lunes, 27 de agosto de 2018

MIT-created programming language Julia 1.0 debuts

After years of tinkering, the dynamic programming language Julia 1.0 was officially released to the public during JuliaCon, an annual conference of Julia users held recently in London.

The release of Julia 1.0 is a huge Julia milestone since MIT Professor Alan Edelman, Jeff Bezanson, Stefan Karpinski, and Viral Shah released Julia to developers in 2012, says Edelman.

 “Julia has been revolutionizing scientific and technical computing since 2009,” says Edelman, the year the creators started working on a new language that combined the best features of Ruby, MatLab, C, Python, R, and others. Edelman is director of the Julia Lab at MIT and one of the co-creators of the language at MIT’s Computer Science and Artificial Intelligence Lab (CSAIL). 

Julia, which was developed and incubated at MIT, is free and open source, with more than 700 active open source contributors, 1,900 registered packages, 41,000 GitHub stars, 2 million downloads, and a reported 101 percent annual rate of download growth. It is used at more than 700 universities and research institutions and by companies such as Aviva, BlackRock, Capital One, and Netflix.

At MIT, Julia users and developers include professors Steven Johnson, Juan Pablo Vielma, Gilbert Strang, Robin Deits, Twan Koolen, and Robert Moss. Julia is also used by MIT Lincoln Laboratory and the Federal Aviation Administration to develop the Next-Generation Airborne Collision Avoidance System (ACAS-X), by the MIT Operations Research Center to optimize school bus routing for Boston Public Schools, and by the MIT Robot Locomotion Group for robot navigation and movement.

Julia is the only high-level dynamic programming language in the “petaflop club,” having achieved 1.5 petaflop/s using 1.3 million threads, 650,000 cores and 9,300 Knights Landing (KNL) nodes to catalogue 188 million stars, galaxies, and other astronomical objects in 14.6 minutes on the world’s sixth-most powerful supercomputer.

Julia is also used to power self-driving cars and 3-D printers, as well as applications in precision medicine, augmented reality, genomics, machine learning, and risk management.

“The release of Julia 1.0 signals that Julia is now ready to change the technical world by combining the high-level productivity and ease of use of Python and R with the lightning-fast speed of C++,” Edelman says. 



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viernes, 24 de agosto de 2018

Chris Caplice and Justin Reich win 2018 MITx Prize for Teaching and Learning in MOOCs

MITx has awarded its second annual Prize for Teaching and Learning in MOOCs (massive open online courses) to two instructors selected from a pool of individuals who made significant contributions to MITx MOOC coursework offered on edX.org during the 2017 calendar year.

The MITx Prize for Teaching and Learning recognizes educators who have developed innovative digital course content that engage online learners around the world through digital classrooms. The award debuted last year as part of the Institute’s effort to encourage the development of new MOOC methods and technologies. 

Chris Caplice, executive director of the MIT Center for Transportation and Logistics, received the award for his work on the MicroMasters Program in Supply Chain Management. MIT launched the MicroMasters credential in fall of 2015. Since then, more than than 25 universities have also launched MicroMasters programs through edX. The MicroMasters Program in Supply Chain Management includes five courses of 13 weeks each, plus a final comprehensive exam.

Individuals who pass the five courses plus the exam earn the MicroMasters credential and may apply for a master’s degree at MIT and other universities. Caplice notes that online learners can access the same exceptional resources as those taking courses on-campus.

“Each course is rigorous and mirrors what we do in the campus classes here at MIT,” he says.

The award for Caplice praises his “dedication to creating a high-quality learner experience both in the courses and beyond, and his work to ensure the value of the credential through rigorous assessment.”

Justin Reich, executive director of the MIT Teaching Systems Lab, was selected for his work on 11.154x (Launching Innovation in Schools), a six-week course targeted to school leaders including teachers, principals, superintendents, school board members, and others.

“It’s for anyone who wants to make their schools better,” Reich says.

