Biology subjects

Grunwald, D.

Publications and source records attributed to Grunwald, D..

6 recordsLinked to original sources

bioRxiv2018

Photon count estimation in single-molecule localization microscopy

Recently, Franke, Sauer and van de Linde1 introduced a way to estimate the axial position of single-molecules (TRABI). To this end, they compared the detected photon count from a temporal radial-aperture-based intensity estimation to the estimated count from Gaussian point-spread function (PSF) fitting to the data. Empirically they found this photometric ratio to be around 0.7-0.8 close to focus and decreasing away from it. Here, we explain this reported but unexplained discrepancy and furthermore show that the photometric ratio as indicator for axial position is susceptible even to typical optical aberrations.

molecular biology↗

bioRxiv2018

An Automated Bayesian Pipeline for Rapid Analysis of Single-Molecule Binding Data

Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. We benchmarked the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We also used the pipeline to extend our understanding of TtAgo by measuring the proteins binding kinetics at physiological temperatures and for target DNAs containing multiple, adjacent binding sites.

molecular biology↗

bioRxiv2017

Fluorescence polarization control for on-off switching of single molecules at cryogenic temperatures

Light microscopy allowing sub-diffraction limited resolution has been among the fastest developing techniques at the interface of biology, chemistry and physics. Intriguingly no theoretical limit exists on how far the underlying measurement uncertainty can be lowered. In particular data fusion of large amounts of images can reduce the measurement error to match the resolution of structural methods like cryo-electron microscopy. Fluorescence, although reliant on a reporter molecule and therefore not the first choice to obtain ultra resolution structures, brings highly specific labeling of molecules in a large assemble to the table and inherently allows the detection of multiple colors, which enable the interrogation of multiple molecular species at the same time in the same sample. Here we discuss the problems to be solved in the coming years to aim for higher resolution and describe what polarization depletion of fluorescence at cryogenic temperatures can contribute for fluorescence imaging of biological samples like whole cells.

biophysics↗

bioRxiv2017

CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics

In contrast to the well-studied condensation and folding of chromosomes during mitosis, their dynamics in interphase are less understood. We developed a sensitive, multicolor system, CRISPR-Sirius, allowing the real-time tracking of the dynamics of chromosomal loci. We tracked loci kilobases to megabases apart and found significant variation in the inter-locus distances of each pair, indicating differing degrees of DNA contortion. We resolved two distinct modes of dynamics of loci: saltatory local movements as well as translational movements of the domain. The magnitude of both of these modes of movements increased from early to late G1, whereas the translational movements were reduced in early S. The local fluctuations decreased slightly in early S and more markedly in mid-late S. These newly observed movements and their cell cycle-dependence are indicative of a hitherto unrecognized compaction-relaxation dynamic of the chromosomal fiber operating concurrently with changes in the extent of observed genomic domain movements.\n\nIN BRIEFDistinct chromosome folding and dynamics during cell cycle progression were dissected by CRISPR-Sirius DNA imaging in living cells.\n\nHIGHLIGHTSO_LICRISPR-Sirius allows tracking of pairs of chromosomal loci having kilobase to megabase inter-locus distances\nC_LIO_LIPair-wise tracking of loci allows measurement of both local and domain dynamics\nC_LIO_LIChromosomal fiber relaxation is positively correlated with local dynamics\nC_LIO_LIGenomic region size contributes to local and domain movements\nC_LIO_LIDistinct chromosome dynamics were uncovered during cell cycle progression in interphase\nC_LI

cell biology↗

bioRxiv2017

Single-molecule FISH in Drosophila muscle reveals location dependent mRNA composition of megaRNPs

Single-molecule fluorescence in-situ hybridization (smFISH) provides direct access to the spatial relationship between nucleic acids and specific subcellular locations. The ability to precisely localize a messenger RNA can reveal key information about its regulation. Although smFISH is well established in cell culture or thin sections, methods for its accurate application to tissues are lacking. The utility of smFISH in thick tissue sections must overcome several challenges, including probe penetration of fixed tissue, accessibility of target mRNAs for probe hybridization, high fluorescent background, spherical aberration along the optical axis, and image segmentation of organelles. Here we describe how we overcame these obstacles to study mRNA localization in Drosophila larval muscle samples that approach 50 m thickness. We use sample-specific optimization of smFISH, particle identification based on maximum likelihood testing, and 3-dimensional multiple-organelle segmentation. The latter allows using independent thresholds for different regions of interest within an image stack. Our approach therefore facilitates accurate measurement of mRNA location in thick tissues.

cell biology↗

bioRxiv2017

Reconstructing Spatial Transport Distributions In The Nuclear Pore Complex From 2D Images -- How Reliable Is It?

Imaging single molecules in living cells and reconstituted cell systems has resulted in a new understanding of the dynamics of nuclear pore complex functions over the last decade. It does, however, fall short on providing insights into the functional relationships between the pore and nucleocytoplasmic cargo in three-dimensional space. This limited ability is the result of insufficient resolution of optical microscopes along the optical axis and limited fluorescent signal due to the short timescales involved in nuclear transport (fractions of a second). To bypass current technological limitations, it was suggested that highly time-resolved 2D single molecule data could be interpreted as projected cargo locations and could subsequently be transformed into a spatial cargo distribution by assuming cylindrical symmetry 1. Such cargo distributions would provide valuable insights into the NPC-mediated transport in cells. This method, termed 3D-SPEED, has attracted large interest inside and beyond the nuclear pore field, but has also been sharply critiqued for a lack of critical evaluation. Here we present such an evaluation, testing the robustness, reconstruction quality and model-dependency.

cell biology↗