Tag Archives: LTEE

They’re back!

They’re back! After a six-month interruption, Devin Lake restarted the long-term evolution experiment and the 12 LTEE lines from the 73,000-generation freezer samples. Now the bacteria are back in their home-sweet-homes: Erlenmeyer flasks with DM25 medium and the shaking incubator set to 37C.

We’re keeping the lab at very low occupancy, and using masks and physical distancing when more than one person is present in a room) until this damn SARS-CoV-2 pandemic is under control.

MSU also has a spit-based surveillence program in place for those entering campus buildings. Each sample is split, and then put into two pools for PCR testing. With each individual’s sample split into two pools, the testing can identify which individual in any reaction that proves to be positive is the source of the virus. That person is then notified and told to isolate and get a definitive diagnostic test.

[Both photos below courtesy of Devin Lake]

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Six Months

It’s been six months since I closed the lab, and temporarily suspended experiments including the LTEE, due to the SARS-CoV-2 pandemic.

The failure to contain this epidemic, especially here in the United States, is truly shocking and sad.

Still, we’ve gotten a lot done. Two superb dissertations completed by Nkrumah Grant and Kyle Card. Several excellent papers submitted, and more on the way. Everyone in the lab remains healthy, and in my own family as well, even as we know that many others have suffered illness and losses.

And please, everyone: Wear your mask and maintain social distancing to protect not only yourself and your own family, but also your community and beyond.

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Celebrating Black in STEM

I have been very fortunate to know and work with outstanding Black scientists throughout my career.  Here are a few of them.

I met Joe Graves when we were undergraduates at Oberlin College.  We took an evolution course together.  I remember discussing with Joe our mutual fascination with evolution and wondering how we might go about studying it.  I met up again with Joe at UC-Irvine, where we were both conducting evolution experiments—Joe using fruit flies, and me with bacteria.  Joe and I reconnected once more when he and I became founding members of the BEACON Center for the Study of Evolution in Action.  Joe now studies bacterial evolution, and we are becoming scientific collaborators as well.

JoAnn White was an ecologist at UNC, studying the life-history and population dynamics of periodical cicadas.  She served on my doctoral advisory committee and was a highly successful faculty member.  Unfortunately, she left academia, even though she had tenure, because it was too frustrating. I was honored that she asked me to write a reference letter when she moved to a new profession.  But it was a terrible loss for academia to lose such an outstanding scientist and role model as JoAnn White.

Paul Turner was one of my first graduate students.  He joined my lab in the Department of Ecology and Evolution at UC-Irvine, and he moved with me to MSU, receiving his Ph.D. in 1995.  Paul has impressed me in many ways, not only as a superb scientist and mentor, but also in his upbeat outlook on life.  Somehow he manages to smile and laugh about the challenges of being a departmental chair and interim dean, even while running a lab that conducts ground-breaking research.

Lynette Ekunwe was my lab manager and technician for seven years after I moved to MSU. She helped to sustain the long-term evolution experiment with E. coli after its move from UC-Irvine, and she helped run my lab group as it grew in size. Lynette moved to Jackson State University when her husband, the late Steve Ekunwe, took a faculty position there. After the move, Lynette earned a doctorate in public health, and she now works in the field of epidemiology.

I first met Scott Edwards when he was a graduate student at UC-Berkeley. I suspected that he was a rising star, and I was right.  Although Scott and I have not collaborated on actual science, we’ve worked together in other ways.  Scott and I served successive terms as Presidents of the Society for the Study of Evolution, and he has been a valued member of the External Advisory Board for the BEACON Center.

Shenandoah Oden was an undergraduate from Detroit when she joined my lab in the 1990s.  She worked with postdoc Santiago Elena on measuring the fitness effects of random insertion mutations in E. coli, leading to a paper in Genetica. What I remember best about Shenandoah is a question she asked me right after Brendan Bohannan presented his dissertation seminar: “How do scientists come up with the questions they ask?” I told her that was the best question that any student had ever asked me.  It reminded me of how Joe Graves and I, when we were undergrads, wondered how we might study evolution. To Shenandoah, I explained the importance of personal curiosity and mentors in finding questions that are both interesting and answerable.