The course was recognized for creating a collaborative environment for educators to take the course in facilitated learning circles, where school leaders are encouraged to take courses and create change together. The course was also lauded for encouraging educators to take specific actions each week that they can implement immediately in their own schools.

“We envision our courses not just a learning experience you do and apply it afterwards,” he explains. “You are encouraged to take what you are learning and immediately start applying it in your context to get feedback and iteratively improve a change initiative together.”

“Chris and I are both really interested in professionals out in the working world who are committed learners,” adds Reich. He also points out that distance learning is not new, having been a part of human learning for over a century from the earliest correspondence courses. “MOOCs like ours are built on that long tradition and we are in our century taking advantage of the new technologies to serve our learners today interested in life-long learning experiences,” he says.

More than 10,000 learners have earned over 20,000 individual course certificates, and 1,062 learners have completed the MicroMasters credential. On June 8, the first group of 40 individuals graduated with a master’s degree in supply chain management under the new blended master’s program.

“This year’s winners reflect the dedication of all of our MITx faculty in sharing the excellence of our on-campus MIT experience with global learners,” says MIT Professor Krishna Rajagopal, dean of digital learning. “Their innovative and timely courses have set a high standard for online learning that influences the whole field of this form of education.”

Anyone interested in more information about MOOCs on MITx is encouraged to visit MIT’s Open Learning site. MIT Open Learning will begin accepting nominations for next year’s prize in early 2019.



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Noelle Selin named director of the MIT Technology and Policy Program

Noelle Selin, an associate professor with a joint appointment in the MIT Institute for Data, Systems, and Society (IDSS) and the Department of Earth, Atmospheric and Planetary Sciences (EAPS), has been appointed the next director for the Technology and Policy Program (TPP) at MIT.

TPP is a two-year, interdisciplinary master of science program that combines science and engineering with social sciences, to educate students whose research addresses important technological issues confronting society. Over more than 40 years, TPP’s more than 1,200 alumni have gone on to work in industry and government as well as academia.

Selin’s own research links science and policy, particularly on the topic of atmospheric pollutants. Her interdisciplinary research aims to inform decision-making on air pollution, climate change, and hazardous substances. A major focus is on mercury pollution, where she has engaged with policy-makers both domestically and internationally. In addition to her work modeling the transport and fate of pollutants, she has published articles and book chapters on the interactions between science and policy in international environmental negotiations, in particular focusing on global efforts to regulate hazardous substances.

“Noelle is an excellent educator and teacher, and has substantially contributed to the curriculum in IDSS and TPP,” said IDSS Director Munther Dahleh, a professor in IDSS and MIT’s Department of Electrical Engineering and Computer Science. While serving as associate director of TPP, Selin managed the admission process and led a curricular development effort that revised the set of course requirements for TPP students. In 2018, she shared the Joseph A. Martore ’75 Award for Exceptional Contributions to Education in IDSS for her contributions to the core TPP course Science, Technology, and Public Policy. She also received TPP’s Faculty Appreciation Award in 2013.

Selin first came to MIT in 2007 as a postdoc at the Center for Global Change Science. She joined the Engineering Systems Division as an assistant professor in 2010 with a joint appointment in EAPS. She joined IDSS as a core faculty member when it was launched in 2015. She was promoted to associate professor with tenure in July 2017.

In the area of policy, Selin had prior appointments as a research associate with the Initiative on Science and Technology for Sustainability at Harvard’s Kennedy School and as a visiting researcher at the European Environment Agency in Copenhagen, Denmark. She also previously worked on chemicals issues at the U.S. Environmental Protection Agency. She holds a BA in environmental science and public policy and an MA and PhD in earth and planetary sciences, all from Harvard University.

Selin received the NSF CAREER Award and two best Environmental Policy paper awards from the journal Environmental Science and Technology (2015 and 2016). She is a Kavli Frontiers of Science Fellow, a member of the Global Young Academy (2014-2018), a fellow of the AAAS Leshner Leadership Institute for Public Engagement (2016-2017), and a Leopold Leadership Fellow (2013).

