Leading Science: Magnifying the Mind

Brandeis Magnify the Mind

Written by Zosia Busé, B.A. ’20

Joshua Trachtenberg, graduated from Brandeis in 1990 and is a leader in studying the living brain in action using advanced imaging technology. After establishing his research laboratory at UCLA, he founded a company – Neurolabware – in order to build the sophisticated custom research microscopes that are needed to perform groundbreaking work in understanding how the brain develops and how diseases and injuries interrupt its normal functioning. His company is created by scientists and for scientists, and is unique in creating high quality microscopes that are easy to use but also have the flexibility to be used in creative ways in innovative experiments, and in combination with a variety of other devices.

Brandeis University is now seeking to acquire one of these advanced microscopes that can observe fundamental processes inside the living brains of animals engaged in advanced behaviors. The reasonant scanning two-photon microscope from Neurolabware allows researchers to understand and image large networks of neurons in order to visualize which cells and networks are involved with specific memories or how these processes go awry in disease. “This approach is unparalleled. There is no other technique around that could possibly touch this,” Trachtenberg says.

Previous two-photon technologies permitted only very slow imaging, allowing scientists to take a picture about every two seconds, but the resonant two-photon technology is a major breakthrough that allows scientists to take pictures at about 30 frames per second. This speed increase is a major game changer. Not only can one observe activity in the brain at a higher speed, but it is possible to take pictures at a speed that is faster than the movement artifacts that must be accounted for, such as breathing or heart beats. Because one can see the movement, it can be corrected, allowing high resolution functional imaging of structures as small as single synaptic spines in the living brain. Further, advances in laser technology and fluorescent labels now allow scientists to see deeper into the brain than ever before, compounding the recent advantages of increased speed.

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New Computational Neuroscience Textbook

Paul Miller bookComputational Neuroscience is an exciting branch of science, which is helping us understand how simple biophysical processes within cells such as neurons lead to complex and sometimes surprising neural responses, and how these neurons, when connected in circuits can give rise to the wide range of activity patterns underlying human thinking and behavior. To bridge the scales from molecules to mental activity, computer simulations of mathematical models are essential, as it is all too easy for us otherwise to produce descriptions of these complex interacting systems that are internally inconsistent. Simulations allow us to ask “given these ingredients, what is possible?”

Simulation showing how weaker input that is localized can produce spiking when stronger dispersed input does not.

The best way to study computational neuroscience is to write the computer codes that model a particular biological phenomenon, then see what the simulation does when you vary a parameter in the model. Therefore, the course I teach at Brandeis (NBIO 136B) is based around a large number of computer tutorials, in which students, some of whom have no computer-coding background, begin with codes of 5-10 lines that simulate charging of a capacitor, and end up completing codes that simulate the neural underpinnings of learning, pattern recognition, memory, and decision-making. It turns out that very few computational principles are needed to build such codes, making these simulation methods far more easily understood and completed than any mathematical analysis of the systems. However, in the absence of a suitable introductory textbook—most computational neuroscience textbooks are designed by Ph.D. physicists and mathematicians for Ph.D. physicists and mathematicians—it proved difficult for me to use the flipped classroom approach (see below). Therefore, my goal was to create a text that students could read and understand on their own.

Different behaviors of a three-unit circuit as connection-strengths are changed. (Multistable constant activity states, multiple oscillating states, chaotic activity, heteroclinic state sequence). Each color represents firing rate of a unit as a function of time.

In keeping with the goal of the course—to help students gain coding expertise and understand biological systems through manipulations of computer codes—I produced over 100 computer codes (in Matlab) for the book, the vast majority of which are freely available online. (All codes used to produce figures and some tutorial solutions are accessible, but I retained over half of the tutorial solutions in case instructors wish to assign tutorials without students being able to seek a solution elsewhere.)

Learn more at MIT Press.

