Tag Archives: Jessica Green

Best post doc position ever: w/ Jessica Green, myself, Jay Stachowicz, Jenna Lang

copied from U. Oregon web site

Postdoctoral Research Scholar
Institute of Ecology and Evolution

Posting: 14431
Location: Eugene
Closes: Open Until Filled

Revised Posting
Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon (http://pages.uoregon.edu/green/) is currently seeking a postdoctoral researcher to collaborate on the Seagrass Microbiome Project (http://seagrassmicrobiome.org).  

Applicants should have a Ph.D. in a biological, computational, mathematical, or statistical field and strong writing skills.  The ideal candidate will have experience developing and applying models to understand the ecology, evolution, and/or function of complex systems.  Experience in the analysis of environmental sequence data is highly desirable, but not required. 
  
The successful candidate will have the opportunity to creatively and independently tackle one or more of the science questions outlined in the Seagrass Microbiome Project grant proposal (http://seagrassmicrobiome.org/2014-grant-proposal/), funded by the Gordon and Betty Moore Foundation.  

The successful candidate will interact regularly with team members Jonathan Eisen (https://phylogenomics.wordpress.com), Jay Stachowicz http://www-eve.ucdavis.edu/stachowicz/stachowicz.shtml, and Jenna Lang (http://jennomics.com/) at the University of California, Davis through weekly tele-conferencing and also through regular visits to the UC Davis campus. 

At the University of Oregon, the candidate will benefit from ongoing microbiome research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).

The position is available for 1 year with the possibility for renewal depending on performance.  The start date is flexible.  Please email questions regarding the position to Jessica Green (jlgreen@uoregon.edu).

To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references 
Submit materials to ie2jobs@uoregon.edu.  Subject: Posting 14431

To ensure consideration, please submit applications by March 10, 2015, but the position will remain open until filled. Women and minorities encouraged to apply.  We invite applications from qualified candidates who share our commitment to diversity. The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

Post-doc w/ me, Jessica Green, Jay Stachowicz, and Jenna Lang on seagrass microbiomes

Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon Green (http://pages.uoregon.edu/green/) is currently seeking a postdoctoral researcher to explore fundamental questions in microbial ecology and evolution. Applicants should have a PhD in a biological, computational, mathematical, or statistical field with extensive training using theory and/or modeling to understand the ecology and evolution of complex biological communities, and strong writing skills. Experience developing and applying quantitative phylogenetic ecological methods is highly desirable, but not explicitly required for candidates who have otherwise demonstrated strong quantitative skills.
The successful candidate will play a key role in the Seagrass Microbiome Project (http://seagrassmicrobiome.org) in collaboration among Jonathan Eisen https://phylogenomics.wordpress.com), Jay Stachowicz http://www-eve.ucdavis.edu/stachowicz/stachowicz.shtml, and Jenna Lang (http://jennomics.com/) at the University of California, Davis. The Seagrass Microbiome Project aims to integrate the long interest in seagrass ecology and ecosystem science with more recent work on microbiomes to produce a deeper, more mechanistic understanding of the ecology and evolution of seagrasses and the ecosystems on which they depend. Our studies of the community of microorganisms that live in and on seagrasses – the seagrass “microbiome” – will contribute to a broader understanding of host-microbe systems biology, and will benefit from ongoing University of Oregon research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).
The position is available for 1 year with the possibility for renewal depending on performance. The start date is flexible. Please email questions regarding the position to Jessica Green (jlgreen).
To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references
Submit materials to ie2jobs. Subject: Posting 14431
To ensure consideration, please submit applications by November 1, 2014, but the position will remain open until filled.
Women and minorities encouraged to apply. We invite applications from qualified candidates who share our commitment to diversity.
The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

Guest post from Ashley Bateman on "Full contact microbes" – Roller Derby

A special guest post from Ashley Bateman.