“I am truly honored to be named as the next Director of TPP,” says Selin. “I see TPP as a hub for education, research, and practice in mobilizing technical expertise to inform policy, within MIT and beyond, and I am excited to help shape its future.”



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MIT-SenseTime Alliance funds projects from all five schools

Faculty and senior researchers at MIT are teaming up in unprecedented ways to help define the next frontier in human and machine intelligence with projects that delve into everything from fundamental research to societal applications for new technologies.

The MIT-SenseTime Alliance on Artificial Intelligence, a program within the MIT Quest for Intelligence, has announced funding for 27 projects involving about 50 principal investigators from departments and labs within engineering, science, architecture and planning, management, and the humanities and social sciences.

SenseTime, a leading artificial intelligence company founded by MIT alumnus Xiao’ou Tang PhD ’96, jointly created the alliance with MIT earlier this year to define the next frontier of human and machine intelligence. The selected projects are of one year in duration that are intended to kick-start new efforts and initiate longer-term work.

“We were thrilled with the range and creativity of the proposals we received,” says Anantha P. Chandrakasan, dean of the MIT School of Engineering and Vannevar Bush Professor of Electrical Engineering and Computer Science, who is heading the MIT-SenseTime Alliance.

“It is particularly exciting to see faculty from so many disciplines join together to embark on projects that speak to the major objectives of the MIT Quest for Intelligence,” he says.

Chandrakasan points to the funded exploratory “moonshot” projects that align with the work of “The Core,” which seeks to advance the science and engineering of human and machine intelligence, explore human intelligence using insights from computer science, and develop new machine-learning algorithms.

One such project features MIT faculty from the Department of Linguistics and Philosophy, the Department of Brain and Cognitive Sciences, and MIT’s Computer Science and Artificial Intelligence Laboratory. These professors are working on a “language moonshot” that explores how insights from linguistic theory can be transformed into machine-learning algorithms to better approximate how people converse.

Several MIT neuroscientists from the McGovern Institute for Brain Research are joining with an MIT physics professor and others in a moonshot project that explores the biological mechanisms subtending learning and how to incorporate that knowledge into more robust machine-learning techniques. Meanwhile, MIT faculty from computer science and brain and cognitive sciences are collaborating in a project focused on how artificial systems, like robots, can learn common sense knowledge.

Also popular were projects described as “mission-driven” that aligned, as Chandrakasan notes, with the MIT Quest for Intelligence’s second key entity, “The Bridge,” which is dedicated to the application of MIT discoveries in natural and artificial intelligence to all disciplines.

Seven principal investigators from disciplines including CSAIL, the Department of Aeronautics and Astronautics, and the Department of Earth, Atmospheric and Planetary Sciences are collaborating on a mission-driven project that will explore drone intelligence for societal applications.

Another mission-driven project features a faculty member from the Sloan School of Management teaming up with an MIT professor of electrical engineering and computer science who proposes to use machine learning to amplify human intelligence and human employment in future manufacturing. Another involves two MIT mechanical engineering faculty focusing on developing tools in product design and systems architecture that capitalize on strategies that combine human intelligence with machine intelligence.

Eight collaborative projects that involve two or more principal investigators also received funding. For example, Media Lab professors will evaluate the use of a social robot as a personalized emotional wellness coach; electrical engineering and computer science professors will use embedded AI to track neurocognitive decline in the elderly; nuclear science and engineering, materials science and engineering, and electrical engineering professors will develop an all-solid device for low-power, fast, brain-like computing; Sloan professors will research dynamic portfolio management with deep learning; and mechanical engineering professors will investigate a specific approach to low-power image regression at the edge for the internet of things.

