Applications open for HHMI Interfaces Scholar Award Lecturer

The Quantitative Biology Program at Brandeis University, supported by a grant from Howard Hughes Medical Institute, is now accepting applications for an award for preparing an outstanding set of three pedagogical lectures on a subject at the interface of the physical and biomedical sciences.  These lectures will be given at the Quantitative Biology Bootcamp, January 26, through January 27, 2013.  The award consists of a cash prize of $2,000.

Any graduate student or postdoctoral research associate currently at Brandeis is eligible to apply.  The application packet should consist of short  curriculum vitae and a one page outline of the three lectures.  QB faculty will work with the successful applicant in preparing the lectures.  Applications should be submitted to Jen Scappini, (jscappin at brandeis dot edu). Due date will be discussed at meeting.

An information session for potential applicants will be held on Friday, October 26th, 9:30-10:00 in Kosow 207

A list of past winners and links to their lecture presentations can be found at


A Cellular Rocket Launcher links Actin, Microtubules, and Cancer

Cells contain thousands of protein “micromachines” performing a bewildering number of chemical reactions every second. The challenge for biologists in the 21st century is to integrate information about multiple – or even all – proteins into holistic models for the entire cell. This is a daunting task. The addition of any new component to a system can alter the behavior of the components already there. This phenomenon is especially familiar to biologists studying the cytoskeleton, a complex system of protein filaments that provide the force for cell division and migration, among other things. The building blocks of the cytoskeleton are simple proteins called tubulin and actin that assemble into a remarkable variety of shapes depending on context. While the basic chemistry of this assembly process has been understood in purified systems for decades, how it happens in cells is not well understood. For example, growth of actin filaments is a two-step process: nucleation, or the formation of a new filament, and elongation, or the extension of that existing filament. Both steps happen just fine when actin is present in pure form in a test tube. In cells, however, proteins called profilin and capping protein block these two steps, respectively. Nucleation and elongation can only occur because other proteins overcome these blocks. Thus, a faithful experimental system to study actin assembly as it would occur in a living cell requires – at a minimum – five purified proteins.

One technological advance of great importance is the ability to literally see single molecules (in this case proteins) using advanced fluorescence imaging. In such an experimental system, many details can be captured. In a recent publication in Science, Dr. Dennis Breitsprecher and colleagues in the Goode and Gelles labs, undertook this challenge and directly visualized the effects of key regulatory proteins helping actin proteins nucleate and grow into filaments in the presence of both profilin and capping protein. A previous study from the Goode lab had shown that two proteins, called APC and mDia1, together stimulate the growth of actin into filaments (Okada et al, 2010). In the present study, Breitsprecher and colleagues examined the mechanism by which APC and mDia1 overcome the profilin and capping protein-imposed blocks. To do this, they ‘tagged’ actin, APC and mDia1 with three different fluorescent dyes, each of a different color, and then filmed these molecules (using triple-color TIRF microscopy) in the act of building an actin filament to learn precisely what they are doing.

The authors began by imaging APC and actin (2 colors) at the same time. APC formed discrete spots on the microscope slide, and growing actin filaments emerged from them, suggesting than APC nucleates actin filament formation. As the filament emerged from the APC spot, APC stayed where it was: remaining stably associated at the site of nucleation. Next, the authors added dye-labeled mDia1 to the system, and observed mDia1 molecules staying attached to and ‘riding’ the fast-growing end of actin filament, while protecting it from capping protein.

The most remarkable result came when they visualized all three labeled molecules together (actin, APC, and mDia1). What they saw was that APC and mDia1 first come together in a stable complex even before actin arrives. Then APC recruits multiple actin subunits to initiate the nucleation of a filament. This complex was resistant to the blocks imposed by both profilin and capping protein. As the filament grew from the APC-mDia1 spot, mDia1 separated from APC and stayed bound to the growing end of the filament – protecting it from capping protein while it grows. Thus, even though APC and mDia1 have different activities, participating in different stages of the growth of a filament, they associate together before actin even arrives, likely so that once the actin filament is born, it is immediately protected from capping protein. This mechanism has been compared to a rocket launcher: APC is the launch pad for an actin filament, which is then propelled forward by mDia1.

Rocket launcher images and cartoon

Rocket launcher mechanism for APC and mDia1 nucleation. Left: Microscopic image of a growing actin filament. APC stays put while mDia1 remains associated with the fast growing end. Right: Model for the rocket launcher mechanism.

The new study provides great detail of the system: for example, the number of APC subunits required to nucleate actin filaments was determined, and the growth rate of actin filaments in the presence and absence of all the other components was measured. Ultimately, all of these data will be required to put together a detailed model of how actin filaments grow inside of real cells: details that would be difficult or impossible to obtain without employing single molecule analysis.

