Symposium Summary

12 03 2009

Unfortunately a hard disk crash prevented detailed note taking at the conference.

Briefly :

Amy Palmer demonstrated a microfluidics device for multiple condition fluorescent assays in single mammalian cells. This will be useful to screen next generation calcium indicators.

Rob Campbell showed off multiplexed FRET imaging in live cells, using new FRET pairs generated in his lab.

Brian Bacskai has been observing how alzheimer’s disease affects astrocyte calcium dynamics in vivo, with bulk loaded dyes. Using Cameleons, he demonstrates the range of intracellular calcium in neuritis in healthy and diseased brain. Alzheimer’s placques cause about 20% of neuritis to have extremely elevated basal calcium levels, with a more pronounced effect closer to the plaque.

I showed some data comparing G-CaMP2, TN-XXL and D3cpv to an improved G-CaMP being developed in the Looger Lab.

Using an improved biotin ligase approach, Alice Ting presented evidence that neurexin/neuroligin is a synaptic stabilizer rather than synapse initiating protein.

Rex Kerr gave a talk on recent progress in planar illumination. In this manner, one can perform calcium imaging (using GECIs) in many neurons in a worm at the same time.

Jin Zhang has a new FRET reporter for JNK Kinase activity. It’s called JNKAR. Get it?

Michael Lin showed new results with bright, monomeric red-shifted fluorescent proteins. They look better then anything else on the market. More importantly, he has improved his TimeSTAMP technology by adding intrinsically fluorescent proteins to it. Bi-molecular fluorescence complementation tags newly synthesized protein be selectively tagged without immunostaining. This should make the in vivo imaging more robust.

Finally, Xiaokun Shu reported a new fluorecent protein that is excited and emits in the near infrared. This will be very powerful for imaging in deep tissues, as the spectra is in the transparency window out beyond the hemoglobin absorbance. Since its coming out in Science soon, I’ll hold off on a complete description of how it works. New scaffold, requires cofactor that is found in mammals.

Madoff fraud closes Picower Foundation

21 12 2008


The Bernie Madoff Ponzi scheme has claimed a victim close to Neuroscience.  The Boston Globe reports that the Picower Foundation had a substantial amount of their endowment invested with Madoff and the losses are suffiecient to  shut down the foundation’s operations immediately. In 2002, the Picower Foundation gave the largest single gift MIT had ever received to that time, $50 million, which currently supports neuroscience research at the  Picower Center for Learning and Memory. I did two years of undergraduate research at the Center for Learning and Memory (the pre-gift name) and Brain Windows has featured research by current PCLM faculty.

The PCLM should be ok, as it appears the gift has been financially mangaed by MIT since 2002.  However, a recurring $200,000 annual gift for support of underrepresented minorities in their doctoral studies in science at MIT will not continue.

Top imaging papers in Chemical Biology 2006-08

10 12 2008

Generation of new sensors for brain imaging often requires application of chemistry. If you are interested in recent developments in biological imaging tools from a chemical perspective, here is a collection of recent papers on the subject in ACS Chemical Biology.  Quite a few familiar faces in the list.


Editor-Selected Papers in IMAGING
“The imaging of biochemical events inside living cells and in vivo is crucial to our understanding of biological processes. Biomolecular imaging relies on appropriate probes and labeling technologies. And although powerful tools for the visualization of various biochemical activities have been developed over the last years, the majority of the cellular processes cannot yet be visualized. This defines one of the main challenges and opportunities in chemical biology.  “Since its introduction, ACS Chemical Biology has become a leading journal for top research papers and reviews that describe the generation and application of innovative tools for biomolecular imaging. The list below highlights some of these papers and we eagerly await the submission of new articles that report on further advances in this exciting field.”   ~ Kai Johnsson, Member, Board of Editors, ACS Chemical Biology
École Polytechnique Fédérale de Lausanne

Reading Dynamic Kinase Activity in Living Cells for High-throughput Screening
Michael D. Allen, Lisa M. DiPilato, Meghdad Rahdar, Yunzhao R. Ren, Curtis Chong, Jun O. Liu, and Jin Zhang
ACS Chem. Biol., (Letter), 2006, 1(6), 371-376. DOI: 10.1021/cb600202f

HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis
Georgyi V. Los, Lance P. Encell, Mark G. McDougall, Danette D. Hartzell, Natasha Karassina, Chad Zimprich, Monika G. Wood, Randy Learish, Rachel Friedman Ohana, Marjeta Urh, Dan Simpson, Jacqui Mendez, Kris Zimmerman, Paul Otto, Gediminas Vidugiris, Ji Zhu, Aldis Darzins, Dieter H. Klaubert, Robert F. Bulleit, and Keith V. Wood
ACS Chem. Biol., (Article), 2008, 3(6), 373-382. DOI: 10.1021/cb800025k

