#Education Articles University

#Education Articles University

Technique identifies electricity-producing bacteria

Posted: 11 Jan 2019 11:00 AM PST

Living in extreme conditions requires creative adaptations. For certain species of bacteria that exist in oxygen-deprived environments, this means finding a way to breathe that doesn't involve oxygen. These hardy microbes, which can be found deep within mines, at the bottom of lakes, and even in the human gut, have evolved a unique form of breathing that involves excreting and pumping out electrons. In other words, these microbes can actually produce electricity.

Scientists and engineers are exploring ways to harness these microbial power plants to run fuel cells and purify sewage water, among other uses. But pinning down a microbe's electrical properties has been a challenge: The cells are much smaller than mammalian cells and extremely difficult to grow in laboratory conditions.

Now MIT engineers have developed a microfluidic technique that can quickly process small samples of bacteria and gauge a specific property that's highly correlated with bacteria's ability to produce electricity. They say that this property, known as polarizability, can be used to assess a bacteria's electrochemical activity in a safer, more efficient manner compared to current techniques.

"The vision is to pick out those strongest candidates to do the desirable tasks that humans want the cells to do," says Qianru Wang, a postdoc in MIT's Department of Mechanical Engineering.

"There is recent work suggesting there might be a much broader range of bacteria that have [electricity-producing] properties," adds Cullen Buie, associate professor of mechanical engineering at MIT. "Thus, a tool that allows you to probe those organisms could be much more important than we thought. It's not just a small handful of microbes that can do this."

Buie and Wang have published their results today in Science Advances.

Just between frogs

Bacteria that produce electricity do so by generating electrons within their cells, then transferring those electrons across their cell membranes via tiny channels formed by surface proteins, in a process known as extracellular electron transfer, or EET.

Existing techniques for probing bacteria's electrochemical activity involve growing large batches of cells and measuring the activity of EET proteins — a meticulous, time-consuming process. Other techniques require rupturing a cell in order to purify and probe the proteins. Buie looked for a faster, less destructive method to assess bacteria's electrical function.

For the past 10 years, his group has been building microfluidic chips etched with small channels, through which they flow microliter-samples of bacteria. Each channel is pinched in the middle to form an hourglass configuration. When a voltage is applied across a channel, the pinched section — about 100 times smaller than the rest of the channel — puts a squeeze on the electric field, making it 100 times stronger than the surrounding field. The gradient of the electric field creates a phenomenon known as dielectrophoresis, or a force that pushes the cell against its motion induced by the electric field. As a result, dielectrophoresis can repel a particle or stop it in its tracks at different applied voltages, depending on that particle's surface properties.

Researchers including Buie have used dielectrophoresis to quickly sort bacteria according to general properties, such as size and species. This time around, Buie wondered whether the technique could suss out bacteria's electrochemical activity — a far more subtle property.

"Basically, people were using dielectrophoresis to separate bacteria that were as different as, say, a frog from a bird, whereas we're trying to distinguish between frog siblings — tinier differences," Wang says.

An electric correlation

In their new study, the researchers used their microfluidic setup to compare various strains of bacteria, each with a different, known electrochemical activity. The strains included  a "wild-type" or natural strain of bacteria that actively produces electricity in microbial fuel cells, and several strains that the researchers had genetically engineered. In general, the team aimed to see whether there was a correlation between a bacteria's electrical ability and how it behaves in a microfluidic device under a dielectrophoretic force.

The team flowed very small, microliter samples of each bacterial strain through the hourglass-shaped microfluidic channel and slowly amped up the voltage across the channel, one volt per second, from 0 to 80 volts. Through an imaging technique known as particle image velocimetry, they observed that the resulting electric field propelled bacterial cells through the channel until they approached the pinched section, where the much stronger field acted to push back on the bacteria via dielectrophoresis and trap them in place.

Some bacteria were trapped at lower applied voltages, and others at higher voltages. Wang took note of the "trapping voltage" for each bacterial cell, measured their cell sizes,  and then used a computer simulation to calculate a cell's polarizability — how easy it is for a cell to form electric dipoles in response to an external electric field.  

From her calculations, Wang discovered that bacteria that were more electrochemically active tended to have a higher polarizability. She observed this correlation across all species of bacteria that the group tested.

"We have the necessary evidence to see that there's a strong correlation between polarizability and electrochemical activity," Wang says. "In fact, polarizability might be something we could use as a proxy to select microorganisms with high electrochemical activity."

Wang says that, at least for the strains they measured, researchers can gauge their electricity production by measuring their polarizability — something that the group can easily, efficiently, and nondestructively track using their microfluidic technique.

Collaborators on the team are currently using the method to test new strains of bacteria that have recently been identified as potential electricity producers.

