Tag Archives: Jeff Lichtman

Nanoscale imaging of a mouse brain

Researchers have developed a new brain imaging tool they would like to use as a founding element for a national brain observatory. From a July 30, 2015 news item on Azonano,

A new imaging tool developed by Boston scientists could do for the brain what the telescope did for space exploration.

In the first demonstration of how the technology works, published July 30 in the journal Cell, the researchers look inside the brain of an adult mouse at a scale previously unachievable, generating images at a nanoscale resolution. The inventors’ long-term goal is to make the resource available to the scientific community in the form of a national brain observatory.

A July 30, 2015 Cell Press news release on EurekAlert, which originated the news item, expands on the theme,

“I’m a strong believer in bottom up-science, which is a way of saying that I would prefer to generate a hypothesis from the data and test it,” says senior study author Jeff Lichtman, of Harvard University. “For people who are imagers, being able to see all of these details is wonderful and we’re getting an opportunity to peer into something that has remained somewhat intractable for so long. It’s about time we did this, and it is what people should be doing about things we don’t understand.”

The researchers have begun the process of mining their imaging data by looking first at an area of the brain that receives sensory information from mouse whiskers, which help the animals orient themselves and are even more sensitive than human fingertips. The scientists used a program called VAST, developed by co-author Daniel Berger of Harvard and the Massachusetts Institute of Technology, to assign different colors and piece apart each individual “object” (e.g., neuron, glial cell, blood vessel cell, etc.).

“The complexity of the brain is much more than what we had ever imagined,” says study first author Narayanan “Bobby” Kasthuri, of the Boston University School of Medicine. “We had this clean idea of how there’s a really nice order to how neurons connect with each other, but if you actually look at the material it’s not like that. The connections are so messy that it’s hard to imagine a plan to it, but we checked and there’s clearly a pattern that cannot be explained by randomness.”

The researchers see great potential in the tool’s ability to answer questions about what a neurological disorder actually looks like in the brain, as well as what makes the human brain different from other animals and different between individuals. Who we become is very much a product of the connections our neurons make in response to various life experiences. To be able to compare the physical neuron-to-neuron connections in an infant, a mathematical genius, and someone with schizophrenia would be a leap in our understanding of how our brains shape who we are (or vice versa).

The cost and data storage demands for this type of research are still high, but the researchers expect expenses to drop over time (as has been the case with genome sequencing). To facilitate data sharing, the scientists are now partnering with Argonne National Laboratory with the hopes of creating a national brain laboratory that neuroscientists around the world can access within the next few years.

“It’s bittersweet that there are many scientists who think this is a total waste of time as well as a big investment in money and effort that could be better spent answering questions that are more proximal,” Lichtman says. “As long as data is showing you things that are unexpected, then you’re definitely doing the right thing. And we are certainly far from being out of the surprise element. There’s never a time when we look at this data that we don’t see something that we’ve never seen before.”

Here’s a link to and a citation for the paper,

Saturated Reconstruction of a Volume of Neocortex by Narayanan Kasthuri, Kenneth Jeffrey Hayworth, Daniel Raimund Berger, Richard Lee Schalek, José Angel Conchello, Seymour Knowles-Barley, Dongil Lee, Amelio Vázquez-Reina, Verena Kaynig, Thouis Raymond Jones, Mike Roberts, Josh Lyskowski Morgan, Juan Carlos Tapia, H. Sebastian Seung, William Gray Roncal, Joshua Tzvi Vogelstein, Randal Burns, Daniel Lewis Sussman, Carey Eldin Priebe, Hanspeter Pfister, Jeff William Lichtman. Cell Volume 162, Issue 3, p648–661, 30 July 2015 DOI: http://dx.doi.org/10.1016/j.cell.2015.06.054

This appears to be an open access paper.

AAAS 2013 meeting in Boston,US and Canadian research excellence

The 2013 annual meeting for the American Association for the Advancement of Science (AAAS) will be held in Boston, Massachusetts from Feb. 14 – 18, 2013 with a much better theme this year, The Beauty and Benefits of Science, than last year’s, Flattening the World. (It didn’t take much to improve the theme, eh?)

Plenary speakers range from AAAS’s president, William N. Press to Nathan Myhrvold, a venture capitalist to astrophysicist, Robert Kirshner to Cynthia Kenyon, a molecular biologist to Sherry Turkle. From the AAAS webpage describing Turkle’s 2013 plenary lecture,

Sherry Turkle

Abby Rockefeller Mauzé Professor of the Social Studies of Science and Technology in the Program in Science, Technology, and Society, MIT

The Robotic Moment: What Do We Forget When We Talk to Machines?

