Archive for the ‘Interesting link’ Category

A little reminder to take life slow sometimes

December 1, 2014 Leave a comment

Awesome timelapse video of some underwater invertibrates doing their thing. Bonus: How many model organisms can you spot?

Vampire Ameboas are all around us

November 17, 2014 Leave a comment

Holy hell these things are nifty


Very cool article from the BBC and Michael Marshall

“Vampire amoebas” were first described in 1865 by the Russian biologist Leon Semenowitj Cienkowski, one of the founders of microbiology. He discovered bright red single-celled creatures, rather like amoebas, which attacked algae by perforating their cell walls and extracting their contents. Evidently conscious of the similarity to vampire folklore, Cienkowski called the microbes Vampyrella.

Their macabre feeding style has fascinated microbiologists for 150 years. A 1926 study describes how Vampyrella lateritia “spreads partly around the doomed cell” and “within a minute or so the transverse walls of the attacked cell begin to bend gradually inward”. When they finally buckle, the vampire amoeba “suddenly swells” due to “the injection of algal cell contents into the animal through an oval opening”.

After they have eaten their fill, vampyrellids build a hard wall around themselves called a cyst. “They stay in an immobile state and digest their food,” says Sebastian Hess of the University of Cologne in Germany. This takes a day or two, and at the same time the cell divides. As a result, when the cyst reopens there may be two vampire amoebas where previously there was just one.

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

Got ugly mug, at least you can take a punch! Males have facial features that were selected to stand up to getting punched

June 9, 2014 Leave a comment

Interesting, if slightly controversial argument that male faces (and other features) were selected through the course of evolution to be more resistant to impacts from violent altercations. Fascinating idea, but I would still cry like a baby if you clocked me right in the face.

Excerpt from “Male faces ‘buttressed against punches’ by evolution” By Jonathan Webb

Fossil records show that the australopiths, immediate predecessors of the human genus Homo, had strikingly robust facial structures.

For many years, this extra strength was seen as an adaptation to a tough diet including nuts, seeds and grasses. But more recent findings, examining the wear pattern and carbon isotopes in australopith teeth, have cast some doubt on this “feeding hypothesis”.

Instead of diet, Prof Carrier and his co-author, physician Dr Michael Morgan, propose that violent competition demanded the development of these facial fortifications: what they call the “protective buttressing hypothesis”.

“Jaws are one of the most frequent bones to break – and it’s not the end of the world now, because we have surgeons, we have modern medicine,” Prof Carrier explained. “But four million years ago, if you broke your jaw, it was probably a fatal injury. You wouldn’t be able to chew food… You’d just starve to death.”

The jaw, cheek, eye and nose structures that most commonly come to grief in modern fist fights were also the most protected by evolutionary changes seen in the australopiths.

Furthermore, these are the bones that show the most differences between men and women, as well as between our male and female forebears. That is how you would expect defensive armour to evolve, Prof Carrier points out.

“In humans and in great apes in general… it’s males that are most likely to get into fights, and it’s also males that are most likely to get injured,” he told BBC News.



Related articles:

Protective buttressing of the hominin face 

David R. Carrier and Michael H. Morgan

When humans fight hand-to-hand the face is usually the primary target and the bones that suffer the highest rates of fracture are the parts of the skull that exhibit the greatest increase in robusticity during the evolution of basal hominins. These bones are also the most sexually dimorphic parts of the skull in both australopiths and humans. In this review, we suggest that many of the facial features that characterize early hominins evolved to protect the face from injury during fighting with fists. Specifically, the trend towards a more orthognathic face; the bunodont form and expansion of the postcanine teeth; the increased robusticity of the orbit; the increased robusticity of the masticatory system, including the mandibular corpus and condyle, zygoma, and anterior pillars of the maxilla; and the enlarged jaw adductor musculature are traits that may represent protective buttressing of the face. If the protective buttressing hypothesis is correct, the primary differences in the face of robust versus gracile australopiths may be more a function of differences in mating system than differences in diet as is generally assumed. In this scenario, the evolution of reduced facial robusticity in Homo is associated with the evolution of reduced strength of the upper body and, therefore, with reduced striking power. The protective buttressing hypothesis provides a functional explanation for the puzzling observation that although humans do not fight by biting our species exhibits pronounced sexual dimorphism in the strength and power of the jaw and neck musculature. The protective buttressing hypothesis is also consistent with observations that modern humans can accurately assess a male’s strength and fighting ability from facial shape and voice quality.