Marwa AdewaMaia Rowles and Kiyana Weatherspoon were three excellent undergraduate researchers in my lab, all of whom were mentored by Zachary Blount. Maia and Kiyana were coauthors on a paper in the Proceedings of the Royal Society, London B, which reported the results of what we call the “all-hands project”—one in which a generation of lab members performed a set of parallel assays to measure the subtle changes in fitness in late generations of the long-term evolution experiment with E. coli. Marwa now works in the field of veterinary medical research, while Maia and Kiyana are pursuing careers with a biomedical focus.

Judi Brown Clarke was, until very recently, the Diversity Director for our BEACON Center. In that role she generated and managed many successful programs that introduced hundreds of students at all levels to evolution and provided them with opportunities to engage in scientific research. She also was a great listener and valuable source of advice for many of us when we faced personal challenges and setbacks. An Olympic medalist, Judi recently became the Chief Diversity Officer at Stony Brook University.

I met Jay Bundy in 2013, at the Evolution meeting in Snowbird, Utah.  Who was this student who was asking so many thoughtful, insightful questions of the speakers?  I ran into Jay as we rushed between talks, introduced myself, and learned that he was a masters student at Penn State.  He wasn’t sure if he was interested in microbes, but I encouraged him to think about joining BEACON.  Jay came to MSU, first as a BEACON staff member contributing to education and outreach activities, and then as a graduate student in the Department of Integrative Biology.  He also contributed to the all-hands project.  However, he switched from studying bacteria to digital organisms, and he’s now performing and analyzing experiments to quantify how the duration of history in an evolving lineage’s previous environment influences its subsequent evolution in a new environment. Stay tuned for Jay’s findings—he’s working on a huge paper. Jay is as deeply thoughtful about science and life as I imagined when I first heard his questions at the Evolution meeting.

I also met Nkrumah Grant in 2013, when he visited MSU while exploring possible graduate programs.  He immediately impressed me with his personal story of overcoming obstacles.  Nkrumah explained to me his love of science as a child, and how he had gotten discouraged and derailed before undertaking a concerted effort to pursue his dream of science and scholarship.  And pursue it he did … and continues to do.  From a G.E.D. to a Ph.D.  Co-author on the all-hands project, co-first-author on a paper just published in eLife, and three more papers posted to bioRxiv in the last few weeks.  He also just defended his dissertation, giving a beautiful public seminar followed by an engaging, collegial exam.  Nkrumah has done all this and more while being a dedicated father and working tirelessly to promote equity and inclusion in science.

Last but not least, Ali Abdel Magid and Jalin Jordan are two of the current generation of superb undergraduate researchers in the lab. Ali is working with Nkrumah on the evolution of bacterial cell size, while Jalin works with Kyle Card on the evolution of antibiotic resistance.  Both Ali and Jalin are also working toward future careers in medicine. This summer, they are reading work that integrates evolution and medicine including the landmark book, Why We Get Sick, by Nesse and Williams, and the path-breaking paper by Tami Lieberman et al. on the evolution of bacteria in the lungs of CF patients.

My science is better, and my life richer, because of all these people, and many more.  How much better science would be, and how much richer all of our lives would be, if we would open more doors, listen more carefully, and live, learn, and work together.

***

After reading a draft of this essay, Nkrumah Grant, Joe Graves, and Jay Bundy all asked me to say more about this:  How can we achieve the aspirations expressed in my closing sentence above? 

I plan to reflect more on their vital question.  In the meantime, I invite readers who have ideas to put them in the comments below.

EDIT: I should also acknowledge two other influences: A high-school teacher, Mrs. Clayton, who taught a Black History class that I took, and who introduced me to Frederick Douglass, whose autobiography I read with awe and admiration.

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Five More Years

The E. coli long-term evolution experiment (LTEE) began in 1988, and it has run for over 32 years with only occasional interruptions. The latest interruption, of course, reflects the temporary closure of my lab during the ongoing coronavirus pandemic. Fortunately, one of the advantages of working with bacteria is that we can freeze population samples and later revive them, which will allow us to resume their daily propagation when it is prudent to do so.  Indeed, we’ve frozen samples of all 12 populations throughout the LTEE’s history, allowing “time travel” to measure and analyze their fitness trajectories, genome evolution, historical contingencies, and more.

