Tuesday, December 2, 2014
Guggenheim 101 (Lees-Kubota Lecture Hall)

PUSD: Annual Open Enrollment

New Center Supports Data-Driven Research

With the advanced capabilities of today's computer technologies, researchers can now collect vast amounts of information with unprecedented speed. However, gathering information is only one half of a scientific discovery, as the data also need to be analyzed and interpreted. A new center on campus aims to hasten such data-driven discoveries by making expertise and advanced computational tools available to Caltech researchers in many disciplines within the sciences and the humanities.

The new Center for Data-Driven Discovery (CD3), which became operational this fall, is a hub for researchers to apply advanced data exploration and analysis tools to their work in fields such as biology, environmental science, physics, astronomy, chemistry, engineering, and the humanities.

The Caltech center will also complement the resources available at JPL's Center for Data Science and Technology, says director of CD3 and professor of astronomy George Djorgovski.

"Bringing together the research, technical expertise, and respective disciplines of the two centers to form this joint initiative creates a wonderful synergy that will allow us opportunities to explore and innovate new capabilities in data-driven science for many of our sponsors," adds Daniel Crichton, director of the Center for Data Science and Technology at JPL.

At the core of the Caltech center are staff members who specialize in both computational methodology and various domains of science, such as biology, chemistry, and physics. Faculty-led research groups from each of Caltech's six divisions and JPL will be able to collaborate with center staff to find new ways to get the most from their research data. Resources at CD3 will range from data storage and cataloguing that meet the highest "housekeeping" standards, to custom data-analysis methods that combine statistics with machine learning—the development of algorithms that can "learn" from data. The staff will also help develop new research projects that could benefit from large amounts of existing data.

"The volume, quality, and complexity of data are growing such that the tools that we used to use—on our desktops or even on serious computing machines—10 years ago are no longer adequate. These are not problems that can be solved by just buying a bigger computer or better software; we need to actually invent new methods that allow us to make discoveries from these data sets," says Djorgovski.

Rather than turning to off-the-shelf data-analysis methods, Caltech researchers can now collaborate with CD3 staff to develop new customized computational methods and tools that are specialized for their unique goals. For example, astronomers like Djorgovski can use data-driven computing in the development of new ways to quickly scan large digital sky surveys for rare or interesting targets, such as distant quasars or new kinds of supernova explosions—targets that can be examined more closely with telescopes, such as those at the W. M. Keck Observatory, he says.

Mary Kennedy, the Allen and Lenabelle Davis Professor of Biology and a coleader of CD3, says that the center will serve as a bridge between the laboratory-science and computer-science communities at Caltech. In addition to matching up Caltech faculty members with the expertise they will need to analyze their data, the center will also minimize the gap between those communities by providing educational opportunities for undergraduate and graduate students.

"Scientific development has moved so quickly that the education of most experimental scientists has not included the techniques one needs to synthesize or mine large data sets efficiently," Kennedy says. "Another way to say this is that 'domain' sciences—biology, engineering, astronomy, geology, chemistry, sociology, etc.—have developed in isolation from theoretical computer science and mathematics aimed at analysis of high-dimensional data. The goal of the new center is to provide a link between the two."

Work in Kennedy's laboratory focuses on understanding what takes place at the molecular level in the brain when neuronal synapses are altered to store information during learning. She says that methods and tools developed at the new center will assist her group in creating computer simulations that can help them understand how synapses are regulated by enzymes during learning.

"The ability to simulate molecular mechanisms in detail and then test predictions of the simulations with experiments will revolutionize our understanding of highly interconnected control mechanisms in cells," she says. "To some, this seems like science fiction, but it won't stay fictional for long. Caltech needs to lead in these endeavors."

Assistant Professor of Biology Mitchell Guttman says that the center will also be an asset to groups like his that are trying to make sense out of big sets of genomic data. "Biology is becoming a big-data science—genome sequences are available at an unprecedented pace. Whereas it took more than $1 billion to sequence the first genome, it now costs less than $1,000," he says. "Making sense of all this data is a challenge, but it is the future of biomedical research."

In his own work, Guttman studies the genetic code of lncRNAs, a new class of gene that he discovered, largely through computational methods like those available at the new center. "I am excited about the new CD3 center because it represents an opportunity to leverage the best ideas and approaches across disciplines to solve a major challenge in our own research," he says.