Dr. Turkle is founder and director of the MIT Initiative on Technology and Self. She received a joint doctorate in sociology and personality psychology from Harvard University and is a licensed clinical psychologist. Her research focuses on the psychology of human relationships with technology, especially in the realm of how people relate to computational objects. She is an expert on mobile technology, social networking, and sociable robotics and a regular media commentator on the social and psychological effects of technology. Her most recent book is Alone Together: Why We Expect More from Technology and Less from Each Other.

Given my experience last year in the 2012 meeting media room, I’m surprised to see a social media session is planned, from the session webpage,

Engaging with Social Media
Communicating Science
Thursday, February 14, 2013: 3:00 PM-4:30 PM
Ballroom A (Hynes Convention Center)

In a constantly changing online landscape, what is the best way for scientists and engineers to engage the public through social media? This session will discuss how people are accessing science information via blogs and social networks and the importance of researchers getting involved directly. [emphasis mine]  Speakers will address the ways that researchers can create meaningful interactions with the public through social media.

Organizer: Cornelia Dean, The New York Times
Co-Organizer: Dennis Meredith, Science Communication Consultant
Moderator: Carl Zimmer, Independent Science Journalist

Speakers:
XXXX Scicurious, Neurotic Physiology
Science Blogging for Fun and Profit
Christie Wilcox, University of Hawaii
Science in a Digital Age
Dominique Brossard, University of Wisconsin
Science and the Public in New Information Environments

I’d love to see how the theme of ‘researcher engaging directly’ gets developed. In theory, I have no problems with the concept. Unfortunately, those words are sometimes code for this perspective, ‘only experts (scientists/accredited journalists) should discuss or write about science’. A couple of quick comments, my Jan. 13, 2012 posting featured an interview with Carl Zimmer, this session’s moderator, about his science tattoo book and Dominique Brossard, one of the speakers, was last mentioned here in my Jan. 24, 2013 posting titled, Tweet your nano, in the context of a research study on social media and nanotechnology.

In keeping with the times (as per my Jan. 28, 2013 posting about the colossal research prizes for the Graphene and Human Brain Project initiatives), the 2012 AAAS annual meeting features a Brain Function and Plasticity thread or subtheme. There’s this session amongst others,

The Connectome: From the Synapse to Brain Networks in Health and Disease
Brain Function and Plasticity
Saturday, February 16, 2013: 8:30 AM-11:30 AM
Room 304 (Hynes Convention Center)

A series of innovative studies are being done to map the brain from the molecular to the systems level both structurally and functionally. At the synaptic level, how neurotransmitters, their receptors, and signaling pathways influence neural function and plasticity is becoming much better understood. Integrating neuronal function at the level of single neurons and groups of neurons into larger circuits at the anatomical level in the mammalian brain, while a daunting task, is being studied by advanced imaging techniques requiring vast amounts of information storage and processing. To integrate local circuit function with whole brain function, understanding the structure and processing of brain networks is critical. A major project to accomplish this task, the Human Connectome Project, is in the process of integrating the structure and function of brain networks using the most advanced imaging and analysis techniques in 1,200 people, including twins and their nontwin siblings. This step will allow for major new insights into not only brain structure and function, but also their genetic underpinnings. Comparing this information in both the normal brain and in different brain disorders such as neurodegenerative diseases is providing novel insights into how understanding brain function from the molecular to the systems level will provide insights into normal brain function and disease pathogenesis as well as provide new treatment strategies.

Organizer:

David Holtzman, Washington University

Speakers:

Mark F. Bear, Massachusetts Institute of Technology
Molecules and Mechanisms Involved in Synaptic Plasticity in Health and Disease
Jeff Lichtman, Harvard University
Connectomics: Developing a Wiring Diagram for the Mammalian Brain
Steve Petersen, Washington University
The Human Connectome Project
Marcus E. Raichle, Washington University
The Brain’s Dark Energy and the Default Mode Network
Nicole Calakos, Duke University
Synaptic Plasticity in the Basal Ganglia in Health and Disease
William W. Seeley, University of California
Brain Networks: Linking Structure and Function in Neurodegenerative Diseases

Then, there’s this session featuring graphene,

What’s Hot in Cold
Sunday, February 17, 2013: 8:30 AM-11:30 AM
Room 308 (Hynes Convention Center)

The study of ultracold atoms and molecules is now the frontier of low-temperature science, reaching temperatures of a few hundred picokelvin above absolute zero. This field was made possible by a technique that did not exist 30 years ago: laser cooling of atoms. It is hardly obvious that the laser, which produces the most intense light on Earth and is routinely used in industrial applications for cutting and welding medal, would also provide the most powerful coolant. Such are the surprises of science, where a breakthrough in one area transforms others in unexpected ways. Since 1997, eight Nobel Laureates in physics have been recognized for contributions to ultracold atomic and molecular science, which has become one of the most vibrant fields in physics, cutting across traditional disciplinary boundaries, e.g., atomic, molecular, and optical; condensed matter; statistical physics; and nuclear and particle physics. This field builds on two accomplishments that it was the first to achieve: first, the production of quantum degenerate matter using a wide range of elements and, second, exquisite control of quantum degenerate matter at the atomic level. These have led to record low temperatures, ultraprecise atomic clocks, and new forms of quantum matter that generalize ideas from magnetism superconductivity and graphene physics.