Even as the experiment is on ice, the lab team continues to analyze recently collected data, prepare papers that report their findings, and make plans for future work. Their analyses use data collected from the LTEE itself, as well as from various experiments spun off from the LTEE.  Nkrumah Grant is writing up analyses of genomic and phenotypic aspects of metabolic evolution in the LTEE populations.  Kyle Card is examining genome sequences for evidence of historical contingencies that influence the evolution of antibiotic resistance. Zachary Blount is comparing the evolution of new populations propagated in citrate-only versus citrate + glucose media. Minako Izutsu is examining the effects of population size on the genetic targets of selection, while Devin Lake is performing numerical simulations to understand the effects of population size on the dynamics of adaptive evolution.  So everyone remains busy and engaged in science, even with the lab temporarily closed.

Today, I’m excited to announce two new developments.  First, the National Science Foundation (NSF) has renewed the grant that supports the LTEE for the next 5 years. This grant enables the continued propagation of the LTEE lines, the storage of frozen samples, and some core analyses of the evolving populations. The grant is funded through the NSF’s Long Term Research in Environmental Biology (LTREB) Program, which “supports the generation of extended time series of data to address important questions in evolutionary biology, ecology, and ecosystem science.” Thank you to the reviewers and program officers for their endorsement of our research, and to the American public and policy-makers for supporting the NSF’s mission “to promote the progress of science.”

Second, Jeff Barrick joins me as co-PI on this grant for the next 5 years, and I expect he will be the lead PI after that period.  In fact, Jeff and his team will take over the daily propagation of the LTEE populations and storage of the sample collection even before then. I’m not planning to retire during the coming grant period. Instead, this transfer of responsibility is intended to ensure that the LTEE remains in good hands for decades to come. In the meantime, Jeff’s group will conduct some analyses of the LTEE lines even before they take over the daily responsibilities, while my team will continue working on the lines after the handoff occurs.

Several years ago I wrote about the qualifications of scientists who would lead the LTEE into the future: “My thinking is that each successive scientist responsible for the LTEE would, ideally, be young enough that he or she could direct the project for 25 years or so, but senior enough to have been promoted and tenured based on his or her independent achievements in a relevant field (evolutionary biology, genomics, microbiology, etc.). Thus, the LTEE would continue in parallel with that person’s other research, rather than requiring his or her full effort, just like my team has conducted other research in addition to the LTEE.”

Jeff is an outstanding young scientist with all of these attributes. Two years ago he was promoted to Associate Professor with tenure in the Department of Molecular Biosciences at the University of Texas at Austin.  He has expertise in multiple areas relevant to the LTEE including evolution, microbiology, genomics, bioinformatics, biochemistry, molecular biology, and synthetic biology. He directs a substantial team of technicians, postdocs, and graduate students, which will provide ample coverage for the daily LTEE transfers (including weekends and holidays). Last but not least, Jeff has participated in the LTEE and made many contributions to it including:

  • Participated in propagating the LTEE lines and related activities while he was a postdoc in my lab from 2006 to 2010.
  • Authored many papers using samples from the LTEE, including almost all of them that have analyzed genome sequences as well as several recent papers examining the genetic underpinnings of the ability to use citrate that evolved in one lineage.
  • Developed the open-source breseq computational pipeline for comprehensively identifying mutations that distinguish ancestral and evolved genomes.

Someone might reasonably ask if the LTEE will work in the same way when it is moved to another site. The answer is yes: the environment is simple and defined, so it is readily reproduced. Indeed, I moved the LTEE from UC-Irvine to MSU many years ago, the lab has moved between buildings here at MSU, and we’ve shared strains with scientists at many other institutions, where measurements and inferences have been satisfactorily reproducible. As an additional check, Jeff’s team at UT-Austin ran a set of the competition assays that we use to measure the relative fitness of evolved and ancestral bacteria, and we compared the new data to data that we had previously obtained here at MSU. The two datasets agreed well, in line with the inherent measurement noise in assessing relative fitness. Fitness is the most integrative measure of performance of the LTEE populations, and it is potentially sensitive to subtle differences in conditions. These results provide further evidence that, when the time comes, the LTEE can continue its journey of adaptation and innovation in its new home.

