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Q&A: Calif. climate champion on her 'Cinderella moment'

ClimateWire News - Mon, 08/12/2019 - 6:43am
A former state lawmaker who played a key role in shaping California's landmark actions on global warming is still battling for action on climate change.

TRANSPORTATION: Amtrak sees opportunity in anti-plane movement

ClimateWire News - Mon, 08/12/2019 - 6:43am
A surprising party wants to capitalize on Greta Thunberg's climate activism: Amtrak.

COURTS: Oil companies push to halt climate cases

ClimateWire News - Mon, 08/12/2019 - 6:43am
Fossil fuel companies embroiled in a climate nuisance lawsuit from the state of Rhode Island are appealing a federal judge's decision to have their case tossed from federal court.

EPA: New oil and gas rule may ignore methane

ClimateWire News - Mon, 08/12/2019 - 6:43am
EPA will tip its hand in the coming weeks on how — or whether — it plans to regulate petroleum industry emissions of the second-most-important greenhouse gas.

ENERGY TRANSITIONS: Trump admin throws wrench into offshore wind plans

ClimateWire News - Mon, 08/12/2019 - 6:43am
The Trump administration is ordering a sweeping environmental review of the burgeoning offshore wind industry, a move that threatens to derail the nation's first major project and raises a host of questions for future developments.

Antarctic iceberg impacts on future Southern Hemisphere climate

Nature Climate Change - Mon, 08/12/2019 - 12:00am

Nature Climate Change, Published online: 12 August 2019; doi:10.1038/s41558-019-0546-1

Climate change will increase meltwater and iceberg discharge from Antarctica, with implications for future climate and sea levels. Iceberg melt will partly offset greenhouse warming in the Southern Ocean and dampen the positive feedback loop between ice-sheet melting and subsurface warming.

Wasting less electricity before use

Nature Climate Change - Mon, 08/12/2019 - 12:00am

Nature Climate Change, Published online: 12 August 2019; doi:10.1038/s41558-019-0558-x

New research finds that global inefficiencies in power transmission and distribution infrastructure result in nearly a gigatonne of CO2-equivalent annually. Countries can use this overlooked mitigation opportunity in their transition to a clean power sector.

Midlatitudes unaffected by sea ice loss

Nature Climate Change - Mon, 08/12/2019 - 12:00am

Nature Climate Change, Published online: 12 August 2019; doi:10.1038/s41558-019-0560-3

Climate scientists cannot agree on what caused a recent spate of severe winters over North America and Eurasia. Now, a simple yet powerful physics-based approach makes it clear that record-low Arctic sea ice coverage was not the root cause.

The climate mitigation opportunity behind global power transmission and distribution

Nature Climate Change - Mon, 08/12/2019 - 12:00am

Nature Climate Change, Published online: 12 August 2019; doi:10.1038/s41558-019-0544-3

Additional electricity generation is required to compensate for losses from inefficient transmission and distribution infrastructure. In this study, emissions from compensatory generation and the potential for reductions are estimated for 142 countries.

Minimal influence of reduced Arctic sea ice on coincident cold winters in mid-latitudes

Nature Climate Change - Mon, 08/12/2019 - 12:00am

Nature Climate Change, Published online: 12 August 2019; doi:10.1038/s41558-019-0551-4

Two independent methods, applied to observations and climate models, suggest that changes in atmospheric circulation drive cold winters in mid-latitudes and coincident mild Arctic winters. Reduced Arctic sea ice causes Arctic warming but has minimal influence on the severity of mid-latitude winters.

Author Correction: Global loss of climate connectivity in tropical forests

Nature Climate Change - Mon, 08/12/2019 - 12:00am

Nature Climate Change, Published online: 12 August 2019; doi:10.1038/s41558-019-0570-1

Author Correction: Global loss of climate connectivity in tropical forests

Nitrogen and phosphorus constrain the CO<sub>2</sub> fertilization of global plant biomass

Nature Climate Change - Mon, 08/12/2019 - 12:00am

Nature Climate Change, Published online: 12 August 2019; doi:10.1038/s41558-019-0545-2

Elevated CO2 increases plant biomass, providing a negative feedback on global warming. Nutrient availability was found to drive the magnitude of this effect for the majority of vegetation globally, and analyses indicated that CO2 will continue to fertilize plant growth in the next century.