 

Roller derby players share their skin microbes during play
Single-celled organisms are intimately associated with multicellular organisms across the tree of life, and human beings are no exception. Making up 90% of our cellular composition, these invisible passengers (our microbiome) contribute to our health and well-being in crucial ways, including aiding our digestion, the education of our immune system, and resistance to pathogens. Despite this importance, we still lack a fundamental understanding of where our host-associated microbes actually come from. We know that infants are born practically sterile; early-life events such as birth mode can contribute to the types of microbial species found on an individual, but these events cannot adequately explain the majority of spatiotemporal variation observed over a host’s lifetime. To be able to accurately describe the processes that drive host-associated microbial community dynamics, we must have an informed understanding of the role of dispersal in structuring host-associated microbial communities.
Where do they come from? How do they get there? Do these changes (if any) last?
The Green Lab at the University of Oregon-Eugene attempted to answer some of these questions in our latest publication “Significant changes in the skin microbiome mediated by the sport of Roller Derby”, released today by PeerJWe decided to use Roller Derby as a model system to investigate the role of contact in dispersing skin microbial communities between hosts. We have known for a long time that pathogens can be transmitted via direct contact; could not our commensal microbial communities be shared in this way?

We swabbed the upper arms (a frequent contact point between players during a bout) of players belonging to 3 geographically distinct derby teams and characterized the skin microbiome of each player using 16s rRNA gene Illumina sequencing. We found that each team’s upper arm microbiome was significantly different from one another before play, and that this difference decreased after bouts were played. Not only did teams’ skin microbiomes become less different from one another after play, but the differences were driven in part “by the presence of unique indicator taxa that are commonly associated with human skin, gut, mouth, and respiratory tract.” There were also environmental bacteria associated with soil and plants found in the skin samples.

Although we weren’t able to show a direct link between contact and transfer of specific microbial taxa, the best explanation of the data seems to be that contact between these players during a one-hour bout effectively resulted in homogenization of their upper arm skin microbiomes.
So much yet to explore! As a 2nd year graduate student in the Green Lab I hope to address some of the questions that the Roller Derby paper has brought to our attention. My dissertation research is gearing up to understand the role of dispersal on our skin microbiome. Are some skin sites more amenable to changes than others? Can we pick up host-associated microbes not just from other individuals, but from objects that other individuals have touched? Can we pick up non-host-associated microbes? If we can pick them up, how long do they stick around? How do they participate in the functions attributed to the skin microbiome?
Hope to keep up the fantastic momentum that has been launched by this latest publication – if you have any thoughts or comments, feel free to contact me at abateman@uoregon.edu, or via Twitter: @microbesrock
And you can check out a stop-motion video I made on the skin microbiome here:

From iSEEM project: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

Quick post.  Another paper is out based on the Gordon and Betty Moore Foundation funded iSEEM project I co-ran with Jessica Green and Katie Pollard.

PLOS Computational Biology: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities.

O’Dwyer JP, Kembel SW, Green JL (2012) Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. PLoS Comput Biol 8(12): e1002832. doi:10.1371/journal.pcbi.1002832.

It has one of my favorite paper figures ever.

Figure 1. The local community and metacommunity framework casts local biodiversity of coexisting species in terms of a sampling process from a larger reference pool, or metacommunity. 

And the paper is definitely worth checking out.

An ecosystem in my house? Yes indeed. And with microbes too. #BostonGlobe #microBEnet

Well I am very excited about this article in the Boston Globe today: Ecosystem, sweet ecosystem – The Boston Globe. By Courtney Humphries the article discusses the Sloan Foundation program in the “Indoor Environment” that is focusing on microbial ecology of the built environment. I am, well, really into this area of work and have a grant from the Sloan Foundation in their program to crete something called “microBEnet” which stands for “microbiology of the Built Environment network.” And in case you were wondering, yes, the BE is supposed to be capitalized and the m in microbe is not. My work in microBEnet is focused on Science 2.0 activities to help boost interaction and communication and outreach relating to studies of microbiology of the built environment. Check out the microBEnet site for more detail on that project (more on this in a bit).
Anyway, a little while ago I was interviewed by Courtney Humphries about studies of microbes in the built environment and the conversation seemed to go pretty well. And I kind of forgot about it due to some family things going on in my life. And then yesterday I saw the article. It is quite nice. It starts off with a nice drawing of a house making it look like an ecosystem

and the headline/lead in is really quite perfect “Ecosystem, sweet ecosystem.” is the headline with the subtitle “What if we studies the indoors as an environment all it’s own”.  She goes on to quite Hal Levin (my collaborator on microBEnet), Jessica Green (the head of the BioBE center in Oregon focusing on biology of the built environment), me, Paula Olsiewski (the Program Officer at Sloan in charge of the Indoor Environment program) and Bill Nazaroff from Berkeley, who is also funded by the Sloan Foundation to work in this area.

