Even in a calm, unchanging environment, cells are not static. Among other actions, cells activate and then deactivate some types of transcription factors—proteins that control the expression of genes—in a series of unpredictable and intermittent pulses. Since discovering this pulsing phenomenon, scientists have wondered what functions it could provide for cells.
Now, a new study from Caltech researchers shows that pulsing can allow two proteins to interact with each other in a rhythmic fashion that allows them to control genes. Specifically, when the expression of the transcription factors goes in and out of sync, gene expression also goes up and down. These rhythms of activation, the researchers say, may also underlie core processes in the cells of organisms from across the kingdoms of life.
"The way transcription factor pulses sync up with one another in time could play an important role in allowing cells to process information, communicate with other cells, and respond to stress," says paper coauthor Michael Elowitz, a professor of biology and biological engineering and an investigator with the Howard Hughes Medical Institute.
The research, led by Caltech postdoctoral scholar Yihan Lin, appears in the October 15 issue of Nature. Other Caltech authors of the paper are Assistant Professor of Chemistry Long Cai; Chang Ho Sohn, a staff scientist in the Cai lab; and Elowitz's former graduate student Chiraj K. Dalal (PhD '10), now at UC San Francisco.
Realizing that many different factors are pulsing in the same cell even in unchanging conditions, the Caltech scientists began to wonder if cells might adjust the relative timing of these pulses to enable a novel sort of time-based regulation. To find out, they set up time-lapse movies to follow two pulsing proteins and a target gene in real time in individual yeast cells.
A three color movie of cells in response to two different stresses (as indicated). Green color corresponds to Msn2 protein, red color corresponds to Mig1 protein, and blue color corresponds to a RNA binding protein that is used to report gene expression. The white circle highlights the cell of interest. (Credit: Michael Elowitz and Yihan Lin/Caltech)
The team tagged two central transcription factors named Msn2 and Mig1 with green and red fluorescent proteins, respectively. When the transcription factors are activated, they move into the nucleus, where they influence gene expression. This movement—as well as the activation of the factors—can be visualized because the fluorescent markers concentrate within the small volume of the nucleus, causing it to glow brightly, either green, red, or both. The color choice for the fluorescent tags was symbolic: Msn2 serves as an activator, and Mig1 as a repressor. "Msn2, the green factor, steps on the gas and turns up gene expression, while Mig1, the red factor, hits the brakes," says Elowitz.
When the scientists stressed the yeast cells by adding heat, for example, or restricting food, the pulses of Msn2 and Mig1 changed their timing with respect to one another, with more or less frequent periods of overlap between their pulses, depending upon the stressing stimulus.
Generally, when the two transcription factors pulsed in synchrony, the repressor blocked the ability of the activator to turn on genes. "It's like someone simultaneously pumping the gas and brake pedals in a car over and over again," says Elowitz.
But when they were off-beat, with the activator pulsing without the repressor, gene expression increased. "When the cell alternates between the brake and the gas—the Msn2 transcription factor in this case—the car can move," says Elowitz. As a result of these stress-altered rhythms, the cells successfully produced more (or fewer) copies of certain proteins that helped the yeast cope with the unpleasant situation.
Previously, researchers have thought that the relative concentrations of multiple transcription factors in the nucleus determine how they regulate a common gene target—a phenomenon known as combinatorial regulation. But the new study suggests that the relative timing of the pulses of transcription factors may be just as important as their concentration.
"Most genes in the cell are regulated by several transcription factors in a combinatorial fashion, as parts of a complex network," says Cai. "What we're now seeing is a new mode of regulation that controls the pulse timing of transcription factors, and this could be critical to understanding the combinatorial regulation in genetic networks."
"There appears to be a layer of time-based regulation in the cell that, because it can only be observed with movies of individual cells, is still largely unexplored," says Lin. "We look forward to learning more about this intriguing and underappreciated form of gene regulation."
In future research, the scientists will try to understand how prevalent this newfound mode of time-based regulation is in a variety of cell types and will examine its involvement in gene regulation systems. In the context of synthetic biology—the harnessing and modification of biological systems for human technological applications—the researchers also hope to develop methods to control such pulsing to program new cellular behaviors.