A single-photon source you can make at home

MIT Latest News - Fri, 08/09/2019 - 1:30pm

Quantum computing and quantum cryptography are expected to give much higher capabilities than their classical counterparts. For example, the computation power in a quantum system may grow at a double exponential rate instead of a classical linear rate due to the different nature of the basic unit, the qubit (quantum bit). Entangled particles enable the unbreakable codes for secure communications. The importance of these technologies motivated the U.S. government to legislate the National Quantum Initiative Act, which authorizes $1.2 billion over the following five years for developing quantum information science.

Single photons can be an essential qubit source for these applications. To achieve practical usage, the single photons should be in the telecom wavelengths, which range from 1,260-1,675 nanometers, and the device should be functional at room temperature. To date, only a single fluorescent quantum defect in carbon nanotubes possesses both features simultaneously. However, the precise creation of these single defects has been hampered by preparation methods that require special reactants, are difficult to control, proceed slowly, generate non-emissive defects, or are challenging to scale.

Now, research from Angela Belcher, head of the MIT Department of Biologicial Engineering, Koch Institute member, and the James Crafts Professor of Biological Engineering, and postdoc Ching-Wei Lin, published online in Nature Communications, describes a simple solution to create carbon-nanotube based single-photon emitters, which are known as fluorescent quantum defects.

“We can now quickly synthesize these fluorescent quantum defects within a minute, simply using household bleach and light,” Lin says. “And we can produce them at large scale easily.”

Belcher’s lab has demonstrated this amazingly simple method with minimum non-fluorescent defects generated. Carbon nanotubes were submerged in bleach and then irradiated with ultraviolet light for less than a minute to create the fluorescent quantum defects.

The availability of fluorescent quantum defects from this method has greatly reduced the barrier for translating fundamental studies to practical applications. Meanwhile, the nanotubes become even brighter after the creation of these fluorescent defects. In addition, the excitation/emission of these defect carbon nanotubes is shifted to the so-called shortwave infrared region (900-1,600 nm), which is an invisible optical window that has slightly longer wavelengths than the regular near-infrared. What's more, operations at longer wavelengths with brighter defect emitters allow researchers to see through the tissue more clearly and deeply for optical imaging. As a result, the defect carbon nanotube-based optical probes (usually to conjugate the targeting materials to these defect carbon nanotubes) will greatly improve the imaging performance, enabling cancer detection and treatments such as early detection and image-guided surgery.

Cancers were the second-leading cause of death in the United States in 2017. Extrapolated, this comes out to around 500,000 people who die from cancer every year. The goal in the Belcher Lab is to develop very bright probes that work at the optimal optical window for looking at very small tumors, primarily on ovarian and brain cancers. If doctors can detect the disease earlier, the survival rate can be significantly increased, according to statistics. And now the new bright fluorescent quantum defect can be the right tool to upgrade the current imaging systems, looking at even smaller tumors through the defect emission.

“We have demonstrated a clear visualization of vasculature structure and lymphatic systems using 150 times less amount of probes compared to previous generation of imaging systems,” Belcher says, “This indicates that we have moved a step forward closer to cancer early detection.”

In collaboration with contributors from Rice University, reearchers can identify for the first time the distribution of quantum defects in carbon nanotubes using a novel spectroscopy method called variance spectroscopy. This method helped the researchers monitor the quality of the quantum defect contained-carbon nanotubes and find the correct synthetic parameters easier.

Other co-authors at MIT include biological engineering graduate student Uyanga Tsedev, materials science and engineering graduate student Shengnan Huang, as well as Professor R. Bruce Weisman, Sergei Bachilo, and Zheng Yu of Rice University.

