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A chemical approach to imaging cells from the inside

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The following press release was issued today by the Broad Institute of MIT and Harvard.

A team of researchers at the McGovern Institute and Broad Institute of MIT and Harvard has developed a new technique for mapping cells. The approach, called DNA microscopy, shows how biomolecules such as DNA and RNA are organized in cells and tissues, revealing spatial and molecular information that is not easily accessible through other microscopy methods. DNA microscopy also does not require specialized equipment, enabling large numbers of samples to be processed simultaneously.

“DNA microscopy is an entirely new way of visualizing cells that captures both spatial and genetic information simultaneously from a single specimen,” says first author Joshua Weinstein, a postdoctoral associate at the Broad Institute. “It will allow us to see how genetically unique cells — those comprising the immune system, cancer, or the gut, for instance — interact with one another and give rise to complex multicellular life.”

The new technique is described in Cell. Aviv Regev, core institute member and director of the Klarman Cell Observatory at the Broad Institute and professor of biology at MIT, and Feng Zhang, core institute member of the Broad Institute, investigator at the McGovern Institute for Brain Research at MIT, and the James and Patricia Poitras Professor of Neuroscience at MIT, are co-authors. Regev and Zhang are also Howard Hughes Medical Institute Investigators.

The evolution of biological imaging

In recent decades, researchers have developed tools to collect molecular information from tissue samples, data that cannot be captured by either light or electron microscopes. However, attempts to couple this molecular information with spatial data — to see how it is naturally arranged in a sample — are often machinery-intensive, with limited scalability.

DNA microscopy takes a new approach to combining molecular information with spatial data, using DNA itself as a tool.

To visualize a tissue sample, researchers first add small synthetic DNA tags, which latch on to molecules of genetic material inside cells. The tags are then replicated, diffusing in “clouds” across cells and chemically reacting with each other, further combining and creating more unique DNA labels. The labeled biomolecules are collected, sequenced, and computationally decoded to reconstruct their relative positions and a physical image of the sample.

The interactions between these DNA tags enable researchers to calculate the locations of the different molecules — somewhat analogous to cell phone towers triangulating the locations of different cell phones in their vicinity. Because the process only requires standard lab tools, it is efficient and scalable.

In this study, the authors demonstrate the ability to molecularly map the locations of individual human cancer cells in a sample by tagging RNA molecules. DNA microscopy could be used to map any group of molecules that will interact with the synthetic DNA tags, including cellular genomes, RNA, or proteins with DNA-labeled antibodies, according to the team.

“DNA microscopy gives us microscopic information without a microscope-defined coordinate system,” says Weinstein. “We’ve used DNA in a way that’s mathematically similar to photons in light microscopy. This allows us to visualize biology as cells see it and not as the human eye does. We’re excited to use this tool in expanding our understanding of genetic and molecular complexity.”

Funding for this study was provided by the Simons Foundation, Klarman Cell Observatory, NIH (R01HG009276, 1R01- HG009761, 1R01- MH110049, and 1DP1-HL141201), New York Stem Cell Foundation, Simons Foundation, Paul G. Allen Family Foundation, Vallee Foundation, the Poitras Center for Affective Disorders Research at MIT, the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, J. and P. Poitras, and R. Metcalfe. 

The authors have applied for a patent on this technology.


Topics: Research, RNA, DNA, Broad Institute, Biological engineering, Brain and cognitive sciences, McGovern Institute, School of Science, School of Engineering, Imaging, Microscopy

Source: http://news.mit.edu/2019/chemical-approach-imaging-cells-inside-0620

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Two Sigma Ventures raises $288M, complementing its $60B hedge fund parent

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Eight years ago, Two Sigma Investments began an experiment in early-stage investing.

The hedge fund, focused on data-driven quantitative investing, was well on its way to amassing the $60 billion in assets under management that it currently holds, but wanted more exposure to early-stage technology companies, so it created a venture capital arm, Two Sigma Ventures.

At the time of the firm’s launch it made a series of investments, totaling about $70 million, exclusively with internal capital. The second fund was a $150 million vehicle that was backed primarily by the hedge fund, but included a few external limited partners.

Now, eight years and several investments later, the firm has raised $288 million in new funding from outside investors and is pushing to prove out its model, which leverages its parent company’s network of 1,700 data scientists, engineers and industry experts to support development inside its portfolio.

The world is becoming awash in data and there’s continuing advances in the science of computing,” says Two Sigma Ventures co-founder Colin Beirne. “We thought eight years ago when when started, that more and more companies of the future would be tapping into those trends.”

Beirne describes the firm’s investment thesis as being centered on backing data-driven companies across any sector — from consumer technology companies like the social networking monitoring application, Bark, or the high-performance, high-end sports wearable company, Whoop.

Alongside Beirne, Two Sigma Ventures is led by three other partners: Dan Abelon, who co-founded SpeedDate and sold it to IAC; Lindsey Gray, who launched and led NYU’s Entrepreneurial Institute; and Villi Iltchev, a former general partner at August Capital.

