 1500s, thousands of years after humans figured out how to brew with S. cerevisiae? The answer came in 2011, with the publication of “Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast” by Libkind et al in Proceedings of the National Academies of Sciences. In it, the researchers analyzed 6 yeast genomes: S. pastorianus, S. cerevisiae, two contaminant Saccharomyces species found in breweries, S. bayanus and S. uvarum, and two wild strains. The scientists knew through prior research that Saccharomyces species thrive on oak trees in Europe. After collecting samples from forests all over the world, they isolated two cold-tolerant yeast strains from the forests of Patagonia in Argentina.

After analyzing the genomes of these cold-tolerant strains, the researchers discovered that they were members of an entirely new species of Saccharomyces yeast, which they namedSaccharomyces eubayanus. The “eubayanus” part is interesting, because what the scientists also determined in this study is that the contaminant strain S. bayanus found in the European brewing environment isn’t, as previously thought, actually its own species. It is a domesticated hybrid strain of this Patagonian yeast. The “eu” part of “eubayanus” is to indicate that the Patagonian strain is the pure progenitor species.

From Eubayanus to Pastorianus Ale yeast and yeast from the forests of Patagonia met in a brewery…and lager was born! 

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

Diego LibkindChris Todd HittingerElisabete ValérioCarla GonçalvesJim DoverMark JohnstonPaula GonçalvesJosé Paulo Sampaio

Domestication of plants and animals promoted humanity’s transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate itSaccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry inNothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement.

Some of this can be summed up by this figure from:

Saccharomyces diversity and evolution: a budding model genus

Chris Todd Hittinger

Relationships of the seven natural species of Saccharomyces and their key industrial hybrids. Populations and lineages that are not regarded as distinct species are discussed in the text but not shown. Note that the S. bayanus species complex includes two natural species (S. uvarum and S. eubayanus) and two hybrids that had been given species names (Saccharomyces pastorianus and S. bayanus).

Basically it seems like S. pastorianus evolved through the actions of human beings and hybridizations of different Saccharomyces species in the context of brewing.

Here is a spread sheet of compiled strain comparisons from different companies. Mostly beer oriented, and very helpful: YeastBot Database thanks to u/Oginme for posting it.

This leads me to a final question: did we select yeast, or did yeast select us?

-Gordon Walker