The article is definitely worth a read.  Only issue really is that I have a feeling people may be distracted by some sort of storm hitting the East Coast right now.  Well, after the storm hits, microbiology of the indoor environment will likely be even more important to pay attention to.

If you want to brush up on studies of microbiology of the built environment check out some of the resources we have made and/or collated at microBEnet including:

Stay tuned for more, from microBEnet, from Sloan funded researchers, and from others studying microbiology of the built environment.  We spend on the order of 90% of our lives in built environments like buildings, cars, trains, etc.  It’s about time we started studying such environments as ecosystems …

Genomics Education highlighted at 14th Annual International Meeting on Microbial Genomics

Just got back from the 14th Annual International Meeting on Microbial Genomics, where I gave talk on microbial symbiont genomics. This was one of the best meetings I have been to in a while. It had the right combination of everything including:

  1. Many excellent talks and posters (OK, in the interest of not upsetting people for not saying their talk or poster was great, I will not make a big list of all the ones I thought were good, but I will give a few highlights below).
  2. Excellent location (UCLAs Lake Arrowhead Conference Center, which is in the mountains east of Los Angeles). This is a place that is very conducive to getting to know colleagues and it almost forces interaction among people. There is one central building where there is a dining hall, a nice deck if you want to eat outside, the conference room, rooms for posters, and a large living room for hanging out. The rooms for sleeping are mostly great (e.g., mine was a split level condo like structure with a living room and a bedroom/bath on floor one and a bedroom/bath on floor 2). And being in the mountains is very pleasant. Plus there is a pool, jacuzzi, and sports facilities that are very nice. The only annoying thing is that the Lake itself, which is 100 yards away, but it really almost private, with most of the shoreline occupied by houses and private docks.
  3. Good food. The food is not spectacular or anything but better than the food at 90% of the conferences I have been at.

In terms of talks, there were quite of few that were both interesting topics and very well presented. For example, Jessica Green from U. C. Merced gave a great talk about spatial distributions of microorganisms, Julian Parkhill from the Sanger Center put together a really nice story about mechanisms by which microbial pathogens generate phenotypic diversity, and Julie Huber from MBL impressed many with her talk about the “Deep Rare Biosphere.”

But to me, the best two talks were ones on science education reform by two people from UCLA. Erin Sanders-Lorenz presented a summary of her course she has been teaching at UCLA that has students doing “phylogenomic” analysis which takes them from isolating and culturing organisms from environmental samples to building evolutionary trees of genes isolated from these cultured species.. This seemed like a very creative, hand on, novel way to teach students the excitement of science and some things about evolution. It sounded so well thought out that I asked for (and got) a copy of her lab manual.

Much as I liked this class, the one described by Cheryl Kerfeld knocked my socks off. She described a program they have developed at UCLA called the Undergraduate Genomics Research Initiative. This is an interdepartmental multi-course collaboration with the central theme involving the sequencing and analysis of the genome of a bacterium called Ammonifex degensii. The various courses are organized around a central course on genome sequencing. The linked courses include ones in many different departments at UCLA as well as various courses at other universities. They have clearly given enormous thought to how to do a truly project based course which likely will catch students attention and interest much more than standard lectures or standard labs.

There have been other successful hands on genome sequencing courses before – perhaps the first being one by Brad Goodner at Hiram College who had students participate in the sequencing and analysis of the genome of Agrobacterium tumefaciens (e.g., see a press release here). The Kerfeld UCLA UGRI program sounds like it has gone to the next level by integrating many courses across departments and by having creative ways to encourage participation of students in multiple aspects of the project. It really is worth giving a look at the UCLA UGRI program’s web site.

Other tidbits about the meeting:

  • Jeffrey H. Miller from UCLA organized it
  • This is the same Jeffrey Miller who identified most of the mutator genes in E. coli with a really creative genetic screen
  • There was another Jeffrey Miller from UCLA at the meeting (will leave this up to google for people to figure out who this other Miller is).