"If the same trend of correlation stands for those newer strains, then this technique can have a broader application, in clean energy generation, bioremediation, and biofuels production," Wang says. 

This research was supported in part by the National Science Foundation, and the Institute for Collaborative Biotechnologies, through a grant from the U.S. Army.

Hair and identity

Posted: 11 Jan 2019 07:40 AM PST

Sefa Yakpo has always been interested in the question of the beauty standards that shape the lives of women of African descent. Growing up in Ghana, Yakpo recalls going with her mother every Sunday to the salon to watch her mother have her hair done. The posters and pictures in hair product commercials showed women and girls with straightened hair, hair that didn't resemble Yakpo's own.

Yakpo begged her mother to let her have her hair straightened. It seemed to her a coming-of-age rite. She wanted to have the sleek, shiny, hair of the girl on the box for the "Beautiful Beginnings" hair products. But in the intervening years, she has pondered whether such rejection of the natural texture and look of her hair was somehow an adaptation to "colonial" or "European" standards of beauty. Yakpo wondered whether her own complicated relationship to her hair might be a microcosm of the broader social and cultural questions facing African women.

A graduating senior majoring in French and management science, Yakpo decided to take up the challenge of doing a senior thesis in French, and to use this opportunity to explore the politics of beauty among Francophone African women. Working with her thesis advisor, Professor M. Amah Edoh, Yakpo decided to investigate criteria of beauty for Black Francophone African women now and in a historical perspective. What informs ideals of beauty? What kind of social, cultural, and economic factors lead to the situation that for women of African descent, a simple matter of hair styling becomes imbued with bigger issues?

Yakpo's research consisted in the analysis of two bodies of primary sources, AWA: la revue de la femme noire, a French-language independent magazine produced in Dakar, Senegal, by a network of African women between 1964 and 1973, and videos from a very popular YouTube channel on black hair created by a young Franco-Senegalese woman. To interpret the findings from her analysis of these primary sources, Yakpo delved into existing academic scholarship on the politics of black hair, drawing from the work of Cameroonian, French, and American scholars such as anthropologist Francis B. Nyamnjoh, sociologist Juliette Sméralda, and media studies scholar Dilip Gaonkar, among others. The resulting thesis, which was written entirely in French, weaved passages describing Sefa's personal relationship to and trajectory with her hair over the course of the year when she worked on the thesis, with discussion and analysis of her research data.

One book in particular had a lot of impact on Yakpo's thinking on her research subject: critical race and gender studies scholar Shirley Anne Tate's book, "Black Beauty: Aesthetics, Stylization, Politics." This book explores the multiple heterogeneous and complex ways in which black women negotiate their relation to social conventions of beauty, or black beauty. The book suggests that there isn't a "one-size-fits-all" approach to understanding how individual women navigate these questions. Yakpo was struck by the author's conclusion that a particular style of hair doesn't imbue the wearer with any inherent meanings. By virtue of being on a black body, any hair style is "black."

Yakpo concluded that meanings behind hair are flexible and reflect a mix of influences that change over time and geography. Africa's colonial past can't be ignored; certainly, for some women, straightening hair can be a conscious or unconscious rejection of their natural hair type. But today many young Francophone African women want the option to play with their hair styles and to alternate between hair textures. To say that there is only one acceptable hair style for women who are proud and self-loving steals their autonomy, Yakpo argues in her thesis.

At a well-attended meeting on Dec. 4, Yakpo presented her findings from her project, titled "Kinks and Identity: Unravelling Francophone African Women's Attitudes to and Perspectives on their hair" ["Cheveux crépus et identité: Démêler les attitudes des femmes d'origine africaine vis-à-vis de leurs cheveux"]. Edoh introduced the presentation by saying that we see in news and popular culture today how the black body, the female body, and the black female body in particular, are routinely politicized. She pointed to the media portrayal of U.S. former first lady, Michelle Obama, or in France, to that of the former Minister of Justice, Christiane Taubira, and the fact that both women's physical appearance has been the focus of political attacks. Indeed, the ways that Obama and her daughters wore their hair became a political issue during U.S. presidential elections, for instance. Yakpo's research on the ideals of beauty for black women, in relation to their hair particularly, Edoh said, thus speaks to a topic of both enduring concern and great political importance. Edoh remarked that with her thesis, Yakpo has realized educators' greatest wish for their students: that they leverage their academic work and their personal experience to mutually elucidate each other and the world around them.

Yakpo's other achievements during her undergraduate career at MIT include internships in France and Belgium, participating in the January Scholars in France IAP program, and winning second place in the 2017 Isabelle de Courtivron Writing Prize for creative or expository student writing about immigrant, diaspora, bicultural, bilingual and/or mixed-race experiences. She was also honored as a Burchard Scholar in 2017. Prior to coming to MIT, Yakpo was winner of the 2014 Math Olympiad in Ghana.

