CAICE IMPACTS 2014

DNA in the Clouds

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.

JMM blog pic[5]
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

CAICE IMPACTS 2014

Approaching the Finish Line…

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

CAICE IMPACTS 2014

Collaboration and teamwork are a key to great discoveries

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.

image001
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

CAICE IMPACTS 2014

Anotha day, anotha dot

Hello from the UCSD Hydraulics lab! The current time is 00:15, and I’m still a good 2 hours from my pillow. My task between now and zzz’s? Figure out how many ice nucleating particles are in the wave flume.

I am a fourth year graduate student in the Department of Atmospheric Science at Colorado State University. I work with Dr. Sonia Kreidenweis, Dr. Paul DeMott, Dr. Tom Hill and several others on ice nucleation. We are in La Jolla with IMPACTS because we want to know more about sea spray ice nucleating particles.

What is an ice nucleating particle (INP)? Well, tiny pure water freezes at -40 C. But, we know that ice crystals exist in clouds at much warmer temperatures than -40C. This is because some (ice nucleating) particles serve as catalysts for ice crystal formation. I am here to operate the continuous flow diffusion chamber (CFDC), which counts the number of INP at a range of temperatures (-32C to -15C). We are also working with several other groups on collecting the INP for post analysis that will look at the chemical composition and shapes of the sea spray INP. We are hoping that by measuring INP through the duration of the phytoplankton bloom, we can observe links between sea spray INP (abundance, chemical and physical characteristics) and changes in the sea surface microlayer (see Josh’s post) and bulk water bacteria and phytoplankton counts.

A challenge of this measurement is INP exist in small numbers in the atmosphere. So, we use an aerosol concentrator, which enhances the number of particles that go into the CFDC and therefore we have a better chance of seeing an INP. It’s a very loud process, it’s like a giant vacuum, and takes all the flow from the system…. Hence the late night shift.

Some of us late nighters have started a saying when we leave the lab at 2 am… “Anotha day, anotha dot.” We do a lot of work everyday for what really may be just a “dot” on a graph showing a timeline or a correlation. But, with a month long study and enough dots, we are hopeful that all the dots will tell a story and lead to some interesting discoveries.

Christina McCluskey, PhD candidate, Department of Atmospheric Science, Colorado State University

CAICE IMPACTS 2014

CAICE Enriches and Challenges Intellectual Capacity

Growing up in a developing country, Rwanda, located in East Africa, who would have thought we could be part of this huge and positively worldwide contributing project?

Authors Grace de Dieu Irumva and Hosiana Abewe with UCSD Chancellor Pradeep Khosla in front of the wave flume

Thanks to CAICE, for opening the doors and providing us the opportunity to profoundly learn about the impact of sea spray aerosols on the climate and environment.

As determined undergraduates, we were intellectually challenged by the change in climate and environment. We longed to know and understand different perspectives and hypotheses on this global issue. One of the hypotheses was to detect if different primary biological seawater particles, such as bacteria, have an impact in chemical and biological composition of the sea spray aerosols released from seawater.

IMG_0606[7]
The authors preparing substrates for MOUDI ( MicroOrifice Uniform Deposit Impactor), an off-site apparatus that collects the aerosols particles on different stages for further microscopical analysis.

To test the above-mentioned hypothesis, different experiments have been designed: two different bacteria strains are pre-cultured on separate medium, thereafter transferred into flasks containing filtered- autoclaved seawater and allowed to grow under the same environmental conditions.

In the meantime, aerosols are collected through bubbling and ultimately analyzed by different analytical instruments, including ATOFMS and WIBS. From these analyses, the data collected will help us detect the chemical and biological composition of the aerosols released, respectively.

Thus far, we have been learning from prestigious scientist researchers, while enriching and challenging both our intellectual and professional capacity. We are certain that this project will nourish and aspire us further to tackle the global environmental problems.

 

Hosiana Abewe and Grace De Dieu Irumva, undergraduate students, Prather Group, Department of Chemistry and Biochemistry.

CAICE IMPACTS 2014

Another world record…?

image001
Jon Trueblood, University of Iowa graduate student, working with one of the MOUDI impactors

I arrived here in San Diego on July 15, 2014 just in time to see everything working!!! This includes phytoplankton blooms occurring in multiple MART systems and of course the 33 m wave flume. I am so impressed with the students and postdocs who were able to get this first time every experiment going – the largest indoor phytoplankton bloom – a world record.   I see many happy (and some tired) faces. What is clear is that everyone is now excited as we are starting to collect very significant data and many new chemistry findings are starting to be realized. These studies will focus on the molecular speciation and chemical complexity of the sea surface microlayer and of sea spray aerosol. A number of off-line and on-line analyses will be done to determine what molecular species are present in order to better understand the transfer of molecules from sea water, and the sea surface microlayer, into sea spray aerosol. This will give us more detailed information on the chemistry of sea spray aerosol. For off-line analysis of sea spray aerosol, a wide range of substrates are being used to collect particles for single particle analysis using a MOUDI impactor to get size resolved composition. Overall, CAICE investigators aim to analyze the chemical composition, structure, phase, hygroscopicity, and reactive properties of as many particles as possible. By the end of the experiment it is estimated that nearly one billion sea spray aerosol particles will be collected. That is right – one billion particles!!! (Another world record???) I can’t wait to see what we learn from these samples in the next few months.