Additional funding was dedicated to 13 projects led by individual faculty from a range of departments, including media arts and sciences, chemistry, computer science, anthropology, physics, brain and cognitive sciences, and more. These projects are wide-ranging and include pursuits such as harnessing artificial intelligence to design vaccines for treating metastatic skin cancer, quantifying the robustness of neural networks, and using AI to increase equity in decision making for agriculture market design.

“These projects are just the beginning of what promises to be one of the most important initiatives MIT has ever started,” says Antonio Torralba, the director of the MIT Quest for Intelligence. “SenseTime’s tremendous support for pivotal research will deepen the footprint of The Quest on campus.”



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jueves, 23 de agosto de 2018

3 Questions: Sasha Costanza-Chock on new “#MoreThanCode” report

Not every technology platform or tool you use, or website you visit, comes straight from a startup or Silicon Valley. Many are developed by nonprofits, government agencies, or advocacy groups practicing community technology, technology for social justice, or “public interest technology.” What can we learn from these community-engaged technology practitioners? How can organizations that work for equity achieve the diversity they often advocate for in society?

Sasha Costanza-Chock, an associate professor in Comparative Media Studies/Writing at MIT, is the lead author of a new report, titled “#MoreThanCode: Practitioners reimagine the landscape of technology for justice and equity,” which delves into these issues. The report distills 109 interviews, 11 focus groups, and data from thousands of organizations into five high-level recommendations for those who want to use technology for the public good. (The report was funded by NetGain, the Ford Foundation, Mozilla, Code for America, and OTI.) MIT News sat down with Costanza-Chock to talk about the report and its recommendations.

Q: Who are the practitioners in this tech ecosystem?

A: “#MoreThanCode” is a report about people working to use technology for social good and for social justice — the space the report’s funders call “public interest technology.” There’s a very wide range of roles for people who use technology to advance the public interest, and it’s not only software developers who are active.

One of our key recommendations is that when funders and organzations — be they city governments or nonprofits or for-profit companies — are putting together teams, they need to think broadly about who is on that team. We found that a good team to develop technology that’s going to advance social justice or the public interest is going to include software developers, graphic designers, researchers, and domain [subject] experts. Domain experts might have formal expertise, but the most important team member is someone with lived experience of the particular condition that technology is supposed to address.

Q: On that note, can you say a little about the current state of social diversity in this sector?

A: Certainly. One of our key goals in the report was to produce baseline knowledge about who’s working in public interest technology. And unfortunately, in terms of hard data, the main finding is that we don’t have it, because many organizations in the space have not published diversity and inclusivity data about who their staff are, who their volunteers are.

And so one recommendation in the report is that everybody who says they’re doing public interest technology, or using technology for good, should be gathering data about, at the very least, race and gender, and publicly releasing it. Gathering and releasing diversity data, and setting time-bound, public targets for diversity and inclusion goals, are two main things that we know work in organizations, from the evidence-based literature. Good intentions aren’t enough.

Although we weren’t able to gather that kind of sector-wide diversity data, we did interview 109 people and conduct focus groups with 79 more, and asked them about their experiences with racism, sexism, transphobia, ableism, and other common forms of systematic marginalization people experience. About half of the people we talked to for the report said they had experiences like that.

The leading recommendation at the end of the report is summed up in a slogan from the disability justice movement, which is, “Nothing about us, without us.” The idea is that when you’re going to develop a technology to help a community, you have to include members of that community from the beginning of your process … and ideally in the governance of the project when it’s deployed.

Q: The report also suggests people should not always look for “silver bullets” or instant answers from technology alone. Why is that, and what are some of the other recommendations from the report?

A: I’m not going to say it’s never about finding a new [technological] solution, but over and over again, the people we interviewed said the projects that were most successful were deployments of resilient, proven technology, rather than some super-exciting new app that’s suddenly supposed to solve everything.

One recommendation is that when organizations set up tech teams, you want someone from the community on the design team, not just at a moment of consultation. That’s a pretty important takeaway. A lot of people told us it was important to go further than just doing initial consultations with a community — having people on the design team from beginning to end is a best practice we recommend.

