Eisen Lab Blog

Lab meeting Tuesday, Jan 22nd 2013

We will be having lab meeting on Tuesday from 1:30 to 3:00pm at the genome center in room 4202.
Russell Neches is presenting.

Back in business

We’ve been sampling every day for Coral Ponds 1 and 2. We are up to almost 500 samples… which means we have a lot of DNA extractions to do.

 

I’ve noticed a few things in the last month. The coral used to be white, but now it is covered with a reddish algae. This is good because clearly things are changing, which is what this study is about! If macroscopic things (for example, the visible algae) are changing, then the microscopic things (microbial community) are most definitely changing as well!

 

On a side note, Matt and I discovered the time it took for a full round of sampling at maximum efficiency. With water filtering being the rate limiting step of our sampling process, we focused on wasting no time with the filtering. By this I mean, we had the next liter of water ready to go instantly after the current liter was done filtering. We also set a timer to remind us to keep adding water to the filter. Out of curiosity, I timed our last filtration and it took 17 minutes and 30 seconds. Overall we were able to complete the sampling in about 1 hour and 50 minutes. Being the mathematician that I am (just kidding), I assumed each filtration (6 total) took about 17 minutes and 30 seconds and calculated the time that water was not being filtered from the time we started to the time we finished: 5 minutes! I’d we were pretty productive.

Progress Report

Coral Pond 1 Graphs copy copyThe first coral pond has been running for 49 days now. We have followed them through their initial construction, the inoculation from an established coral tank and now the addition of live rock so that more corals can be added. Our collection of over 400 samples is continuing to grow and we are seeing nice trends in our water chemistry parameters.  We are excited to start looking at the DNA and have been extracting a number of samples.

Here is a quick look at coral pond one. I believe David has already shown some of this data. The red dot is the time point when we inoculated the coral ponds with microbes from an established coral reef tank.

Evolutionary Biology of the Built Environment Working Group: Call for Participants

Call for participants: Evolutionary Biology of the Built Environment Working Group.  Details copied from the announcement pasted below:

The Basics: We need your help. We are organizing the first working group aimed at understanding the evolutionary biology of the built environment—our bedrooms, our houses, our backyards and our cities. This working group will occur June 10 – 14, 2013, in Durham, North Carolina. We are now inviting applications for participants in the working group.
Why: As recently as one hundred thousand years ago the indoor environment did not exist. Yet, this is now where most humans spend the majority of their life. One might imagine that in its relatively short history the built environment might have had time to accumulate very few species. Far from the case, an emerging body of literature shows that hundreds of multicellular species and thousands of unicellular species can be found in houses and buildings more generally. Among the species found in homes are those whose presence (or absence) is likely to have a large impact on human health and well-being, species including beneficial microbiota on the body but also pathogens and potential pathogens or toxic species such as extremophilic fungi. Yet, with the exception of a few deadly pathogens (such as MRSA), the evolutionary history of most of the species with which we most intimately interact in our homes remains unknown. To remedy our lack of knowledge and take advantage of recent advances in disparate fields we will bring together scientists studying both the fauna (microbiologists, entomologists, mammalogists, and any other -ologists you can convince us have some bearing on house biomes) and environment (engineers, architects) along with social scientists (anthropologists) and evolutionary biologists (e.g. theoreticians, bioinformaticians, geneticists) to begin to build a framework for the evolution of the indoor and more generally built biome. Our goal is to develop a framework for a comprehensive understanding of the evolution of the species we most intimately interact with, particularly in the context of considering how to build and design our environments so as to favor beneficial (rather than dangerous) evolutionary trajectories. We aim to understand both how to prevent the extinction of beneficial species and to favor the evolution of lineages and species with beneficial attributes, whether those be ecological functions, health benefits or simply aesthetic value.
Who: We’d like to convene a diverse group of scientists and practitioners at various stages in their careers, from graduate students and post-docs to senior scientists, representing an array of disciplines including the organismal -ologies (e.g. microbiology, entomology, etc.), engineering, architecture, anthropology, evolution, genetics, bioinformatics, art and design. We want to be inclusive of any field that you can convince us has something to bear on studying evolution in the built environment.
How: We are currently accepting applications to be part of this working group. If you are interested, you can apply online apply online here, but do so soon. We will select a group of 30 scholars and practitioners from the applicant pool who will meet in Durham with the goal of producing a series of general audience and peer-reviewed publications about the evolutionary biology of the built environment.
Sponsored by a partnership between the Sloan Foundation and the National Evolutionary Synthesis Center.
Have questions? Drop us a note at yourwildlife@gmail.com.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

At #UCDavis: Ary Hoffmann-1/16-17th Climate change, Dengue, Wolbachia and more

Ary Hoffman flyer FN.PDF

Phyloseminar: ""Language phylogenies and cultural evolution" Online 1/16 2 PM PST

From phyloseminar.org home

“Language phylogenies and cultural evolution”

Simon Greenhill (Australian National University)

“Charles Darwin famously noted that there were many curious parallels between the evolution of species and languages. Since then evolutionary biology and historical linguistics have used trees to conceptualise evolution. However, whilst evolutionary biology developed the vast discipline of phylogenetic methods, linguistics dabbled with computational methods before rejecting them. The last decade or so has seen the introduction of phylogenetic methods into linguistics, often with some startling results. In this talk I will present some of these studies, and discuss how phylogenetics can help us grapple with the problems of linguistic and cultural evolution. These problems range from testing population dispersal hypotheses, to investigating the shape of cultural evolution, to inferring the rates at which languages change.