In addition to the great science we continue to give tours to everyone who wants to see what we are doing. Saturday morning a group of high school and undergraduate students came by to view the wave flume here in the hydraulics lab at SIO. It was fun to see how they were excited to see the experiment and to talk to them about it. We discussed the importance of chemistry and the molecular fundamental knowledge needed to understand sea spray aerosol. We then all went out to the pier to see where the sea water came from and to take look at the other experiments there. We also enjoyed the beautiful view – what a great way to spend a Saturday morning!

 

Vicki Grassian, F. Wendell Miller Professor of Chemistry at the University of Iowa and CAICE, Co-Director

image003image004

CAICE IMPACTS 2014

CAICE IMPACTS a UCSD Undergrad

After finishing my second year of undergrad at UCSD, I am thrilled to already be a part of the CAICE IMPACTS experiments. My interests revolve around understanding the surface chemistry of seawater and its impact on the selective transfer of species from the bulk seawater to the surface seawater and ultimately to the sea spray aerosols during the phytoplankton bloom in the wave-flume.

A Tensiometer measuring the surface tension of surface seawater via a Platinum plate
A Tensiometer measuring the surface tension of surface seawater via a Platinum plate

To get a sense of the changes occurring in the surface of the seawater, I have been measuring the surface tension in the sea-surface microlayer (upper most millimeter of the surface) and the bulk seawater (the water beneath the surface) using a tensiometer shown in the image on the right. Surface tension can be thought of as the force that causes a liquid’s surface to pull closely together for minimal surface area, and the tensiometer uses a platinum plate to measure the force the liquid exerts on it. I am looking for changes in the surface tension day-by-day in the wave-flume as the phytoplankton bloom progresses to see how this surface property changes and how it impacts the chemical properties of the surface water and sea spray aerosols.

image003
A preliminary infrared spectrum of dehydrated bulk seawater

To determine the changing chemical and biological composition of bulk seawater, sea-surface microlayer, and sea spray aerosols, I am using infrared (IR) spectroscopy, which essentially uses light in the infrared region to cause molecules to vibrate. These vibrations can be seen as peaks in the IR spectrum shown on the right, and each peak corresponds to a certain chemical group. It should be interesting to see if changes in functional groups are apparent to better understand the transfer of molecules from the surface of the ocean to sea spray aerosols.

While learning all of the chemistry behind CAICE is exciting, the true nature of its impact on my undergrad experience comes from the diversity and perseverance of everyone I have met. From biologists to oceanographers, I am so grateful to be around this atmosphere of scientists coming together to work on the impact sea spray aerosols have on our climate and environment. I have met numerous PIs, postdocs, and grad students, and they have all given me insight into what I want to do in the future. I want to continue to explore and help determine the true impact the changing environment has on our lives and how we can all make the effort to improve our understanding of the world’s scientific complexity.

Joshua L. Cox, Undergraduate Researcher, Prather Group, Dept. of Chemistry and Biochemistry, UCSD

CAICE IMPACTS 2014

How science gets done

A lack of sleep, lots of laughs, and a room full of loud pumps: how science gets done!

What a whirlwind the past few weeks have been! It’s hard to believe that we are already about halfway through IMPACTS (Investigation into Marine Particle Chemistry and Transfer Science), the Center for Aerosol Impacts on Climate and the Environment (CAICE) summer 2014 intensive campaign. The hydraulics lab at Scripps Institution of Oceanography has been overtaken by students, postdocs, and instrumentation (and TONS of noisy pumps!) in hopes of measuring changes in various chemical and physical properties of sea spray aerosol over the course of a phytoplankton bloom and understanding how these changes may influence the climate and environment.

I am a grad student, just starting my 3rd year at UC San Diego in Timothy Bertram’s research group. Most of the researchers here are interested in measuring sea spray aerosols; however, particles are not the only interesting component generated and released from the ocean surface.

IMG_0077
The author, Nicole Campbell, poses with the CITOFMS, which measures trace marine gases

The ocean also emits various gas-phase species; the specific trace gases that are produced can change as a function of the biological conditions present at the sea surface. Once introduced to the atmosphere, gas-phase molecules can undergo interesting chemistry; some gases can even serve as precursors for new aerosol particle formation! I am operating a piece of instrumentation to measure these trace marine gases, a chemical ionization time of flight mass spectrometer (the CITOFMS), which allows for real-time, simultaneous detection of gas-phase molecules in a specific mass range of interest.

