Biology subjects

Myers, E. W.

Publications and source records attributed to Myers, E. W..

4 recordsLinked to original sources

bioRxiv2018

Multi-scale coordination of planar cell polarity in planarians

Polarity is a universal design principle of biological systems that manifests at all organizational scales. Although well understood at the cellular level, the mechanisms that coordinate polarity at the tissue or organismal scale remain poorly understood. Here, we make use of the extreme body plan plasticity of planarian flatworms to probe the multi-scale coordination of polarity. Quantitative analysis of ciliary rootlet orientation in the epidermis reveals a global polarization field with head and tail as independent mediators of anteroposterior (A/P) polarization and the body margin influencing mediolateral (M/L) polarization. Mathematical modeling demonstrates that superposition of separate A/P- and M/L-fields can explain the global polarity field and we identify the core planar cell polarity (PCP) and Ft/Ds pathways as their specific mediators. Overall, our study establishes a mechanistic framework for the multi-scale coordination of planar polarity in planarians and establishes the core PCP and Ft/Ds pathways as evolutionarily conserved 2D-polarization module.

cell biology↗

bioRxiv2017

Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy

Fluorescence microscopy is a key driver of discoveries in the life-sciences, with observable phenomena being limited by the optics of the microscope, the chemistry of the fluorophores, and the maximum photon exposure tolerated by the sample. These limits necessitate trade-offs between imaging speed, spatial resolution, light exposure, and imaging depth. In this work we show how image restoration based on deep learning extends the range of biological phenomena observable by microscopy. On seven concrete examples we demonstrate how microscopy images can be restored even if 60-fold fewer photons are used during acquisition, how near isotropic resolution can be achieved with up to 10-fold under-sampling along the axial direction, and how tubular and granular structures smaller than the diffraction limit can be resolved at 20-times higher frame-rates compared to state-of-the-art methods. All developed image restoration methods are freely available as open source software in Python, FO_SCPLOWIJIC_SCPLOW, and KO_SCPLOWNIMEC_SCPLOW.

bioinformatics↗

bioRxiv2017

Cell Dynamics Underlying Oriented Growth Of The Drosophila Imaginal Wing Disc

Quantitative analysis of the dynamic cellular mechanisms shaping the Drosophila wing during its larval growth phase has been limited, impeding our ability to understand how morphogen patterns regulate tissue shape. Such analysis requires imaging explants under conditions that maintain both growth and patterning, as well as methods to quantify how much cellular behaviors change tissue shape. Here, we demonstrate a key requirement for the steroid hormone 20-hydroxyecdysone (20E) in the maintenance of numerous patterning systems in vivo and in explant culture. We find that low concentrations of 20E support prolonged proliferation in explanted wing discs in the absence of insulin, incidentally providing novel insight into the hormonal regulation of imaginal growth. We use 20E-containing media to directly observe growth and apply recently developed methods for quantitatively decomposing tissue shape changes into cellular contributions. We discover that while cell divisions drive tissue expansion along one axis, their contribution to expansion along the orthogonal axis is cancelled by cell rearrangements and cell shape changes. This finding raises the possibility that anisotropic mechanical constraints contribute to growth orientation in the wing disc.

developmental biology↗

bioRxiv2017

Non Hybrid Long Read Consensus Using Local De Bruijn Graph Assembly

While second generation sequencing led to a vast increase in sequenced data, the shorter reads which came with it made assembly a much harder task and for some regions impossible with only short read data. This changed again with the advent of third generation long read sequencers. The length of the long reads allows a much better resolution of repetitive regions, their high error rate however is a major challenge. Using the data successfully requires to remove most of the sequencing errors. The first hybrid correction methods used low noise second generation data to correct third generation data, but this approach has issues when it is unclear where to place the short reads due to repeats and also because second generation sequencers fail to sequence some regions which third generation sequencers work on. Later non hybrid methods appeared. We present a new method for non hybrid long read error correction based on De Bruijn graph assembly of short windows of long reads with subsequent combination of these correct windows to corrected long reads. Our experiments show that this method yields a better correction than other state of the art non hybrid correction approaches.

bioinformatics↗