Monthly Archives: August 2012

Orchid Symbioses Symposium and Workshop, Spring 2013

Those that know me know that I’ve got a thing for orchids.  From my point of view, what’s not to like: they have exceptionally diverse morphology, have complicated natural histories, have equally diverse interactions with pollinating insects, and – most important for me – are obligate mycorrhizal formers with a wide array of fungal symbionts.  I’m quite surprised we don’t have more scientists studying them.

orchid symbioses header

The journal New Phytologist has already sponsored 30 symposia on plant biology – the 31st symposium has been announced and will be focused on orchids and their interactions with mycorrhizal fungi and insects.  The goal of this meeting will be to bring together scientists studying orchids and advance the study of orchids and their symbiotic fungi and co-evolved insects.  As someone who has attended in the past, I cannot place enough emphasis on how rewarding these New Phytologist symposia have been to me.  There is plenty of time to register and apply for a travel grant.

orchid workshop header

This particular symposium will be held in conjunction with the 5th International Orchid Workshop this upcoming spring.  Both meetings will be held back to back at very close locales in Italy.

My Philosophy On Attending Scientific Meetings

I enjoy going to academic meetings and very frequently post information about upcoming meetings and symposia.  Some people have recently asked me why I put so much emphasis on meeting information on the blog and others have asked how I decide which meetings to attend, including this recent comment.  I go to meetings for many reasons – some of which I will cover here – but, specifically for me, the main reason I go to meetings is to interact with other scientists in my discipline.

I believe going to scientific meetings is a vital part of mastering how to communicate your research.  The types of communication you have the opportunity to master can range from giving an oral presentation to hundreds (or perhaps thousands!) of other scientists to speaking with someone for 30 seconds in an elevator.  Academic meetings give you an opportunity to master your communication skills.

MSA 2011 presentations

Meetings are also great places to learn about the cutting edge of your research area.  Often scientists will present their most recent findings prior to publication.  You might be able to learn about new technologies or novel ways to analyze data before you read about them in publications.  Often during the question and answer portion of talks, theories and controversial topics are discussed, with a debate in real time.  I tend to return from meetings mentally energized with lots of new ideas to investigate and think about.

Meetings are great places to network and meet people in your research area.  It’s easier to strike up a conversation or collaboration via email if you’ve met someone in person at a meeting.  Also, if you are in academia, the people you speak with at meetings will likely be the ones who are reading your grant proposals and reviewing your manuscripts.  Future job contacts and impromptu pre-interviews happen at meetings.  Most importantly, there’s the added bonus of developing friendships with your fellow scientists.

Lastly, I enjoy traveling, so going to academic meetings is a way for me to mix business with pleasure, so to speak.  I’ve gotten to see some truly beautiful places under the auspices of attending scientific meetings.

rhodes_at_dawn

If you are a student or a post-doc – or have been asked to present a talk – there may often be registration discounts for meetings and symposia.  You may be able to get a discount if you volunteer to help out at the registration desk or other planned events.  You might also be asked to provide financial need.  You should check with the meeting organizers as soon after the meeting is announced for these types of discounts.

When it comes to choosing a meeting to attend, I personally prefer smaller more intimate meetings, with a range of participants in the hundreds, and not in the thousands like you tend to find at large meetings.  Large meetings can be valuable, but I personally find that it’s more difficult to attend all the talks you want to and to locate the people you want to speak with.  I will often speak to people who have attended specific meetings in the past and ask them about their experiences in order to gauge if a meeting will be a valuable one to attend.

Before going to a conference, I usually get an idea of which talks I would like to see and who I would like to speak with at the meeting.  This can happen before I leave for a meeting if the conference booklet is posted online, but it typically happens right after I arrive at the registration desk.  Some people prepare by bringing business cards, and although I haven’t used business cards, this could help people remember you after the meeting.  You also want to prepare your “talk” – whether it’s for a speaking presentation, a poster presentation, or just speaking in the hallways or at a dinner of the meeting – you should be able to communicate your research clearly in many different formats.

During the meeting, I have different strategies depending on the meeting size and the types of talks.  I try to pick the talks that are most relevant to my interests, but sometimes this leaves me running between sessions.  This can be a great time to “bump” into someone you want to speak with, but you may also miss important talks this way too.  Sometimes, particularly at the end of meetings when my mind is overwhelmed, I sit through entire sessions just to see if there is something interesting in a disparate research area that can be applied to my research.  I’ve gotten some great ideas listening to talks I thought would not be pertinent to my research.  I take notes and make sure to write down literature to look up and read when I get home from the meeting.

After the meeting is over it’s important to follow up with those you have started collaborations with and those whose research papers you want to read.  If you’ve taken notes, review them and think about posting them to a public forum, like a blog, so that others can share in on your meeting experience.