From the Preface of the book:

I designed this book to help beginning students access the exciting and blossoming field of computational neuroscience and lead them to the point where they can understand, simulate, and analyze the quite complex behaviors of individual neurons and brain circuits. I was motivated to write the book when progressing to the “flipped” or “inverted” classroom approach to teaching, in which much of the time in the classroom is spent assisting students with the computer tutorials while the majority of information-delivery is via students reading the material outside of class. To facilitate this process, I assume less mathematical background of the reader than is required for many similar texts (I confine calculus-based proofs to appendices) and intersperse the text with computer tutorials that can be used in (or outside of) class. Many of the topics are discussed in more depth in the book “Theoretical Neuroscience” by Peter Dayan and Larry Abbott, the book I used to learn theoretical neuroscience and which I recommend for students with a strong mathematical background.

The majority of figures, as well as the tutorials, have associated computer codes available online, at github.com/primon23/Intro-Comp-Neuro, and at my website. I hope these codes may be a useful resource for anyone teaching or wishing to further their understanding of neural systems.

 

Lorenz Studer to receive the 2018 Gabbay Award on October 9

Lorenz Studer, Director for the Center for Stem Cell Biology and a member of the Developmental Biology Program at Memorial Sloan Kettering Cancer Center will receive the 2018 Gabbay Award on October 9, 2018 at 4:00 PM at the Shapiro Campus Center Theater. At that time, Studer will deliver a talk titled “Building and Repairing the Human Brain: from Pluripotency to Cell Therapy.”

Lorenz Studer is receiving the award “in recognition of his innovative and transformative contributions to the fields of stem cell biology and patient-specific, cell-based therapy”.

The Gabbay Award was created in 1998 by the Jacob and Louise Gabbay Foundation in order to recognize scientists working in academia, medicine or industry for their outstanding achievements developing scientific content and significant results in the biomedical sciences.

“Lessons from the Lobster” details Eve Marder’s research

Lessons from Lobster. Photo courtesy of MIT.By Eve Marder

Students often tell me that they don’t want to be scientists because it is too lonely. That always surprises me, because laboratories are filled with people. One of the conclusions that readers of Charlotte Nassim’s “Lessons from the Lobster” should take from the book is that laboratories are communities of scholars of all ages. Lifelong friendships are often formed and sustained as laboratory colleagues may spend as much time together as they do with other friends and family. When Charlotte approached me about writing the story of my research, I was very surprised because there are many eminent neuroscientists, including many other eminent female neuroscientists. What convinced me to work with Charlotte was her wish to reach teenage girls, before they decided that a career in science was not for them. And this decision was validated when a few days ago, one of the students (now working in a neighboring lab) whom I had taught in NBio 140, Principles of Neuroscience, told me that she loved the book, but wished she had had it when she was in high school. We agreed that after she finished the book, that she would donate it to her small home town library, in the hopes that it would encourage other high school students to consider becoming scientists.

Charlotte’s book is a piece of science history. She read our lab notebooks, and talked to many ex-lab members. Her choices of what to emphasize and how to frame the scientific issues speak as much about what she finds scientifically and sociologically interesting as it does about what I was thinking. By reading deeply, she relied not only on my flawed memory, but on what I and others had written. For me, it is an extraordinary reminder that even scientists who revere data have only partial recollections of their own intellectual paths.

2018 Prizes and Awards Announced

Congratulations to all recipients of the 2018 prizes and awards for the Division of Science and the departments and programs within the Division.