This is my first field study, and it has definitely been an eye-opening experience, filled with the full spectrum of emotions. I have learned SO much during the past few weeks, not only about science, but also about teamwork and collaboration. This experiment has been a huge undertaking for everybody involved and has definitely tested the patience of many, but I can honestly say that I couldn’t have asked for a better group of people to spend a month of 15+ hour workdays with. The creativity, dedication, positivity (most of the time…don’t get me wrong, there have been some challenging moments for sure!), and excitement of the grad students, postdocs, professors, facility staff, and visitors is incredible and has made this such a fun and exciting environment to work in. I can’t wait to see what we learn and the story that unfolds in the coming months!

Nicole R. Campbell, graduate student, Bertram Group at UC San Diego, Department of Chemistry and Biochemistry

CAICE IMPACTS 2014

CAICE IMPACTS 2014

I have the privilege of writing the very first blog for our major 2014 NSF Center for Aerosol Impacts on Climate and the Environment (CAICE) summer intensive named IMPACTS (Investigation into Marine PArticle Chemistry and Transfer Science). Things have been incredibly busy with many people working long days (phytoplankton don’t sleep!). We are now at the mid-point in the study. We have about 40 students, ranging from high school through graduate school, and postdoctoral fellows working on this project. They came from many places with their unique instrumentation to work with us at UCSD/SIO including U. of Iowa, U. of Wisconsin, Colorado State University, UC Davis, UC Berkeley, Colby College, and Rwanda via Cal Baptist College. It is an exciting but very challenging experiment where we are setting out to produce the world’s largest indoor phytoplankton bloom in 3000 gallons of seawater in a 33 m wave flume equipped with real breaking waves. Phytoplankton are tiny microscopic plants (just think of the ocean as an underwater forest) that fix carbon from the atmosphere and produce almost 50% of the oxygen we breathe.  Chlorophyll is an indicator of the quantity of phytoplankton that is present. When a bloom occurs, scientists can watch chlorophyll change from space using satellite imagery.

image001
Red tide phytoplankton bloom off the Scripps Pier at UC San Diego

The image on the left shows what a phytoplankton bloom (called a red tide) looks like off the Scripps Institution of Oceanography pier. When these blooms occur, they can cover large regions of the ocean and dramatically change ocean chemistry. The ultimate goal of our study is to investigate the transfer of chemical and biological species from seawater into sea spray aerosols and measure how this chemistry evolves over the course of a phytoplankton bloom. Over the past 2 years, we have found we can reproducibly induce phytoplankton blooms in much smaller tanks. It turns out it is much more challenging in a wave flume! This is due to the fact that the tank is filled with a myriad of species (bacteria, phytoplankton, viruses) all competing for nutrients (i.e. food) we initially put in the tank. Another major challenge is the large “grazers” that are like little Pacmen that go around and consume the phytoplankton before they can grow into a bloom. Once we get a bloom and sea spray is emitted, we measure the ability of the particles to undergo chemical reactions, induce ice cloud formation, form cloud droplets, as well as interact with sunlight. The grand challenge involves understanding how the chemical complexity of the seawater changes and how this impacts climate and reactivity properties of the sea spray. The premise for CAICE is to perform the next generation of lab studies where we learn about the real world by bringing its true complexity into the lab where we can control many of the parameters at a level that cannot be done in the field. I believe this has to be one of the most challenging experiments ever done in a laboratory setting due to how difficult it is to rely on the complexity of biological processes to naturally evolve under lab conditions (less light, changing temperatures, etc.)….the good news is I think we have finally done it!

IMPACTS-2014: graph showing growth of phytoplankton over time as indicated by chlorophyll-a concentrations in CAICE ocean-atmosphere wave flume in July 2014. This represents the world's largest indoor ocean phytoplankton bloom in natural seawater equipped with breaking waves
IMPACTS-2014: graph showing growth of phytoplankton over time as indicated by chlorophyll-a concentrations in CAICE ocean-atmosphere wave flume in July 2014. This represents the world’s largest indoor ocean phytoplankton bloom in natural seawater equipped with breaking waves

After waiting nervously for almost 2 weeks of “background” measurements, the bloom started taking off on July 10 and it has been growing since then. We know this by monitoring chlorophyll levels which have been increasing over time. We are all very excited that we are finally getting to measure what we set out to measure. That is not always the case in complex “field studies” and certainly not the case just because this one is in the lab. Now chemists are positioned to directly measure the chemical composition and physical properties of complex sea spray aerosol in ways that have never been done before. This was made possible by a devoted team that has been brought together through CAICE. Finally on a personal note, I will say that the last month has been one of the most challenging ones I have faced as a professor; yet, it has been the most rewarding research experience I have ever been involved in. I have so enjoyed the day-to-day interactions with this team of young scientists and getting the opportunity to work in the trenches with them to help make a difficult experiment take off. Their drive and positive can-do attitudes make it clear to me that the next generation of scientists is well equipped to tackle the complex environmental problems that we will be facing. In subsequent blogs, you will get to hear from other CAICE scientists about their experiences and measurements and how they are trying to address the questions above. I hope you enjoy following the CAICE IMPACTS-2014 blog over the next couple of weeks.

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

CAICE Intensive 2011

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

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)