Introduction to Microfluidics Technology – June 13-17, 2016

2016 MRSEC Summer Course Announcement

Registration for our annual, one-week summer course, “Introduction to Microfluidics Technology” at Brandeis University, near Boston, MA, is now open. The application deadline is March 31, 2016.

Introduction to Microfluidics Technology is a hands-on laboratory course sponsored by the National Science Foundation’s Bioinspired Soft Materials Research Science and Engineering Center (MRSEC) at Brandeis. It will be offered during the week of June 13 ‐ 17, 2016. The course is intended for graduate students, post docs, faculty, and industrial scientists/engineers interested in utilizing microfluidic technology in their work, both in the physical and life sciences. The course does not assume any specific prerequisites.

“Introduction to Microfluidics Technology” (June 13 – 17, 2016)
will be taught by Dr. Nathan Tompkins.

The $750 fee covers course tuition, housing in double-occupancy rooms, and breakfast/lunch/coffee from Monday through Friday. Single rooms are not available. Local students who do not need housing will pay a non-resident fee of $500 (cash and check only please).

More information is available.

Lipids hit a “sweet spot” to direct cellular membrane remodeling.

Lipid membrane reshaping is critical to many common cellular processes, including cargo trafficking, cell motility, and organelle biogenesis. The Rodal lab studies how dynamic membrane remodeling is achieved by the active interplay between lipids and proteins. Recent results, published in Cell Reports, demonstrate that for the membrane remodeling protein Nervous Wreck (Nwk), intramolecular autoregulation and membrane charge work together in surprising ways to restrict remodeling to a limited range of lipid compositions.

F-BAR (Fes/Cip4 homology Bin/Amphiphysin/Rvs) domain family proteins are important mediators of membrane remodeling events. The F-BAR domain forms a crescent-shaped α-helical dimer that interacts with and deforms negatively charged membrane phospholipids by assembling into higher-order scaffolds. In this paper, Kelley et al. have shown that the neuronal F-BAR protein Nwk is autoregulated by its C-terminal SH3 domains, which interact directly with the F-BAR domain to inhibit membrane binding. Until now, the dogma in the field has been that increasing concentrations of negatively charged lipids would increase Nwk membrane binding, and thus would induce membrane deformation.

Surprisingly, Kelley et al. found that autoregulation does not mediate this kind of simple “on-off” switch for membrane remodeling. Instead, increasing the concentration of negatively charged lipids increases membrane binding, but inhibits F-BAR membrane deforming activities (see below). Using a combination of in vitro assays and single particle electron microscopy, they found that the Nwk F-BAR domain efficiently assembles into higher-order structures and deforms membranes only within “sweet spot” of negative membrane charge, and that autoregulation elevates this range. The implication of this work is that autoregulation could either reduce membrane binding or promote higher-order assembly, depending on local cellular membrane composition. This study suggests a significant role for the regulation of membrane composition in remodeling.

Brandeis authors on the study included Molecular and Cell Biology graduate students Charlotte Kelley and Shiyu Wang, staff member Tania Eskin, and undergraduate Emily Messelaar ’13 from the Rodal lab; postdoctoral fellow Kangkang Song, Associate Professor of Biology Daniela Nicastro (currently at UT Southwestern), and Associate Professor of Physics Michael Hagan.

Kelley CF, Messelaar EM, Eskin TL, Wang S, Song K, Vishnia K, Becalska AN, Shupliakov O, Hagan MF, Danino D, Sokolova OS, Nicastro D, Rodal AA. Membrane Charge Directs the Outcome of F-BAR Domain Lipid Binding and Autoregulation. Cell reports. 2015;13(11):2597-609.

Visualizing a protein decision complex in actin filament length control

Seen at the Gelles Lab Little Engine Shop blog this week, commentary on a new paper in Nature Communicationspublished in collaboration with the Goode Lab and researchers from New England Biolabs.

“Single-molecule visualization of a formin-capping protein ‘decision complex’ at the actin filament barbed end”

Regulation of actin filament length is a central process by which eukaryotic cells control the shape, architecture, and dynamics of their actin networks. This regulation plays a fundamental role in cell motility, morphogenesis, and a host of processes specific to particular cell types. This paper by recently graduated [Biophysics and Structural Biology] Ph.D. student Jeffrey Bombardier and collaborators resolves the long-standing mystery of how formins and capping protein work in concert and antagonistically to control actin filament length. Bombardier used the CoSMoS multi-wavelength single-molecule fluorescence microscopy technique to to discover and characterize a novel tripartite complex formed by a formin, capping protein, and the actin filament barbed end. Quantitative analysis of the kinetic mechanism showed that this complex is the essential intermediate and decision point in converting a growing formin-bound filament into a static capping protein-bound filament, and the reverse. Interestingly, the authors show that “mDia1 displaced from the barbed end by CP can randomly slide along the filament and later return to the barbed end to re-form the complex.” The results define the essential features of the molecular mechanism of filament length regulation by formin and capping protein; this mechanism predicts several new ways by which cells are likely to couple upstream regulatory inputs to filament length control.

Single-molecule visualization of a formin-capping protein ‘decision complex’ at the actin filament barbed end
Jeffrey P. Bombardier, Julian A. Eskin, Richa Jaiswal, Ivan R. Corrêa, Jr., Ming-Qun Xu, Bruce L. Goode, and Jeff Gelles
Nature Communications  6:8707 (2015)

The capping protein expression plasmid described in this article is available from Addgene.

Readers interested in this subject should also see a related article by Shekhar et al published simultaneously in the same journal.  We are grateful to the authors of that article for coordinating submission so that the two articles were published together.