Division of Science Prizes and Awards

  • Doris Brewer Cohen Award: Richard Haburcak (Math, Chemistry)
  • Rishon M. BIaler ’64 Memorial Prize: Abraham Cheloff (Biology, Neuroscience, Chemistry)
  • Schiff Memorial Award in Science: Meisui Liu (Biology) and Kathryn Shangraw (Biology)
  • Division of Science Prize for Outstanding Research Accomplishment: Heather Schiller (Biology, Neuroscience) and Jordan Saadon (Biology, Neuroscience)
  • Dr. Ralph Berenberg ’65 Prize (dentistry): Brandon Tran
  • Elihu A. Silver Prize (junior research): Julia Tartaglia (Biochemistry)
  • Steinberg Prize (Physical Science with interest in History): Mihir Khanna (Physics, Art History minor)

Biochemistry Prizes and Awards

  • Nathan O. Kaplan Prize in Biochemistry: Jessie Moore (Senior)
  • Professor Dagmar Ringe Biochemistry Award: Miriam Hood (Senior)
  • William P. Jencks Award in Biochemistry: Senmiao Sun (Senior)

Biology Prizes and Awards

  • Biology Department Award For Excellence in Research: Jason Xin
  • Chandler Fulton Prize for Undergraduate Research: Theresa Weis

Chemistry Prizes and Awards

  • Anatol Zhabotinsky Memorial Prize: Sumner Alperin-Lea
  • American Chemical Society Division of Physical Chemistry 2018 Undergraduate Award: Sumner Alperin-Lea
  • Chemistry Department Excellence Award: Samantha Shepherd
  • Melvin M. Snider Prize in Chemistry: Jamie Soohoo
  • American Chemical Society Division of Inorganic Chemistry 2018 Undergraduate Award: Elishua D. Litle
  • American Chemical Society Division of Organic Chemistry 2018 Undergraduate Award: Elishua D. Litle
  • Emily Dudek Undergraduate Teaching Assistant Award: Miriam Hood; Steven Wilhelm

Mathematics Prizes and Awards

  • Jerome Levine Thesis Prize (given annually to a graduate student in mathematics finishing with an outstanding PhD thesis): Yan Zhuang
  • Arnold Shapiro Prize in Mathematics (to a senior who has shown unusual talent and accomplishments in mathematical studies): Richard Haburcak

Neuroscience Prizes and Awards

  • Reis and Sowul Family Prize in Neuroscience: Amanda Shilton
  • John Lisman ’66 Memorial Award for Excellence in Neuroscience Research: Megan Leubner and Casey Lamar

Physics Prizes and Awards

  • Stephan Berko Memorial Prize (This endowed prize was established in 1991 by the family of the late Dr. Berko to annually recognize an outstanding student in Physics): Ali Aghvami (graduate); Carl Merrigan (graduate); Zachary Sustiel (undergraduate)
  • David L. Falkoff Prize (The Falkoff  Prize annually recognizes a graduate student in Physics who demonstrates excellence in teaching): Daichi Hayakawa
  • Physics Faculty Prize (Awarded to a graduating senior for excellence in Physics): Guillermo Narvaez Paliza; Liana Simpson

 

 

Raul Ramos Pays It Forward in His Home State of Texas


photo credit: Simon Goodacre

Helen Wong | Graduate School of Arts and Sciences

Raul Ramos, a fourth-year Ph.D. candidate in Neuroscience, spent the five-hour flight from Boston to Austin, Texas trying to think of what to say to a classroom full of adolescents who had been sentenced to juvenile detention, like he had been once when he was a teenager.

“I was trying to get into the mindset of it all,” he says of those nerve-wracking hours before arriving in Austin. “I was trying to remember how I felt when I had been in their shoes.” He had put together a talk and a script, but the moment he entered the first classroom at the Austin Alternative Learning Center, all of it went out the window. “Instead of giving a lecture, I had an actual conversation with the kids,” says Ramos. “They could relate to me. I was someone who looked like them, talked like them, moved like them. So they listened when I told them about my story and how, despite what they were facing now, their outcomes could be different too.”

Ramos first started working with high school students after he moved to Waltham. Anique Olivier-Mason PhD’12, Director of Education, Outreach and Diversity at the Materials Research Science and Engineering Center had arranged “Pizza Talks,” a program where graduate students in the sciences visit classrooms at Waltham High School and discuss their decisions to pursue careers in science, their experiences as investigators and their research. The program has been a great success and now serves as the model for similar talks taking place nationally, sponsored by the American Association for the Advancement of Science (AAAS). Ramos volunteered to give a talk when he first heard about the program.

