Why are not all E. coli resistant to antibiotics?

Last summer gave a talk at a Gordon Conference about transmission and evolution of drug resistance in HIV and E. coli. When I was done with my talk, there was time for questions. Dmitri Petrov asked what I thought about why resistant and susceptible strains of bacteria co-exist. I had to admit that I hadn’t really thought about that.

This question of co-existence (why aren’t all bacteria resistant or all of them susceptible?) it not a new one. In fact, about a week after the Gordon Conference, I talked to Marc Lipsitch who has worked on this question for many years. It was just not on my radar. Until last summer.

The question of co-existence marinated in my head for over the summer. I read papers about it. Looked at the data I was analyzing. And then sometime in the fall it suddenly hit me! I saw a solution to the question that was real easy. This is what I think may be happening: Resistance evolves when a bacterial strain finds itself in a person who is treated with antibiotics. But because most of us aren’t on antibiotic treatment most of the time, these resistant strains tend to have lower R0 values than susceptible strains (that is, the resistant strains don’t spread as effectively). Therefore in the human population at large, existing resistant strains are losing against the susceptible strains.

I had been studying the many origins of resistance (resistance in E. coli and other bacteria evolves very often – lots of convergent evolution), and I had been studying the cost of resistance (I think most resistant E. coli strains tend to die out – thought this is not easy to prove). These two ingredients together can explain the co-existence of resistant and susceptible strains.

Early October I emailed Dmitri: “Dmitri, I think I have the answer to your question!”. Dmitri answered: “Exciting! But you forgot to attach the manuscript”. Me: “Oh, I didn’t write it up yet! It is just in my head.”

So I started writing because that’s how academic science works!

The manuscript now lives on Medrxiv. I have submitted it to Nature (desk-rejected) and to Science (reviewed and rejected). Traditionally, after a rejection from a high-profile journal, one would send a manuscript to another journal right away, but one of the reviewers from Science suggested using a particular Norwegian dataset, instead of the Enterobase data I had used for the manuscript. I really liked that idea (as well as some other ideas from the reviewers). So I decided to pause and do more analysis. Some of the new data made their way into my talk for the TAGC conference in Washington DC last week.

If you are curious to hear where I am at with this project, here is the video of my talk:

Thoughts on the first Women in Computational Biology conference

Earlier this week I went to the first Women in Computational Biology conference at Janelia Research Campus. When I got the invite, I said yes immediately, but then I had some doubts. I wondered: why have a conference just for women? And then I worried: would it be only Ivy-league trained white women? Would this conference actually contribute to diversity in our field?

Now the conference has happened and I am back in SF, so I thought I share some thoughts.

1. While the conference was not just Ivy-league trained white women, it was still fairly white and certain groups were clearly underrepresented (e.g., Black and Latina women).

2. The conference was super interesting! I learned about image analysis, cancer genomics and machine learning. I met some great scientists. It got me excited to try new things.

3. If I were in neurobiology or image analysis, I would seriously consider applying for a job at Janelia. It is luxurious and beautiful and they have great food and amazing staff.

4. I very much enjoyed being at a women-only conference. One reason is that normally at conferences, I spend time and energy worrying that the guys in the room will be the only ones asking questions. No worries here! Or, I worry about the guys at the dinner table dominating the conversations. No worries here! Then, when a guy is giving a talk and clearly not giving proper credit to his postdocs, I wonder whether I should say something about it. At many conferences, I worry a lot, and most of that worry was absent at this conference. In addition, it was nice to feel safe to talk about women stuff. Our dinner conversation went from breast pumps to programming languages without skipping a beat. SO COOL! Being part of the majority for once is nice.

5. Being at this conference, and enjoying the safety of being surrounded by women, makes me even more motivated to help create safe spaces for my students and colleagues of color. I already make an effort to send my students to conferences for minority scientists such as SACNAS and ABRCMS. But I also want to try (again) to organize a meeting for people of color in evolutionary biology. Evolutionary biology is still a very white field with a racist history (eugenics). I think it’d be a good idea to organize a regular conference for people of color in our field. A few years ago, I applied for money to do this, but I was not successful. I will try again!