This work was supported by grants from the Marble Center for Cancer Nanomedicine, the Koch Institute Frontier Research Program, Frontier, the National Science Foundation, and the Welch Foundation.

The music of the spheres

MIT Latest News - Fri, 08/09/2019 - 1:25pm

Space has long fascinated poets, physicists, astronomers, and science fiction writers. Musicians, too, have often found beauty and meaning in the skies above. At MIT’s Kresge Auditorium, a group of composers and musicians manifested their fascination with space in a concert titled “Songs from Extrasolar Spaces.” Featuring the Lorelei Ensemble — a Boston, Massachusetts-based women’s choir — the concert included premieres by MIT composers John Harbison and Elena Ruehr, along with compositions by Meredith Monk and Molly Herron. All the music was inspired by discoveries in astronomy.

“Songs from Extrasolar Spaces,” part of an MIT conference on TESS — the Transiting Exoplanet Survey Satellite, launched in April 2018. TESS is an MIT-led NASA mission that scans the skies for evidence of exoplanets: bodies ranging from dwarf planets to giant planets that orbit stars other than our sun. During its two-year mission, TESS and its four highly-sensitive cameras survey 85 percent of the sky, monitoring more than 200,000 stars for the temporary dips in brightness that might signal a transit — the passage of a planetary body across that star.

“There is a feeling you get when you look at these images from TESS,” says Ruehr, an award-winning MIT lecturer in the Music and Theater Arts Section and former Guggenheim Fellow. “A sense of vastness, of infinity. This is the sensation I tried to capture and transpose into vocal music.” 

Supported by the MIT Center for Art, Science and Technology’s Fay Chandler Creativity Grant; MIT Music and Theater Arts; and aerospace and technology giant Northrop Grumman, which also built the TESS satellite, the July 30 concert was conceived by MIT Research Associate Natalia Guerrero. Both the conference and concert marked the 50th anniversary of the Apollo 11 moon landing — another milestone in the quest to chart the universe and Earth’s place in it.

A 2014 MIT graduate, Guerrero manages the team finding planet candidates in the TESS images at the MIT Kavli Institute for Astrophysics and Space Research and is also the lead for the MIT branch of the mission’s communications team. “I wanted to include an event that could make the TESS mission accessible to people who aren’t astronomers or physicists,” says Guerrero. “But I also wanted that same event to inspire astronomers and physicists to look at their work in a new way.”

Guerrero majored in physics and creative writing at MIT, and after graduating she deejayed a radio show called “Voice Box” on the MIT radio station WMBR. That transmission showcased contemporary vocal music and exposed her to composers including Harbison and Ruehr. Last year, in early summer, Guerrero contacted Ruehr to gauge her interest in composing music for a still-hypothetical concert that might complement the 2019 TESS conference.

Ruehr was keen on the idea. She was also a perfect fit for the project. The composer had often drawn inspiration from visual images and other art forms for her music. “Sky Above Clouds,” an orchestral piece she composed in 1989, is inspired by the Georgia O’Keefe paintings she viewed as a child at the Art Institute of Chicago. Ruehr had also created music inspired by David Mitchell’s visionary novel “Cloud Atlas” and Anne Patchett’s “Bel Canto.” “It’s a question of reinterpreting language, capturing its rhythms and volumes and channeling them into music,” says Ruehr. “The source language can be fiction, or painting, or in this case these dazzling images of the universe.”

In addition, Ruehr had long been fascinated by space and stars. “My father was a mathematician who studied fast Fourier transform analysis,” says Ruehr, who is currently composing an opera set in space. “As a young girl, I’d listen to him talking about infinity with his colleagues on the telephone. I would imagine my father existing in infinity, on the edge of space.”

Drawing inspiration from the images TESS beams back to Earth, Ruehr composed two pieces for “Songs from Extrasolar Spaces.” The first, titled “Not from the Stars,” takes its name and lyrics from a Shakespeare sonnet. For the second, “Exoplanets,” Ruehr used a text that Guerrero extrapolated from the titles of the first group of scientific papers published from TESS data. “I’m used to working from images,” explains Ruehr. “First, I study them. Then, I sit down at the piano and try to create a single sound that captures their essence and resonance. Then, I start playing with that sound.”