But the most valuable findings from the center could be those that stem not from a single project, but from the multidisciplinary collaborations that CD3 will enable, Djorgovski says. "To me, the most interesting outcome is to have successful methodology transfers between different fields—for example, to see if a solution developed in astronomy can be used in biology," he says.

In fact, one such crossover method has already been identified, says Matthew Graham, a computational scientist at the center. "One of the challenges in data-rich science is dealing with very heterogeneous data—data of different types from different instruments," says Graham. "Using the experience and the methods we developed in astronomy for the Virtual Observatory, I worked with biologists to develop a smart data-management system for a collection of expression and gene-integration data for genetic lines in zebrafish. We are now starting a project along similar methodology transfer lines with Professor Barbara Wold's group on RNA genomics."

And, through the discovery of more tools and methods like these, "the center could really develop new projects that bridge the boundaries between different traditional fields through new collaborations," Djorgovski says.

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Caltech and City of Hope Formalize Collaboration

Caltech and City of Hope have signed a memorandum of understanding, formalizing a relationship that encourages researchers from the two institutions to collaborate and share resources in the interest of furthering both basic scientific research and translational projects—those with a medical application.

"Bringing together Caltech and City of Hope researchers will surely result in transformative science and hopefully also new approaches to medical care," says Jacqueline K. Barton, the Arthur and Marian Hanisch Memorial Professor of Chemistry and chair of the Division of Chemistry and Chemical Engineering at Caltech.

"The complementary nature of this partnership is a natural fit between our two institutions," says David Horne, vice provost and associate director of the Beckman Research Institute at City of Hope. "The translational opportunities in therapeutics and devices have never been greater, and this partnership comes at an opportune time to advance health care in oncology, diabetes, and HIV, which are City of Hope's major focus areas."

As a result of the new agreement, City of Hope researchers will have access to several unique Caltech facilities, including the Molecular Observatory, an X-ray crystallography resource with an automated beamline at the Stanford Synchrotron Radiation Laboratory; the Center for Catalysis and Chemical Synthesis, a synthetic-chemistry center that offers robotic instrumentation for high-throughput screening and analysis of chemical entities; and the Center for the Chemistry of Cellular Signaling, which analyzes the systems of molecules that dictate how cells behave and react to their surroundings.

Likewise, Caltech scientists and engineers will be able to access City of Hope's array of core research services, including resources such as the Pathology Core, a facility that provides access to preserved tumors and normal tissues; the Analytical Pharmacology Core Facility, which conducts pharmacokinetic and pharmacodynamic studies for chemotherapy clinical trials and peer-reviewed preclinical studies; the Animal Tumor Model Core, which creates various cancer models in mice for testing novel experimental therapies; and the Translational Research Laboratory, which helps with the design of clinical trials and basic research studies using samples from clinical trials.

"This is a very timely event, and I see it as building a bridge between Caltech and City of Hope that is natural both in proximity and in the way we complement each other," says Peter Dervan, Caltech's Bren Professor of Chemistry. "Caltech has always been very strong in basic fundamental research. But today, Caltech scientists and engineers are genuinely interested in taking the discoveries that we make in chemistry, biochemistry, biology, and bioengineering to real-world practical applications. City of Hope is a renowned medical research center that is only 20 minutes away and can work with us collaboratively on these translational problems. This is going to be a win-win partnership."

The memorandum establishes the Arthur D. Riggs Distinguished Lectureship series, which will bring scientists from across the country to speak at Caltech and City of Hope on current projects in basic research as well as on efforts to predict, prevent, diagnose, treat, and cure such diseases as cancer, diabetes, and HIV.

The first lecture in that series will be delivered on Wednesday, November 19, by a distinguished molecular biologist who knows both Caltech and City of Hope well: Riggs himself. Riggs completed his doctoral work in biochemistry at Caltech in 1966; at City of Hope, he is now a professor of cancer biology and chair of the Department of Diabetes and Metabolic Diseases Research as well as director emeritus of the Beckman Research Institute at City of Hope.

"We are really excited that Art has agreed to be the kickoff lecturer," says Dervan. "By sharing interest in the lectures, researchers at Caltech and City of Hope will share ideas, and I think at the end of the day we're going to be sharing students—postdoctoral coworkers and graduate students—on collaborative projects."

Riggs's lecture, " Reflections on a Career of Collaboration, Mostly with Caltech," will begin at 4 p.m. in Gates Annex 22 at Caltech and is open to the public.