Evolve, LTEE, evolve!

LTEE flasks repeating

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Time to restart the LTEE, this virus be damned

The LTEE ran for over 32 years and more than 73,000 generations, without missing a beat. Then this stupid coronavirus came along and made me shut down the lab and stop the experiment. Well, I think it’s high time for everyone to return to the lab and get back to work.

We’ve wasted a hell of a lot of time here.  The LTEE lines were frozen on March 9th.  That’s 23 days ago, for crying out loud.  Do you know how many generations have been lost?  With 100-fold daily dilution and regrowth, that’s ~6.7 generations per day.  So we’ve already lost over 150 generations. And with 12 populations that’s a net loss of more than 1,800 generations.

Another way of looking at it is that each population produces around half a billion new cells each day.  So that’s 23 x 12 x 500,000,000 cells that went missing. You get the picture, that’s a sh*t-load (a technical term for those of us who study E. coli) of baby bacteria that never got born!

I’ve gotten in enough trouble already with a certain crowd for our claim to have observed evolution. If they find out we’ve denied these adorable baby bacteria their existence, there’s no telling what letters they might send me.

Plus, speaking as a scientist, I have this premonition that something really big would have happened during those missing generations. I’ve been expecting them to evolve the ability to produce palladium from citrate. They could then use the palladium for cold fusion, which would surely get some attention. Stupid virus!

Heigh-ho, heigh-ho, it’s back to work I go.  I sure hope you have a nice day at home.

Calendar April

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We Interrupt This Experiment

Today I made the decision to close the lab and temporarily suspend our experiments, including the LTEE, in light of the expanding SARS-CoV-2 outbreak.

I started to say it was a difficult decision, but really it was not all that difficult.  Several considerations led me to this decision.

1/ The SARS-CoV-2 outbreak appears to be taking off in many countries, including the USA, despite the substantial containment that has been orchestrated in Wuhan and elsewhere in China.

2/ The absence of evidence of any local cases is not as comforting as it might be, given the near-absence of testing here and in most of the USA.

3/ MSU students just returned from spring break today.  Some of the superb undergrads who work in my lab went to places that have confirmed cases. None of the places they went are among the locations with intense outbreaks, but the confirmed cases in at least one location have grown noticeably in the past week. They also flew on planes to and from their vacations.

4/ As a team, we’re connected not only to one another, but also to people who are health-care workers and others with increased vulnerabilities to infections. (Not to mention that I’m over 60 …) When you think about it, pretty much everyone has those connections.

5/ We’re very lucky because our work is easy to stop and re-start. Our study organisms can be frozen away and revived whenever we see fit.  In the meantime, everyone has classes to take, papers to read and write, data to analyze, etc.  And a little extra time, hopefully, to reflect on and maintain the health and well-being of our friends, families, and selves.  So, we will all be busy, but doing things a bit differently than we had planned.

6/ As we freeze away the long-term lines, the lab notebook will record:  “On this day, the LTEE was temporarily halted and frozen down for the coronavirus pandemic of 2020.”

Hopefully, some future historian of science will look back on today’s entry and say: “What the hell was that all about?”

Freezing LTEE for SARS

[Devin Lake putting the LTEE populations into the ultra-low freezer, where they will stay until they are called back into action … evolution in action.]

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The Lenski Lab Health Plan for the New Coronavirus Outbreak

The future is unknown, as it always is.  We do know that the SARS-CoV-2 virus is spreading around the globe, but we don’t know how many people will be infected.  Some experts are predicting that something like half of the adult population will be infected, although not all at the same time.  We also know that many cases are relatively mild (like a cold or the usual flu), and some infections may be asymptomatic. However, we also know that some other cases—perhaps 20% or so—are very serious, and some of those are life-threatening.

See MSU’s coronavirus page for University policy, information, and advice.

What can we do, as individuals and a lab group, to protect ourselves, our families, each other, our communities, and our research?  Here are my current thoughts, with an emphasis on activities related to our laboratory and our academic setting.

1/ If you haven’t done so already, get your flu shot. It won’t protect against the coronavirus, and it doesn’t provide perfect protection against the influenza virus, but it will reduce the chance of getting the flu (and save health-care resources for others in need).

