Biology subjects

Ehmke, N.

Publications and source records attributed to Ehmke, N..

3 recordsLinked to original sources

bioRxiv2024

Automated high-throughput selection of DNA aptamers using a common optical next-generation sequencer

Aptamers are conventionally selected via Systematic Evolution of Ligands by Exponential Enrichment (SELEX). This process is, however, laborious, time-consuming, and has a relatively low efficacy. Here, we developed an automated high-throughput screening platform for the selection of DNA aptamers which consists of an optical next-generation sequencer with a modified software and hardware to automatically perform fluorescence-based binding assays on the displayed DNA sequences subsequent to sequencing. Using this platform, after only three to five SELEX rounds we selected highly affine DNA aptamers for the lectins LecA and LecB of Pseudomonas aeruginosa as well as for the Pseudomonas Exotoxin A. In comparison, twelve rounds of conventional SELEX resulted in three-fold less affine aptamers for LecA and PEA and none for LecB. Our high throughput-approach bears great potential to augment SELEX as it significantly increases time efficiency, enabling the selection of aptamers within only one week.

biochemistry↗

bioRxiv2020

VarFish - Collaborative and Comprehensive Variant Analysis for Diagnosis and Research

VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of panel and exome variant data for rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Filtered variants are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows user to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the softwares extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g., after update of genotype or phenotype databases.

bioinformatics↗

bioRxiv2018

Thrombocytopenia Microcephaly Syndrome - a novel phenotype associated with ACTB mutations

Introductory paragraphUntil recently missense germ-line mutations in ACTB, encoding the ubiquitously expressed {beta}-cytoplasmic actin (CYA), were exclusively associated with Baraitser-Winter Cerebrofrontofacial syndrome (BWCFF), a complex developmental disorder1,2. Here, we report six patients with previously undescribed heterozygous variants clustered in the 3-coding region of ACTB. These patients present with clinical features different from BWCFF, including thrombocytopenia, microcephaly, and mild developmental disability. Patient derived cells are morphologically and functionally distinct from controls. Assessment of cytoskeletal constituents identified a discrete filament population altered in these cells, which comprises force generating and transmitting actin binding proteins (ABP) known to be associated with thrombocytopenia3-8. In silico modelling and molecular dynamics (MD)-simulations support altered interactions between these ABP and mutant {beta}-CYA. Our results describe a new clinical syndrome associated with ACTB mutations with a distinct genotype-phenotype correlation, identify a cytoskeletal protein interaction network crucial for thrombopoiesis, and provide support for the hypomorphic nature of these actinopathy mutations.

genetics↗