You walk by a bakery, smell the scent of fresh cookies, and are immediately reminded of baking with your grandmother as a child. The seemingly simple act of learning to associate a smell with a good or bad outcome is actually quite a complicated behavior—one that can begin as a single synapse, or junction, where a signal is passed between two neurons in the brain.
Assistant Professor of Neuroscience Betty Hong is interested in how animals sense cues in their environment, process that information in the brain, and then use that information to guide behaviors. To study the processing of information from synapse to behavior, her work focuses on olfaction—or chemical sensing via smell—in fruit flies.
Hong, who received her bachelor's degree from Caltech in 2002 and her doctorate from Harvard in 2009, came from a postdoctoral position at Harvard Medical School to join the Caltech faculty in June. We spoke with her recently about her work, her life outside the laboratory, and why she is looking forward to being back at Caltech.
How did you initially become interested in your field?
It's rather circuitous. I was initially drawn to neuroscience because I was interested in disease. I had family who passed away from Alzheimer's disease, and it's clear that with the current demographic of our country, diseases associated with aging—like Alzheimer's—are going to have a large impact on society in the next 20 to 30 years. Working at the Children's Hospital Boston in graduate school, I also became increasingly interested in understanding the rise of neurodevelopmental disorders like autism.
I really wanted to understand the mechanistic basis for neurological disease. And then it became clear to me that part of the problem of trying to understand neurological disorders was that we really had no idea how the brain is supposed to work. If you were a mechanic who didn't know how cars work, how could you fix a broken car? That led me to study increasingly more basic mechanisms of how the brain functions.
Why did you decide to focus your research on olfaction?
Although we humans have evolved to move away from olfaction—humans and primates are very visual—the whole rest of the animal kingdom relies on olfaction heavily for all of its daily survival and functions. Even the lowliest microbe relies on chemical sensing to navigate its way through the environment. We study olfaction in an invertebrate model—the fruit fly Drosophila. We do that for a couple of reasons. One is that it has a very small brain, and so its circuits are very compact, and that small size and numerical simplicity lets us get a global overview of what's happening—a view that you could never get if you're looking at a big circuit, like a mouse brain or a human brain.
The other reason is that there are versatile genetic tools and new technologies that have allowed us to make high-resolution electrical and optical recordings of neural activity in the brains of fruit flies. That very significant technical hurdle had to be crossed in order to make it a worthwhile experimental model. With electrophysiological access to the brain, and genetic tools that allow you to manipulate the circuits, you can watch brain activity as it's happening and ask what happens to neural activity when you tweak the properties of the system in specific ways. And the fly also has a robust and flexible set of behaviors that you can relate to all of this.
What are some of the behaviors that you are interested in studying?
We're very interested in understanding how flies can associate an odor with a pleasant or unpleasant outcome. So, in the same way that you might associate wonderful baking smells with something from your childhood, flies can learn to arbitrarily associate odors with different outcomes. And to know "when I smell this odor, I should run away," or "based on what happened to me the last time I smelled this odor, this might be an indicator of food"—that's actually a fairly sophisticated behavior that is a basic building block for more complex higher-order cognitive tasks that emerge in vertebrates.
There are many animals that are inflexibly wired. In other words, they smell something, and through evolution, their circuits have evolved to tell them to move toward it or go away from it. Even if they are in an unusual environment, they can't flexibly alter that behavior. The ability to flexibly adapt our behavior to new and unfamiliar environments was a key transition in the evolution of the nervous system.
You are also a Caltech alum. What drew you back as a faculty member?
Yes, it seems like such a long time ago, but I was an undergraduate here—a biology major in Page House—from 1998 to 2002. I was also a SURF student with [Professor of Biology] Bruce Hay and later with David Baltimore [president emeritus and Robert Andrews Millikan Professor of Biology]. It's kind of wild to have as your colleagues people who were your mentors a decade ago, but I think the main reason I chose Caltech was the community of scholars here—on the level of faculty, undergraduate students, graduate students, and postdocs—that I will be able to interact with. In the end, you mainly just want to be with smart, motivated people who want to use science to make a difference in the world. And I think that encapsulates what Caltech does.
Do you have any interests or hobbies that are outside of the lab?
