The miraculous biodiversity bubbling in your sourdough starter

I made it through four weeks of Los Angeles’ COVID-19 shelter in place order before I climbed aboard the isolation sourdough bandwagon. It took more effort than expected just to stay on.

I followed a protocol provided on the King Arthur Flour website to ferment my own starter from flour mixed with water. Twice a day, from March into April, I transferred a bit of starter to a fresh jar, and added fresh flour and water, with no apparent progress. I moved the starter around my little kitchen, searching for a sufficiently warm nook. I restarted the whole process from scratch. I ran through two five-pound bags of all-purpose flour I scrounged at a neighborhood grocery store (everyone else in Los Angeles had taken up baking, too), and when, visiting Costco on a friend’s membership, I lucked into a 25-pound sack, I didn’t pause to wonder where I’d find space for it in the pantry.

And then, finally, one afternoon, I checked the jar in the oven (heat off, light on, a nice steady 70°F) and saw that the starter had surged above the rubber band I put around the jar to mark its beginning volume. I baked bread the next day.

I am no manner of microbiologist, but I knew in a general way that sourdough starter is a microbial culture, and the rising is, of course, due to the metabolism of those microbes — carbohydrates in, carbon dioxide out. I also knew enough to recognize the process of establishing a starter as something like a serial passage protocol: sample the microbes in a batch of flour, give them periodic infusions of fresh growth medium, and let them duke it out for supremacy until the population growth rate was enough to leaven a batch of bread. What I am, though, is a molecular ecologist — and so I naturally started wondering what was known about the population and community genetics bubbling in that blue glass jar.

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It’s the city life for me… or maybe not.

Michael Fitch wrote this post as part of Dr. Stacy Krueger-Hadfield’s Evolution course at the University of Alabama at Birmingham. He completed a B.S. in Biology from the UAB and is currently considering entering the Master’s program.  Current interests… all over the place.

As urban sprawl expands and consumes the last wild places, do we pause to think about the consequences? 

Take apex predators, as an example. How does urbanization affect animals that likely range over large areas?

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Posted in bioinformatics, blogging, community ecology, comparative phylogeography, conservation, ecology, evolution, genomics, mammals, population genetics, Science Communication | Tagged , , , , , , , | Leave a comment

Kelp connections

Aisha O’ Connor wrote this post as part of Dr. Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Currently a MS student in the Krueger-Hadfield lab, she is interested in algae and conservation. Aisha tweets @Aisha_MOC.

We can all think of barriers to dispersal, such as mountains, rivers, or even urban sprawl. Other barriers may be less visible, but can be just as important for gene flow. 

For example, what about currents? In the ocean, they can form strong barriers!

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Posted in bioinformatics, blogging, conservation, demography, ecology, evolution, haploid-diploid, Science Communication | Tagged , , , , | Leave a comment

The Molecular Ecologist Podcast: Color me viral edition

A screenshot from a Google-powered tool that can generate color palettes from images of artworks.

A new episode of The Molecular Ecologist Podcast is now out on Anchor.fm. In this episode,

You can find the podcast hosted on Anchor.fm, or on Apple PodcastsPocket Casts, and Spotify — or you can add the RSS feed directly to your podcast-management app of choice. Whatever service you use, consider taking a moment to rate or even review the podcast, which will help us build an audience.

You can also listen right here on the blog, with the widget below:

The music in this episode is Leroy Anderson’s “The Syncopated Clock,” performed on piano by Markus Staab and available under a Creative Commons license via Musopen.

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Pre-NewPI Summer To Do List

As my last postdoc summer begins (holy sh*t), I’ve been thinking a lot about how to prepare for the fall – what should I be doing in now to set myself up for success in my first year on the tenure-track? For those of us in this position, obviously we’re still wrapping up postdocs or PhDs or other jobs, but I’m not the only one trying to answer this question. There is an entire channel dedicated to #PreNewPI questions and planning on the FuturePI Slack. I’ve read those posts, watched this helpful video from iBiology, talked to friends and co-workers, and I think I’ve got a super comprehensive list, sorted by effort required, for those of us in this position, which you can use as a starting place. As with all of my posts, your mileage will vary – some items on this list may not apply to you, or I may have missed something. But I hope you can take this list, cut the things that don’t apply to you, and have at least the start of a roadmap!