Ruehr was particularly pleased to compose music about space for the Lorelei Ensemble. “There’s a certain quality in a women’s choir, especially the Lorelei Ensemble, that is perfectly suited for this project,” says Ruehr. “They have an ethereal sound and wonderful harmonic structures that make us feel as if we’re perceiving a small dab of brightness in an envelope of darkness.”

At the 2019 MIT TESS conference, experts from across the globe shared results from the first year of observation in the sky above the Southern Hemisphere, and discussed plans for the second-year trek above the Northern Hemisphere. The composers and musicians hope “Songs from Extrasolar Spaces” brought attention to the TESS missions, offers a new perspective on space exploration, and will perhaps spark further collaborations between scientists and artists. George Ricker, TESS principal investigator; Sara Seager, TESS deputy director of science; and Guerrero presented a pre-concert lecture. “Music has the power to generate incredibly powerful emotions,” says Ruehr. “So do these images from TESS. In many ways, they are more beautiful than any stars we might ever imagine.”

TESS is a NASA Astrophysics Explorer mission led and operated by MIT in Cambridge, Massachusetts, and managed by Goddard Spaceflight Center. Additional partners include Northrop Grumman, based in Falls Church, Virginia; NASA’s Ames Research Center in California’s Silicon Valley; the Harvard-Smithsonian Center for Astrophysics in Cambridge; MIT Lincoln Laboratory; and the Space Telescope Science Institute in Baltimore, Maryland. More than a dozen universities, research institutes, and observatories worldwide are participants in the mission.

Yearlong hackathon engages nano community around health issues

MIT Latest News - Fri, 08/09/2019 - 11:45am

A traditional hackathon focuses on computer science and programming, attracts coders in droves, and spans an entire weekend with three stages: problem definition, solution development, and business formation. 

Hacking Nanomedicine, however, recently brought together graduate and postgraduate students for a single morning of hands-on problem solving and innovation in health care while offering networking opportunities across departments and research interests. Moreover, the July hackathon was the first in a series of three half-day events structured to allow ideas to develop over time.

This deliberately deconstructed, yearlong process promotes necessary ebb and flow as teams shift in scope and recruit new members throughout each stage. “We believe this format is a powerful combination of intense, collaborative, multidisciplinary interactions, separated by restful research periods for reflecting on new ideas, allowing additional background research to take place and enabling additional people to be pulled into the fray as ideas take shape,” says Brian Anthony, associate director of MIT.nano and principal research scientist in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Mechanical Engineering.

Organized by Marble Center for Cancer Nanomedicine Assistant Director Tarek Fadel, Foundation Medicine’s Michael Woonton, and MIT Hacking Medicine Co-Directors Freddy Nguyen and Kriti Subramanyam, the event was sponsored by IMES, the Koch Institute’s Marble Center for Cancer Nanomedicine, and MIT.nano, the new 200,000-square-foot nanoscale research center that launched at MIT last fall.

Sangeeta Bhatia, director of the Marble Center, emphasizes the importance of creating these communication channels between community members working in tangentially-related research spheres. "The goal of the event is to galvanize the nanotechnology community around Boston — including MIT.nano, the Marble Center, and IMES — to leverage the unique opportunities presented by miniaturization and to answer critical questions impacting health care,” says Bhatia, who is also the John J. and Dorothy Wilson Professor of Health Sciences and Technology at MIT.

At the kickoff session, organizers sought to create a smaller, workshop-based event that would introduce students, medical residents, and trainees to the world of hacking and disruptive problem solving. Representatives from MIT Hacking Medicine started the day with a brief overview and case study on PillPack, a successful internet pharmacy startup created from a previous hackathon event.

Participants then each had 30 seconds to develop and pitch problems highlighting critical health care industry shortcomings before forming into five teams based on shared interests. Groups pinpointed a wide array of timely topics, from the nation’s fight against obesity to minimizing vaccine pain. Each cohort had two hours to work through multifaceted, nanotechnology-based solutions. 