West Coast USA:14:00 (02:00 PM) on Wednesday, January 16
East Coast USA:17:00 (05:00 PM) on Wednesday, January 16
UK:22:00 (10:00 PM) on Wednesday, January 16
France:23:00 (11:00 PM) on Wednesday, January 16
Japan:07:00 (07:00 AM) on Thursday, January 17
New Zealand:11:00 (11:00 AM) on Thursday, January 17

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Today at #UCDavis: The True Cost of Oil talk by Garth Lenz

Forwarding this:

This is a final reminder about the awesome opportunity you have to see the talk by Garth Lenz TODAY, Tuesday, Jan 15th at 5:10pm.

Garth Lenz <

> on these issues and his work, and will be visiting UC Davis to share a slideshow of his photos and talk to us about this important environmental issue. It is a pertinent topic, as the country moves toward a final decision about the XL pipeline which would drive the expansion of the mining operations in the Tar Sands. And hearing this story from a world-renown photojournalist like Garth is truly a unique opportunity.

His talk is being sponsored by the Society for Conservation Biology, Davis and the Geology Students. It is titled “The True Cost of Oil: Images of Beauty and Devastation”

Join us on TODAY, Jan 15th at 5pm in 2 Wellman Hall to see his presentation. Free admission to students and the public.

Please bring your own coffee cup if you can!

Garth Lenz poster with UCD.pdf

 

Lab meeting Jan 15th 2013

We will be having lab meeting from 1:30 to 3pm in the Genome Center, room 4202.
Jenna Morgan Lang is presenting.

10 things you can do to REALLY support #OpenAccess #PDFTribute

I wrote a post earlier today in relation to the #PDFTribute movement: Ten simple ways to share PDFs of your papers #PDFtribute.  I wrote it largely to give people an outlet and information and ideas about how to better share PDFs of their academic work.  I think the more people share the better.

However, I also got shit from my brother Michael – co founder of PLoS on Twitter about how this is partly a “feel good” action.  I do think he underestimates the surge of anger over the death of Aaron Swartz and the momentum right now in the semi-civil disobedience being seen in the #PDFTribute movement.  But I also think he is right in part. So, I thought I would follow up with suggestions for what people should do in the future to really support full and open access to the academic literature.

  1. Only publish in fully open access journals.  See DOAJ — Directory of Open Access Journals.
  2. Do not do ANY work for non open access journals. That includes reviewing, suggesting reviewers, etc. 
  3. Cancel all subscriptions to closed access journals. The subscription model is part of the problem. 
  4. Work for open access journals. 
  5. Embrace openness in other aspects of your academic work. See for example Open science – Wikipedia, the free encyclopedia and Open Humanities Alliance
  6. Learn the difference between “open” and “freely available.” See Peter Suber, Open Access Overview (definition, introduction) and Open Access | PLOS
  7. Reward people in job hiring, merits and promotions for their level of openness.  Do not reward them for closed activities.
  8. Lobby for more open access requirements at the Federal, State, and Institutional level.  Make sure they are not mealy mouthed or mediocre. See What the UC “open access” policy should say for example.
  9. Embrace other changes in scientific publishing such as post-publication review that enable more rapid sharing of publications (see The Glacial Pace of Change in Scientific Publishing). 
  10. Read up on what else you can do (e.g., Peter Suber, What you can do to promote open access) and come up with your own ideas.  Oh and share them.  Openly.

Related posts from The Tree of Life


Other ideas? Please post in comments.


——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Introduction and my first day of sampling: Undergraduate Aquarium Project

Hello Everyone!

Since I am new to the lab and not many of you know me, I thought of positing a quick introduction along with my first day experiences with sampling.

My name is Lakshmi Bharadwaj, you’ll probably see a lot of me this quarter.

IMG_9470

(That is how I look like if you find me walking into the lab, you can say hello!)

I hope that I get to work in the lab with all of you at least once. Here’s a little bit about me:

I am a senior Biomedical Engineering major and I love photography, writing, swimming and microbes! Currently, I am extremely curious about bacteria, and my senior design project is all about how they infect your bloodstream, their clinical relevance and detection. I haven’t really dealt with a lot of microbial procedures: my time in engineering lab has been mostly machine work. So I’m really excited to learn from all of you and also observe how things work in a biology lab!

My first day in the lab was exciting because I hadn’t really seen anything like it before. I got introduced to the basics. I learnt how to correctly obtain the water, sediment and wipe samples. I learnt of the rate-limiting step in the procedure, proper techniques etc. Then, David taught me some lab protocols that I needed to follow. I was really glad with the pipettes that the lab uses because I find it extremely convenient. The only one time I have used micropipettes before involved stops and was slightly confusing. I find our pipettes so much easier to use.

I also got a basic understanding of what water chemistry involved. I learnt about how there were different tests for different chemicals and all of them required a different procedure. Although I couldn’t perform all the procedures, I got a pH reading and observed how oxygen levels were tested for.  I hope to perform each test individually and learn it in greater detail next time.

I was half-way through testing, but I had to abandon it last minute because of incorrect dilution. I did obtain a fair understanding of how this should be done in my two and a half hours in the laboratory though.

During my time in the lab and with the genome project, I hope to use this blogging space to document my observations and have it act as my notes/log book. You should expect a blogpost from me weekly.

I wish to come in every week, probably on Tuesdays or Wednesday mornings and I look forward to meeting everybody.