All in all, I think the conference was worth my time and a great way to meet other women in computational biology.

 

Five Reasons why you should attend the Annual SACNAS National Conference

Guest post by: Bridget Hansen, SFSU undergraduate researcher

First, who am I? What is SACNAS?

My name is Bridget Hansen and I am an undergraduate in Microbiology at San Francisco State University, doing research at the Romberg Tiburon Center for Environmental Studies. Over the summer, I participated in the Howard Hughes Medical Institute Excellent Research Opportunity Program (HHMI-ExROP) summer research and the AMGEN program at the University of California, Berkeley. I worked on a project that I then presented at the SACNAS Conference this past October.

SACNAS stands for the Society for Advancing Chicanos/Hispanics and Native Americans in Science. This society, made up of many successful Chicanos and Native Americans in science related careers, puts on a national conference once a year. The conference has opportunities for scientists at all levels, from undergraduates to professors and researchers. Many graduate school recruiters and other professional organizations come to this conference to recruit, providing a great platform for networking.

I used this opportunity to network for graduate schools! I will be attending a PhD program in the fall, in part, thanks to my interactions that I had at SACNAS.

What happens at the SACNAS National Conference?

Students from all over the country submit abstracts for the opportunity to present their work, either in the form of a poster or an oral presentation. The students had a scheduled time and room to present. Other than presentations, the meat of the conference was geared towards guest speakers and networking. The whole goal of the conference was to introduce young students to the world of research and science related careers! The best part is the graduate student recruiter booths where you have the opportunity to chat with recruiters, professors, and students from that university.

Five reasons why I recommend SACNAS

1. The networking

There were hundreds of booths set up, all stocked with professors, recruiters, graduate students and pamphlets listing the reasons why you should come to their school. Nearly every research institution was in attendance, looking for the next round of graduate students to apply to their programs. They want you to apply to their programs but most importantly, they want to make sure their school lines up with your research interests. You can ask them about the programs, the application process, what it is like to live in that part of the United States and any funding opportunities. Exchanging business cards or information is very common and the badge that you are given upon arriving even has a scanner square that the recruiters can use to keep in touch with you (they scan your badge and your e-mail is logged with them).

I spoke to over a dozen booths about their programs and had all my questions answered. I was even recruited during my poster session presentation! Which brings me to my next point.

2. The presentations

The presentations are great for two reasons: 1. You have an opportunity to talk about your work and receive feedback on your presentation skills and 2. Other schools can come by your presentation and see you as a researcher. This is fantastic! I am not the best on paper in some ways, so having other schools approach me based on my science, reassures me that I am more than just my GPA or my GRE scores. Not only that, I received written evaluations based on my presentation skills and my poster, which were all constructive and positive!

3. The seminars

The guest speakers focus on their journeys as minorities in the sciences and how their transforming experiences have brought them to where they are today. They inspire us to continue to pursue our passions and create a sense of community, which I will get to in a minute. The seminars are also great opportunities for junior scientists, like myself, because they offer an opportunity to check out new areas of research, hear about different paths in science outside of academia and get insights into how to be successful. There are workshops on how to give a compelling interview, what to expect in graduate school and how to master networking. All of these skills are important ones that give you a competitive edge.

4. The experience

The experience itself was wonderful. Surrounded by 3,600 other students, mentors and researchers, the conference felt grand. I say grand because the conference center was massive, the sheer number of attendees was at times, a bit overwhelming, and the hotel that we were assigned to left me in awe. The Gaylord National Conference Center in Washington D.C. was an incredible place to hold this conference this year. As apart of the conference fees, we were fed in a large hall, which also created a sense of community.

5. The sense of community

The SACNAS conference creates a sense of community for young scientists; a community that they can be a part of throughout their careers in the sciences. The idea of having a supportive community that I can be part of is a great feeling, especially coming from a background that does not have any college graduates. It can be lonely sometimes, walking into a completely new field that no one you grew up around, has any experience in. So, when I attended the conference with other San Francisco State students who were also presenting, they immediately considered me one of the group, even though we had just met. Similarly, other students from other places also welcomed conversation with open arms. The inclusion that occurs at SACNAS is excellent.