Mentors Cicely Fadel, a clinical researcher at the Wyss Institute for Biologically Inspired Engineering and neonatologist at Beth Israel Deaconess Medical Center, and David Chou, a hematopathologist at Massachusetts General Hospital and clinical fellow at the Wyss Institute, roamed the room during the solution phase, offering feedback on feasibility based on their own clinical experience.

At the conclusion of the problem-solving block, each of the five teams presented their solution to a panel of expert judges: Imran Babar, chief business officer of Cydan; Adama Marie Sesay, senior staff engineer of the Wyss Institute; Craig Mak, director of strategy at Arbor Bio; Jaideep Dudani, associate director of Relay Therapeutics; and Zen Chu, senior lecturer at the MIT Sloan School of Management and faculty director of MIT Hacking Medicine. 

Given the introductory nature of the event, judges opted to forego the traditional scoring rubric and instead paired with each team to offer individualized, qualitative feedback. Event sponsors note that the decision to steer away from a black-and-white, ranked-placing system encourages participants to continue thinking about the pain points of their problem in anticipation of the next hackathon in the series this fall.

During this second phase, participants will further develop their solution and explore the issue’s competitive landscape. Organizers plan to bring together local business and management stakeholders for a final event in the spring that will allow participants to pitch their project for acquisition or initial seed funding. 

Founded in 2011, MIT Hacking Medicine consists of both students and community members and aims to promote medical innovation to benefit the health care community. The group recognizes that technological advancement is often born out of collaboration rather than isolation. Monday’s event accordingly encouraged networking among students and postdocs not just from MIT but institutions all around Boston, creating lasting relationships rooted in a commitment to deliver crucial health care solutions.

Indeed, these events have proven successful in fostering connections and propelling innovation. According to MIT Hacking Medicine’s website, more than 50 companies with over $240 million in venture funding have been created since June 2018 thanks to their hackathons, workshops, and networking gatherings. The organization’s events across the globe have engaged nearly 22,000 hackers eager to disrupt the status quo and think critically about health systems in place.

This past weekend, MIT Hacking Medicine hosted its flagship Grand Hack event in Washington. Over the course of a weekend, like-minded students and professionals across a range of industries will join forces to tackle issues related to health care access, mental health and professional burnout, rare diseases, and more. Sponsors hope that Monday’s shorter, intimate event will garner enthusiasm for larger hackathons like this one to sustain communication among a diverse community of experts in their respective fields. 

Optimus Ride’s autonomous system makes self-driving vehicles a reality

MIT Latest News - Fri, 08/09/2019 - 11:36am

Some of the biggest companies in the world are spending billions in the race to develop self-driving vehicles that can go anywhere. Meanwhile, Optimus Ride, a startup out of MIT, is already helping people get around by taking a different approach.

The company’s autonomous vehicles only drive in areas it comprehensibly maps, or geofences. Self-driving vehicles can safely move through these areas at about 25 miles per hour with today’s technology.

“It’s important to realize there are multiple approaches, and multiple markets, to self-driving,” says Optimus Ride CEO Ryan Chin MA ’00, SM ’04, PhD ’12. “There’s no monolithic George Jetson kind of self-driving vehicle. You have robot trucks, you have self-driving taxis, self-driving pizza delivery machines, and each of these will have different time frames of technological development and different markets.”

By partnering with developers, the Optimus team is currently focused on deploying its vehicles in communities with residential and commercial buildings, retirement communities, corporate and university campuses, airports, resorts, and smart cities. The founders estimate the combined value of transportation services in those markets to be over $600 billion.

“We believe this is an important, huge business, but we also believe this is the first addressable market in the sense that we believe the first autonomous vehicles that will generate profits and make business sense will appear in these environments, because you can build the tech much more quickly,” says Chin, who co-founded the company with Albert Huang SM ’05, PhD ’10, Jenny Larios Berlin MCP ’14, MBA ’15, Ramiro Almeida, and Class of 1948 Career Development Professor of Aeronautics and Astronautics Sertac Karaman.