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Kimm Fesenmaier
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Wednesday, October 29, 2014
Center for Student Services 360 (Workshop Space)

Meet the Outreach Guys: James & Julius

Figuring Out How We Get the Nitrogen We Need

Caltech Chemists Image Nitrogenase's Active Site At Work

Nitrogen is an essential component of all living systems, playing important roles in everything from proteins and nucleic acids to vitamins. It is the most abundant element in Earth's atmosphere and is literally all around us, but in its gaseous state, N2,, it is inert and useless to most organisms. Something has to convert, or "fix," that nitrogen into a metabolically usable form, such as ammonia. Until about 100 years ago when an industrial-scale technique called the Haber-Bosch process was developed, bacteria were almost wholly responsible for all nitrogen fixation on Earth (lightning and volcanoes fix a small amount of nitrogen). Bacteria accomplish this important chemical conversion using an enzyme called nitrogenase.

"For decades, we have been trying to understand how nitrogenase can interact with this inert gas and carry out this transformation," says Doug Rees, Caltech's Roscoe Gilkey Dickinson Professor of Chemistry and an investigator with the Howard Hughes Medical Institute (HHMI). To fix nitrogen in the laboratory, the Haber-Bosch process requires extremely high temperatures and pressures, yet bacteria are able to complete the conversion under physiological conditions. "We'd love to understand how they do this," he says. "It's a great chemical mystery."

But cracking that mystery has proven extremely difficult using standard chemical techniques. We know that the enzyme is made up of two proteins, the molybdenum iron (MoFe-) protein and the iron (Fe-) protein, which are both required for nitrogen fixation. We also know that the MoFe-protein consists of two metal centers and that one of those is the FeMo-cofactor (also known as  "the cofactor") at the active site, where the nitrogen binds and the chemical transformation takes place.

In 1992, Rees and his graduate student, Jongsun Kim (PhD '93), were the first to determine the structure of the MoFe-protein using X-ray crystallography.

"I think that there was a feeling that once you solved the structure, you'd understand how it worked," Rees says. "What we can say 22 years later is that was certainly not the case."

The dream would be to have atmospheric nitrogen bind to the FeMo-cofactor and to stop time so that chemists could sneak a peak at the chemical structure of the protein at that intermediate point. Since it is not possible to freeze time and because the reaction proceeds too quickly to study by standard crystallographic methods, researchers have come up with an alternative. Chemists have been trying to get carbon monoxide, an inhibitor that halts the enzyme's activity but also closely mimics the structure and electronic makeup of N2, to bind to the cofactor and to then crystallize the product relatively quickly so that the structure can be analyzed using X-ray crystallography.

Unfortunately, the cofactor has stubbornly refused to cooperate. "We've demonstrated more times than we'd like that the form of this protein as isolated doesn't bind substrates," explains Rees. "Usually if you want to know how something binds to a protein, you just add it to your protein and study the crystal structure with X-ray crystallography. But we just couldn't get anything bound to this cofactor."

But in order for the cofactor to exist in a form that would bind to a substrate or an inhibitor, several other conditions must be met—for example, the Fe-protein has to be there. In addition, ATP—a molecule that provides energy for many life processes—must be present, along with yet another enzyme system that regenerates the ATP consumed in the reaction and a source of electrons. So although the aim in crystallography is typically to isolate a purified protein, the chemists had to muddy their samples by adding all these other needed components.

After joining Rees's group as a postdoctoral scholar in 2012, Thomas Spatzal spent months working on this problem, tweaking the method he used for trying to get the carbon monoxide to bind to the cofactor and for crystallizing the product. He adjusted parameters such as the protein concentrations, the temperature under which the samples were prepared, and the amount of time he allowed for the crystals to form. Every week, he sent a new set of crystals, frozen with liquid nitrogen, to be analyzed on an X-ray beamline at the Stanford Synchrotron Radiation Lightsource (SSRL) constructed as part of Caltech's Molecular Observatory with support from the Gordon and Betty Moore Foundation. And every week he worked up the data that came back and looked to see if any of the carbon monoxide bound to the active site.

"People have been seeing the resting state of the active site, where nothing was bound, for years," Spatzal says. "It's always the same thing. It never looks any different."

But on a recent Friday morning, Spatzal processed the latest batch of data, and lo and behold, he finally saw what he had been looking for.

"There was a moment where I looked at it and said, 'Hold on. Something looks different there,'" says Spatzal. "I wondered, 'Am I crazy?' You just don't expect it at first."