Overall, I highly recommend attending a SACNAS national conference. It looks great on your CV, it is great for your future scientific career and definitely gives you an edge when applying for graduate school. Bring your own business cards!

If you have any questions about SACNAS, please refer to the SACNAS website: http://sacnas.org .

Hope to see you there next year! I will be attending as a graduate student!

Feel free to contact me with questions at: blhansen “at” mail.sfsu.edu or missbridgette4 “at” aol.com. and indicate you read this blog so I know where the questions are coming from!

 

2014 NESCent Evolution Video Contest: the finalists

For the fourth time, NESCent organizes the NESCent Evolution Video Contest. For me, this was a good motivation to make a new video just in time to send it in.

Now twelve video’s were chosen by NESCent to be shown next week at the Evolution meeting in Raleigh. I am happy that my video (number 10) is amongst the finalists! Have a look at the videos and if you’re in Raleigh next week, go and vote for your favorite! (Saturday 21 June, 8-10 p.m., Room 402, popcorn provided!)

All the entries can be found on the NESCent website. Here are the twelve finalists:

1. Sex-y Science: Sex Ratios in Patchy Populations

Allison Neal

Sex-y Science: Sex Ratios in Patchy Populations from Allison Neal on Vimeo.

2. Exaptations versus Adaptations

Renske Onstein

Evolution: Exaptations versus Adaptations from Renske Onstein on Vimeo.

3. Please Tap Again

Ana Endara

Video not available 😦

4. Bird Clines

Osmond, et al (Univ. of British Columbia)

Bird Clines from Luc Luc on Vimeo.

5. Using Fitness Landscapes to Visualize Evolution in Action

Randy Olson and Bjørn Østman

Using fitness landscapes to visualize evolution in action from Bjørn Østman on Vimeo.

6. Selfish Gene

Shankar Meyer, Guillaume Vandenesch, Adrien Bernheim

Selfish Gene from François Maginial on Vimeo.

7. Genetic Drift with Origami Ducks

Flo Débarre

Genetic Drift with Origami Ducks from Flo Débarre on Vimeo.

8. Drift

Will Ryan, et al (Florida State University)

Drift from Julia Kunberger on Vimeo.

9. The Adaptive Radiation of Darwin’s Finches

Andrew Hendry

The Adaptive Radiation of Darwin’s Finches – NSESCent/Evolution 2014 edit from Andrew Hendry on Vimeo.

10. Selective Sweeps in HIV

Pleuni Pennings

Selective sweeps in HIV from Pleuni Pennings on Vimeo.

11. The Genetics of Mouse Burrowing

Ariana Kam

The Genetics of Mouse Burrowing from Ariana Kam on Vimeo.

12. Dinosaur

Lori Henriques and Joel Henriques

Dinosaur from Lori Henriques on Vimeo.

(Almost) 100 things we did to make the BAPGX conference a success

(Also posted on http://stanfordcehg.wordpress.com/)
I love working with a team to organize an event. The tenth Bay Area Population Genomics conference (BAPGX) was a fun event to organize. It is part of a successful series of conferences and there was plenty of support, both at Stanford and from the community, to organize it. Five Stanford postdocs volunteered to help out and did a great job.

I think the conference was a success. Here are some of the things we did to make it that success.

How it got started

1.     Dmitri Petrov (who initiated the BAPG series) asked me (Pleuni) if I could organize the conference.
2.     Dmitri and I picked a date (not realizing it was Memorial day weekend!) and after that I was free to organize it the way I wanted.
3.     I asked the CEHG mailing list for volunteers and –within 10 minutes!– found five postdocs who were willing to help me organize the event. We were ready to get started!