Optimus Ride currently runs fleets of self-driving vehicles in the Seaport area of Boston, in a mixed-use development in South Weymouth, Massachusetts, and, as of this week, in the Brooklyn Navy Yard, a 300-acre industrial park that now hosts the first self-driving vehicle program in the state.

Later this year, the company will also deploy its autonomous vehicles in a private community of Fairfield, California, and in a mixed-use development in Reston, Virginia.

The early progress — and the valuable data that come with it — is the result of the company taking a holistic view of transportation. That perspective can be traced back to the founders’ diverse areas of focus at MIT.

A multidisciplinary team

Optimus Ride’s founders have worked across a wide array of departments, labs, and centers across MIT. The technical validation for the company began when Karaman participated in the Defense Advanced Research Projects Agency’s (DARPA) Urban Challenge with a team including Huang in 2007. Both researchers had also worked in the Computer Science and Artificial Intelligence Laboratory together.

For the event, DARPA challenged 89 teams with creating a fully autonomous vehicle that could traverse a 60 mile course in under six hours. The vehicle from MIT was one of only six to complete the journey.

Chin, who led a Media Lab project that developed a retractable electric vehicle in the Smart Cities group, met Karaman when both were PhD candidates in 2012. Almeida began working in the Media Lab as a visiting scholar a year later.

As members of the group combined their expertise on both self-driving technology and the way people move around communities, they realized they needed help developing business models around their unique approach to improving transportation. Jenny Larios Berlin was introduced to the founders in 2015 after earning joint degrees from the Department of Urban Studies and Planning and the Sloan School of Management. The team started Optimus Ride in August that year.

“The company is really a melting pot of ideas from all of these schools and departments,” Karaman says. “When we met each other, there was the technology angle, but we also realized there’s an important business angle, and there’s also an interesting urban planning/media arts and sciences angle around thinking of the system as a whole. So when we formed the company we thought, not just how can we build fully autonomous vehicles, but also how can we make transportation in general more affordable, sustainable, equitable, accessible, and so on.”

Karaman says the company’s approach could only have originated in a highly collaborative environment like MIT, and believes it gives the company a big advantage in the self-driving sector.

“I knew how to build autonomous systems, but in interacting with Ryan and Ramiro and Jenny, I really got a better understanding of what the systems would look like, what the smart cities that utilize the systems would look like, what some of the business models would look like,” Karaman says. “That has a feedback on the technology. It allows you to build the right kind of technology very efficiently in order to go to these markets.”

Optimus Ride's self-driving vehicles can travel on many public roads. Courtesy of Optimus Ride

First mover advantage

Optimus Ride’s vehicles have a suite of cameras, lasers, and sensors similar to what other companies use to help autonomous vehicles navigate their environments. But Karaman says the company’s key technical differentiators are its machine vision system, which rapidly identifies objects, and its ability to fuse all those data sources together to make predictions, such as where an object is going and when it will get there.

Optimus Ride's vehicles feature a range of cameras and sensors to help them navigate their environment. Courtesy of Optimus Ride

The strictly defined areas where the vehicles drive help them learn what Karaman calls the “culture of driving” on different roads. Human drivers might subconsciously take a little longer at certain intersections. Commuters might drive much faster than the speed limit. Those and other location-specific details, like the turn radius of the Silver Line bus in the Seaport, are learned by the system through experience.

“A lot of the well-funded autonomous driving projects out there try to capture everything at the same time and tackle every problem,” Karaman says. “But we operate the vehicle in places where it can learn very rapidly. If you go around, say, 10,000 miles in a small community, you end up seeing a certain intersection a hundred or a thousand times, so you learn the culture of driving through that intersection. But if you go 10,000 miles around the country, you’ll only see places once.”

Safety drivers are still required to be behind the wheels of autonomous vehicles in the states Optimus Ride operates in, but the founders hope to soon be monitoring fleets with fewer people in a manner similar to an air traffic controller.