I used to play horn in the wind ensemble and orchestra, including the time when I was here as an undergraduate. But these days, any time that I'm not in the office, I'm with my two young kids. Right now, we're really excited about exploring all the fun and exciting things to do outdoors in Southern California. We've done a lot of hiking and exploring the natural beauty here. The kids have gotten into fishing lately, so our latest thing has been scoping out the best places to fish. I would love to hear from members of the community what their favorite spots are!
On October 1, the National Institutes of Health (NIH) announced its second round of funding in furtherance of President Obama's Brain Research through Advancing Innovative Neurotechnology—or BRAIN—Initiative. The new awards totaled more than $38 million. Included among the 67 funded projects are two led by Caltech researchers.
"Development of a scalable methodology for imaging neuropeptide release in the brain" — U01-MH109147
David Anderson, Seymour Benzer Professor of Biology; Investigator, Howard Hughes Medical Institute
Anderson and his colleagues aim to develop and test a new technology for visualizing the release of neuropeptides from neurons. Neuropeptides are a class of signaling molecules that communicate information between neurons, called neuromodulators. Neuropeptides control fundamental behavioral processes like eating and mood. These chemical signals can fundamentally alter neural computations in brain circuits and have previously been difficult to study using existing methods.
Anderson also received an NIH BRAIN grant in 2014 for developing a detailed, publicly available database characterizing the genetic, physiological, and morphological features of the various cell types in the brain that are involved in circuits controlling sensations and emotions.
"Tracing brain circuits by transneuronal control of transcription" — R21-EY026432
Neurons in the brain are wired together like a complex electronic circuit, but it is unknown exactly what that circuit looks like. This project aims to utilize a new method to investigate the brain's wiring diagram. A new genetic system has been developed that will allow researchers to map the connections between neurons in the brain. Identifying how neurons in brain circuits are connected to one another is crucial to understanding how the brain processes information involved in perception, movement, or emotion. Recent research indicates that aberrant neuronal wiring may be the cause of several neurodevelopmental disorders, including autism and schizophrenia, further emphasizing the importance of identifying the wiring diagrams of brain circuits.
Lois also received an NIH BRAIN grant in 2014 to investigate the genetic mechanisms responsible for the evolution of the brain by comparing the genomic and biophysical properties of neurons across different mammalian species.
Arthur B. McDonald (PhD '70), director of the Sudbury Neutrino Observatory (SNO) in Ontario, Canada, and Takaaki Kajita, at the University of Tokyo, Kashiwa, Japan, have shared the 2015 Nobel Prize in Physics for the discovery that neutrinos can change their identities as they travel through space.
McDonald and Kajita lead two large research teams whose work has upended the standard model of particle physics and settled a debate that has raged since 1930, when the neutrino's existence was first proposed by physicist Wolfgang Pauli. Pauli initially devised the neutrino as a bookkeeping device—one to carry away surplus energy from nuclear reactions in stars and from radioactive decay processes on Earth. In order to make the math work, he gave it no charge, almost no mass, and only the weakest of interactions with ordinary matter. Billions of them are coursing through our bodies every second, and we are entirely unaware of them.
There are three types of neutrinos—electron, muon, and tau—and they were, for many years, assumed to be massless and immutable. The technology to detect electron neutrinos emerged in the 1950s, and it slowly became apparent that as few as one-third of the neutrinos the theorists said the sun should be emitting were actually being observed. Various theories were proposed to explain the deficit, including the possibility that the detectable electron neutrinos were somehow transmuting into their undetectable kin en route to Earth.
Solving the mystery of the missing neutrinos would require extremely large detectors in order to catch enough of the elusive particles to get accurate statistics. Such sensitive detectors also require enormous amounts of shielding to avoid false readings.
The University of Tokyo's Super-Kamiokande neutrino detector, which came online in 1996, was built 1,000 meters underground in a zinc mine. Its detector, which counts muon neutrinos and records their direction of travel, found fewer cosmic-ray neutrinos coming up through the Earth than from any other direction. Since they should not be affected in any way by traveling through the 12,742-kilometer diameter of our planet, Kajita and his colleagues concluded that the extra distance had given them a little extra time to change their identities.
