Signals on the move

A hallmark feature of eukaryotic cells is their intricate subcellular membrane compartmentalization, which biochemically and spatially isolates cellular processes including signal transduction, protein synthesis, and energy production. Membrane-spanning proteins such as growth factor receptors are transported through these compartments by the actions of a host of membrane binding proteins that bend, pinch and move bits of cargo-containing membrane from one compartment to another. Growth factor receptors change their signaling properties as they transit through these different compartments, and so cells can turn growth factor signaling up or down by regulating the rate of transit. The challenge is to understand how networks of hundreds of interacting membrane deforming proteins work to control cargo traffic, and how these proteins might themselves be regulated by the cell to reroute cargo.

Live imaging of dynamic interactions between subcellular compartments in fly neurons.
(click to watch movie)

Now, in a recent study published in the Journal of Cell Biology, new Biology faculty member Avital Rodal, together with Troy Littleton at MIT, identify a novel interaction between two membrane-binding proteins, Nervous Wreck (Nwk) and Sorting Nexin 16 (SNX16), that are critical for controlling the traffic of growth factor receptors that drive the expansion of neuronal arbors. Using the neurons that innervate muscles in fruit fly larvae as a model, Rodal and colleagues show that a physical association between these two proteins is necessary to turn off signaling by receptors that have been previously activated by growth factors. Perplexingly, though Nwk and SNX16 must physically interact to execute their role in driving membrane movements, they appear to reside in different subcellular compartments, in different locations within the neuron. To solve this conundrum, Rodal and colleagues took advantage of the spinning disk confocal microscope in the Brandeis Correlative Light and Electron Microscopy facility to look at the dynamic behavior of these compartments in living neurons in larvae. They found that the two distinct compartments inhabited by Nwk and SNX16 undergo dynamic and transient interactions, which represent the point in space and time that signaling receptor cargo is transferred between compartments. These receptor trafficking events are implicated in diseases ranging from neurodegenerative disease to mental retardation and addiction, underlining the health importance of understanding how signal transduction is modulated by intracellular membrane traffic in neurons.

Brandeis Profs are Pretty Fly

Last week the Genetics Society of America (or GSA) held their annual Drosophila Research Conference in sunny San Diego.  Following a 52 year tradition, the meeting brought together some of the world’s greatest scientific minds to discuss all things fruit fly (formally known as Drosophila melanogaster).  Brandeis Professor Leslie Griffith and alumnus Giovanni Bosco (PhD ’98), now at the University of Arizona, were among the meeting’s head organizers, and were visible figures throughout the course of the entire conference.

Brandeis was also a commanding presence throughout the keynote talks, with Biologist Michael Rosbash kicking off the first night’s festivities.  His lecture, which documented the history of fruit fly behavioral research, recounted a number of both professional and personal experiences with some of history’s most renowned Drosophila researchers, including Seymour Benzer and Brandeis’ own Jeff Hall.  Neuroscientist Paul Garrity further represented Brandeis with his keynote address, titled “From the Cambrian to the Sushi bar: TRPA1 and the Evolution of Thermal and Chemical Sensing”.   The talk, which discussed the molecular underpinnings of thermosensation in fruit flies, also demonstrated that these mechanisms are well conserved between many invertebrate and vertebrate species, and likely date back to a common ancestor that walked (crawled?) the earth millions of years before humans existed.  Other presentations encompassed a number of exciting topics, including aging, immunity, population genetics, evolution, and models of human disease.

Brandeis Professors Michael Rosbash (left) and Paul Garrity (right), both of whom were featured in this year’s Drosophila Research Conference Keynote Lectures.


The next meeting will be held on March 7-11, 2012 in Chicago, Illinois.  For more information, visit

Claude Desplan to speak in Bauer Distinguished Lecturer Series

Claude Desplan, Silver Professor and Professor of Biology at NYU, will visit Brandeis the week of March 21-25 as part of the M.R.Bauer Foundation Distinguished Lecturer Series. Desplan’s work focuses on developmental biology in insects, and is particularly concerned with pattern formation. A recent topic of interest is the development of the neural network that supports color vision in the optic lobe of the fruit fly.

Desplan will speak on Monday, March 21 at 4:00 pm in Gerstenzang 121. The title of his talk will be “Processing of Color Information in Drosophilia”. Desplan will speak again at Neurobiology Journal Club on March 22 at 12:05 pm in Gerstenzang 121.

According to a post at

Desplan is the funniest, nicest guy ever. At first you may not be able to understand him too too easily due to his french accent but after a few days that’s not a problem. Desplan went pretty slow and went over concepts that people didn’t seem to understand. Even then he held very helpful review sessions. Great professor.


Turning germline cells into neurons

Piali Sengupta discusses the most recent research in how nerve cells are programmed to develop in “Cellular reprogramming: chromatin puts on the brake“, published in the Feb 22 issue of Current Biology.

Fishing for neurons

Let’s say you’re a fisherman/woman trawling for tuna out on the azure-blue waters of the Pacific. Tuna’s your desired catch, but as you drag your net through the water you notice that all manner of aquatic life gets ensnared, to say nothing of styrofoam flotsam, plastic bottles, used automotive parts, and syringes. The FDA has guidelines about these sorts of things and the folks back at Trader Joe’s won’t tolerate even trace amounts of dolphin in their tuna. Bottom line is – you need your tuna to be pure. However, fishing individual tuna out of the sea one by one is extremely labor intensive, and though it may achieve high purity, you’ll be hard pressed to meet your production quotas.  The point of all this?