FOXO links stress to the innate immune response in flies

Life is tough. Every living thing is constantly dealing with insults that damage or disrupt homeostasis. At the cellular level these insults, or stresses, come in multiple forms: starvation, oxidative stress, heat shock, radiation damage, and infection. In response to these stresses, organisms have evolved numerous mechanisms to promote survival. Broadly speaking, an insult stimulates various signaling cascades that alter gene expression in the cell.

One way this is achieved is through the “turning on” of transcription factors. One such transcription factor is FOXO, which is activated under many types of stress, both metabolic and environmental. Another way gene expression can be accomplished is the post-transcriptional control of gene expression. An important player of post-transcriptional control is the small RNA pathways composed of the RNA interference (RNAi), micro RNA (miRNA), and PIWI RNA (piRNA) branches. In a recent article from the Marr lab titled “FOXO regulates RNA interference in Drosophila and protects from RNA virus infection”, published in PNAS this November, the authors identify a new connection between both the transcriptional and small RNA mediated post-transcriptional mechanisms that respond to stress.

Screen Shot 2015-11-16 at 9.22.43 AM

RNAi efficiency is enhanced in a dFOXO-dependent manner. For full explanations, see Fig. 2 in Spellberg & Marr (2015)

Using Drosophila as a model system, the authors identify FOXO as a transcription factor that regulates important genes in the small RNA pathways in response to stress. This is the first transcription factor identified to control these genes. Despite being a hot and competitive field for over 15 years, work in small RNA pathways had yet to reveal the transcriptional regulation of the core protein machinery that are involved in small RNA biogenesis and utilization. Under stress conditions, FOXO directly binds the promoters of core small RNA pathway genes, such as Ago1, Ago2, and Dicer 2, leading to increases in their expression. As one might expect, this is followed by an increase in RNAi efficiency and post-transcriptional control of gene expression.

A known physiological role for RNAi is to fight off viral infections as part of an innate immune response. The authors find that FOXO is activated by viral infection to promote this anti-viral response. In addition, animals deleted for the FOXO gene are more susceptible to a viral infection. Theses results are consistent with the notion that virally-activated FOXO stimulates RNAi gene transcription as a mechanism to enhance viral immunity.

Finally, the work in this paper identifies integration between metabolic and stress signaling and the innate immune response, with FOXO serving the bridge. There is evidence that acute stress can confer a protective effect against infection in humans. If the identified role of FOXO is conserved, perhaps it can be utilized therapeutically.

Spellberg MJ, Marr MT, 2nd. FOXO regulates RNA interference in Drosophila and protects from RNA virus infection. Proc Natl Acad Sci U S A. 2015

DUB inhibitors _or_ why you should you eat your broccoli

Eat your broccoli!

We’re constantly bombarded by advice on which foods to eat or not eat, but skeptics among us often find compelling evidence for a convincing mechanism of how the foods promote health hard to come by – food has many components, and there are many different cells and metabolic pathways in those cells with which those components interact.

phenethyl isothiocyanate (a component of cruciferous vegetables)

phenethyl isothiocyanate (PEITC, a component of cruciferous vegetables)

Consider broccoli. It is well established that cruciferous vegetables have wide-ranging health benefits, apparently reducing cancer risks and lowering inflammation.  One set of phytochemicals responsible for the potent anti-cancer and anti-inflammatory properties are called isothiocyanates or ‘ITCs’.  It is now four decades since the discovery of ITCs, yet a molecular understanding of what ITCs do in a cell has proven elusive.

In a paper published this month in Cancer Research, Brandeis research scientist Ann Lawson, working in Liz Hedstrom’s laboratory, together with graduate students Marcus Long (Biochem) and Rory Coffey (Mol Cell Biol) and scientists from UbiQ and from Boston College, has shown that ITCs block the action of deubiquitinating enzymes (DUBs),  including the tumorigenesis-associated enzymes USP9x and UCH37, at physiologically relevant concentrations and time scales.

DUB inhibition provides a simple, unifying explanation that can account for many of the diverse health effects of ITCs. Understanding of how ITCs work at the molecular level may, one day, lead to new drug therapies for illnesses such as cancer, chronic inflammation, and neurodegenerative diseases.

Are you ready for your broccoli now? Me, I think I’ll have some kale sprouts.

Lawson AP, Long MJ, Coffey RT, Qian Y, Weerapana E, El Oualid F, Hedstrom L. Naturally occurring isothiocyanates exert anticancer effects by inhibiting deubiquitinating enzymes. Cancer Res. 2015

Physics students win awards

The Physics Department recently held its annual Student Research Symposium in Memory of Professor Stephan Berko. At the symposium, the undergraduate speakers describe their senior thesis honors research as the final step in gaining an honors degree in physics. The graduate student speakers are in the middle of their PhD research, and describe their progress and goals.

The prize winners are nominated and chosen by the faculty for making particularly noteworthy progress in their research. Here are the Berko prize winners for 2015:

Undergraduate Prize Winners:

Adam Wang
Title: “Controlling Coupled Chemical Oscillators: Toward Synchronization Engineering and Chemical Computation”
video

Jacob Gold
Title: “Inhibitively Coupled Chemical Oscillators as a Substrate for Logic Gates and Larger Circuits”
video

Graduate Prize Winners:

Lishibanya Mohapatra
Title: “How cells control the size of their organelles?”
video

Feodor Hilitski
Title: “Measuring mechanics of active microtubule bundles, one filament at a time”
video

Other Physics Prize winners this year:

Cesar A. Agon Falkoff prize
Hannah Herde Falkoff prize
Matthew Cambria Physics Faculty prize
Stefan Stanojevic Physics Faculty prize

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