McDonald's SNO, built 2,100 meters deep in a nickel mine, began taking data in 1999. It has two counting systems. One is exclusively sensitive to electron neutrinos, which are the type emitted by the sun; the other records all neutrinos but does not identify their types. The SNO also recorded only about one-third of the predicted number of solar electron-type neutrinos—but the aggregate of all three types measured by the other counting systems matched the theory.
The conclusion, for which McDonald and Kajita were awarded the Nobel Prize, was that neutrinos must have a nonzero mass. Quantum mechanics treats particles as waves, and the potentially differing masses associated with muons and taus gives them different wavelengths. The probability waves of the three particle types are aligned when the particle is formed, but as they propagate they get out of synch. Therefore, there is a one-third chance of seeing any particular neutrino in its electron form. Because these particles have this nonzero mass, their gravitational effects on the large-scale behavior of the universe must be taken into account—a profound implication for cosmology.
McDonald came to Caltech in 1965 to pursue a PhD in physics in the Kellogg Radiation Laboratory under the mentorship of the late Charles A. Barnes, professor of physics, emeritus, who passed away in August 2015. "Charlie Barnes was a great mentor who was very proud of his students," says Bradley W. Filippone, professor of physics and a postdoctoral researcher under Barnes. "It is a shame that Charlie didn't get to see Art receive this tremendous honor."
A native of Sydney, Canada, McDonald received his bachelor of science and master's degrees, both in physics, from Dalhousie University in Halifax, Nova Scotia, in 1964 and 1965, respectively. After receiving his doctorate, he worked for the Chalk River Laboratories in Ontario until 1982, when he became a professor of physics at Princeton University. He left Princeton in 1989 and became a professor at Queen's University in Kingston, Canada; the same year, he became the director of the SNO. In 2006, he became the holder of the Gordon and Patricia Gray Chair in Particle Astrophysics, a position he held until his retirement in 2013.
Among many other awards and honors, McDonald is a fellow of the American Physical Society, the Royal Society of Canada, and of Great Britain's Royal Society. He is the recipient of the Killam Prize in the Natural Sciences; the Henry Marshall Tory Medal from the Royal Society of Canada, its highest award for scientific achievement; and the European Physics Society HEP Division Giuseppe and Vanna Cocconi Prize for Particle Astrophysics.
To date, 34 Caltech alumni and faculty have won a total of 35 Nobel Prizes. Last year, alumnus Eric Betzig (BS '83) received the Nobel Prize in Chemistry.
Caltech biologists have developed a nonsurgical method to deliver long-term contraception to both male and female animals with a single shot. The technique—so far used only in mice—holds promise as an alternative to spaying and neutering feral animals.
The approach was developed in the lab of Bruce Hay, professor of biology and biological engineering at Caltech, and is described in the October 5 issue of Current Biology. The lead author on the paper is postdoctoral scholar Juan Li.
Hay's team was inspired by work conducted in recent years by David Baltimore and others showing that an adeno-associated virus (AAV)—a small, harmless virus that is unable to replicate on its own, that has been useful in gene-therapy trials—can be used to deliver sequences of DNA to muscle cells, causing them to produce specific antibodies that are known to fight infectious diseases, such as HIV, malaria, and hepatitis C.
Li and her colleagues thought the same approach could be used to produce infertility. They used an AAV to deliver a gene that directs muscle cells to produce an antibody that neutralizes gonadotropin-releasing hormone (GnRH) in mice. GnRH is what the researchers refer to as a "master regulator of reproduction" in vertebrates—it stimulates the release of two hormones from the pituitary that promote the formation of eggs, sperm, and sex steroids. Without it, an animal is rendered infertile.
In the past, other teams have tried neutralizing GnRH through vaccination. However, the loss of fertility that was seen in those cases was often temporary. In the new study, Hay and his colleagues saw that the mice—both male and female—were unable to conceive after about two months, and the majority remained infertile for the remainder of their lives.
"Inhibiting GnRH is an ideal way to inhibit fertility and behaviors caused by sex steroids, such as aggression and territoriality," says Hay. He notes that in the study, his team also shows that female mice can be rendered infertile using a different antibody that targets a binding site for sperm on the egg. "This target is ideal when you want to inhibit fertility but want to leave the individual otherwise completely normal in terms of reproductive behaviors and hormonal cycling."