Adding Dropbox To Remote Machines At The Command Line

When I was recently at Titus Brown’s Next-Generation Sequencing and Data Analysis Workshop we were using remote computers at the command line for our workshop exercises.  In the workshop we used Dropbox to transfer files from one computer to another.  I had no idea that I could easily install and utilize Dropbox at the command line on remote machines.  I’ve reproduced the tutorial from the workshop here with some minor changes of my own.

Knowing how connect Dropbox to remote machines has saved me some time transferring files and it’s been extremely helpful on many different levels.  I can quickly pipe or send output text or images right to numerous shared devices.  I can check on the progression of a pipeline running on a remote server with my mobile phone by looking at output images or files (or even quickly checking file sizes).  Visualization at the command line is non-existant, so if I want to see an output figure, I can look at data output graphs quickly from Dropbox, and, if I choose to do so, can put images in a shared folder for a colleague to inspect in a matter of seconds.  Before you use Dropbox at the command line, you’ll have to set up a Dropbox account.

To link Dropbox at the command line on your home computer or, perhaps more importantly, on a remote machine, you should start at the location where you want to put your Dropbox folder, such as your home directory on your machine.

$ cd

Next, you’ll want to download Dropbox (here, for Linux-based machines):

$ wget -O dropbox.tar.gz "http://www.dropbox.com/download/?plat=lnx.x86_64"

…and extract the zipped file:

$ tar -xvzf dropbox.tar.gz

Next, you should run the dropboxd program:

$ ~/.dropbox-dist/dropboxd &

After running the program, you should see a message like this:

$ This client is not linked to any account... Please visit https://www.dropbox.com/cli_link?host_id=XXXXX to link this machine.

You will next want to copy and paste that URL into your Web browser.  While in your browser log into dropbox.  BAM!  The folder ~/Dropbox is now linked to your home directory!

By accessing Dropbox in your browser you can modify which computers will be linked to your Dropbox account by accessing the “My Computers” tab in Account Settings option.

I prefer to use Dropbox and most of my colleagues do too, but I’m sure you can do this with other file sharing platforms such as Google Drive or SugarSync.

Seasonal Trends In Bryophyte-Associated Fungal Communities

I recently returned from the Mycological Society of America annual meeting – this year held at Yale University in New Haven.  There were lots of great talks about fungal genomics, systematics, and ecology – and it’s always good to see old mycological friends and make new ones.

Håvard Kauserud of The University of Oslo, who spoke about recent research from his laboratory, gave one of my favorite talks of the meeting.  His talk took place during a very rewarding afternoon session on fungal ecology.  Already highly prolific, there’s been an increase in the flood of papers to come out of the Kauserud lab over the last year.  Just this month, there’s a nice commentary on the phenomenon of metagenomic tag switching during amplicon sequencing published in the journal Fungal Ecology.

Another paper published this month in the journal New Phytologist is the study “Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing”, authored by Davey et al., a group of researchers both members and affiliates of the Kauserud laboratory, and it is this paper I will address here.

Davey et al 2012 header

Bryophytes represent a portion of the dominant vegetation in boreal forests, but very little is understood about the taxonomy, seasonality, or biomass of the fungi associated with them.  Additionally, microbes associated with mosses may be responsible for nitrogen fixation and nutrient immobilization as epiphytes or on forest soils.  A previous study from the Kauserud lab reported high levels of fungal biomass and active plant cell wall degrading enzymes identified from moss-associated fungi.

Figure One

As I have mentioned here numerous times, fungi are notoriously hard to identify by cultural and morphological means and are extremely diverse.  To understand this diversity, the authors performed 454 pyrosequencing of the ITS2 region of the ribosomal DNA operon for molecular taxonomic identification against a database of known fungal sequences.  This sequencing was done in concert with an ergosterol HPLC assay that is used to estimate living fungal biomass.

Figure Two

The authors identified a large numbers of fungi, some presumably moss associated, and the total amount of fungi recognized was comparable to that found in forest soils.  The majority of fungi were identified as Ascomycetes, which agrees with other studies investigating vascular plant phyllosphere communities using the primer pair ITS3 and ITS4.  Additionally, this study identified a consistent taxonomic profile as a previous study from the Kauserud laboratory using a cloning strategy and Sanger sequencing approach.  Not surprisingly, this study reports orders of magnitude more fungi but identified roughly the same groups of fungi (Helotiales, Chaetothyriales, Agaricales, and Tremellales).

Figure Three

The researchers addressed seasonal variation by sampling every eight weeks between April and January over the course of a year.  Quite interestingly, there is a strong consensus in this study with other research that provides evidence that fungi not only survive under snowpack, but also continue to grow during the winter months.  While the researchers found consistent trends with regard to season, there were fluctuations in fungal biomass when considering host bryophyte.  By using principle component analyses, the authors show that the fungal communities are structured mainly by host plant and secondarily by the type of bryophyte tissue that was sampled.  This paper is an important contribution to the growing literature that show that plant-associated fungi are extremely diverse, dynamic, and show complex relationships with host plants.