Organizer:

Charles W. Clark, Joint Quantum Institute

Speakers:

Markus Greiner, Harvard University
Quantum Simulation: A Microscopic View of Quantum Matter
Ana Maria Rey, University of Colorado
Atomic Clocks: From Precise Timekeepers to Quantum Simulators
Daniel Greif, ETH Zurich
Exploring Dirac Points with Ultracold Fermions in a Tunable Honeycomb Lattice
Gretchen Campbell, Joint Quantum Institute
Superflow in Bose-Einstein Condensate Rings: Tunable Weak Links in Atom Circuits
Benjamin Lev, Stanford University
New Physics in Strongly Magnetic Ultracold Gases

Amongst all these other sessions, there’s a session about Canadian science,

Introduction to Canadian Research Excellence: Evidence & Examples
Friday, February 15, 2013: 11:00 AM-12:00 PM
Room 205 (Hynes Convention Center)

The Canada Pavilion in the Exhibit Hall gives a taste of what lies north of Boston and the 49th parallel. Join us at this workshop to learn about opportunities in Canada for research and study. Canada recently completed a comprehensive analysis of its domestic science and technology strengths. The final report of the expert panel of the Council of Canadian Academies will be presented, including the use of global benchmarks and insights on international collaborations. Two of the drivers for Canadian excellence will be introduced: large-scale science facilities in key fields and a system of targeted fellowships and research chairs that recruit globally.

Coordinator:

Tim Meyer, TRIUMF

Presenters:

Tim Meyer, TRIUMF,
Chad Gaffield, Social Sciences and Humanities Research Council of Canada
Eliot Phillipson, University of Toronto

“Introduced,” really? Large scale science facilities are not new in Canada or anywhere else for that matter and the programmes of targeted fellowships have been around long enough and successful enough that it is being copied.

First, there was the Canada Research Chair programme, which was instituted in 2000. From the About Us page (Note: A link has been removed),

The Canada Research Chairs program stands at the centre of a national strategy to make Canada one of the world’s top countries in research and development. [emphasis mine]

In 2000, the Government of Canada created a permanent program to establish 2000 research professorships—Canada Research Chairs—in eligible degree-granting institutions across the country.

The Canada Research Chairs program invests $300 million per year to attract and retain some of the world’s most accomplished and promising minds.

This was programme was followed up with the Canada Excellence Research Chairs Program in 2008, from the Background page (Note: A link has been removed),

Launched in 2008, the Canada Excellence Research Chairs (CERC) Program supports Canadian universities in their efforts to build on Canada’s growing reputation as a global leader in research and innovation. The program awards world-renowned researchers and their teams up to $10 million over seven years to establish ambitious research programs at Canadian universities. These awards are among the most prestigious and generous available globally.

In May 2010, the first group of Canada Excellence Research Chairs was announced. Selected through a rigorous, multilevel peer review process, these chairholders are helping Canada build a critical mass of expertise in the four priority research areas of the federal government’s science and technology strategy …

Here’s an excerpt from my Feb. 21, 2012 posting,

Canadians have been throwing money at scientists for some years now (my May 20, 2010 posting about the Canada Excellence Research Chairs programme). We’ve attempted to recruit from around the world with our ‘research chairs’ and our ‘excellence research chairs’ and our Network Centres of Excellence (NCE) all serving as enticements.

The European Research Council (ERC) has announced that they will be trying to beat us at our own game at the AAAS 2012 annual meeting in Vancouver (this new ERC programme was launched in Boston, Massachusetts in January 2012).

The Canadian report these folks will be discussing was released in Sept. 2012 and was  featured here in a two-part commentary,

The State of Science and Technology in Canada, 2012 report—examined (part 1: the executive summary)

The State of Science and Technology in Canada, 2012 report—examined (part 2: the rest of the report)

My Sept. 27, 2012 posting features my response to the report’s launch on that day.

As for the AAAS 2013 annual meeting, there’s a lot, lot more of it and it’s worth checking out, if for no other reason than to anticipate the types of science stories you will be seeing in the coming months.