Hay's team has dubbed the new approach "vectored contraception" and says that there are many other proteins that are thought to be important for reproduction that might also be targeted by this technique.
The researchers are particularly excited about the possibility of replacing spay–neuter programs with single injections. "Spaying and neutering of animals to control fertility, unwanted behavior, and population numbers of feral animals is costly and time consuming, and therefore often doesn't happen," says Hay. "There is a strong desire in many parts of the world for quick, nonsurgical approaches to inhibiting fertility. We think vectored contraception provides such an approach."
As a next step, Hay's team is working with Bill Swanson, director of animal research at the Cincinnati Zoo's Center for Conservation and Research of Endangered Wildlife, to try this approach in female domestic cats. Swanson's team spends much of its time working to promote fertility in endangered cat species, but it is also interested in developing humane ways of managing populations of feral domestic cats through inhibition of fertility, as these animals are often otherwise trapped and euthanized.
Additional Caltech authors on the paper, "Vectored antibody gene delivery mediates long-term contraception," are Alejandra I. Olvera, Annie Moradian, Michael J. Sweredoski, and Sonja Hess. Omar S. Akbari is also a coauthor on the paper and is now at UC Riverside. Some of the work was completed in the Proteome Exploration Laboratory at Caltech, which is supported by the Gordon and Betty Moore Foundation, the Beckman Institute, and the National Institutes of Health. Olvera was supported by a Gates Millennium Scholar Award.
Hong and colleagues aim to reveal neural mechanisms related to olfaction
Over the summer, Betty Hong, assistant professor of neuroscience, spent a week at the Janelia Research Campus in Ashburn, Virginia, interacting and brainstorming with other researchers from around the country interested in olfaction, our sense of smell. Invited to participate by the National Science Foundation (NSF), these 30 computational and experimental neuroscientists came up with innovative ways to approach some of the mysteries about how the brain processes odors and uses that information to guide behavior.
The five-day session was an example of the agency's new funding mechanism, the Ideas Lab. At these meetings, a multidisciplinary group of researchers is charged with generating potentially transformative proposals on a focused research topic. Now the NSF has awarded $15 million to three projects from the Olfactory Ideas Lab. Hong is coprincipal investigator on one titled "Using natural odor stimuli to crack the olfactory code." The awards expand NSF's investments in President Obama's BRAIN Initiative.
"I am grateful to have had the opportunity to be thrown together for a week with such a smart, diverse group of scientists who approach olfaction from so many different angles," says Hong (BS '02), adding that without the Ideas Lab, it is unlikely that she would have ever established collaborations with her coinvestigators. "I am also extremely grateful to the NSF for including junior investigators like myself who are just kicking off their research program. This unique funding mechanism will enable us to tackle really challenging and innovative research right at the start of our careers."
Olfactory scientists typically use simple synthetic odors involving single molecules for their experiments because natural odors—those that we smell around us every day—are too difficult to reproduce in a reliable way under controlled conditions. However, those simplified stimuli may not trigger the full range of neural computations that constitute olfaction.
Therefore, Hong and her colleagues aim to use comprehensive chemical analysis and computational methods to construct reproducible synthetic odorants in the lab that mimic naturally occurring smells in terms of eliciting typical behavioral responses in honey bees, fruit flies, and fly larvae. (Hong specializes in studies of the fruit fly Drosophila.) These synthetic odor blends can then be used to investigate how the brain processes smells and orders specific adaptive behaviors.
"We believe probing the olfactory circuit with naturalistic stimuli will reveal long-hidden computational features of the circuit," Hong explains. "Much as higher-order visual neurons only respond to complex stimuli like faces or hands, and not to simple bars and dots, we hypothesize that naturalistic odor stimuli will reveal novel features of odor space that the olfactory system encodes, which may only become apparent once appropriate sets of stimuli are used."
Along with Hong, additional principal investigators on the project are Brian Smith of Arizona State University; Aravinthan Samuel of Harvard University; and Tatyana Sharpee of the Salk Institute for Biological Studies. The project will receive $3.6 million over three years.