For the future, the authors have set their sights on even more challenging experiments aimed at elucidating the mysterious link between tubulin and actin fibers. APC and mDia1 are implicated in this linkage in living cells, but almost nothing is known about how they physically link and/or communicate information between the two systems. Since APC is mutated in some 80% of colon cancer tumors, understanding its multiple roles is of clinical as well as intellectual importance. This will be an exciting, if challenging, endeavor for the future.

Using PhADE in single molecule fluorescence imaging

Anna Loveland, a postdoc in the Grigorieff Lab, has a new paper, A general approach to break the concentration barrier in single-molecule imaging” that appeared today in Nature Methods online. The paper is based on her PhD work, which was done jointly in the labs of Antoine van Oijen and Johannes Walter at Harvard.

Single-molecule fluorescence imaging is often incompatible with physiological protein concentrations, as fluorescence background overwhelms an individual molecule’s signal. Loveland et al. employ a new imaging approach called PhADE (photoactivation, diffusion and excitation). A protein of interest is fused to a photoactivatable protein (mKikGR) and introduced to its surface-immobilized substrate. After photoactivation of mKikGR near the surface, rapid diffusion of the unbound mKikGR fusion out of the detection volume eliminates background fluorescence, whereupon the bound molecules are imaged. The authors labeled the eukaryotic DNA replication protein flap endonuclease 1 with mKikGR and added it to replication-competent Xenopus laevis egg extracts. PhADE imaging of high concentrations of the fusion construct revealed its dynamics and micrometer-scale movements on individual, replicating DNA molecules. Because PhADE imaging is in principle compatible with any photoactivatable fluorophore, it should have broad applicability in revealing single-molecule dynamics and stoichiometry of macromolecular protein complexes at previously inaccessible fluorophore concentrations.

Anna B Loveland, Satoshi Habuchi, Johannes C Walte & Antoine M van Oijen (2012) A general approach to break the concentration barrier in single-molecule imaging. Nature Methods

How does a hard-wired simple circuit generate multiple behaviors?

In a paper appearing in last week’s issue of Neuron, members of the Sengupta Lab and their collaborators from the Bargmann Lab describe how a fixed neural circuit produces multiple behaviors in a context-dependent manner.  The study was led by former Brandeis post-doctoral fellow Kyuhyung Kim in the Sengupta Lab (currently Assistant Professor at DGIST, Korea) and Rockefeller student Heeun Jang in the Bargmann Lab. Also involved in the study were current Brandeis MCB students Scott Neal and Danna Zeiger, and Dongshin Kim, the head of the Brandeis Microfluidics Facility.

For this study the researchers used the nematode Caenorhabditis elegans. The nervous system of C. elegans consists of only 302 neurons (in the adult hermaphrodite) whose anatomical connectivities are well-mapped. Despite its relatively small nervous system, C. elegans exhibits a wide range of behaviors in response to environmental stimuli. For instance, C. elegans exhibits varied responses to pheromones – small chemical substances used for intra-specific communication. Some pheromones are repulsive to adult hermaphrodite C. elegans but neutral to male C. elegans. However, reducing the function of the neuropeptide Y-like receptor NPR-1 results in hermaphrodites now exhibiting neutral pheromone responses and males becoming strongly attracted. The researchers asked how the sex and neuromodulatory state of the animal allows it to interpret the pheromone stimulus differently to generate distinct behavioral responses.

To answer this question, the researchers used behavioral assays, genetic manipulations of neuronal output, and in vivo measurements of pheromone-induced neuronal activity (using genetically encoded calcium sensors and customized microfluidics devices designed by the Brandeis Microfluidics Facility). They found that flexible output of a neuronal ‘hub-and-spoke’ circuit motif was responsible for generating these distinct pheromone responses under different conditions.

In this circuit, pheromone-sensing neurons ASK and ADL are connected to the central RMG motor/interneuron by gap junctions (see Figure). Jang et al. showed that in hermaphrodites with high levels of NPR-1 activity, the ADL sensory neurons respond strongly to a specific pheromone component and drive avoidance behavior via their chemical synapses to command interneurons for locomotion. However, sexual dimorphism in the circuit results in males having reduced ADL pheromone responses.  Moreover, Jang et al. showed that ADL synaptic output in males is further decreased via RMG and ASK-mediated antagonism (see Figure). As a result, males are indifferent to this pheromone.

The next issue the authors addressed is the role of NPR-1 activity in regulating pheromone responses. The Bargmann Lab had previously shown that high NPR-1 activity inhibits RMG, and under these conditions, pheromone responses of the ASK sensory neurons are low. Conversely, when NPR-1 activity is reduced or absent, ASK pheromone responses are enhanced. Jang et al. found that in the absence of NPR-1 activity, ADL chemical synaptic output in response to pheromones is antagonized by the RMG-ASK gap junction circuit. In other words, avoidance mediated by ADL chemical synaptic output is balanced by attraction mediated by the RMG-ASK gap junction circuit, resulting in hermaphrodites being neither attracted to nor avoiding this pheromone. In males with reduced NPR-1 activity the same effects are observed, however, since the ADL pheromone response is already lower in males, the RMG-ASK attraction-mediating arm “wins” resulting in attraction to pheromones.  The authors refer to these as overlapping ‘push-pull’ circuits in analogy with electronic circuits.