For now, though, they’re focused on scaling their current model. The contract in Reston, Virginia is part of a strategic partnership with one of the largest real estate managers in the world, Brookfield Properties. Chin says Brookfield owns over 100 locations where Optimus Ride could deploy its system, and the company is aiming to be operating 10 or more fleets by the end of 2020.

“Collectively, [the founders] probably have around three decades of experience in building self-driving vehicles, electric vehicles, shared vehicles, mobility transportation, on demand systems, and in looking at how you integrate new transportation systems into cities,” Chin says. “So that’s been the idea of the company: to marry together technical expertise with the right kind of policymaking, the right kind of business models, and to bring autonomy to the world as fast as possible.”

An emerging view of RNA transcription and splicing

MIT Latest News - Fri, 08/09/2019 - 11:30am

Cells often create compartments to control important biological functions. The nucleus is a prime example; surrounded by a membrane, it houses the genome. Yet cells also harbor enclosures that are not membrane-bound and more transient, like oil droplets in water. Over the past two years, these droplets (called “condensates”) have become increasingly recognized as major players in controlling genes. Now, a team led by Whitehead Institute scientists helps expand this emerging picture with the discovery that condensates play a role in splicing, an essential activity that ensures the genetic code is prepared to be translated into protein. The researchers also reveal how a critical piece of cellular machinery moves between different condensates. The team’s findings appear in the Aug. 7 online issue of Nature.

“Condensates represent a real paradigm shift in the way molecular biologists think about gene control,” says senior author Richard Young, a member of the Whitehead Institute and professor of biology at MIT. “Now, we’ve added a critical new layer to this thinking that enhances our understanding of splicing as well as the major transcriptional apparatus RNA polymerase II.”

Young’s lab has been at the forefront of studying how and when condensates form as well as their functions in gene regulation. In the current study, Young and his colleagues, including first authors Eric Guo and John Manteiga, focused their efforts on a key transition that happens when genes undergo transcription — an early step in gene activation whereby an RNA copy is created from the genes’ DNA template. First, all of the molecular machinery needed to make RNA, including a large protein complex known as RNA polymerase II, assembles at a given gene. Then, specific chemical modifications to RNA polymerase II allow it to begin transcribing DNA into RNA. This shift from so-called transcription initiation to active transcription also involves another important molecular transition: As RNA molecules begin to grow, the splicing apparatus must also move in and carry out its job.

“We wanted to step back and ask, ‘Do condensates play an important role in this switch, and if so, what mechanism might be responsible?’” explains Young.

For roughly three decades, it has been recognized that the factors required for splicing are stored in compartments called speckles. Yet whether these speckles play an active role in splicing, or are simply storage vessels, has remained unclear.

Using confocal microscopy, the Whitehead team discovered condensates filled with components of the splicing machinery in the vicinity of highly active genes. Notably, these structures exhibited similar liquid-like characteristics to those condensates described in prior studies from Young’s lab that are involved in transcription initiation. 

“These findings signaled to us that there are two types of condensates at work here: one involved in transcription initiation and the other in splicing and transcriptional elongation,” said Manteiga, a graduate student in Young’s lab.

With two different condensates at play, the researchers wondered: How does the critical transcriptional machinery, specifically RNA polymerase II, move from one condensate to the other?

Guo, Manteiga, and their colleagues found that chemical modification, specifically the addition of phosphate groups, serves as a kind of molecular switch that alters the protein complex’s affinity for a particular condensate. With fewer phosphate groups, it associates with the condensates for transcription initiation; when more phosphates are added, it enters the splicing condensates. Such phosphorylation occurs on one end of the protein complex, which contains a specialized region known as the C-terminal domain (CTD). Importantly, the CTD lacks a specific three-dimensional structure, and previous work has shown that such intrinsically disordered regions can influence how and when certain proteins are incorporated into condensates.

