Biology subjects

Bouwens, A.

Publications and source records attributed to Bouwens, A..

3 recordsLinked to original sources

bioRxiv2024

DynaMAP: Dynamic Microbiome Abundance Profiling through high density optical mapping

Microbial abundance profiling is rapidly becoming an essential method in biomedical research, though it is often costly and time intensive. We present DynaMAP, a rapid approach for microbiome profiling that uses single-molecule imaging to develop an optical map of metagenomic DNA. DynaMAP achieves strain-level taxonomic profiling without requiring base-by-base sequencing and with a one-day turnaround time. In doing so, it delivers microbiome profiling that is comparable to shotgun sequencing but operates more efficiently, strongly expanding the possibility for microbiome analysis.

microbiology↗

bioRxiv2021

Self-contained and modular structured illumination microscope

We present a modular implementation of structured illumination microscopy (SIM) that is fast, largely self-contained and that can be added onto existing fluorescence microscopes. Our instrument, which we call HIT-SIM, can theoretically deliver well over 50 super-resolved images per second and is readily compatible with existing acquisition software packages. We provide a full technical package consisting of schematics, a list of components and an alignment scheme that provides detailed specifications and assembly instructions. We illustrate the performance of the instrument by imaging optically large samples containing sequence-specifically stained DNA fragments.

biophysics↗

bioRxiv2019

Identifying microbial species by single-molecule DNA optical mapping and resampling statistics

Single molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Secondly, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Thirdly, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.

genomics↗