Tapping the MIT talent pool for the future of fusion

Posted: 11 Jan 2019 07:00 AM PST

MIT graduate student Caroline Sorensen is using her talent for mechanical engineering to help advance a novel project within the domain of applied science: the commercialization of fusion energy.

"There are a lot of cool things to be done from a technical perspective," she says. "Plus this work holds the possibility of making a huge impact on the world. This is exactly the kind of project that I came to MIT hoping to find."

Many of the researchers at MIT's Plasma Science and Fusion Center (PSFC) are plasma physicists and nuclear engineering researchers, she says, but not all. "There are a few of us from other areas who are jumping over here," says Sorensen, who earned a master's degree at MIT in a MechE lab but is based at the PSFC for doctorate work. "People are super excited about the future of fusion, and there is this vibe of positivity and hopefulness that what we're doing is really going to make a difference."

Fusion technology has long held the promise of producing safe, abundant, carbon-free electricity but a pivotal challenge exists: Researchers must create and harness fusion reactions to produce net energy gain. In order to fast track an innovative solution, MIT announced plans last March to work with a new private company, Commonwealth Fusion Systems (CFS), to carry out rapid, staged research leading to a new generation of fusion experiments and power plants based on advances in high-temperature superconductors.

The Italian energy company Eni, a founding member of the MIT Energy Initiative, invested $50 million in CFS, which is funding fusion research at MIT as part of a joint collaboration focused on rapidly commercializing fusion energy and establishing a new industry. Meanwhile Eni has also funded additional fusion research projects run out of PSFC's newly created Laboratory for Innovation in Fusion Technologies (LIFT). This is where Sorensen and colleagues are helping to perfect the design and economics of compact fusion power plants.

"There is the plasma physics and magnet technology side of things — but there are also engineering challenges where people like me can play an important role in making fusion plants significantly better in design. I see many exciting opportunities for collaboration," she says.

Engineering challenges

Sorensen is studying a key element of the fusion pilot plant: the liquid immersion blanket, essentially a flowing pool of molten salt that completely surrounds the fusion energy core. The purpose of this blanket is threefold: to convert the kinetic energy of fusion neutrons to heat for eventual electricity production; to produce tritium — a main component of the fusion fuel; and to prevent the neutrons from reaching other parts of the machine and causing material damage.

"I'm working on the blanket because for me that's where the rubber meets the road," says Sorensen. "We need to figure out this kind of technology in order to make fusion plants functional and economical." Researchers must be able to predict how the molten salt in such an immersion blanket would move when subjected to high magnetic fields such as those found within a fusion plant, she says.

The cutting-edge technology projects underway within LIFT are crucial, says Dennis Whyte, the director of PSFC and the Hitachi America Professor of Engineering at MIT. "We need to be working on a host of integrated technologies to actually make fusion economically viable. So that's what we're doing through LIFT. We are involving faculty from throughout Course 22 and from other departments within the School of Engineering and across the Institute."

Time is of the essence

Whyte described a growing fusion ecosystem in which researchers across disciplines — mechanical engineering, electrical engineering, aero-astro — are working together to achieve a mutual goal of fusion energy in time to make a difference. "This is exactly the kind of innovative research and development that we should be doing," he says.

Advances in high-temperature superconducting magnets that can access higher fields and smaller machines have enabled rapid cycles of learning and development — an approach embodied in the SPARC concept, which was developed at the PSFC and forms the foundation of CFS's aggressive effort to demonstrate energy-gain fusion by the mid-2020s and produce practical power plant designs by the early 2030s.

Martin Greenwald, deputy director of the PSFC and a veteran fusion researcher, says that if fusion is going to have an impact on climate change, time is of the essence. "One of the big advantages of working on this project at MIT is that we have all this potential energy to tap into — if we can get people across the Institute excited about having something really worthwhile to work on."

In a series of lightning talks seven experts will discuss the current "MIT Fusion Landscape" on Jan. 22 between 1 pm and 3 pm at 50 Vassar Street (MIT 34-101). Topics will range from engineering and scientific underpinnings to finance, entrepreneurship and social impact. People are welcome to attend to learn about MIT's smarter, sooner path to fusion energy.

Scope advance gives first look through all cortical layers of the awake brain

Posted: 11 Jan 2019 02:30 AM PST

Just like doctors seek to scan deeper into the body with sonograms, CT, and MRI, and astronomers seek to look farther out into the universe with space-based telescopes, adaptive optics, and different wavelengths of light, neuroscientists pursue new ways to watch brain cells at work deep inside the brain. Three-photon microscopy recently emerged to give them a deeper look at brain cells than ever before.

Now, based on a substantial refinement of the technology, scientists at MIT have conducted the first-ever study of stimulated neural activity in an awake mouse through every visual cortex layer and notably the mysterious subplate below.