A Comparative Study of Bioorthogonal Reactions with Azides
Nicholas J. Agard, Jeremy M. Baskin, Jennifer A. Prescher, Anderson Lo, and Carolyn R. Bertozzi
ACS Chem. Biol., (Letter), 2006, 1(10), 644-648. DOI: 10.1021/cb6003228

Measuring Picomolar Intracellular Exchangeable Zinc in PC-12 Cells Using a Ratiometric Fluorescence Biosensor
Rebecca A. Bozym, Richard B. Thompson, Andrea K. Stoddard, and Carol A. Fierke
ACS Chem. Biol., (Article), 2006, 1(2), 103-111. DOI: 10.1021/cb500043a

A Survey of Single-Molecule Techniques in Chemical Biology
Peter V. Cornish and Taekjip Ha
ACS Chem. Biol., (Review), 2007, 2(1), 53-61. DOI: 10.1021/cb600342a

Fluorogenic Label for Biomolecular Imaging
Luke D. Lavis, Tzu-Yuan Chao, and Ronald T. Raines
ACS Chem. Biol., (Article), 2006, 1(4), 252-260. DOI: 10.1021/cb600132m

Chemical Tools for Biomolecular Imaging
Nils Johnsson and Kai Johnsson
ACS Chem. Biol., (Review), 2006, 2(1), 31-38. DOI: 10.1021/cb6003977

Mechanism-Based Probe for the Analysis of Cathepsin Cysteine Proteases in Living Cells
Howard C. Hang, Joana Loureiro, Eric Spooner, Adrianus W. M. van der Velden, You-Me Kim, Annette M. Pollington, Rene Maehr, Michael N. Starnbach, and Hidde L. Ploegh
ACS Chem. Biol., (Article), 2006, 1(11), 713-723. DOI: 10.1021/cb600431a

Fluorogenic Phospholipids as Head Group-Selective Reporters of Phospholipase A Activity
Tyler M. Rose and Glenn D. Prestwich
ACS Chem. Biol., (Article), 2006, 1(2), 83-92. DOI: 10.1021/cb5000014

Imaging Distinct Conformational States of Amyloid- Fibrils in Alzheimer’s Disease Using Novel Luminescent Probes
K. Peter R. Nilsson, Andreas Åslund, Ina Berg, Sofie Nyström, Peter Konradsson, Anna Herland, Olle Inganäs, Frantz Stabo-Eeg, Mikael Lindgren, Gunilla T. Westermark, Lars Lannfelt, Lars N. G. Nilsson, and Per Hammarström
ACS Chem. Biol., (Article), 2007, 2(8), 553-560. DOI: 10.1021/cb700116u

Evolving the Substrate Specificity of O6-Alkylguanine-DNA Alkyltransferase through Loop Insertion for Applications in Molecular Imaging
Christian Heinis, Simone Schmitt, Maik Kindermann, Guillaume Godin, and Kai Johnsson
ACS Chem. Biol., (Article), 2006, 1(9), 575-584. DOI: 10.1021/cb6003146

Novel Genetically Encoded Biosensors Using Firefly Luciferase
Frank Fan, Brock F. Binkowski, Braeden L. Butler, Peter F. Stecha, Martin K. Lewis, and Keith V. Wood
ACS Chem. Biol., (Letter), 2008, 3(6), 346-351. DOI: 10.1021/cb8000414

An Integrated-Molecule-Format Multicolor Probe for Monitoring Multiple Activities of a Bioactive Small Molecule
Sung Bae Kim, Yoshio Umezawa, Kira A. Kanno, and Hiroaki Tao
ACS Chem. Biol., (Article), 2008, 3(6), 359-372. DOI: 10.1021/cb800004s

Coiled-Coil Tag–Probe System for Quick Labeling of Membrane Receptors in Living Cells
Yoshiaki Yano, Akiko Yano, Shinya Oishi, Yukihiko Sugimoto, Gozoh Tsujimoto, Nobutaka Fujii, and Katsumi Matsuzaki
ACS Chem. Biol., (Letter), 2008, 3(6), 341-345. DOI: 10.1021/cb8000556

Molecular Electron Microscopy: State of the Art and Current Challenges
Henning Stahlberg and Thomas Walz
ACS Chem. Biol., (Review), 2008, 3(5), 268-281. DOI: 10.1021/cb800037d

Bright Ideas for Chemical Biology
Luke D. Lavis and Ronald T. Raines
ACS Chem. Biol., (Review), 2008, 3(3), 142-155. DOI: 10.1021/cb700248m

Simultaneous Recording of Multiple Cellular Events by FRET
Alen Piljic and Carsten Schultz
ACS Chem. Biol., (Letter), 2008, 3(3), 156-160. DOI: 10.1021/cb700247q

Notes : Structural Biochemistry

26 11 2008

I TA’ed a course in structural biochemistry at UCSD.  I spent a lot of time making cool handouts for the students (at least until the last 2 weeks when my own finals sapped all my time and energy).  Found these buried online.  Nothing too mind-blowing, but I figured I’d post them to preserve them.