The BAPGX committee, Pleuni Pennings (@pleunipennings), Maria Avila (@maricugh), Carlo Artieri (@Carlo_Artieri), David Enard (@DavidEnard), Dave Yuan (@13bee_slurpee), Bridget Algee-Hewitt (@BridgetAH), Dmitri Petrov (@PetrovADmitri, not in the picture).

The BAPGX committee

4.     The BAPGX committee met 3 times. The first meeting was mostly to brainstorm, the other meetings were more focused on logistics.
5.     We sent many (many!) emails within the committee.
6.     We kept notes and files in a shared folder on Google Drive.
7.     We split tasks: Bridget was in charge of communication with speakers and participants.
8.     Carlo was in charge booking the location, catering, and poster boards.
9.     Maria was in charge of mugs and name stickers.
10. David was in charge of the logo and photography during the event.
11. Dave was in charge of wine and cheese and printing the schedules and signs.
12. Pleuni was in charge of the website, Facebook, twitter and the money.
13. We decided on the program (and many other things) together.

There was a BAPGX mug for every participant.

Logistics

14. We looked at several lecture halls at Stanford and chose M106 in the Alway building, even though it wasn’t fancy, because it had the right size (140 seats) and was adjacent to a courtyard (great for registration, breaks and posters). It was also good because people could take their coffee with them into the room and because we could order food from an outside vendor.
15. We decided to start the conference at 10AM, so that it was convenient for people who wanted to take the Caltrain (the first arrived at 9:17 in Palo Alto).
16. We put travel instructions on the website and also sent them by e-mail:http://evolgenomecehg.wordpress.com/bapgx-map-and-travel-instructions/
17. We put up some signs to make it easier for people to find the Alway building.
18. We encouraged people to ride share and included a column in the registration Google doc with ride share information.
19. We had two of our committee members (Maria and David) in and at the Caltrain to guide people to the lecture hall.
20. We made sure the lecture hall would be open on the day of the conference.
21. Two of us washed all the mugs and four of us went to Costco two days before the conference.
    

    Dave and David are preparing the registration area.

Registration

22. Registration was free and open to all.
23. We decided to cap participation at 150 (even though we had only 140 seats) under the assumption that some people would cancel or not show.
24. To sign up, people simply added their name, email, affiliation, food preference, whether they’d bring a poster and ride shareride share info to a Google doc.
25. A few days before the conference we “locked” the Google doc and asked people to email us instead.
26. We reached 150 registrations around one week before the conference. After that approximately 10 people canceled and around 5 additional people were admitted. A few people didn’t show up and a few crashed the conference, but this was no problem as we had enough seats and food.

A full lecture hall.

Using social media to build momentum

One of the great things about working with an active community and a motivated committee is that we could build a lot of momentum before the conference.

27. We had a simple website (http://evolgenomecehg.wordpress.com/bapgx/)
28. The committee communicated with the community through emails (to individual people, to the speakers and the poster presenters and to the BAPG Google group).
29. We hoped for participation from many different universities and made additional efforts to encourage people from SFSU, Santa Clara and UCSC to sign up. We also had participants from UCSF, UC Davis, UC Berkeley, the Cal Academy of Sciences, Ancestry.com, Stanford and a few other institutions.
30. We used twitter (all committee members are on twitter).
31. We decided on a twitter hashtag early on (#BAPGX).
32. We used Facebook (through the CEHG Facebook page).
33. We tried to keep everyone updated on the program and everything else we were working on (logo, mugs, cheese etc.) to show that we were working hard and that we were excited about the conference.
34. We asked three active tweeters from the community to live-tweet the conference (@razibkhan, @mwilsonsayres and @JeremyJBerg)
    

    One of many tweets on the day of #BAPGX

Money

35. We received financial support from Ancestry.com and from CEHG (thank you!!).
36. For the CEHG money we had to write a short proposal, but basically used the same text as we already had on the website.
37. We spent money on food and coffee ($2,266), water, juice, soda, wine and grapes ($711), cheese ($430), mugs ($715), and name stickers ($76).
38. We saved money by buying water, juice, soft drinks, wine, crackers, grapes, paper plates and plastic cups at Costco.
39. We also saved money by using stickers as badges (instead of more fancy badges).
40. We saved money by not video-recording anything.
41. We decided not to spend any money on inviting an outside speaker or gifts for speakers.
42. We got help with the financial administration from CEHG (Cody Sam) and from Elena Yujuico (Dmitri’s admin).