What he saw was a first—a crystal structure revealing carbon monoxide bound to the FeMo-cofactor. Spatzal, Rees, and their colleagues describe that structure and their methodology in the September 26 issue of the journal Science.

Spatzal figured out a way to optimize the crystallization process by using tiny crystal seeds to accelerate the rate of crystal growth and conducting all manipulations in the presence of carbon monoxide, allowing him to grow nice crystals of the MoFe-protein and then to see where the carbon monoxide was bound to the cofactor.

What he found was surprising. The carbon monoxide took the place of one of the sulfur atoms in the cofactor's original structure, bridging two of its iron atoms. Many people had expected that the carbon monoxide would bind differently, so that it would stick out, adding extra density to the structure. But because it displaced the sulfur, the cofactor only took on a slightly different arrangement of atoms.

In addition, Spatzal showed that when the carbon monoxide is removed, the sulfur can reattach, reactivating the cofactor so that it can once again fix nitrogen.

"As astonishing as this structure was—that the carbon monoxide replaced the sulfur—I think it's even more astonishing that Thomas was able to establish that the cofactor could be reactivated," Rees says. "I don't think anyone had imagined that you would get this sort of rearrangement of the cofactor as part of the interaction."

"You could imagine that if you put an inhibitor on a system, it could damage the metal center and inactivate the protein so that it would no longer do its job. The fact that we can get it back into an active state means that it's not permanently damaged, and that has physiological meaning in terms of how nitrogen fixation occurs in nature," says Spatzal.

The researchers note that this result would still be a long way off without the X-ray crystallography resources of Caltech's Molecular Observatory, which has abundant dedicated time on a beamline at SSRL. "We were really fortunate that the Moore Foundation funded this access to the beamline," says Rees. "That was really essential for this project because it took a lot of optimization to work everything out. We were able to keep regularly sending samples and right away get feedback about how things were working. It's an unbelievable resource."

Additional Caltech authors on the paper, "Ligand binding to the FeMo-cofactor: Structures of CO-bound and reactivated nitrogenase," are Kathryn A. Perez, a graduate student, and James Howard, a visiting associate who is also affiliated with the University of Minnesota and where Rees was a postdoc. Oliver Einsle of the Institut fur Biochemie in Freiburg, Germany, and the Albert-Ludwigs-Universität Freiburg, was a postdoc with Rees as well as Spatzal's thesis advisor and is a coauthor on the paper. Spatzal is an associate with HHMI.

This work was supported by grants from the National Institutes of Health, Deutsche Forschungsgemeinschaft, and the European Research Council N-ABLE project. The Molecular Observatory is supported by the Gordon and Betty Moore Foundation, the Beckman Institute, and the Sanofi-Aventis Bioengineering Research Program at Caltech. Microbiology research at Caltech is supported by the Center for Environmental Microbial Interactions

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Kimm Fesenmaier
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Stoltz Wins Synthetic Chemistry Award

Professor of Chemistry Brian Stoltz has been named the winner of the 2015 Mukaiyama Award from the Society of Synthetic Organic Chemistry, Japan. He was noted for "the discovery and development of new reactions and processes for the synthesis of natural products and non-naturally occurring bioactive structures," according to the award citation.

Stoltz's work is aimed at developing new strategies for creating complex molecules with interesting structural, biological, and physical properties. The goal is to use these complex molecules to guide the development of new reaction methodology to extend fundamental knowledge and to potentially lead to useful biological and medical applications.

The Mukaiyama Award, named in honor of Japanese synthetic chemist Teruaki Mukaiyama, comes with a $5,000 award, a medallion, and a certificate. It is given to an individual 45 years old or younger who has made outstanding contributions to synthetic organic chemistry. Each year, two winners are selected, one each from Japanese and non-Japanese nominees. Also being honored this year is Professor Shigehiro Yamaguchi of Nagoya University.

 

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Wednesday, October 29, 2014
Avery Courtyard

Fall Family Festival

Friday, October 17, 2014
Center for Student Services 360 (Workshop Space)

TA Training: fall make-up session

Alumnus Eric Betzig Wins 2014 Nobel Prize in Chemistry

Eric Betzig (BS '83), a group leader at the Howard Hughes Medical Institute's Janelia Farm Research Campus in Ashburn, Virginia, has been awarded the 2014 Nobel Prize in Chemistry along with Stefan W. Hell of the Max Planck Institute for Biophysical Chemistry and William E. Moerner of Stanford University. The three were honored "for the development of super-resolved fluorescence microscopy," a method that allows for the creation of "super-images" with a resolution on the order of nanometers, or billionths of a meter. In essence, the work turns microscopy into "nanoscopy."

