Checking the First Data from OCO-2

On July 2, NASA successfully launched its first satellite dedicated to measuring carbon dioxide in Earth's atmosphere. The Orbiting Carbon Observatory-2 (OCO-2) mission—operated by NASA's Jet Propulsion Laboratory—will soon provide atmospheric carbon dioxide measurements from thousands of points all over the planet. Last week, the satellite reached its proper orbit—meaning that it is now beginning to return its first data to Earth.

Data from the satellite will be used to help researchers understand the anthropogenic and natural sources of CO2, and how changing levels of the greenhouse gas may affect Earth's climate. But before OCO-2 provides scientists with such a global picture of the carbon cycle—where carbon is being produced and absorbed on Earth—researchers have to convert raw satellite data into a CO2 reading and then, just as importantly, make sure that the reading is accurate. A team of Caltech researchers is playing an instrumental role in this effort.

As it orbits, OCO-2 provides data about levels of atmospheric CO2 by measuring the sunlight that reflects off Earth, below. "OCO-2 measures something that is related to the CO2 measurement we want but it's not directly what we want. So from the reflected light, we have to extract the information about CO2," says Yuk Yung, the Smits Family Professor of Planetary Science.

The process begins with the satellite's instrument, a set of high-resolution spectrometers that measure the intensity of sunlight at different wavelengths, or colors, after it has passed twice through the atmosphere—once from the sun to the surface, and then back from the surface to space. As the satellite orbits, systematically slicing over sections of Earth's atmosphere, it will collect millions of these measurements.

"OCO-2 will provide the measurements of this light at different wavelengths in millions of what we call spectra, but spectra aren't what we really want—what we really want is to know how much carbon dioxide is in the atmosphere," Yung says. "But to get the CO2 information from the spectra, we have to do what's called data retrieval—and that's one of my jobs."

The data retrieval method that Yung and his colleagues designed for OCO-2 compares the light spectra collected by the satellite to a model of how light spectra would look—based on the laws of physics and knowledge of how efficiently CO2 absorbs sunlight. This knowledge, in turn, is derived from laboratory measurements made by Caltech professor of chemical physics Mitchio Okumura and his colleagues at JPL and the National Institute of Standards and Technology.

"To make scientifically meaningful measurements, OCO-2 has to detect CO2 with better than 0.3 percent precision, and that has meant going back to the lab and measuring the spectral properties with extraordinarily high precision," Okumura says. From this retrieval, the researchers determine the amount of CO2 in the atmosphere above each of OCO-2's sampling points.

However, when OCO-2 sends its first CO2 measurements back to Earth for analysis, they'll still have to go through one more check, says Paul Wennberg, the R. Stanton Avery Professor of Atmospheric Chemistry and Environmental Science and Engineering.

"Although the OCO-2 retrieval will calculate the amount of carbon dioxide above the point where the spectrometers pointed, we know that these initial numbers will be wrong until the data are calibrated," Wennberg says. Wennberg and his team provide this calibration with their Total Carbon Column Observing Network (TCCON), a ground-based network of instruments that measure atmospheric CO2 from approximately 20 locations around the world.

TCCON and OCO-2 provide the same type of CO2 measurement—what is called a column average of CO2. This measurement provides the average abundance of CO2 in a column from the ground all the way up through Earth's atmosphere.

About once per day, the OCO-2 instrument will be commanded to point at one of TCCON's stations continuously as it passes overhead. By comparing the Earth-based and space-based measurements, researchers will evaluate the data that they receive from the satellite and improve the retrieval method.

The complete, high-quality information OCO-2 provides about global CO2 levels will be important for researchers and policymakers to determine how human activity influences the carbon cycle—and how these activities contribute to our changing planet.

"A lot of the very first satellites were developed to study astronomy and planets far away. But there has been a shift. Our changing climate means that we now have a big need to study Earth," and the information OCO-2 provides about our atmosphere will be an important part of filling that need, says Yung.

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Study of Aerosols Stands to Improve Climate Models

Aerosols, tiny particles in the atmosphere, play a significant role in Earth's climate, scattering and absorbing incoming sunlight and affecting the formation and properties of clouds. Currently, the effect that these aerosols have on clouds represents the largest uncertainty among all influences on climate change.