These results begin to explain how a small fixed circuit can generate a remarkable range of behaviors via alteration of sensory response properties as well as choice of specific synaptic output pathway as a function of neuromodulatory state and sex. The general theme of a circuit functioning differently under different neuromodulatory conditions has been extensively studied in the Marder Lab in the crustacean nervous system, and is an important principle to be kept in mind when interpreting functionality from structurally described connectomes.

Jang H(*), Kim K(*), Neal SJ, Macosko E, Kim D, Butcher RA, Zeiger DM, Bargmann CI, Sengupta P. Neuromodulatory State and Sex Specify Alternative Behaviors through Antagonistic Synaptic Pathways in C. elegans. Neuron. 2012;75(4):585-92.

Call for Speakers: Summer Life Science Seminar Series

Postdoctoral fellows Yuliya Sytnikova and Joana Enes write:

Dear Brandeis researchers,

Do you feel that summer is quite empty without seminars? Are you interested in learning about the research done in the life science departments at Brandeis? Then this is for you.

We proudly announce a series of Life Sciences Summer Seminars! This is intended to give opportunities mainly to postdoc students to present their work to the Brandeis scientific community, although young group leaders and last year’s graduate students are also encouraged to present.

WHEN?    On Mondays at 12 pm, from July 9th to August 20th

WHERE?    Rosenstiel 118


If you are interested in presenting, please reply to this email indicating your name, lab, department and title of the talk. Also, let us know of any dates that are not convenient for you. Spots are limited to 14 (2 per week), a minimum of 8 spots will be allocated to postdoc students on a first come first served basis.

We are also considering organizing a poster session to take place on the last day of the series. Please let us now if you would be interested in presenting a poster.

We look forward to seeing you in attendance at this great seminar series!

Joana and Yuliya

To sleep, perchance to learn?

Sleep deprivation is ubiquitous in today’s society, and we have all felt the effects of sleep loss on our ability to function optimally, physically and especially mentally. In particular, it has become clear that the brain requires sleep to efficiently establish many forms of long-term memory. However, it is still unknown what sleep deprivation actually does to the brain to impair its function. In a recently published review in the journal Cellular Signalling, authors Christopher G. Vecsey from Brandeis University and Robbert Havekes and Ted Abel from the University of Pennsylvania have tried to capture the current state of our knowledge about the molecular and cellular effects of sleep deprivation that could explain why sleep loss is so detrimental for memory formation. The review focuses primarily on memories for events and places, which are thought to be formed and stored in the area of the brain called the hippocampus.

A key approach to learn about the nitty-gritty effects of sleep deprivation has been research in rodents. Therefore, the authors begin by summarizing how sleep deprivation studies are carried out in rodents, and how sleep deprivation affects memory and several signaling pathways in the brain. Notably, they review the effects of sleep loss on neurotransmitter systems such as acetylcholine, glutamate, and GABA, all of which could potentially modulate learning and memory. The authors also discuss some of the newest and most exciting studies on the topic of sleep loss, including a handful of experiments in which researchers have been able to reverse the effects of sleep deprivation through pharmacological treatments. For example, the authors describe one of their own studies in which sleep deprivation in mice caused memory deficits and reduced signaling through the cAMP pathway, which is known to be crucial for long-term memory. This molecular effect was likely caused by accelerated breakdown of cAMP by phosphodiesterase 4 (PDE4). When mice were treated with a PDE4 inhibitor during the period of sleep deprivation, memory formation remained unaffected. Rescue of memory defects were also obtained in separate studies in which rodents were treated either with nicotine, caffeine, or CPT, an antagonist of the adenosine A1 receptor. Two related studies also found that the effects of sleep deprivation on memory could be ameliorated by prevention of transmitter release from cells in the brain called glia. This was the first indication that brain cells other than neurons are impacted by sleep deprivation and that they contribute to the effects of sleep loss on the ability to remember new information.

As the authors mention, goals for studies in the immediate future will be to identify additional ways that sleep deprivation affects the brain, determine why sleep deprivation targets these molecules, and discover how these targets interact with each other to impair the normal function of the brain. Finally, hopefully our growing knowledge can be used to develop treatments for the cognitive deficits produced by sleep loss in people, especially those who have impaired sleep due to a medical condition, such as insomnia, chronic pain, sleep apnea, or one of the many neurodegenerative or psychiatric disorders associated with disturbed sleep patterns.

Christopher G. Vecsey is a postdoctoral fellow in the Griffith Lab at Brandeis, where he continues to work on interactions between sleep and learning. Chris is supported by a postdoctoral fellowship from the National Institute of Mental Health.

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