Biology subjects

Schoennenbeck, P.

Publications and source records attributed to Schoennenbeck, P..

4 recordsLinked to original sources

bioRxiv2025

CryoVIA - An image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs

Imaging of lipid structures and associated protein complexes using electron cryo-microscopy (cryo-EM) is a common visualization and structure determination technique. The quantitative analysis of the membrane structures, however, is not routine and time consuming in particular when large amounts of data are involved. Here, we introduce the automated image-processing software cryo-vesicle image analyzer (CryoVIA) that parametrizes lipid structures of large data sets from cryo-EM images. This toolkit combines segmentation, structure identification with methods to automatically perform a large-scale data analysis of local and global membrane properties such as bilayer thickness, size, and curvature including membrane shape classifications. We included analyses of exemplary data sets of different lipid compositions and protein-induced lipid changes through an ESCRT-III membrane remodeling protein. The toolkit opens new possibilities to systematically study structural properties of membrane structures and their modifications from cryo-EM images.

bioinformatics↗

bioRxiv2024

Structural plasticity of bacterial ESCRT-III protein PspA in higher-orderassemblies

Eukaryotic members of the endosome sorting complex required for transport III (ESCRT-III) family have been shown to form diverse oligomeric assemblies. The bacterial phage shock protein A (PspA) has recently been identified as a bacterial member of the ESCRT-III superfamily, and monomeric PspA homo-oligomerizes to form large rod-shaped assemblies. As observed for eukaryotic ESCRT-III, PspA forms different tubular assemblies with varying diameters. Using electron cryo-microscopy (cryo-EM), we determined a total of 61 PspA structures and observed in molecular detail how structural plasticity of PspA rods is mediated by conformational changes at three hinge regions in the monomer and by the fixed as well as changing molecular contacts between protomers. Moreover, we reduced and increased the structural plasticity of PspA rods by removing the loop connecting helices 3/4 and the addition of nucleotides, respectively. Based on our analysis of PspA-mediated membrane remodeling, we suggest that the observed mode of structural plasticity is a prerequisite for the biological function of ESCRT-III superfamily members. SummaryA series of cryo-EM structures of PspA rods with induced diameter modulations reveals the molecular basis of structural plasticity.

biophysics↗

bioRxiv2021

Precise estimation of genome size from NGS data

Precise estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. We present here a fast, easy-to-implement and precise method to estimate genome size from the number of bases sequenced and the mean sequence coverage. To estimate the latter, we take advantage of the fact that a precise estimation of the Poisson distribution parameter lambda is possible from truncated data, restricted to the part of the coverage distribution representing the true underlying distribution. With simulations we could show that reasonable genome size estimates can be gained even from low-coverage (10X), highly discontinuous genome drafts. Comparison of estimates from a wide range of taxa and sequencing strategies with flow-cytometry estimates of the same individuals showed a very good fit and suggested that both methods yield comparable, interchangeable results.

genomics↗

bioRxiv2021

tbg - a new file format for genomic data

MotivationThe question of determining whether a Single-Nucleotide Polymorphism (SNP) or a variant in general leads to a change in the amino acid sequence of a protein coding gene is often a laborious and time-consuming challenge. Here, we introduce the tbg file format for storing genomic data and tbg-tools, a user-friendly toolbox for the faster analysis of SNPs. The file format stores information for each nucleotide in each gene, allowing to predict which change in the amino acid sequence will be caused by a variant in the nucleotide sequence. Our new tool therefore has the potential to make biological sense of the unprecedented amount of genome-wide genetic variation that researchers currently face. ResultsThe new tab-separated file for storing the nucleotide data can be easily analyzed and used for a wide variety of biological research. It is also possible to automate some of these analyses using the additional analysis tools from tbg-tools Availabilitytbg-tools is written in Python and allows the installation from the command line. It can be found on https://github.com/Croxa/tbg-tools. Contactpschoenn@students.uni-mainz.de

genomics↗