2/ Make sure you and your household are prepared for a period of self-isolation or quarantine lasting 2 weeks, or perhaps longer.  This means stocking up on food staples and, importantly, any medicines that you and your household need.  For medicines, I suggest having at least a full month’s supply, maybe longer, in case there are disruptions to availability.  Talk to your doctor about extending prescriptions or any other special needs you might have.

3/ If you develop symptoms of a cold or flu—even mild symptoms—please stay at home and don’t come into the office or the lab.  We don’t want you to spread the infection.  Just email the group list to let us know what’s up, and work from home on your writing and reading if you feel up to it. You won’t impress me, or anyone, by trying to work while you’re sick.

4/ If a member of your household becomes ill, see and follow point 3 above.

5/ Let’s all start practicing more restrained physical interactions, and thus set good examples not only among ourselves but also for our colleagues and friends. That means skipping hugs and handshakes, for the time being.  Instead, you might put your own hands together and bow your head slightly to greet or congratulate someone. Or maybe an elbow bump, if you really must make contact.  Foot bumps are apparently another new thing, too.

6/ Be prepared to stop your lab work on short notice.  In the meantime, I guess March might be a good time to get a week-long or two-week experiment done, before the epidemic grows too large (if it does).  However, I suggest holding off, for the time being, on any plan to start a large and/or long experiment.

7/ Speaking of long experiments, you will recall that we have a certain long-term experiment in our lab.  The LTEE will soon hit 73,500 generations, at which time the samples will be frozen as usual.  After that date, I’d like population samples to be frozen more often, say, every 2 or 3 weeks.  Just freeze away a copy of each population (no need to plate cells)—basically, so we have samples to restart in the event that people get sick, or if the university should at some point curtail certain activities for a while.

8/ Be prepared to cancel your attendance at scientific conferences and other academic or social events as new information arises. Even if an event organizer decides to push ahead, you don’t have to go if you feel it is risky for you personally. As an aside, I recommend delaying purchases of airfares until an event is closer in time, given the current uncertainty.  (Refundable tickets on most airlines are very expensive, and other tickets have restrictions.)  Hotel reservations can usually be cancelled on shorter notice (a day or week, check to be sure), but not if they were booked through a discounter.

9/ And maybe the hardest advice of all is to practice good personal hygiene. Cover your mouth with your forearm or the inside of your elbow when you cough or sneeze unexpectedly.  (If you know you’re sick, then you should have disposable tissues handy. Use those to cover your nose and mouth completely, and dispose of a tissue after one use.) If you find yourself coughing or sneezing repeatedly, see point 3 above. Wash your hands thoroughly [Click that link, with the sound on, and stay for the end!] after you’ve touched shared surfaces, especially before eating. And most difficult of all, avoid touching your own face.  This coronavirus can survive for hours as tiny droplets on surfaces, which we may inadvertently touch (“fomite transmission”). Then, when we touch our mouth, nose, or eyes, we can infect ourselves.

10/ ADDED: Follow the news, and get your news from trustworthy, reliable sources. If it becomes clear that infections are spreading locally, or even if you are just concerned about that possibility, then avoid crowded public venues. (But this does not mean that you should follow the news obsessively, as that can be exhausting. h/t Carl Bergstrom.)

11/ ADDED: If you do isolate yourself, whether because of illness or concern, make sure to maintain frequent social contact with your family, friends, and the lab via phone, email, or whatever works best for you. Don’t let physical isolation and loneliness make you feel miserable. We are all stronger together, even if we might have to be physically apart.

12/ ADDED: Please read these Words of Wisdom, regarding preparedness for infectious disease outbreaks, from Michael Leavitt, a former Secretary of Health and Human Services.

13/ ADDED:  This one is for those of you in science or other relevant scholarly fields.  Do you have data in your lab notebooks and/or on computers accessible only in the lab?  Are the datasets ones that you might need for your analyses and writing if, say, you end up confined at home for a few weeks?  If so, I recommend that you copy it (but only if it’s allowed in the case of certain types of sensitive data!) by scanning it and/or copying it to your personal computer. That way, you can use it while working from home if you decide, or are required, to do so.

Take care everyone.  Please let me know of any errors, omissions, and practical suggestions.

 

 

 

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