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The last Last Dance

A faculty job application trilogy! Have you also been reading Katie’s recent blog posts on the costs of applying for a faculty job? One is about the workload of applying, the second one about the financial cost, and the last and maybe most moving one is about the emotional cost. I was eagerly waiting every week for another episode. Almost as good as Netflix’s recent series “The Last Dance” about Michael Jordan leading his team to become the NBA champions. A parallel I immediately saw is Katie writing her posts after she successfully got the job and Netflix committing to a series after Michael won six championships.

But who remembers Bill Cartwright? There is no Netflix series about Bill. As there is also no blog post about all the postdocs who applied but did not get that faculty job yet.

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Tapping social networks to explore biological systems

Bharat Mishra is wrote this post as part of Dr. Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. He is currently pursuing his PhD in the lab of Dr. Shahid Mukhtar. He earned an undergraduate degree at SRM University and a MS in Bioinformatics from the Indian Institute of Information Technology – Allahabad. Bharat research interests are bioinformatics, non-coding RNAs and network systems biology.

Have you ever wondered how you received suggestions from a friend-of-a-friend or your distant family member in Facebook?

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Yeast 2-Hybrid: Discovering Protein-Protein Interactions from Yeast to West

Thomas Detchemendy wrote this post as part of Dr. Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. He is a PhD student under the mentorship of Dr. Shahid Mukhtar. He is currently studying plant-microbial interactions in efforts to further elucidate bacterial-mediated redistribution of nutrients in Arabidopsis thaliana. Thomas earned his B.S. in Biology at the University of Tennessee at Chattanooga.

When they’re not being used to brew beer or bake bread, yeast can serve as a convenient model for discovering new information in molecular biology, such as protein-protein interactions among various biological systems. 

In the central dogma of molecular genetics, DNA is transcribed into RNA, which is then translated into a protein. After a protein is translated it may also interact with another protein to form a functional complex or dimer. 

This protein-protein interaction (PPI) could take place between two friendly proteins from the same cell, or between a pathogenic protein targeting another protein within its host. 

So, proteins interact, but how can we determine specifically, which proteins can bind together?

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Applying for a faculty job is a full-time job – the emotional cost

My last few posts have described my experiences with the time required and financial cost of applying for faculty positions as a postdoctoral fellow. The amount of time it takes to submit X number of applications and how much it costs to interview for X number of positions is something that can be quantified – it can be tracked and tallied, although your personal mileage will vary. Today’s post, however, is not going to be that straight forward. Today I’m going to describe the emotional destruction that makes applying for faculty jobs so incredibly hard. Few people talk about how it feels to apply for jobs beyond “it’s stressful,” and even I, with my commitment to transparency, am more than a little afraid to post this piece.

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Victoria Sork awarded the 2020 Molecular Ecology Prize

Valley oak, Quercus lobata, an iconic California endemic that has been one focus of Victoria Sork’s research (Flickr: Philip Bouchard)

The Molecular Ecology Prize Committee has announced the 2020 recipient of the award, which recognizes an outstanding scientist who has made significant contributions to the still-young field of molecular ecology:

We are pleased to announce that the 2020 Molecular Ecology prize has been awarded to Dr. Victoria Sork, Distinguished Professor in Ecology and Evolutionary Biology, Dean of Life Sciences, and Director of the Mildred E. Mathias Botanical Garden at University of California Los Angeles. Throughout her career, Dr. Sork has made substantial and diverse scientific contributions to the field of molecular ecology – from working to build the foundation of landscape genetics, to pioneering the use of molecular markers in tracking plant dispersal, to unraveling the genomic and epi-genomic basis of climate adaptation in non-model organisms. With well over 100 publications, she has proven herself to be a preeminent scholar in her field for decades, while serving as a role model and mentor for many early career scientists, and as a continual advocate for increasing diversity and inclusion in STEM.

Dr. Sork joins previous winners Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf , Louis Bernatchez, Nancy Moran, Robin Waples, and Scott Edwards.

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