Some people talked about creating tech clinics, modeled after legal clinics in education. That would be something a place like MIT could think about. Law schools often require students to spend a certain number of hours providing legal services pro bono to people in different domains who otherwise can’t afford lawyers. It would be interesting to consider whether there could be a [similar] tech clinic concept.

Our final recommendation was about recognizing organizational models beyond traditional startups, government offices, or 501c3 nonprofits — for example, consider tech cooperatives, or ad hoc networks that emerge around a crisis moment. These are hard for investors or foundations to fund: Whom do you fund? And yet a lot of really important technology projects are informal. In the wake of Hurricane Maria in Puerto Rico, there were hundreds of developers, techies, and community organizers doing everything they could, ad hoc, to get communications infrastructure back up.

People should develop strategies for supporting those kinds of networks when they do spring up. For funders, that may mean setting up a crisis response fund with a mechanism to rapidly dispense smaller amounts of funds. And members of the MIT community who are creating new companies to bring “tech for good” innovations to market should consider worker-owned cooperatives, platform co-ops, and other models that internally mirror the kind of world they’d like to build.



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Pushing the plasma density limit

For decades, researchers have been exploring ways to replicate on Earth the physical process of fusion that occurs naturally in the sun and other stars. Confined by its own strong gravitational field, the sun’s burning plasma is a sphere of fusing particles, producing the heat and light that makes life possible on earth. But the path to a creating a commercially viable fusion reactor, which would provide the world with a virtually endless source of clean energy, is filled with challenges.

Researchers have focused on the tokamak, a device that heats and confines turbulent plasma fuel in a donut-shaped chamber long enough to create fusion. Because plasma responds to magnetic fields, the torus is wrapped in magnets, which guide the fusing plasma particles around the toroidal chamber and away from the walls. Tokamaks have been able to sustain these reactions only in short pulses. To be a practical source of energy, they will need to operate in a steady state, around the clock.

Researchers at MIT’s Plasma Science and Fusion Center (PSFC) have now demonstrated how microwaves can be used to overcome barriers to steady-state tokamak operation. In experiments performed on MIT’s Alcator C-Mod tokamak before it ended operation in September 2016, research scientist Seung Gyou Baek and his colleagues studied a method of driving current to heat the plasma called Lower Hybrid Current Drive (LHCD). The technique generates plasma current by launching microwaves into the tokamak, pushing the electrons in one direction — a prerequisite for steady-state operation.

Furthermore, the strength of the Alcator magnets has allowed researchers to investigate LHCD at a plasma density high enough to be relevant for a fusion reactor. The encouraging results of their experiments have been published in Physical Review Letters.  

Pioneering LHCD

“The conventional way of running a tokamak uses a central solenoid to drive the current inductively,” Baek says, referring to the magnetic coil that fills the center of the torus. “But that inherently restricts the duration of the tokamak pulse, which in turn limits the ability to scale the tokamak into a steady-state power reactor.”

Baek and his colleagues believe LHCD is the solution to this problem.

MIT scientists have pioneered LHCD since the 1970s, using a series of “Alcator” tokamaks known for their compact size and high magnetic fields. On Alcator C-Mod, LHCD was found to be efficient for driving currents at low density, demonstrating plasma current could be sustained non-inductively. However, researchers discovered that as they raised the density in these experiments to the higher levels necessary for steady-state operation, the effectiveness of LHCD to generate plasma current disappeared.

This fall-off in effectiveness as density increased was first studied on Alcator C-Mod by research scientist Gregory Wallace.

“He measured the fall-off to be much faster than expected, which was not predicted by theory,” Baek explains. “The last decade people have been trying to understand this, because unless this problem is solved you can’t really use this in a reactor.”

Researchers needed to find a way to boost effectiveness and overcome the LHCD density limit. Finding the answer would require a close examination of how lower hybrid (LH) waves respond to the tokamak environment.