Pattern, severity and aetiology of injuries in victims of assault.

Although the incidence of assault and other violent crime is increasing in the UK, the cause and overall pattern of injury, and the need for admission have not been defined in adult victims who attend hospital. In a prospective study, all 539 adult victims of assault attending a major city centre Accident & Emergency department in 1986 were therefore interviewed and examined. Facial injury was extremely common: 83% of all fractures, 66% of all lacerations and 53% of all haematomas were facial. The upper limb was the next most common site of injury (14% of all injuries). Twenty-six per cent of victims sustained at least one fracture and nasal fractures were the most frequently observed skeletal injuries (27%) followed by zygomatic fractures (22%) and mandibular body (12%), angle (12%) and condyle (9%) fractures. Seventeen per cent of victims required hospital admission. Overall, the type of injury observed correlated with the alleged weapon used (P = less than 0.001) though 20% of victims who reported attacks with sharp weapons sustained only haematomas or fractures. Injury most often resulted from punching (72% of assaults) or kicking (42% of assaults). Only 6% of victims reported injury with knives but 11% were injured by broken drinking glasses. Those who were kicked were most likely to need hospital admission.


The soap and skin paradox: the human skin microbiome may have changed drastically with the use of detergents

May 28, 2014 Leave a comment

This is a pretty interesting concept, essentially that we used to have bacteria capable of metabolizing ammonia and making our BO less offense. The science seems relatively compelling, however I’m still not entirely sold on the idea of foregoing a nice long hot shower for spraying myself twice daily with a suspension of bacteria. Certainly an interesting concept but I’ll stick to soap for the time being.

Like with most probiotic/microbiome products the biggest hurdle will be getting permanent colonization of the environment after the product is not longer being used, or the environment faces a disruption.

Maybe for a backpacking trip where I can experiment away from civilized society. Cool stuff.

Excerpt from “My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment” by By Julia Scott

Whitlock gathered his samples and brought them back to his makeshift home laboratory, where he skimmed off the dirt and grew the bacteria in an ammonia solution (to simulate sweat). The strain that emerged as the hardiest was indeed an ammonia oxidizer: N. eutropha. Here was one way to test his “clean dirt” theory: Whitlock put the bacteria in water and dumped them onto his head and body.

Some skin bacteria species double every 20 minutes; ammonia-oxidizing bacteria are much slower, doubling only every 10 hours. They are delicate creatures, so Whitlock decided to avoid showering to simulate a pre-soap living condition. “I wasn’t sure what would happen,” he said, “but I knew it would be good.”

The bacteria thrived on Whitlock. AO+ was created using bacterial cultures from his skin.

And now the bacteria were on my skin.

I had warned my friends and co-workers about my experiment, and while there were plenty of jokes — someone left a stick of deodorant on my desk; people started referring to me as “Teen Spirit” — when I pressed them to sniff me after a few soap-free days, no one could detect a difference. Aside from my increasingly greasy hair, the real changes were invisible. By the end of the week, Jamas was happy to see test results that showed the N. eutropha had begun to settle in, finding a friendly niche within my biome.



The company website AOBiome

Reasons for a Nightmare PhD

September 12, 2013 Leave a comment

Common Reasons for Nightmare PhDs by 

From pre-doc to postdoc, there are many instances that can transform a perfectly good PhD program into a nightmarish one. Here are the most common scenarios to watch out for in graduate school – and some ideas about how to deal with them when they pop up.

I wanted to get my PhD but didn’t realize how much work was involved!

Few leap into graduate programs just for the final prize, only to discover that the workload is more than they bargained for. Looking back, the student realizes their heart wasn’t in it from the start. And while they may still be determined to finish, the five years program now feels as if it will take 50.