“Waltham High has a large Hispanic student population,” says Ramos. “These groups underrepresented in science. I really liked going to speak to them and talking about my own journey and its relation to my identity.” AAAS became aware of this community outreach and contacted the university to learn more. Ramos has always been open about the troubles in his own past, so when AAAS were looking for scientists to speak to students in alternative learning centers in Austin, they asked him if he would like to go. “I said yes, of course,” says Ramos. “I’m from Texas originally, so I agreed to fly down and talk to the kids.”

What began as originally just one or two schools became six upon his arrival in Austin as word got around of his visit. During the trip, Ramos gave sixteen talks and spoke to around two hundred students. “I went to juvie centers, alternative learning centers, drug rehabilitation facilities,” he says. “The level of engagement was amazing. For every kid that didn’t want to engage, there were a few more who wanted to talk to me and learn about how I’d gotten to where I am. One of the most frequent questions they asked me was, ‘Sir, what do I do when I get out of here?’ and I would tell them the truth. I told them that once they got out, they would have to actively avoid situations and people that would get them in trouble. I said that if that meant having to hole up in their room to study and get away from it all, then doing that would absolutely be worth it in the long run. Their environment matters.”

But even after telling them his advice, Ramos knew that advice alone wasn’t going to be enough for many of the kids he was speaking to. “You need a support network,” he says. “A lot of these kids don’t have that. Some of them are safer in detention than at home. So many of them are angry–why wouldn’t they be? They’re supposed to become upstanding members of society, but the way the system goes about that is to lock them up and isolate them. That’s not how rehabilitation should work.”

At some of the facilities he visited, Ramos saw kids as young as eleven or twelve being escorted by armed guards from classroom to classroom despite some of them being barely half his size. For Ramos, the sight was jarring. “It looks like overkill,” says Ramos. “I know they’re here because they did something wrong, but at the end of the day, they’re just kids.”

It also struck Ramos, as he made the rounds in each facility, that the kids incarcerated at these centers were all people of color despite Austin being in a majority white part of Texas. “Brandeis is all about recruiting underrepresented minorities into its science programs,” he says. However, the challenges of recruiting students of color for doctoral programs in science are significant, and Ramos realized during his trip to Texas that “part of the reason for the absence of black and brown individuals in science was that so many of them, who could potentially be scientists someday, are stuck in juvie–stuck in environments that deprive them of opportunities and healthy role models.

“And people like me that manage to get an education, we make it out and we leave. We come over here to go to college, we leave Laredo [Ramos’ hometown], and these kids don’t get to have good role models. They make mistakes fueled by a terrible home environment and get stuck in the juvie-to-prison pipeline. They repent and feel bad in juvie, but once they get out, if they don’t have a support network, it starts all over again. The system tries them as full adults at seventeen, when they’re not even old enough to vote. Things have to change. I want to help make that happen and to show them that right now, there are still opportunities open to them.”

Despite all of the system’s shortcomings, the alternative learning centers and similar institutions are making a tangible difference. “The system’s not perfect,” says Ramos. “It’s deeply flawed. But things are already better now than when I was in. Back then, I was put in what would conventionally be considered a prison cell. At least most of these kids get an education, space to walk, and are surrounded by people who care about them. Everyone working at the Austin Alternative Learning Center was so motivated and clearly cared about the kids.”

Upon his return to Brandeis, Ramos decided that he would dedicate more time to community outreach and consider the possibility of working in science policy after earning his doctorate. He wants to do work that not only has value in the scientific world, but that also actively helps bolster diversity and inclusion in the field, helping fight back against larger societal and institutional structures that disadvantage people of color.

“We need representation to show kids that the journey is possible,” says Ramos. “The cards feel like they’re stacked almost the entire way through. I’m going to do whatever I have to do to get the message out there to those kids who are hardest to reach and who need to hear from us the most.”

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