Trapping individual cell types in the mouse brain

Lines labeling cortical subplate, mesencephalic, and diencephalic cell types

Lines labeling cortical subplate, mesencephalic, and diencephalic cell types (see Fig. 7 in Shima et al.)

The complexity of the human brain depends upon the many thousands of individual types of nerve cells it contains. Even the much simpler mouse brain probably contains 10,000 or more different neuronal cell types. Brandeis scientists Yasu Shima, Sacha Nelson and colleagues report in the journal eLife on a new approach for genetically identifying and manipulating these cell types.

Cells in the brain have different functions and therefore express different genes. Important instructions for which genes to express, in which cell types, lie not only in the genes themselves, but in small pieces of DNA called enhancers found in the large spaces between genes. The Brandeis group has found a way to highjack these instructions to express other artificial genes in particular cell types in the mouse brain. Some of these artificially expressed genes (also called transgenes) simply make the cells fluorescent so they can be seen under the microscope. Other transgenes are master regulators that can be used to turn on or off any other gene of interest. This will allow scientists to activate or deactivate the cells to see how they alter behavior, or to study the function of specific genes by altering them only in some cell types without altering them everywhere in the body. In addition to developing the approach, the Brandeis group created a resource of over 150 strains of mice in which different brain cell types can be studied.


Shima Y, Sugino K, Hempel C, Shima M, Taneja P, Bullis JB, Mehta S, Lois C, Nelson SB. A mammalian enhancer trap resource for discovering and manipulating neuronal cell types. eLife. 2016;5.

Simons Foundation funds Brandeis Math, Physics collaborations

In 2014, the Simons Foundation, one of the world’s largest and most prominent basic science philanthropies, launched an unprecedented program to fund multi-year, international research collaborations in mathematics and theoretical physics. These are $10M grants over four years, renewable, that aim to drive progress on fundamental scientific questions of major importance in mathematics, theoretical physics, and theoretical computer science. There were 82 proposals in this first round. In September 2015, two were funded. Both involve Brandeis.

Matthew Headrick (Physics) is deputy director of the Simons Collaboration It from Qubit, which involves 16 faculty members at 15 institutions in six countries. This project is trying from multiple angles to bring together physics and quantum information theory, and show how some fundamental physical phenomena (spacetime, black holes etc.) emerge from the very nature of quantum information. Fundamental physics and quantum information theory remain distinct disciplines and communities, separated by significant barriers to communication and collaboration. “It from Qubit” is a large-scale effort by some of the leading researchers in both communities to foster communication, education and collaboration between them, thereby advancing both fields and ultimately solving some of the deepest problems in physics. The overarching scientific questions motivating the Collaboration include:

  • Does spacetime emerge from entanglement?
  • Do black holes have interiors?
  • Does the universe exist outside our horizon?
  • What is the information-theoretic structure of quantum field theories?
  • Can quantum computers simulate all physical phenomena?
  • How does quantum information flow in time?

Bong Lian (Mathematics) is a member of the Simons Collaboration on Homological Mirror Symmetry, which involves nine investigators from eight different institutions in three countries. Mirror Symmetry, first discovered by theoretical physicists in late ‘80s, is a relationship between two very different-looking physical models of Nature, a remarkable equivalence or “duality” between different versions of a particular species of multidimensional space or shape (Calabi-Yau manifolds) that seemed to give rise to the same physics. People have been trying to give a precise and general mathematical description of this mirroring ever since, and in the process have generated a long list of very surprising and far-reaching mathematical predictions and conjectures. The so-called “Homological Mirror Symmetry Conjecture” (HMS) may be thought of as a culmination of these efforts, and Lian was a member of the group (including S.-T. Yau) that gave a proof of a precursor to HMS in a series of papers in the late ‘90s.

