Tag Archives: LTEE

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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We Interrupt this Nasty Virus with Some Good News about Bacteria

Today is the 32nd birthday of the E. coli long-term evolution experiment (LTEE).  I started it on February 24th, 1988, when I was at the University of Califonia, Irvine.

Notebook entry start of LTEEIt also happens to be daily transfer number 11,000 for the experiment.  But wait, you ask: Is 365 x 32 really equal to 11,000?  (Not to mention the complication of leap years.)

LTEE flasks repeating

No!  365 x 32 = 11,680.  We’re almost 2 years behind perfection!  Over the years, we missed daily transfers for various reasons including the fact the experiment was frozen for several months around the time of my move from Irvine to Michigan State University, as well as some missed transfers and various mishaps (including contamination) along the way that have led us to restart the experiment from frozen samples.

Luckily, we don’t have to go back to the beginning–the LTEE wouldn’t have survived if we did. We freeze whole-population samples every 75 days, and those provide the backups that keep us going when needed.

So the LTEE is 32 years old today.  The evolving bacteria lineages, though, are younger, at a little over 30 years (11,000 / 365).  I prefer to think of them as timeless, though … having survived in and adapted to their tiny flask worlds for more than 73,000 generations.

Here’s grad student and lab manager Devin Lake doing today’s transfer.

Devin LTEE 32 years

And here’s Devin & me with the lab notebook. Devin is pointing to today’s entries.

Devin and Rich with LTEE notebook for 32nd birthday

And here’s what we wrote:

LTEE notebook 32nd birthday

For those with pathogens on their mind (and that’s a lot of us, with the new coronavirus spreading), you might wonder: Aren’t E. coli dangerous?  The short answer is only rarely. All of us have harmless or even beneficial strains of E. coli and many other bacterial species in our GI tract. The LTEE uses one of these harmless strains, one that has been studied in many labs for close to a century without problems. There are some strains of E. coli, though, that are nasty, and which are usually acquired by eating contaminated foods.  So wash your raw fruits and vegetables, cook your meats, and don’t worry about the LTEE bacteria … Just wish them a happy birthday today, and many more years of scientific discovery.

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Revisiting Telliamed

I started this blog, Telliamed Revisited, back in August of 2013, after attending a conference at which a colleague emphasized the value of social media in science.

I recall being questioned on Twitter by someone who expressed skepticism whether my blog would last or quickly be dropped. (Hey, I had already been running the LTEE for a quarter of a century at that point, so you’d think I’d get a little slack.) Anyhow, I said I didn’t really know, and that this blog was a personal experiment in communication.  In any case, I’ve now kept it up for six years, but with only occasional posts … about 100 in total so far.

If you want to follow a regular blog that is focused on science and related issues, I highly recommend Dynamic Ecology.  Jeremy Fox, Meg Duffy, and Brian McGill discuss interesting issues multiple times almost every week.  Impressive!

Anyhow, reflecting on my blog experiment as we head into a new decade, I was interested to see which of my posts had been viewed most often.  Here are the top 10:

Here are five more that are among my own favorites, but which didn’t make the top 10:

Also, if you’re wondering about the name of this blog, see the following post:

Last but not least, Happy New Year—and New Decade—to one and all!

Telliamed

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Freezer Burn

One of the more challenging aspects of running a microbiology lab, in my opinion, is freezer management.  There’s a lot to keep track of, both in terms of quantity and quality.  My lab team and I take great pride in the quality control of our work that has allowed us, for example, to keep the LTEE running for over 30 years and 70,000 generations without contamination.  Or rather, as I’ve posted before, we’ve had occasional accidents including cross-contamination of the replicate lines, but we’ve caught those mistakes and, using frozen samples, restarted as needed to keep things going smoothly and cleanly.

With my lab group now running for ~34 years (I started at UCI in 1985), and with so many hard-working students and postdocs, we’ve filled up lots of –80C freezers.  And that’s despite shipping many strains to scientific collaborators and former lab members who’ve continued to work on the various projects—the LTEE is only one (albeit the longest) of the many projects we’ve done in my lab.  Adding to the storage challenge, we’ve got duplicates of most samples in case we have a problem with the primary sample (say, someone drops a vial on the floor).  Also, to avoid compromising our primary or backup samples, I ask that everyone who plans to use any sample (usually a set of many samples) more than once make his or her own working copies of the samples.

And freezers sometimes fail, despite our best efforts to maintain them in tip-top shape.  So over the years, I’ve always tried to keep a freezer’s worth of spare capacity across our multiple freezers, so when one fails, everything can be moved into a functioning freezer.

On Sunday, one of our workhorse freezers failed. Most of our freezers have alarms that send out an email alert to members of the lab that something is amiss.  This one did not (oops!), but fortunately undergraduate Jessica Baxter (working hard even on the weekend), noticed that it had “warmed up” to –40C or so.  I was off visiting grandkids, but Jessica was able to reach Devin Lake, who manages the lab’s operations extremely well, even as he does double-duty as a grad student.  Devin and Jessica were able to find enough spare capacity to get everything into one of the surviving freezers, so nothing was lost.

But that meant we had no more spare capacity.  We can buy a new freezer, although my experience (and hearing about many other failures) is that they don’t make them like they used to.  And what if another freezer were to fail before we got a new one?

I knew we had many freezer racks full of now-unimportant samples—working copies made by people who’ve left the lab, as well as samples from abandoned experiments and various long-ago projects that won’t be revisited.  So I asked Devin to look through the freezers for the identifiers on various racks (besides the LTEE and any associated with current lab members) that would give me ideas of what we could discard to free up some space that we will need for ongoing projects … as well as the possibility of another freezer failure.  (But please not that!  I’m not trying to tempt fate—I just want to be prepared.)  It turns out there were lots of possibilities, so Devin and I spent a couple of hours checking boxes and then removing about 20 freezer racks, most holding 6 to 10 boxes, and most of those with dozens of small vials, each holding many millions or even billions of bacterial cells.  Seeing the names of former lab members on the boxes, and the numbers on all those vials, was a humbling reminder of all the hard work that so many have done over the years.  Devin carted three loads of discards down to one of our workrooms, where hardworking tech John Baltusis emptied each box and prepared the vials for the sterilization (autoclaving at high temperature) that’s required before they can be discarded.

Thanks to the hard work of Jessica, Devin, and John, the lab avoided any setback. In fact, our freezer collection is now a little more manageable than it was before.

[Devin Lake, in front, with one of three cartloads of samples to discard, while John Baltusis removes the samples from one box before autoclaving.]

Devin, John, and freezer mess

 

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