Driving the current

Lower hybrid waves drive plasma current by transferring their momentum and energy to electrons in the plasma.

Head of the PSFC’s Physics Theory and Computation Division, senior research scientist Paul Bonoli compares the process to surfing. 

“You are on a surf board and you have a wave come by. If you just sit there the wave will kind of go by you,” Bonoli says. “But if you start paddling, and you get near the same speed as the wave, the wave picks you up and starts transferring energy to the surf board. Well, if you inject radio waves, like LH waves, that are moving at velocities near the speed of the particles in the plasma, the waves start to give up their energy to these particles.”

Temperatures in today’s tokamaks — including C-Mod — are not high enough to provide good matching conditions for the wave to transfer all its momentum to the plasma particles on the first pass from the antenna, which launches the waves to the core plasma. Consequently, researchers noticed, the injected microwave travels through the core of the plasma and beyond, eventually interacting multiple times with the edge, where its power dissipates, particularly when the density is high.

Exploring the scrape-off layer

Baek describes this edge as a boundary area outside the main core of the plasma where, in order to control the plasma, researchers can drain — or “scrape-off” — heat, particles, and impurities through a divertor. This edge has turbulence, which, at higher densities, interacts with the injected microwaves, scattering them, and dissipating their energy.

“The scrape-off layer is a very thin region. In the past RF scientists didn’t really pay attention to it,” Baek says. “Our experiments have shown in the last several years that interaction there can be really important in understanding the problem, and by controlling it properly you can overcome the density limit problem.”

Baek credits extensive simulations by Wallace and PSFC research scientist Syun’ichi Shiraiwa for indicating that the scrape-off layer was most likely the location where LH wave power was being lost.

Detailed research on the edge and scrape-off-layer conducted on Alcator C-Mod in the last two decades has documented that raising the total electrical current in the plasma narrows the width of the scrape-off-layer and reduces the level of turbulence there, suggesting that it may reduce or eliminate its deleterious effects on the microwaves.

Motivated by this, PSFC researchers devised an LHCD experiment to push the total current by from 500,000 Amps to 1,400,000 Amps, enabled by C-Mod’s high-field tokamak operation. They found that the effectiveness of LCHD to generate plasma current, which had been lost at high density, reappeared. Making the width of the turbulent scrape-off layer very narrow prevents it from dissipating the microwaves, allowing higher densities to be reached beyond the LHCD density limit.

The results from these experiments suggest a path to a steady-state fusion reactor. Baek believes they also provide additional experimental support to proposals by the PSFC to place the LHCD antenna at the high-field (inboard) side of a tokamak, near the central solenoid. Research suggests that placing it in this quiet area, as opposed to the turbulent outer midplane, would minimize destructive wave interactions in the plasma edge, while protecting the antenna and increasing its effectiveness. Principal Research scientist Steven Wukitch is currently pursuing new LHCD research in this area through PSFCs’ collaboration with the DIII-D tokamak in San Diego.

Although existing tokamaks with LHCD are not operating at the high densities of C-Mod, Baek feels that the relationship between the current drive and the scrape-off layer could be investigated on any tokamak.

“I hope our recipe for improving LHCD performance will be explored on other machines, and that these results invigorate further research toward steady-state tokamak operation,” he says.



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Tissue architecture affects chromosome segregation

All growth and reproduction relies on a cell’s ability to replicate its chromosomes and produce accurate copies of itself. Every step of this process takes place within that cell.

Based on this observation, scientists have studied the replication and segregation of chromosomes as a phenomenon exclusively internal to the cell. They traditionally rely on warm nutritional cultures that promote growth but bear little resemblance to the cell’s external surroundings while in its natural environment.

New research by a group of MIT biologists reveals that this long-held assumption is incorrect. In a paper published this week, they describe how some types of cells rely on signals from surrounding tissue in order to maintain chromosome stability and segregate accurately. 