(Almost) glitches

43. We didn’t realize until fairly late that we planned the conference in Memorial Day weekend.
44. We didn’t think about Wi-Fi access for guests until the night before the conference. On the day itself we created a guest login for the Stanford network and that worked.
45. We were not consistent about the length of the normal talks. We originally announced that they’d be 12 minutes (+3 minutes for questions), but then this somehow became 15 minutes (+5 minutes for questions).

Talks

46. We allowed for normal talks (15 min) and mini talks (5 min) and got an equal number of abstracts for both.
47. We set a deadline for talk submissions (4 weeks before conference) and another deadline for registration (one week before conference).
48. We asked people to submit abstracts (this was not done for previous BAPG conferences. At previous BAPG conferences, people were encouraged to add their name in a Google doc to sign up for a talk, but we thought that making the process a little more formal would get us different speakers and potentially more well-prepared speakers).
49. We accepted all talks that were submitted before the deadline (but none that were submitted after).
50. Our program was a bit longer than previous BAPG programs, because we decided to accept all submitted abstracts and because we wanted to be sure there was ample time for questions.
51. We asked speakers to send us their slides (only Powerpoint or PDF allowed) a few days before the conference (in the end we had all files before the start of the conference!)
52. We organized a practice-your-talk session for the speakers from Stanford.

Posters

53. Participants were encouraged to bring a poster. No titles or abstracts needed, just a “yes” in the right column in the Google doc.
54. 11 People signed up to bring a poster, in the end there were 9 posters.
55. We borrowed simple poster boards from the Beckman center and brought pins and tape (We considered higher quality poster boards, but they would have cost around $500 rental fee at Stanford).
56. Posters were up the whole day (from the coffee break in the morning).
    

The day itself

57. All of the committee (except Maria who was on the Caltrain) met at 7:30 to set up everything for the day.
58. We made sure we each had all the other phone numbers.
59. We brought several computers, VGA cables, thumb drives etc (but in the end all worked from the computer that was already in the lecture hall).
60. We brought plates and knives for the cheese and grapes.
61. We asked Dmitri Petrov to say something at the start of the conference.
62. We split chairing between three members of the organizing committee (Carlo, Maria, David).
63. Bridget and Pleuni “manned” the registration table from 9 till 10:30 and explained to everyone how to indicate their affiliation on their name sticker.

Name sticker with associations indicated (a yellow dot at the approximate location of Stanford and a green dot at the location of SFSU).

64. We had fairly long breaks and allowed plenty of time for questions. Each session ran a few minutes late, but we caught up during the breaks.
65. Each of the members of the organizing committee missed at least one of the sessions to be outside to handle food.
66. Our three designated twitter volunteers did a great job live-tweeting the conference and many others joined in. The result was storified here: https://storify.com/mwilsonsayres/bay-area-population-genomics-x
67. David brought his camera (photo’s will follow!).
68. Originally we had someone (not the chair) assigned the task of keeping track of time during the talks, but in the end we decided that it worked better if the chair did it him/herself.

After the conference

69. We all stayed till the end and cleaned up the mess.
70. We found a home for the leftover mugs & the leftover wine and cheese.
71. We wrote this document.
72. We sent an email to all participants to thank them for coming & for great talks and posters & to tell them about the storified tweets.
73. We plan to have a nice lunch or dinner with the committee to celebrate the success of the conference.
74. We’ll publish the photos.
75. We’ll round up the financial administration.

Other notes

76. The talks were of very high quality (thank you, speakers!!). The fact that we asked presenters to send us their slides beforehand may have contributed to that.
77. We got a lot of positive feedback about the mini talks (lightning talks), so it may be a good idea to keep that as part of BAPG.
78. Many people stayed for the posters and cheese. The cheese may have helped with that; we had a Toma (cow’s milk cheese from Pointe Reyes), Comte (cow’s milk cheese from France), Brabander (goat’s milk Gouda from Holland) and Casatica (buffalo milk soft cheese from Italy).