"By optimizing the optical design and other features for parameters for making measurements in the live brain, we were able to actually make novel discoveries that were not possible before," says co-corresponding author Mriganka Sur, the Newton Professor of Neuroscience in the Picower Institute for Learning and Memory. The paper's co-lead authors are postdocs Murat Yildirim and Hiroki Sugihara. The other corresponding author is Peter So, professor of mechanical engineering and biological engineering.

"The concept has existed, but the question was how do you make it work," Sur says.

In the study, published in Nature Communications, the team showed that as mice watched visual stimuli, their human observers could measure patterns of activity among neurons in all six layers of visual cortex and the subplate, providing new data about their role in how mammals process vision. Moreover, through a series of careful experiments, the researchers were able to show that the light they sent in, as well as the light that came back out, neither damaged, nor even altered, the cells they measured.

In all, the paper describes a new three-photon microscope optimized to deliver rapid, short, low-power pulses of light capable of reaching deep targets without causing any functional disturbance or physical damage, and then to detect the resulting fluorescence emitted by cells with high efficiency to produce images with sharp resolution and a fast frame rate.

"We were motivated to show what we could do with three-photon microscope technology for an animal in an awake condition so we could ask important questions of neuroscience," Yildirim says. "You could think you have the best microscope in the world, but until you ask those questions you don't know what results you are going to get."

Femtoseconds and nanojoules

The theory behind multiphoton microscopy dates back to the 1931 doctoral dissertation of Maria Goeppert-Mayer, whose work showed that a simultaneous combination of lower-energy photons could excite an atom or molecule to a higher energy state just like a single higher energetic photon could. In 1990 Cornell University scientists applied that insight to biological imaging in the two-photon microscope and again in 2013 with a three-photon scope. These allowed neuroscientists to see deeper into the brain because lower energy, higher wavelength photons are less susceptible than higher-energy, shorter-wavelength photons to being scattered by cellular molecules like lipids.

Sur and So's labs at MIT have joined in pushing the frontiers of multiphoton microscopy. In the new study they show they've now taken it far enough to study live neural activity. To do that, the team sought to refine many different parameters of both the laser light and the scope optics, based on meticulous measurements of properties of the brain tissue they were imaging.

For instance, they not only measured the energy at which cells started to show overt damage (about 10 nanojoules), but also measured the power at which cells would start to behave differently, thereby producing data influenced by the measurement (2 to 5 nanojoules). With precision and purpose to deliver lower energy levels, the scientists optimized the scope to emit incredibly short pulses of light lasting for a "pulse width" of only 40 femtoseconds, or quadrillionths of a second, and painstakingly arranged the optics to maximize the collection of the light that molecules, excited by the incoming laser energy, would emit back.

Unprecedented neuroscience

After carefully validating that the optimized three-photon scope's measurements agreed with those of two-photon scopes (in shallower layers of the cortex) and electrophysiology (which can go deeper, but blindly), the team set out to do some unprecedented neuroscience — direct visual observation of neural activity in all cortical layers of awake, behaving animals.

In the lab they showed mice some grating patterns in 12 different rotated orientations and two directions of motion across a screen. With their optimized three-photon scope, they watched neurons in each layer of the cortex — going more than a millimeter deep — to see how the cells reacted to this standard visual input. They could see the activity of the cells because they had engineered them to glow upon elevated calcium activity, using a label called GCaMP6s. They could see other tissues like blood vessels and white matter via a phenomenon researchers call "third harmonic generation."

With the capability to see the deepest layers they observed that layer 5 neurons are broadly tuned for orientation, meaning they respond to a wide variety of orientations, rather than just one or two specific ones. Layer 5 neurons also had more spontaneous activity than cells in other layers and more connections to deeper parts of the brain. Meanwhile, layer 6 neurons had somewhat sharper orientation tuning than neurons in other layers, meaning they are more specific in their response to distinct orientations.

Subplate surprise

The most surprising finding was that the subplate, a thin layer of mostly neural white-matter fibers, was home to a population of neurons with patterns of activity that were weakly and broadly tuned to the visual input. The finding was revelatory, the researchers said, in that many neuroscientists believed that subplate neurons were mostly only active during development. The layer is also too thin, Yildirim said, to be measured with electrophysiology.

"So far, subplate neurons in the mature brain have not been studied at all due to the technical challenges of imaging these cells in vivo," the researchers wrote.

Sugihara recalls the first time Yildirim showed him that subplate neurons were active in the mature mice. "What are they doing there?" he recalls asking in surprise.

Now they are continuing to use their new scope to answer that question.

The National Institutes of Health, the National Science Foundation, a Picower Institute Engineering Collaboration Grant, and the Massachusetts Life Sciences Initiative supported the research.