Is science your passion? Live vicariously through a graduate student while working in a lab as a research assistant for a year. You’ll share in their joys, their trials, and discover if you’re ready to take on your own gauntlet of unpredictable late night and weekend work, and writing (lots of writing!). The transition from research staff to grad student is easy. And if you come to the realization that graduate school isn’t the route for you, that’s OK too!

I really don’t like my current project anymore…

You love being a graduate student, but the current project is about as exciting as watching paint dry. It’s hard to be motivated when your heart isn’t in it, although in grad school there’s lots of help! First and second year projects are to expose you to a variety of new experiences. Your thesis project is longer. And if parts of that become mundane, seek out more established scientists to glimpse the bigger picture, including the societal impact that your work will have. That’s inspirational!

My project is a disaster! If only it were planned and executed properly.

Suppose you’re learning a new technique and decide to use the most valuable samples. You hope everything will run perfectly but with one misstep you’ve suddenly set yourself back by months. Time and reagents are wasted…now you have to start again from the very beginning, hoping not to make the same mistake twice!

With a good plan every experiment can be a success. Consider these ideas before executing your next experiment:

ñ Projects can easily take on a life of their own so define endpoints where no matter the outcome you know comfortable places to stop experimentation

ñ Remember your positive & negative controls

ñ While the experiment is fresh on your mind, make a goal to analyze raw data soon after it’s collected

ñ You can save $$$ or time when ordering supplies, but usually not both

ñ Think ahead: Murphy’s Law is ruthless.

ñ Lab calendars make equipment scheduling simple

And of course, practice makes perfect. Master new techniques using samples set aside just for practice.

Arrgh!!! These experiments just don’t work. At all.

Experimental design looked impressive on paper, but in practice it didn’t pan out. After burning the midnight oil for countless nights you realize that the experiments aren’t novel enough for your thesis. You had a backup plan, right? No? Oh…

Time to switch gears quickly, lest you spend even more years working towards the PhD. Instead of a frantic scramble to plan and execute last minute experiments, take some time at the beginning of your program to design a second project. It may be that you’ll never have to use it, but it’s there for your peace of mind to fall back on, just in case.

My advisor and I rarely see eye-to-eye…

Because sometimes personalities clash. And sometimes the advisor wants to keep a student in the lab as long as possible (as inexpensive labor). Whatever the reason, the student/advisor relationship is toxic and forward progress is stalled.

Thankfully you have an advising team and can turn to the others for guidance. In the rare case that your differences are irreconcilable, there is one last ditch option: pull together a new advising team, seek out a new lab that is willing to take you on as a graduate student, and effectively “fire” those that are stunting your educational growth. Do note that is quite an unpopular choice to have to make, and one not to be made lightly.

My advisor is never around when I need them most!

What can be more agonizing than a floundering graduate program is one where the Advisor has vanished, leaving you with a foreboding sense of abandonment. Whether they’re taking every Friday off, whether they’re vacationing halfway around the world, they remain your Advisor and mentor until the very end.

Don’t wait for their reappearance to flood them with questions, data, and meetings; instead, keep a steady line of communication going. In today’s ever connected world, that’s easy to do: E-mail for casual correspondence and for submitting data and writing samples; phone calls for the more immediate lab matters; and face-to-face Internet video conferencing for the full experience of praise, lively discussion, and furrowed brows.

Finally! Is there enough time to start…and finish…writing my thesis?

Graduation is so close, but what holds you back now is the written portion of your thesis. In the span of a month you’ll develop a solid writer’s block, maybe even overdose on caffeine while trying to write 24/7. Did you leave yourself enough time to make edits based on advisor feedback?

When you do 5 minutes of experimental work to wait 30 on incubation, dedicate the extra time to writing. For thesis sections like the introduction, background, and experimental design, that can be started early on, leaving individual experiments, data and discussion, conclusion and a polishing touch towards the end. Good luck

Categories: Interesting link Tags: ,

Great link with advice for graduate students

July 29, 2013 1 comment

Stephen Stearns is a professor in ecology and evolutionary biology at Yale.

Besides being a professor he also has an interesting piece on his lab website with advice for graduate students..

Here is his introductory class in evolution for undergraduates at Yale.

Categories: Interesting link