“It is well-documented that phosphorylation acts as a signal to help regulate the activity of RNA polymerase II,” says Guo, a postdoc in Young’s lab. “Now, we’ve shown that it also acts as a switch to alter the protein’s preference for different condensates.”

In light of their discoveries, the researchers propose a new view of splicing compartments, where speckles serve primarily as warehouses, storing the thousands of molecules required to support the splicing apparatus when they are not needed. But when splicing is active, the phosphorylated CTD of RNA Pol II serves as an attractant, drawing the necessary splicing materials toward the gene where they are needed and into the splicing condensate.

According to Young, this new outlook on gene control has emerged in part through a multidisciplinary approach, bringing together perspectives from biology and physics to learn how properties of matter predict some of the molecular behaviors he and his team have observed experimentally. “Working at the interface of these two fields is incredibly exciting,” says Young. “It is giving us a whole new way of looking at the world of regulatory biology.”

Support for this work was provided by the U.S. National Institutes of Health, National Science Foundation, Cancer Research Institute, Damon Runyon Cancer Research Foundation, Hope Funds for Cancer Research, Swedish Research Council, and German Research Foundation DFG.

Eight from MIT honored in 2019 Technology Review 35 Innovators Under 35

MIT Latest News - Fri, 08/09/2019 - 10:20am

Earlier this summer, MIT Technology Review released its annual list of 35 Innovators Under 35, and the 2019 roster has a strong MIT presence. At least eight MIT alumni and current or former postdocs were named to this year’s group.

According to MIT Technology Review, "35 Innovators Under 35," now in its 19th year, is a list of the most promising young innovators around the world whose accomplishments are poised to have a dramatic impact on the world. The list is split into five categories: Inventors, Entrepreneurs, Visionaries, Humanitarians, and Pioneers.

Postdocs and alumni honored for 2019 are:

Anurag Bajpayee SM ’08, PhD ’12 (Entrepreneurs) The founder of Gradient, Bajpayee's approaches can treat dirty wastewater and can make desalination more efficient.

Cesar de la Fuente Nunez, 2015 postdoc (Pioneer) An assistant professor at the University of Pennsylvania, De la Fuente Nunez developed algorithms that follow Charles Darwin’s theory of evolution to create optimized artificial antibiotics.

Grace X. Gu SM ’14, PhD ’18 (Pioneers) Now at the University of California at Berkeley, Gu is using artificial intelligence to help dream up a new generation of lighter, stronger materials.

Qichao Hu ’07, 2012 postdoc (Entrepreneur) Hu, founder and CEO of SolidEnergy Systems, is on the cusp of one of the most highly anticipated developments in industry: the next battery revolution.

Raluca Ada Popa ’10, MEng ’10, PhD ’14 (Visionaries) Now at the University of California at Berkeley, Popa's computer security method could protect data, even when attackers break in. 

Ritu Raman, postdoc (Inventor) A researcher at MIT's Koch Institute, Raman has developed inchworm-size robots made partly of biological tissue and muscle. 

Brandon Sorbom PhD ’17 (Inventor) Chief scientist at Commonwealth Fusion Systems, Sorbom's high-temperature superconductors could make fusion reactors much cheaper to build. 

Archana Venkataraman ’07, MEng ’07, PhD ’12 (Inventor) We still don’t know much about neurological disorders. Venkataraman, now at the Johns Hopkins University, is using artificial intelligence to change that.

For more on the connection between the Institute and MIT Technology Review's Innovators Under 35, see Slice of MIT's lists from 2018201720162015201420132012, and 2010.

A version of this article originally appeared on the Slice of MIT blog.

MICHIGAN: Environmental sustainability effort boosted

ClimateWire News - Fri, 08/09/2019 - 6:41am
State government in Michigan is stepping up efforts to boost environmental sustainability by using energy saving efforts at prisons, converting state parks and fish hatcheries to renewable energy, and taking other steps.

GERMANY: Report: Government weighs new debt to fund climate package

ClimateWire News - Fri, 08/09/2019 - 6:41am
Germany's finance ministry said there has been no government decision to abandon its policy of running a balanced budget.

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