The technique developed by the trio overcomes the so-called Abbe diffraction limit, which describes a physical restriction on the sizes of the structures that can be resolved using optical microscopy, showing that, essentially, nothing smaller than one-half the wavelength of light, or about 0.2 microns, can be discerned by these scopes. The result of the Abbe limit is that only the larger structures within cells—organelles like mitochondria, for example—can be resolved and studied with regular microscopes but not individual proteins or even viruses. The restriction is akin to being able to observe the buildings that make up a city but not the city's inhabitants and their activities.

Betzig, building on earlier work by Hell and Moerner, found that it was possible to work around the Abbe limit to create very-high-resolution images of a sample, such as a developing embryo, by using fluorescent proteins that glow when illuminated with a weak pulse of light. Each time the sample is illuminated, a different, sparsely distributed subpopulation of fluorescent proteins will light up and, because the glowing molecules are spaced farther apart than the Abbe diffraction limit, a standard microscope would be able to capture them. Still, each of the images produced in this way has relatively low resolution—that is, they are blurry. Betzig, however realized that by superimposing many such images, he would be able to obtain a sharp super-image, in which nanoscale structures are clearly visible. The new technique was first described in a 2006 paper published in the journal Science.

After Caltech, Betzig, a physics major from Ruddock House, earned an MS (1985) and a PhD (1988) from Cornell University. He worked at AT&T Bell Laboratories until 1994, when he stepped away from academia and science to work for his father's machine tool company. Betzig returned to research in 2002 and joined Janelia in 2005.

To date, 33 Caltech alumni and faculty have won a total of 34 Nobel Prizes. Last year, alumnus Martin Karplus (PhD '54) also received the Chemistry Prize. 

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Kathy Svitil
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Orchestrating the Healing Process in a Damaged Cornea

It is safe to say that the eye is an amazing biological system. One reason is its keratocyte cells—specialized cells that make up the bulk of the cornea. Unlike most of the other cells in our body, those in the cornea are transparent, making sight possible. Should something happen to make the cornea opaque, blindness results.

Sadly, injuries to the cornea do occur, sometimes in the simplest of ways, such as getting sand in one's eyes and scratching the cornea. The scar tissue that then grows to heal the cornea may have the unwanted side effect of being opaque. This does not happen, however, if the cornea and the tissue around it heal in a very orderly fashion. The question, then: Is it possible to encourage this orderly healing after an injury, thus preserving vision?

Professor of Chemical Engineering Julia Kornfield and graduate student Amy Fu are very much hoping that this is the case. To find out, they have assigned a few students, including Caltech senior and recent SURF fellow Jacqueline Masehi-Lano, to experiment with various growth factors that might inhibit the formation of scar tissue and promote orderly wound healing.

"We chose three growth factors to test because Amy Fu and I read several papers on growth factors that have been able to suppress some types of scar tissue," Masehi-Lano says. "In particular, we want to inhibit the formation of alpha smooth muscle actin, the type of stress fiber that creates opaque scars over corneal wounds. So far, the experiments I've done with cell cultures have worked pretty well, so it looks promising."

Eventually, the researchers hope to encapsulate the growth factors in a hydrogel that is reminiscent of the native cornea. "Our hydrogel starts out as a liquid and gels in situ on the eye," explains Masehi-Lano.

Masehi-Lano is enthusiastic about her experience with the SURF program. This past summer was her second in Kornfield's lab, and last year she was a recipient of an Amgen scholarship. "I'm really grateful that my mentor and my co-mentor have entrusted me with my own project and have allowed me to conduct my own experiments. And since it was my second summer in this lab, I was able to take up a leadership role by training a new SURF student," she says. "For me, SURF has gone beyond research. I've been able to improve my ability to present my research to the general public, which I think is extremely important." Indeed, Masehi-Lano was awarded the Caltech Doris S. Perpall SURF Speaking Competition for delivering the most outstanding oral research presentation.

Masehi-Lano plans to continue in bioengineering and is contemplating an MD/PhD program. "I've always been interested in the medical field, and though I'm committed to doing research," she explains, "I'd like to be able to do clinical trials and directly apply new medical technologies to people."

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