Tag Archives: thorsten wohland

Bayesian Model Selection Applied to the Analysis of FCS Data of Fluorescent Proteins in vitro and in vivo

by Guangyu Sun,†$ Syuan-Ming Guo, Cathleen Teh,§ Vladimir Korzh,§# Mark Bathe, and Thorsten Wohland*,†$#

Department of Chemistry, National University of Singapore, 117543 Singapore, $Centre for Bioimaging Sciences, National University of Singapore, 117557 Singapore, Laboratory for Computational Biology and Biophysics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States, §Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673 Singapore, #Department of Biological Sciences, National University of Singapore, 117543 Singapore

Sun et al. – Anal. Chem. 87 (2015) 4326−4333

Fluorescence Correlation Spectroscopy (FCS) is a powerful technique to investigate molecular dynamics with single molecule sensitivity. In particular, in the life sciences it has found widespread application using fluorescent proteins as molecularly specific labels. However, FCS data analysis and interpretation using fluorescent proteins remains challenging due to typically low signal-to-noise ratio of FCS data and correlated noise in autocorrelated datasets. As a result, naive fitting procedures that ignore these important issues typically provide similarly good fits for multiple competing models without clear distinction of which model is preferred given the signal-to-noise ratio present in the data. Recently, we introduced a Bayesian model selection procedure to overcome this issue with FCS data analysis. The method accounts for the highly correlated noise that is present in FCS datasets and additionally penalizes model complexity to prevent over interpretation of FCS data. Here, we apply this procedure to evaluate FCS data from fluorescent proteins assayed in vitro and in vivo. Consistent with previous work, we demonstrate that model selection is strongly dependent on the signal-to-noise ratio of the measurement, namely excitation intensity and measurement time, and is sensitive to saturation artifacts. Under fixed, low intensity excitation conditions physical transport models can unambiguously be identified. However, at excitation intensities that are considered moderate in many studies, unwanted artifacts are introduced that result in non-physical models to be preferred. We also determined the appropriate fitting models of a GFP tagged secreted signaling protein, Wnt3, in live zebrafish embryos, which is necessary for the investigation of Wnt3 expression and secretion in development. Bayes model selection therefore provides a robust procedure to determine appropriate transport and photophysical models for fluorescent proteins when appropriate models are provided, to help detect and eliminate experimental artifacts in solution, cells and in living organisms.

Read the entire article.

Learn more about Thorsten Wohland’s research.

Characterization of Lipid and Cell Membrane Organization by the Fluorescence Correlation Spectroscopy Diffusion Law

by Xue Wen Ng1,3, Nirmalya Bag2,3, Thorsten Wohland1,2,3,*

1 Department of Chemistry, National University of Singapore, Singapore, 2 Department of Biological Sciences, National University of Singapore, Singapore, 3 NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore

Ng et al – CHIMIA (2015), 69 (3) 112-119

The plasma membrane organization of live cells defines a plethora of cellular processes important for cell functionality. Many membrane structures that define this organization exist at a spatial resolution below the optical diffraction limit and are highly dynamic. Therefore, a method with millisecond time resolution and nanometer spatial resolution is required for the investigation of plasma membrane organization. However, spatial and temporal resolutions of the currently available biophysical techniques are often mutually exclusive. In a novel realization, Lenne and coworkers developed a spot-variation modality of fluorescence correlation spectroscopy (FCS), also known as FCS diffusion law, to harvest nanoscopic information from microscopic measurements. The FCS diffusion law, so far, has been instrumental to decode the physico-chemical origin of membrane organization and its relationship with biological processes. Overall, the structural information of plasma membrane obtained by FCS diffusion law provides a better understanding of its coupling to the underlying cellular processes.

Read the entire article.

Learn more about Thorsten Wohland’s research.

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

by Tapan Kumar Mistri1, 2, 3, Devasia Arun George2, Lee Thean Chu2, Wei Ping Ng1, Florian Halbritter3, Ben Martynoga4, Simon R Tomlinson3, Ian Chambers3,#, Paul Robson2, 5,*, Thorsten Wohland1, 5, 6 x

1Department of Chemistry, National University of Singapore, Singapore, 2Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore. 3MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, Scotland, United Kingdom, 4Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, England, United Kingdom, 5Department of Biological Sciences and 6Centre for Bioimaging Sciences, National University of Singapore, Singapore.

EMBO Rep. 2015 Sep;16(9):1177-91. doi: 10.15252/embr.201540467. Epub 2015 Aug 11

Embryonic stem cell (ESC) identity is orchestrated by the co-operative activity of the transcription factors (TFs) Sox2 and the class V POU TF, Oct4 at composite Sox/Oct motifs. Neural stem cells (NSCs) lack Oct4 but express class III POU TF Oct4-homologs, Oct6, Brn1 and Brn2 as well as Sox2. This raises the question of how Sox2 interacts with POU TFs to selectively activate the ESC or NSC-specific transcriptional state. Here we show that Oct4 alone binds equally well to the Sox/Oct motif and to the octamer-containing ‘More palindromic Oct factor regulatory element’ (MORE). Sox2 binding selectively increases the affinity of Oct4 for the Sox/Oct motif. In contrast, Oct6 binds preferentially to the MORE, and is unaffected by Sox2. Genome-wide chromatin localisation in NSCs shows the most enriched motif for Oct6, Brn1 and Brn2 is in each case the MORE, with no evidence of a Sox/Oct motif. Moreover, MORE sub-types with C-A substitutions in positions 4 and 9, and a sub-type with a single base insertion between half-sites, are evident. These results suggest that in NSCs, co-operativity between Sox2 and class III POU TFs may not occur and that POU TF driven gene regulation uses predominantly the MORE cis architecture. Thus, distinct interactions between Sox2 and POU-TF subclasses distinguish pluripotent ESCs from multipotent NSCs, providing molecular insight into how Oct4 alone can convert NSCs to pluripotency.

Read the entire article.

Learn more about Thorsten Wohland’s research.