Biology subjects

Willems, R.

Publications and source records attributed to Willems, R..

4 recordsLinked to original sources

bioRxiv2023

Precision sampling of discrete sites identified during in-vivo functional testing in the mammalian heart

Ventricular arrhythmias after myocardial infarction (MI) originate from discrete areas within the MI border zone (BZ), identified during functional electrophysiology tests. Accurate sampling of arrhythmogenic sites for ex vivo study remains challenging, yet is critical to identify their tissue, cellular and molecular signature. In this study, we developed, validated, and applied a targeted sampling methodology based on individualized 3D prints of the human-sized pig heart. To this end, 3D anatomical models of the left ventricle were created from magnetic resonance imaging and fused with biplane fluoroscopy. Regions of interest for sampling were annotated on the anatomical models, from which we created a unique 3D printed cast with custom slits identifying the annotated regions for sampling. The methodology was validated by retrieving ablation lesions created at predefined locations on the anatomical model. We applied the methodology to sample arrhythmia-vulnerable regions after MI during adrenergic stimulation. A novel pipeline of imaging was developed to create a 3D high-resolution map of each sample, highlighting the complex interplay of cellular organization, and altered innervation in the BZ.

bioengineering↗

bioRxiv2023

S100A8-enriched microglia populate the brain of tau-seeded and accelerated aging mice

Long considered to fluctuate between pro- and anti-inflammatory states, it has now become evident that microglia occupy a variegated phenotypic landscape with relevance to aging and neurodegeneration. However, whether specific microglial subsets converge in or contribute to both processes that eventually affect brain function is less clear. To investigate this, we analyzed microglial heterogeneity in a tauopathy mouse model (K18-seeded P301L) and an accelerated aging model (senescence accelerated mouse prone 8, SAMP8) using cellular indexing of transcriptomes and epitopes by sequencing. We found that widespread tau pathology in K18-seeded P301L mice caused a significant change in the number and morphology of microglia, but only a mild overrepresentation of disease-associated microglia. At the cell population-level, we observed a marked upregulation of the calprotectin-encoding genes S100a8 and S100a9. In 9-months-old SAMP8 mice, we identified a unique microglial subpopulation that showed partial similarity with the disease-associated microglia phenotype and was additionally characterized by a high expression of the same calprotectin gene set. Immunostaining for S100A8 revealed that this population was enriched in the hippocampus, correlating with the cognitive impairment observed in this model. However, incomplete colocalization between their residence and markers of neuronal loss suggests regional specificity. Importantly, S100A8-positive microglia were also retrieved in brain biopsies of human AD and tauopathy patients as well as in a biopsy of an aged individual without reported pathology. Thus, the emergence of S100A8-positive microglia portrays a conspicuous commonality between accelerated aging and tauopathy progression, which may have relevance for ensuing brain dysfunction. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/566543v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@d1e4e1org.highwire.dtl.DTLVardef@98adeorg.highwire.dtl.DTLVardef@7c15aaorg.highwire.dtl.DTLVardef@7265ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Conditionally essential genes for survival during starvation in Enterococcus faecium E745

The nosocomial pathogen Enterococcus faecium can survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability of E. faecium to spread among patients in hospitals. Because there is currently a lack of data on the mechanisms that are responsible for the ability of E. faecium to survive in the absence of nutrients, we performed a high-throughput transposon mutant library screening (Tn-seq) to identify genes that have a role in long-term survival during incubation in phosphate-buffered saline (PBS) at 20{degrees}C. A total of 18 genes were identified by Tn-seq to contribute to survival in PBS, with functions associated with the general stress response, DNA repair, metabolism, and membrane homeostasis. The gene which was quantitatively most important for survival in PBS was usp (locus tag: EfmE745_02439), which is predicted to encode a 17.4 kDa universal stress protein. After generating a targeted deletion mutant in usp, we were able to confirm that usp significantly contributes to survival in PBS and this defect was restored by in trans complementation. As usp is present in 99% of 1644 E. faecium genomes that span the diversity of the species, we postulate that this gene is a key determinant for the remarkable environmental robustness of E. faecium. Further mechanistic studies into usp and other genes identified in this study may shed further light on the mechanisms by which E. faecium can survive in the absence of nutrients for prolonged periods of time.

microbiology↗

bioRxiv2019

R-DECO: An open-source Matlab based graphical user interface for the detection and correction of R-peaks

Many of the existing ECG toolboxes focus on the derivation of heart rate variability features from RR-intervals. By doing so, they assume correct detection of the QRS-complexes. However, it is highly likely that not all detections are correct. Therefore, it is recommended to visualize the actual R-peak positions in the ECG signal and allow manual adaptations. In this paper we present R-DECO, an easy-to-use graphical user interface for the detection and correction of R-peaks. Within R-DECO, the R-peaks are detected by an adaptation of the Pan-Tompkins algorithm. Instead of using all the pre-processing steps of the latter algorithm, the proposed algorithm uses only an envelope-based procedure to flatten the ECG and enhance the QRS-complexes. The algorithm obtained an overall sensitivity of 99.60% and PPV of 99.69% on the MIT/BIH arrhythmia database. Additionally, R-DECO includes support for several input data formats for ECG signals, three basic filters, the possibility to load other R-peak locations and intuitive methods to correct ectopic, wrong, or missed heartbeats. All functionalities can be accessed via the graphical user interface and the analysis results can be exported as Matlab or Excel files. The software is publicly available. Through its easy-to-use-graphical user interface, R-DECO allows both clinicians and researchers to use all functionalities, without previous knowledge.

bioengineering↗