Lian and his Simons collaborators are determined to prove HMS in full generality and explore its applications. One consequence of HMS says that if one starts from a “complex manifold” (a type of even-dimensioned space that geometers have been studying since Riemann described the first examples in 1845), then all its internal geometric structures can in fact be described using a certain partner space, called a “symplectic manifold”. The latter type of space was a mathematical edifice invented to understand classical physics in the mid-1900s. This connection goes both ways: any internal geometric structure of the symplectic partner also has an equally compelling description using the original complex partner. No one had even remotely expected such a connection, especially given that the discoveries of the two types of spaces — complex and symplectic — were separated by more than 100 years and were invented for very different reasons. If proven true, HMS will give us ways to answer questions about the internal geometric structure of a complex manifold by studying its symplectic partner, and vice versa.

Proving HMS will also help resolve many very difficult problems in enumerative geometry that for more than a century were thought to be intractable. Enumerative geometry is an ancient (and until recently moribund) branch of geometry in which people count the number of geometric objects of a particular type that can be contained inside a space. Mirror symmetry and HMS have turned enumerative geometry into a new way to characterize and relate shapes and spaces.

Two Science Students Are Fulbright Fellows

Two of the five Brandeis undergraduates and recent alumni that have been selected to teach English overseas as Fulbright Fellows are Division of Science students.

Abby Brooks ’16 and Joel Burt-Miller ’16 have received English Teaching Assistantships through the Fulbright grant program. Brooks is a double major in biology and history. She will be teaching in Laos. Joel Burt-Miller ’16 is a double major in biology and Health: Science, Society and Policy. He will be teaching in India.

Find more information about our soon-to-be graduates and the Fulbright program on BrandeisNow.

7th Annual Jay Pepose Award to be presented April 12 at 12:30 pm

David WilliamsDavid Williams from the University of Rochester has been selected to receive the 7th annual Jay Pepose ’75 Award in Vision Sciences. Williams will be presented with the Pepose award on Tuesday, April 12th at 12:30 pm in Gerstenzang 121. The celebration will include David Williams talk titled, “Seeing Through the Retina”.

Williams’ research has improved the effectiveness of laser refractive surgery, the design of contact lenses, and enabled the imaging of single cells in the retina.

Yoshinori Ohsumi to Receive Rosenstiel Award Wednesday, April 6

ohsumi220Biologist Yoshinori Ohsumi will receive the 45th Rosenstiel Award for Distinguished Work in Biomedical Science this Wednesday, April 6th at 4:00 pm in Gerstenzang 123. At that time, he will present a lecture titled, “Lessons from yeast: Cellular recycling system, autophagy”.

Ohsumi is a cell biologist and professor at the Tokyo Institute of Technology’s Frontier Research Center in Japan. He is one of leading experts in the world on autophagy, a process that allows for the degradation and recycling of cellular components. The Rosenstiel Award is being given to Ohsumi in recognition of his pioneering discoveries in autophagy.

Learn more about Professor Ohsumi and his research at BrandeisNow.

Fruit flies alter their sleep to beat the heat

Do you have trouble sleeping at night in the summer when it is really hot?

Does a warm sunny day make you want to take a nap?

You are not alone — fruit flies also experience changes in their sleep patterns when ambient temperature is high. In a new paper in Current Biology, research scientist Katherine Parisky and her co-workers from the Griffith lab show that hot temperatures cause animals to sleep more during the day and less at night, and then investigate the mechanisms governing the behavior.

The increase in daytime sleep is caused by a complex interplay between light and the circadian clock. The balance between daytime gains and nighttime losses at high temperatures is also influenced by homeostatic processes that work to keep total daily sleep amounts constant. This study shows how the nervous system deals with changes caused by environmental conditions to maintain normal operations.

Parisky KM, Agosto Rivera JL, Donelson NC, Kotecha S, Griffith LC. Reorganization of Sleep by Temperature in Drosophila Requires Light, the Homeostat, and the Circadian Clock. Curr Biol. 2016.

Four Brandeis Science Grads Receive 2016 NSF Graduate Fellowships

GRFP_logoA science education at Brandeis University can be a springboard to future science achievements. We would like to congratulate four of our science graduates who have received the prestigious National Science Foundation Graduate Research Fellowships for 2016.