Recent investments in the firm’s portfolio include Firedome, an endpoint security company; NewtonX, which provides a database of experts; Radar, a location-based data analysis company; and Terray Therapeutics, which uses machine learning for drug discovery.

Other companies in the firm’s portfolio are farther afield. These include the New York-based Amper Music, which uses machine learning to make new music; and Zymergen, which uses machine learning and big data to identify genetic variations useful in pharmaceutical and industrial manufacturing.

Currently, the firm’s portfolio is divided between enterprise investments, consumer-facing deals and healthcare-focused technologies. The biggest bucket is enterprise software companies, which Beirne estimates represents about 65% of the portfolio. He expects the firm to become more active in healthcare investments going forward.

“We really think that the intersection of data and biology is going to change how healthcare is delivered,” Beirne says. “That looks dramatically different a decade from now.”

To seed the market for investments, the firm’s partners have also backed the Allen Institute’s investment fund for artificial intelligence startups.

Together with Sequoia, KPCB and Madrona, Two Sigma recently invested in a $10 million financing to seed companies that are working with AI. “This is a strategic investment from partner capital,” says Beirne.

Typically startups can expect Two Sigma to invest between $5 million and $10 million with its initial commitment. The firm will commit up to roughly $15 million in its portfolio companies over time.

Read more: https://techcrunch.com/2020/01/22/two-sigma-ventures-raises-288-million-complementing-its-60-billion-hedge-fund-parent/

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German football league Bundesliga teams with AWS to improve fan experience

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Germany’s top soccer (football) league, Bundesliga, announced today it is partnering with AWS to use artificial intelligence to enhance the fan experience during games.

Andreas Heyden, executive vice president for digital sports at the Deutsche Fußball Liga, the entity that runs Bundesliga, says that this could take many forms, depending on whether the fan is watching a broadcast of the game or interacting online.

“We try to use technology in a way to excite a fan more, to engage a fan more, to really take the fan experience to the next level, to show relevant stats at the relevant time through broadcasting, in apps and on the web to personalize the customer experience,” Heyden said.

This could involve delivering personalized content. “In times like this when attention spans are shrinking, when a user opens up the app the first message should be the most relevant message in that context in that time for the specific user,” he said.

It also can help provide advanced statistics to fans in real time, even going so far as to predict the probability of a goal being scored at any particular moment in a game that would have an impact on your team. Heyden thinks of it as telling a story with numbers, rather than reporting what happened after the fact.

“We want to, with the help of technology, tell stories that could not have been told without the technology. There’s no chance that a reporter could come up with a number of what the probability of a shot [scoring in a given moment]. AWS can,” he said.

Werner Vogels, CTO at Amazon, says this about using machine learning and other technologies on the AWS platform to add to the experience of watching the game, which should help attract younger fans, regardless of the sport. “All of these kind of augmented customer fan experiences are crucial in engaging a whole new generation of fans,” Vogels told TechCrunch.

He adds that this kind of experience simply wasn’t possible until recently because the technology didn’t exist. “These things were impossible five or 10 years ago, mostly because now with all the machine learning software, as well as how the [pace of technology] has accelerated at such a [rate] at AWS, we’re now able to do these things in real time for sports fans.”

Bundesliga is not just any football league. It is the second biggest in the world in terms of revenue, and boasts the highest stadium attendance of all football teams worldwide. Today’s announcement is an extension of an ongoing relationship between DFL and AWS, which started in 2015 when Heyden helped move the league’s operations to the cloud on AWS.

Heyden says that it’s not a coincidence he ended up using AWS instead of another cloud company. He has known Vogels (who also happens to be a huge soccer fan) for many years, and has been using AWS for more than a decade, even well before he joined the DFL. Today’s announcement is an extension of that long-term relationship.

Read more: https://techcrunch.com/2020/01/24/german-football-league-bundesliga-teams-with-aws-to-improve-fan-experience/

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Delta Air Lines startup partnerships are fueling innovation

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For the first time, this year Delta Air Lines had a large presence at CES. The carrier used much of its space to highlight the “parallel reality” screens developed by Misapplied Sciences and Sarcos Robotics, which brought its latest Guardian exoskeleton. At the show, I sat down with COO Gil West, an industry veteran with years of experience at a number of airlines and airplane manufacturers, to talk about how the company works with these startups.

Like all large companies, Delta has gone through a bit of a digital transformation in recent years by rebuilding a lot of the technical infrastructure that powers its internal and external services (though like all airlines, it also still has plenty of legacy tech that is hard to replace). This work enabled the company to move faster, rethink a lot of its processes and heightened the reality that a lot of this innovation has to come from outside the company.

“If you think about where we are as a world right now, it’s a Renaissance period for transportation,” West said. “Now, fortunately, we’re right in the middle of it, but if you think about the different modes of transportation and autonomous and electrification — and the technologies like AI and ML — everything is converging. There’s truly, I think, a transportation revolution — and we’ll play in it.

Read more: https://techcrunch.com/2020/01/14/delta-air-lines-startup-partnerships-are-fueling-innovation/

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