DNA in the Clouds

25 07 2014

As a third year graduate student in a biochemistry lab, I don’t often get experiences like this. A giant wave-generating tank is novel to me and quite a bit different than the pipet-land I usually live in. Walking into the transformed hydraulics lab always leaves an impression on me. The facility has come alive. It is crammed full with buzzing whirring equipment, and buzzing, whirring people. Scientists and students from all over the country all pointed at a common goal. Every time I walk in there, I step back and really understand what I am a part of. I’m proud. This experience hasn’t always been easy, but it has been rewarding. Certainly, the unwavering dedication of everyone down at the waveflume day to day is truly inspiring.

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Author Jennifer Michaud in the lab extracting DNA


I am not the only biochemist/biologist involved in IMPACT, but definitely my work stands apart from what others are doing. The name of my game is DNA. My efforts are to collect cells from the waveflume and extract their DNA, which will then be used to identify all the species present.   I would like to characterize not only what microbes are there, but also how they change across a bloom and relate to a natural ocean phytoplankton bloom. More specifically, I am interested to learn which species transfer from bulk to the sea surface to aerosols (airborne particles) and how this changes in conjunction with the growth of phytoplankton and correspondingly bacteria. My highest hope is that certain phenomenon, like ice nuclei, particle types, and interesting organic molecules, might be able to be connected to the predominance of a species or group at the time of their occurrence.

To do this I collect water samples. Harvesting cells is done by vacuum filtration under sterile conditions serially with different sized filters to fractionate the samples into phytoplankton, bacteria, and viruses and vesicles. The major hurdle to my sampling is having enough. Cells are not overly abundant in the marine environment and many liters of water are generally required for DNA analysis. Here we are trying to optimize our methods so that that we get as much DNA from minimal sample amounts so that other analyses are not disrupted. Additionally, sampling cells from aerosols poses its separate challenges. We are using a SpinCon PAS 450-10A Wet Cyclone Portable Air Samplers (Sceptor Industries, Kansas City, MO) to concentrate cells in the aerosols. This instrument has previously been used to sample air above a NY city high-rise and other sites for microbes. The instrument pumps aerosols into a glass chamber containing buffer creating a vortex in which cells are trapped which then are collected by our standard methods. DNA is isolated using an optimized phenol chloroform extraction. Then our precious samples will be sent away for sequencing to identify species.

Yesterday was big sample collection day for me. Lots of filtration. Today, I am extracting DNA from the aerosol samples. I hope they have lots!

Jennifer Michaud, Graduate Student, Burkart Group, Department of Chemistry and Biochemistry, UC San Diego





Approaching the Finish Line…

25 07 2014

Although it was a ton of hard work, I have enjoyed being part of the CAICE (Center for Aerosol Impacts on Climate and the Environment) IMPACTS (Investigation into Marine Particle Chemistry and Transfer Science) 2014 intensive. Professors and students from all over the country are gathered here to better understand the link between ocean biology and the composition and physical properties of particles emitted from sea spray.

10457561_692410517491553_292097329586178028_n[2]I am a 3rd year graduate student in Chris Cappa’s group at UC Davis. I came to UC San Diego to investigate how much these particles grow as a result of humidification using a cavity ring-down spectrometer (CRD). The larger these particles grow, the more light they scatter. By scattering solar radiation, these particles cool the planet and are therefore important for understanding the Earth’s climate. Particles emitted from sea spray take up a lot of water because they are mostly composed of salt. However, the biology of the ocean impacts what these particles are made of and, by making the particle less “salty,” can decrease the how much water they take up.

The "beach" area of the wave flume in the Hydraulic Lab at SIO

The “beach” area of the wave flume in the Hydraulic Lab at SIO

My goal is to quantify how changes in particle composition due to biological processes in seawater influence how much these particles grow due to humidification.
During this unique, once-in-a-lifetime experiment, everyone I have worked with has been incredibly positive and fun to be around. At the end of IMPACTS, I will leave with both exciting data and many new friends.

 

Sara Forestieri, Graduate Student, Cappa Group, Department of Civil and Environmental Engineering at UC Davis





Collaboration and teamwork are a key to great discoveries

23 07 2014

Dozens of instruments from many universities, this is what it takes to do real science! Nowadays, great discoveries are not possible within one laboratory working in isolation. Collaborations of research teams that have various techniques, approaches, and backgrounds from multiple scientific disciplines are necessary for innovations and advances. This summer professors, graduate and undergraduate students from all over the country came to Scripps Institution of Oceanography at University of California, San Diego to participate in 2014 NSF Center for Aerosol Impacts on Climate and the Environment (CAICE) IMPACTS (Investigation into Marine PArticle Chemistry and Transfer Science) campaign.