Noam Saper

Noam was an outstanding student graduating summa cum laude with highest honors in Chemistry in 2015. At Brandeis, Noam worked in the labs of Prof. Barry Snider and Prof. Christine Thomas. He co-authored 3 publications with Snider and Thomas.

Noam received multiple awards including the Barry M. Goldwater Scholarship (2014); the Elihu A. Silver Prize (2014); and the Doris Brewer Cohen Endowment Award (2015).

Following graduation and enthralled by the mysteries of the west coast, he decided to attend the University of California, Berkeley. Noam is working on mechanistic studies of Ni-catalyzed diaryl ether hydrogenolysis in Professor John Hartwig’s laboratory.

Alexandra Sun

Another outstanding Chemistry student, Alexandra Sun graduated magna cum laude with highest honors in 2015. Alexandra also worked in Christine Thomas’ lab where she carried out research on Transition Metal Complexes Featuring a Redox-Active Bidentate Amido-Phosphido Ligand. Alexandra received the Melvin M. Snider Prize in Chemistry in 2015.

She is currently a first-year student in the Chemistry Department at the University of Michigan working with Professor Corey Stephenson on developing new methods in photoredox catalysis.

Abigail Zadina

Abigail received her BS/MS in Neuroscience in 2013. Working in Michael Rosbash’s lab, she was a co-author on 2 publications and received numerous awards including the Doris Brewer Cohen award and the Elihu Silver Prize. In 2013, Abigail discussed her science experience in the Brandeis publication Imprint.

Following graduation, Abigail worked at Columbia in Richard Axel’s lab. She is currently a PhD student in Neurobiology and Behavior at Columbia University.

Joseph Jacobowitz

Joseph Jacobowitz received his BS/MS in 2014, graduating summa cum laude with Highest Honors in Biochemistry. While a Brandeis undergraduate, Joseph co-authored a publication with his faculty mentor, Doug Theobald. In 2013, Joseph received the Division of Science Prize for Outstanding Research Accomplishment and the William P. Jencks  Award in Biochemistry in 2014.

Joseph is in the Biology PhD program at MIT, working for Jing-Ke Weng on the origins of chemodiversity in plants.

Summer Research at Brandeis

All four science graduates had the opportunity to jump start their careers by doing summer research at Brandeis. Noam, Alexandra and Joseph were Division of Science Summer Undergraduate Research Fellows (SURF). Abigail received a Computational Neuroscience Traineeship.

These undergraduate research programs enable students to spend their summers at Brandeis engaged in intensive undergraduate training and summer research. Both programs provide a stipend, faculty mentoring and full-time lab research. The Summer Undergraduate Research Fellows work culminates in a poster presentation summarizing their work. The SURF program is funded by generous donations from alumni. The Computational Neuroscience Traineeship program begins in the summer and runs through the following academic year. It is funded through a grant from the National Institute on Drug Abuse. 

Acid, Base and Electrical Charge at the Water Surface

Liquid water seems simple, but there’s a lot of chemistry going on in it.
It is common knowledge that, in pure water, under ordinary conditions, 1 in every 10 million H2O molecules is dissociated into the acid ion H+ and the base ion OH. However, what preference, if any, these self-ions of water have to sit at the air water interface has been the subject of lengthy and heated debate. The question is consequential in a wide range of contexts, including on the surface of droplets in the atmosphere and at the surfaces of biomolecules.  The Herzfeld group has now bridged the gap between experiment and theory by using a model that efficiently balances three subtle features of water molecules (polarizability, H+ sharing, and H+ transfer) that control the ambient behavior of the liquid. The model predicts that OH– prefers the air-water interface while H+ avoids it, consistent with observations of the response of air bubbles in water to an applied electric field.
Bai C, Herzfeld J. Surface Propensities of the Self-Ions of Water. ACS Central Science. 2016.

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