Scientists in the Nelson Lab at Brandeis fish for neurons. And not just any neurons, mind you, but very specific types. The end goal is to harvest their mRNA in order to “read out” their global gene expression using microarrays or sequencing based methods. They’re not alone in these pursuits; on the contrary, cell-type-specific gene expression profiling is a burgeoning field. However, like the analogy of fish in the sea, neurons exist in a complex and crowded environment, and isolating specific cell types requires some ingenuity. Different labs have used very different methods. In a recent study published in PLoS ONE, Okaty et al. compiled and re-analyzed all of the publicly available mouse brain, cell-type-specific microarray data (including their own) in order to ask the question: can they detect evidence of contamination, “stress effects” (more on that below), or any other kind of peculiar artifacts stemming from the purification (“fishing”) methods themselves? The short answer: Yes they can.

Some methods are fairly low throughput – fishing out one cell at a time.  The Manual cell sorting method (a home grown method) dissociates brain tissue, keeps the cells alive in artificial cerebrospinal fluid (almost literally seawater), and then the cell fisherman/woman hand picks labeled cells from the cell suspension with a glass pipette under a microscope (how they’re labeled isn’t terribly relevant to this discussion). This would be like collecting seawater, transferring the fish to less dense holding tanks with artificial seawater and then sorting the yellowfin tuna from the chub mackerel, etcetera. Another of the lower throughput methods is called Laser Capture Microdissection (LCM), where the extracted mouse brain is preserved through formalin fixation or flash freezing. Then thin tissue sections are made with a microtome, and individual cells are carved out of these tissue sections with a laser beam. This would be roughly approximate to freezing a volume of seawater, and then carving out the frozen fish of choice with a laser beam (sounds complicated). The primary difference between these two methods is that Manual sorts dissociated cells, whereas LCM extracts cells from intact, but preserved tissue.  Methods like fluorescence activated cell sorting (FACS) and immunopanning (PAN) also sort dissociated cells, and with the aid of flow cytometry, automated fluorometry, and/or the power of antibody selection (cell-type-specific bait), these methods greatly exceed the yields afforded by Manual cell sorting (imagine a dense network of narrow canals in which each fish is entrained in a high velocity stream, and an automated detection system diverts tuna into one channel, chub mackerel into another, and dolphin into another). Finally, a method called translating ribosome affinity purification (TRAP) bypasses the need to sort cells and “pulls down” tagged ribosomes, mRNAs in tow, from non-preserved tissue homogenate (a process which defies fishing analogy).

As you might expect, Manual cell sorting, along with FACS and PAN, achieve the highest purity (lowest amount of contamination), whereas LCM and TRAP show strong evidence of contamination from off-target cell types. Another concern is that the stress of dissociating cells or maintaining them in artificial media may perturb gene expression (think nervous, angry, wild fish in a cramped fish tank). However, only in the case of PAN data is there evidence of these effects (elevated levels of stress-response, cell death, and immediate early genes). Finally, the TRAP method extracts only mRNAs that are actively being translated, thus differences between TRAP data and data obtained by other methods may also reveal patterns of posttranscriptional regulation. For the full story, please refer to the paper.

addendum: see also Okaty et al. J.Neurosci. 31(19):6939-6943, 2011

How much torque is on my elbow?

A recent article in l. Biomech. Eng. by Davide Piovesan, a former post-doctoral fellow in Brandeis’ Ashton Graybiel Spatial Orientation Laboratory, with Alberto Pierobon, a staff engineer, and Paul DiZio and James Lackner, the laboratory’s directors has advanced the empirical and analytic tools used to quantify human arm segment inertias.  The new methodology enables studies of the neuromotor control of naturalistic reaching movements unfettered by heretofore necessary laboratory constraints, in healthy and clinical populations,

Arm segment inertias are key parameters of inverse dynamics equations which compute movement kinetics (joint torques and muscle forces) from measurements of movement kinematics.  Existing methods for estimating arm segment parameters did not provide sufficient resolution for calculation of a class of joint torques called interaction torques.  During natural reaching, interaction torques are generated by an arm segment’s motion relative to other moving segments, in addition to  normal inertial torques which are due to motion relative to fixed space.  The technical solution provided in this paper involves statistical techniques for partitioning variance in inertial estimates due to task-related (arm angular acceleration) and extraneous factors (different estimation techniques and subject body shape variations) and eliminating the extraneous sources.

The Graybiel Lab researchers have previously shown that current neuromotor models of muscle activation fail to account for movement errors that occur when large interaction torques are experimentally induced, and the new methods will enable development of better experiments and models.

Multi-body representation of the torso and arm during planar reaching.  Joint torques (τ) and forces (θ) of this multi-link sysytem can be computed knowing the motions and the inertial properties (mass, center of mass, and moment of inertia) of each segment.  The torso frame of reference is at the shoulder (S), and each other segment’s reference frame (x‑y) is fixed at its center of mass.  The environmental frame of reference (E) is shown at the upper left.

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