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The author, Olga, and her group mate Jon preparing for particle collection on MOUDI


I came from the University of Iowa where I just started my fifth year of graduate school in Dr. Vicki Grassian research group. My area of interest is phase, composition and hygroscopicity of individual sea spray aerosol particles. We collect particles generated during wave breaking and then take them back to Iowa for detailed micro-structural analysis with a variety of microscopic and spectroscopic techniques. Atomic force microscopy is a tool to image the surface of particles at the nanoscale and it is exceptionally noteworthy that it can reveal 3D shape of particles. Scanning electron microscopy and transmission electron microscopy can image particles down to 1 nm resolution and when used with energy-dispersive X-ray spectroscopy can reveal spatial elemental composition of particles. Raman microspectroscopy gives information about vibrations of functional groups thus revealing chemical composition of particles as small as several hundred nanometers. Elemental and molecular composition derived from these techniques can be combined with on-line measurements such as aerosol time-of-flight mass spectrometry to get the most complete information about particles’ composition. All microscopy techniques can be performed in chambers where relative humidity is be controlled and size of particles is monitored using microscope. Therefore, we can detect how particles grow in humid environment. Raman microspectrometer can detect the water in particles spectroscopically and thus can be additionally used to monitor water content of particles as relative humidity changes. It is very important to know how particles interact with water as it determines how particles will interact with light, form clouds and react with trace gases in the atmosphere (which can be fairly humid). Finally, as we learn about the dependence of particles’ properties on their detailed chemical composition we can understand and more importantly predict their properties in the environment better!

As I have already mentioned collaboration is a key for breakthrough research discoveries. Collaboration and teamwork! This picture illustrates teamwork in action where Jon and Olga (author) are putting together stages to collect sea spray aerosol particles. This is a great campaign that unites many research groups and I look forward to analyzing our particles and working with other participating groups to shade more light on marine atmosphere.

Olga Laskina, Research Assistant, Grassian Research Group, Department of Chemistry at University of Iowa





Just the beginning in our quest to understand complex chemistry impacts on climate……

24 11 2011

As I sit here on Thanksgiving morning thinking of all I am thankful for, I think of many things but the CAICE intensive, just completed a little more than one week ago, keeps springing to mind.  We ran a few days longer than we expected, but on November 15, we officially stopped sampling with all instruments.

Due to the dedication of the team of scientists involved in this project, we took full advantage of the suite of measurements to run experiments 24/7 for the final 10 days.  In the final 5 days, thanks to input (and samples) from our biology colleagues, we ran a complete mesocosm experiment, studying how a mixture of bacteria, viruses, and other ocean critters affect the chemistry of the seawater and in turn, these changes affect the chemistry of sea spray.  Our experiments went from “simple” filtered seawater to single “critter” additions covering a range of properties to the full complexity of a real mesocosm bloom. We did all that we set out to do and more with many exciting surprises along the way.  I will say that the one thing that sticks out in my mind is how much easier it is to see instantaneous changes and make sense of the chemical complexity when you know for a fact you are looking at one source, in this case, sea spray.  This study has already helped our group explain critical observations we have seen countless times in field studies but never been able to explain.  It reinforces exactly why we moved the real world to the lab to perform complex chemistry experiments.  I think

Chemical complexity...the soup of bacteria, viruses, protozoa, organics, salts...formed some very interesting aerosols...

we will be able to clearly show how this represents a new approach for  “integrating reductionist and complexity approaches to solve complicated problems”, one of the grand NSF challenges we set out to address.

Everyone is recovering now, but feeling extremely rewarded by all we have accomplished as a collective group.  The fruits of all of our labor will become evident in the coming weeks and months, as we merge all we have found into one set of stories.  I want to personally thank everyone who has been involved in this study, Hlab staff, grad, undergrad, postdocs, faculty, and advisors, for your dedication to this CAICE project.

It has been a wonderful experience, one of the best of my 20 year career, working with everyone involved and I look forward to digging more deeply into the results together.  Today, I am thankful for all we were able to accomplish together–but I can’t help feeling that this is just the beginning of a long and productive scientific journey….

Here’s to hoping everyone has a wonderful Thanksgiving…

Kimberly A. Prather, Director of CAICE (http://caice.ucsd.edu)