But now researchers from Caltech and the Jet Propulsion Laboratory have provided a global observational study of the effect that changes in aerosol levels have on low-level marine clouds—the clouds that have the largest impact on the amount of incoming sunlight that Earth reflects back into space. The findings appear in the advance online version of the journal Nature Geoscience.

Changes in aerosol levels have two main effects—they alter the amount of clouds in the atmosphere and they change the internal properties of those clouds. Using measurements from several of NASA's Earth-monitoring satellites from August 2006 through April 2011, the researchers quantified for the first time these two effects from 7.3 million individual data points.

"If you combine these two effects, you get an aerosol influence almost twice that estimated in the latest report from the Intergovernmental Panel on Climate Change," says John Seinfeld, the Louis E. Nohl Professor and professor of chemical engineering at Caltech. "These results offer unique guidance on how warm cloud processes should be incorporated in climate models with changing aerosol levels."

The lead author of the paper, "Satellite-based estimate of global aerosol-cloud radiative forcing by marine warm clouds," is Yi-Chun Chen (Ph.D. '13), a NASA postdoctoral fellow at JPL. Additional coauthors are Matthew W. Christensen of JPL and Colorado State University and Graeme L. Stephens, director of the Center for Climate Sciences at JPL. The work was supported by funding from NASA and the Office of Naval Research.

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Watching Nanoscale Fluids Flow

At the nanoscale, where objects are measured in billionths of meters and events transpire in trillionths of seconds, things do not always behave as our experiences with the macro-world might lead us to expect. Water, for example, seems to flow much faster within carbon nanotubes than classical physics says should be possible. Now imagine trying to capture movies of these almost imperceptibly small nanoscale movements.

Researchers at Caltech now have done just that by applying a new imaging technique called four-dimensional (4D) electron microscopy to the nanofluid dynamics problem. In a paper appearing in the June 27 issue of Science, Ahmed Zewail, the Linus Pauling Professor of Chemistry and professor of physics, and Ulrich Lorenz, a postdoctoral scholar in chemistry, describe how they visualized and monitored the flow of molten lead within a single zinc oxide nanotube in real time and space.

The 4D microscopy technique was developed in the Physical Biology Center for Ultrafast Science and Technology at Caltech, created and directed by Zewail to advance understanding of the fundamental physics of chemical and biological behavior. 

In 4D microscopy, a stream of ultra-fast-moving electrons bombards a sample in a carefully timed manner. Each electron scatters off the sample, producing a still image that represents a single moment, just a femtosecond—or a millionth of a billionth of a second—in duration. Millions of the still images can then be stitched together to produce a digital movie of nanoscale motion.

In the new work, Lorenz and Zewail used single laser pulses to melt the lead cores of individual zinc oxide nanotubes and then, using 4D microscopy, captured how the hot pressurized liquid moved within the tubes—sometimes splitting into multiple segments, producing tiny droplets on the outside of the tube, or causing the tubes to break. Lorenz and Zewail also measured the friction experienced by the liquid in the nanotube.

"These observations are particularly significant because visualizing the behavior of fluids at the nanoscale is essential to our understanding of how materials and biological channels effectively transport liquids," says Zewail. In 1999, Zewail won the Nobel Prize for his development of femtosecond chemistry.

The paper is titled "Observing liquid flow in nanotubes by 4D electron microscopy." The work was supported by the National Science Foundation, the Air Force Office of Scientific Research, and the Gordon and Betty Moore Foundation. Lorenz was partially supported by a fellowship from the Swiss National Science Foundation.

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Growing Unknown Microbes One by One

A new technique developed at Caltech helps grow individual species of the unknown microbes that live in the human body.

Trillions of bacteria live in and on the human body; a few species can make us sick, but many others keep us healthy by boosting digestion and preventing inflammation. Although there's plenty of evidence that these microbes play a collective role in human health, we still know very little about most of the individual bacterial species that make up these communities. Employing the use of a specially designed glass chip with tiny compartments, Caltech researchers now provide a way to target and grow specific microbes from the human gut—a key step in understanding which bacteria are helpful to human health and which are harmful.

The work was published the week of June 23 in the Proceedings of the National Academy of Sciences.