Handout 1 – Aqueous Solutions, Amino Acids & Secondary Protein Structure

Handout 2 – Protein, DNA & RNA Structure

Handout 3 – RNA continued, Mono- & Polysaccharides

Handout 4 – Cell Membrane Components and Structure Determination

Handout 5 – Enzyme Kinetics & Serine Proteases including Chymotrypsin

Handout 7 – Ion Channels

Handout 8 – Bacterial Recation Center & Molecular Dynamics

Raw Notes : Gyorgy Buzsaki at SFN

20 11 2008

Comparative Neuroanatomy with Buzsaki

Comparative Neuroanatomy with Buzsaki

Large Scale recording of neuronal activity in behaving rodents

Want to separate the types neurons of they record from and control.

Step 1 : extract single neurons from extracellular electrodes

Extracellular electrode arrys give best spatiotemporal resolution at depth in awake freely moving rodent.

Neurons are not point sources of action potentials. The action potential back propagates to dendrites.

Extracellular fields of many neurons strongly overlap.

Can be fooled if you look just in one layer, an action potential recorded in layer IV may actually originate in layer 5. 

Try to infer intracellular features from extracellular recording properties.

Depolarization of the cell during AP chages its intracellular waveform and is refelected in the extracellular waveform. Hence wave-shape sorting algorhitms can be fooled by changing depolarization levels.

Use multidimensional clustering to figure out which spikes come from which neurons.  

Step 2 : From single neurons to neuron types (taxonomy)

Compare the timing of spiking of each neuron relative to the theta cycle.  Also compare in the sharp wave cycle.  

After 6 years of works, they classify constellations of neurons involved in different network patterns.  

Interneurons : Timers and segreators.  Timing is locked to theta cycle.  

Looking at the assembly patterns you can predict the choice of an animal.

see Pastalkova, Science 2008.

In prefrontal cortex.  Use cross-correlation techniques across the population that is recorded.

Short latency large narrow peak indicates monosynaptic excitatory connection. Pyramidal -> Interneurons.  

Short latency spike suppression indicates monosynaptic inhibition. Inter-> Pyr

Has a database of >2500 neurons.  Comparte peak latency and waveshape to the correlation data that defines each as inhibitory or excitatory.  These two groups cluster in the peak latency vs. waveshape space.  So now they have a signature to classify excitatory or inhibitory neurons.

Interacting with circuits

Determine the neuron types

Perturb the correlations with optogenetics to test hypotheses

Simultaneous recoding and stimulation with optical fiber attached to silicon probe (Sebastian Royer @ Janelia)

Figure 8 maze.  

Can record place cells that have characteristic firing pattern during running through the maze.  Can see CHr2 stimulation in some cells.  Neurons fire in stereotyped pattern with theta cycle except when stimulated with ChR2, then it follows the ChR2 stimulation cycle.


Better probes, stimulating on every shank rather than just one shank.  

Larger density recording sites

Further volume reduction

Identification of neurons

Light activation and scilencing of neurons

Improved neurron clustering algorithims

SFN Neuroscience Picower MIT Party 2008

10 11 2008

Lots of people searching for “SFN MIT party” for this information in google… Here’s the answer you are looking for.  Right next to the convention center. Much more convenient than three years ago at Cobalt.  No excuse to be late…

Someone send me an invite to the Neuron, Nature and Emory parties, pretty please! 


Is that a man in a tuxedo wearing stilts?

Is that a man in a tuxedo wearing stilts?



The Picower Institute, The McGovern Institute, and the Department of Brain and Cognitive Sciences at MIT

Invite you to the sixth annual party at the 2008 meeting of the Society for Neuroscience

Monday, November 17th, 2008  

9pm – 2am  

Avenue Nightclub
649 New York Ave NW

Washington, DC

Brain Cell Biology – Optogenetics Probes Issue

7 11 2008

Most of the articles for the Optogenetics Probes Issue of Brain Cell Biology, edited by Ryohei Yasuda and George Augustine are out now. This journal used to be called the Journal of Neurocytology, but they have rebranded it.  Having a full issue devoted to the hot topic of optogenetic probes will doubtlessly raise the impact factor.


G-CaMP2 characteristics

G-CaMP2 characteristics



The issue include two papers on engineered Halorhodopsins with improved expression from Deisseroth and Feng. Also, there are reviews of genetically-encoded calcium, chloride, cyclic nucleotide and voltage sensors. There are a few papers reporting new findings with applications of these probes.

My own contribution is part-review, part fresh data, part modeling of genetically-encoded calcium indicators.  We examine the properties of these indicators, what things to consider when selecting them and where improvements will likely be made. If you are currently using a GECI or are planning to in the future, its probably worth a read.  Feedback welcome!