My itinerary for ESEB 2013

I usually set goals for conferences (see here), but not a specific itinerary. Inspired by other bloggers (such as Jeremy Fox on Dynamic Ecology), I decided to plan my itinerary for the ESEB conference next week. ESEB stands for the European Society for Evolutionary Biology, and the ESEB conference takes place every other year in a different city. This year it’s in Lisbon!

I am sure it’ll be a great conference!

Monday Aug 19th

Arrival, some sightseeing, maybe a work meeting with a collaborator. Registration and then to the welcome reception! I hope to see all the speakers & poster presenters of the drug resistance symposium there!

Tuesday Aug 20th

On this day I have no difficult choices to make 🙂

The day starts with a plenary talk by Juliette de Meaux, who will talk about “reconciling molecular and evolutionary biology” using Arabidopsis as a model system.

Then I am off to Symposium 22: The evolution and genetics of drug resistance which I co-organize with Sarah Cobey, Fredrik Inglis and Gabriel Perron.  You can find the schedule here. During the Tuesday poster session I’ll probably hang around the Symposium 22 posters most of the time.

I will try to write a separate post about all the great talks & posters of our symposium. I hope to see many of you there!

Wednesday Aug 21st

The day starts with a plenary by Dieter Ebert on the “population genetics of host-parasite coevolution.”

Then I will head to Symposium 10 on genomics and experimental evolution, with talks about adaptation in bacteria in hosts and in the lab.

After lunch I will move to Symposium 13 on rapid evolution, and look forward especially to Richard Neher’s talk on “HIV coevolution with the host immune system” and Hildegard Uecker’s talk on “evolutionary rescue in structured populations”. Unfortunately, I will have to miss this talk by Sally Otto and this one by Claudia Bank, both on “adaptive mutations in/to different environments.”

There is a poster session in the afternoon, where I will certainly go see this poster by Ricardo Ramiro about adaptation to the gut of the mouse, and this poster by Frederic Hopital about detecting selection in chickens.

I also plan to look at this poster about diversity in SIV (George Shireff), this one about experimental evolution in mice (Mirian Linnenbrink), and two posters about the evolutionary advantage of sex (one by Su-Chan Park and one by Daniel Weissman).

Thursday Aug 22nd

Thursday starts with a plenary talk about evolution in cancer by Mel Greaves.

The rest of the morning I’ll spend at Symposium 1 which focuses on experimental evolution and fitness landscapes.

Thursday afternoon is free for sightseeing or organized tours!

Friday Aug 23rd

The plenary speaker of this day is Trudy Mackay. I have never seen her talk, so I am excited to see this famous geneticist speak about the genotype-phenotype map of fruit flies. There is a great little video about her on YouTube.

After the plenary I will go back to Symposium 1 which focuses on experimental evolution and fitness landscapes, where I will also stay after lunch.

I am still undecided for the rest of Friday afternoon.

Later on Friday there is another poster session. I plan to go see this poster on fixation probabilities (Ivo Chelo) and many others in the experimental evolution symposium (Symp 1).

Saturday Aug 24rd

The last day of the conference. The plenary speaker is Virpi Lummaa and she talks about longevity in humans.

I’ll then go to Symposium 8 on epigenetic variation.

Saturday afternoon is filled with more plenaries about speciation (Roger Butlin), species selection (Rochard FitzJohn) and a talk by Rolf Hoekstra with the great title: “♀ ♂ + –“. At night there is the conference dinner.

Your itinerary?

The ESEB website is really nice and I encourage everyone to spend some time with it before flying to Portugal. I’d love to hear where others are planning to go! I hope there will be a pdf version of the entire program soon.

I will be following the #ESEB2013 hashtag on Twitter to find out about the sessions I’ll be missing. Let’s hope there will be wifi!