Although a few bacterial species are easy to grow in the laboratory, needing only a warm environment and plenty of food to multiply, most species that grow in and on the human body have never been successfully grown in lab conditions. It's difficult to recreate the complexity of the microbiome—the entire human microbial community—in one small plate (a lidded dish with nutrients used to grow microbes), says Rustem Ismagilov, Ethel Wilson Bowles and Robert Bowles Professor of Chemistry and Chemical Engineering at Caltech.

There are thousands of species of microbes in one sample from the human gut, Ismagilov says, "but when you grow them all together in the lab, the faster-growing bacteria will take over the plate and the slow-growing ones don't have a chance—leading to very little diversity in the grown sample." Finding slow-growing microbes of interest is like finding a needle in a haystack, he says, but his group wanted to work out a way to "just grow the needle without growing the hay."

To do this, Liang Ma, a postdoctoral scholar in Ismagilov's lab, developed a way to isolate and cultivate individual bacterial species of interest. He and his colleagues began by looking for bacterial species that contained a set of specific genetic sequences. The targeted gene sequences belong to organisms on the list of "Most Wanted" microbes—a list developed by the National Institutes of Health (NIH) Human Microbiome Project. The microbes carrying these genetic sequences are found abundantly in and on the human body, but have been difficult to grow in the lab.

To grow these elusive microbes, the Caltech researchers turned to SlipChip, a microfluidic device previously developed in Ismagilov's lab. SlipChip is made up of two glass slides, each the size of a credit card, that have tiny etched grooves which become channels when the grooved surfaces are stacked atop one another. When a sample—say, a jumbled-up assortment of bacteria species collected from a colonoscopy biopsy—is added to the interconnected channels of the SlipChip, a single "slip" of the top chip will turn the channels into individual wells, with each well ideally holding a single microbe. Once sequestered in an isolated well, each individual bacterium can divide and grow without having to compete for resources with other types of faster-growing microbes.

The researchers then needed to determine which compartment of the SlipChip contained a colony of the target bacterium—which is not a simple task, says Ismagilov. "It's a Catch-22—you have to kill the organism in order to find its DNA sequence and figure out what it is, but you want a live organism at the end of the day, so that you can grow and study this new microbe," he says. "Liang solves this in a really clever way; he grows a compartment full of his target microbe in the SlipChip, then he splits the compartment in half. One half contains the live organism and the other half is sacrificed for its DNA to confirm that the sequence is that of the target microbe."

The method of creating two halves in each well in the SlipChip will be published separately in an upcoming issue of the journal Integrative Biology.

To validate the new methodology, the researchers isolated one specific bacterium from the Human Microbiome Project's "Most Wanted" list. The investigators used the SlipChip to grow this bacterium in a tiny volume of the washing fluid that was used to collect the gut bacteria sample from a volunteer. Since bacteria often depend on nutrients and signals from the extracellular environment to support growth, the substances from this fluid were used to recreate this environment within the tiny SlipChip compartment—a key to successfully growing the difficult organism in the lab.

After growing a pure culture of the previously unidentified bacterium, Ismagilov and his colleagues obtained enough genetic material to sequence a high-quality draft genome of the organism. Although a genomic sequence of the new organism is a useful tool, further studies are needed to learn how this species of microbe is involved in human health, Ismagilov says.

In the future, the new SlipChip technique may be used to isolate additional previously uncultured microbes, allowing researchers to focus their efforts on important targets, such as those that may be relevant to energy applications and the production of probiotics. The technique, says Ismagilov, allows researchers to target specific microbes in a way that was not previously possible.

The paper is titled "Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa." In addition to Liang and Ismagilov, other coauthors include, from Caltech, associate scientist Mikhail A. Karymov, graduate student Jungwoo Kim, and postdoctoral scholar Roland Hatzenpichler, and, from the University of Chicago department of medicine, Nathanial Hubert, Ira M. Hanan, and Eugene B. Chang. The work was funded by NIH's National Human Genome Research Institute. Microfluidic technologies developed by Ismagilov's group have been licensed to Emerald BioStructures, RanDance Technologies, and SlipChip Corporation, of which Ismagilov is a cofounder.

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