Monday, June 26, 2006

CMCI Mailing List

I asked the network group for a CMCI mailing list. Currently, there are 86 people on the list. 6 of them are from outside EMBL. This list will be used mainly for notifications for CMCI seminars, courses and questions for wide audience related to imaging.

Theoretical paper.

An optimal number of molecules for signal amplification and discrimination in a chemical cascade
Yoshihiro Morishita, Tetsuya J. Kobayashi, and Kazuyuki Aihara
Biophys. J. published 23 June 2006, 10.1529/biophysj.105.070797

How molecular fluctuation is treated during signal amplification.

Friday, June 16, 2006

"read all biological file formats" PlugIn for ImageJ

seems to be pretty useful. One must download two files to the PlugIn folder.
http://www.loci.wisc.edu/ome/formats.html

Thursday, June 15, 2006

spot counting

I was thinking about how to automatically count the number of ERES within cell. One way I initially thought was to do it by Gaussian fitting. Scan through 2D plane and find positions where Gaussian fitting works well (probably evaluate by chi-sq or Q value). Another way is simple particle analysis after processing image by (1) anisotropic diffusion (2) background subtraction (3) then do particle analysis.

wrote a Igor procedure to calculate average distances between ERES from a list of xy coordinates. (K_distancestats(xpos, ypos))

Wednesday, June 14, 2006

Wrote a short notes for a talk two weeks later and linked the document to the CMCI website. The talk is about how to measure and analyze dynamics using time lapse sequeces. Here is the LINK.

Monday, June 12, 2006

Picks from Biophysical J. Online Alerts

******* for the period 26 May 2006 to 2 Jun 2006 ****************

Measurements of Molecular dynamics

Probing diffusion laws within cellular membranes by Z-scan fluorescence correlation spectroscopy
Jana Humpolikova et al.
Biophys. J. published 2 June 2006, 10.1529/biophysj.106.089474

abstract:
"The plasma membrane of various mammalian cell types is heterogeneous in structure and may contain microdomains, which can impose constraints on the lateral diffusion of its constituents. Fluorescence correlation spectroscopy (FCS) can be used to investigate the dynamic properties of the plasma membrane of living cells. Very recently L. Wawrezieck et al [Biophys. J. 89 (2005) 4029-4042] described a method to probe the nature of the lateral microheterogeneities of the membrane by varying the beam size in the FCS instrument. The dependence of the width of the autocorrelation function at half maximum, i.e. the diffusion time, on the transverse area of the confocal volume gives information on the nature of the imposed confinement. We describe an alternative approach which yields essentially the same information and which can readily be applied on commercial FCS instruments by measuring the diffusion time and the particle number at various relative positions of the cell membrane with respect to the waist of the laser beam, i.e. by performing a Z-scan."

Molecular Dynamics and substrate curvature

Molecular Dynamics study of MscL interactions with a curved lipid bilayer

Grischa R Meyer, Justin Gullingsrud, Klaus Schulten, and Boris Martinac
Biophys. J. published 2 June 2006, 10.1529/biophysj.106.080721

The Role of Flexible Tethers in Multiple Ligand-Receptor Bond Formation Between Curved Surfaces
Nathan W Moore and Tonya L Kuhl
Biophys. J. published 2 June 2006, 10.1529/biophysj.105.079871



simulation of small gaseous ligands propagation through single protein molecule.

Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin
Jordi Cohen, Anton Arkhipov, Rosemary I Braun, and Klaus Schulten
Biophys. J. published 2 June 2006, 10.1529/biophysj.106.085746



******* for the period 2 Jun 2006 to 9 Jun 2006 *******

Measurements of Molecular dynamics FRET

Analysis of Single-molecule FRET Trajectories Using Hidden Markov Modeling
Sean A McKinney et al
Biophys. J. published 9 June 2006, 10.1529/biophysj.106.082487


quote from the abstract
"We have developed an analysis scheme that casts single-molecule time-binned FRET trajectories as hidden Markov processes, allowing one to determine, based on probability alone, the most likely FRET-value distributions of states and their interconversion rates while simultaneously determining the most likely time sequence of underlying states for each trajectory. Together with a transition density plot and Bayesian information criterion we can also determine the number of different states present in a system in addition to the state-to-state transition probabilities. Here we present the algorithm and test its limitations with various simulated data and previously reported Holliday junction data. The algorithm is then applied to the analysis of the binding and dissociation of three RecA monomers on a DNA construct."


Membrane structure and vesicle fusion.

Phospholipid vesicle fusion on micropatterned polymeric bilayer substrates
Takashi Okazaki et al.
Biophys. J. published 9 June 2006, 10.1529/biophysj.105.080507


******* for the period 19 May 2006 to 26 May 2006 *******

Force generaiton by Actin Dynamics

Diffusion rate limitations in actin-based propulsion of hard and deformable particles
Richard Dickinson and Daniel L. Purich
Biophys. J. published 26 May 2006, 10.1529/biophysj.106.082362


"In the "actoclampin" filament end-tracking motor model, particle-surface-bound filament end-tracking proteins are involved in load-insensitive processive insertion of actin subunits onto elongating filament plus-ends that are persistently tethered to the surface. In contrast, the "Tethered Ratchet" model assumes working filaments are untethered and grow as thermal ratchets in a load-sensitive manner. This paper presents a model for the diffusion and consumption of actin monomers during actin-based particle propulsion in order to predict the monomer concentration field around the motile particle. The results demonstrate that the various behaviors of biomimetic particles, including dynamic saltatory motion of hard particles and oscillatory vesicle deformations, can be quantitatively and self-consistently explained by load-insensitive, diffusion-limited elongation of (+)-end-tethered actin filaments, consistent with predictions of the 'actoclampin' end-tracking model."

Friday, June 09, 2006

Picks from ImageJ News

1. New PlugIn: FRETcalc - FRET by acceptor photobleaching

2. New PlugIn: Leica TIFF Sequence plugin

2. New Tip: Macros in the plugins folder with an ".ijm"
extension (ImageJ Macro), and an underscore in the name, are
installed in the Plugins menu at startup (> v 1.37g).