Kristin Knouse, a fellow at the Whitehead Institute, is the lead author of the paper, which was published online in the journal Cell on Aug. 23. Angelika Amon, the Kathleen and Curtis Marble Professor in Cancer Research in the Department of Biology and a member of the Koch Institute for Integrative Cancer Research, is the senior author.

“The main takeaway from this paper is that we must study cells in their native tissues to really understand their biology,” Amon says. “Results obtained from cell lines that have evolved to divide on plastic dishes do not paint the whole picture.”

When cells replicate, the newly duplicated chromosomes line up within the cell and cellular structures pull one copy to each side. The cell then divides down the middle, separating one copy of each chromosome into each new daughter cell.

At least, that’s how it’s supposed to work. In reality, there are sometimes errors in the process of separating chromosomes into daughter cells, known as chromosome mis-segregation. Some errors simply result in damage to the DNA. Other errors can result in the chromosomes being unevenly divided between daughter cells, a condition called aneuploidy.

These errors are almost always harmful to cell development and can be fatal. In developing embryos, aneuploidy can cause miscarriages or developmental disorders such as Down syndrome. In adults, chromosome instability is seen in a large number of cancers.

To study these errors, scientists have historically removed cells from their surrounding tissue and placed them into easily controlled plastic cultures.

“Chromosome segregation has been studied in a dish for decades,” Knouse says. “I think the assumption was … a cell would segregate chromosomes the same way in a dish as it would in a tissue because everything was happening inside the cell.”

However, in previous work, Knouse had found that reported rates for aneuploidy in cells grown in cultures was much higher than the rates she found in cells that had grown within their native tissue. This prompted her and her colleagues to investigate whether the surroundings of a cell influence the accuracy with which that cell divided.

To answer this question, they compared mis-segregation rates between five different cell types in native and non-native environments.

But not all cells’ native environments are the same. Some cells, like those that form skin, grow in a very structured context, where they always have neighbors and defined directions for growth. Other cells, however, like cells in the blood, have greater independence, with little interaction with the surrounding tissue.

In the new study, the researchers observed that cells that grew in structured environments in their native tissues divided accurately within those tissues. But once they were placed into a dish, the frequency of chromosome mis-segregation drastically increased. The cells that were less tied to structures in their tissue were not affected by the lack of architecture in culture dishes.

The researchers found that maintaining the architectural conditions of the cell’s native environment is essential for chromosome stability. Cells removed from the context of their tissue don’t always faithfully represent natural processes.

The researchers determined that architecture didn’t have an obvious effect on the expression of known genes involved in segregation. The disruption in tissue architecture likely causes mechanical changes that disrupt segregation, in a manner that is independent of mutations or gene expression changes.

“It was surprising to us that for something so intrinsic to the cell — something that's happening entirely within the cell and so fundamental to the cell's existence — where that cell is sitting actually matters quite a bit,” Knouse says.

Through the Cancer Genome Project, scientists learned that despite high rates of chromosome mis-segregation, many cancers lack any mutations to the cellular machinery that controls chromosome partitioning. This left scientists searching for the cause of the increase of these division errors. This study suggests that tissue architecture could be the culprit.

Cancer development often involves disruption of tissue architecture, whether during tumor growth or metastasis. This disruption of the extracellular environment could trigger chromosome segregation errors in the cells within the tumor.

“I think [this paper] really could be the explanation for why certain kinds of cancers become chromosomally unstable,” says Iain Cheeseman, a professor of biology at MIT and a member of the Whitehead Institute, who was not involved in the study.

The results point not only to a new understanding of the cellular mechanical triggers and effects of cancers, but also to a new understanding of how cell biology must be studied.

“Clearly a two-dimensional culture system does not faithfully recapitulate even the most fundamental processes, like chromosome segregation,” Knouse says. “As cell biologists we really must start recognizing that context matters.”

This work was supported by the National Institutes of Health, the Kathy and Curt Marble Cancer Research Fund, and the Koch Institute Support (core) Grant from the National Cancer Institute.



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