Biology subjects

ter Horst, J.

Publications and source records attributed to ter Horst, J..

3 recordsLinked to original sources

bioRxiv2024

Stopping Speed as State, Not Trait: Exploring Within-Animal Varying Stopping Speeds in a Multi-Session Stop-Signal Task

Being able to reactively stop ongoing movements is important for safe navigation through the environment. Reactive stopping is typically studied using the stop-signal task, where participants are occasionally instructed to stop initiated movements. The speed of stopping, also referred to as the stop-signal reaction time (SSRT), is not observable because successful stopping lacks a response, but can be estimated. Researchers most often acquire one session of data per participant to estimate the speed of stopping, but sometimes more sessions of data are acquired to maximize the signal-to-noise ratio, for example when the task is combined with neural recordings such as electrophysiology. However, it is unknown whether the estimated stopping speed is a fixed trait or a state that can vary under identical experimental conditions. In this study, we investigate whether a separately estimated SSRT for each acquired session is statistically meaningful compared to estimating an across-session SSRT, by collecting many sessions in which male rats performed a stop-signal task. Results revealed that within-animal stopping speeds meaningfully changed from session to session and were not following a trend over time (e.g., due to task learning). Single-session SSRT estimates with lower reliabilities were associated with higher go trial response time variabilities, lower skewness levels of the go trial response time distribution, and lower stop accuracies. We also explored which factors explained changing SSRTs, and showed that motivation, shared motor dynamics, and attention could play a role. In conclusion, we encourage researchers to treat SSRTs as state-like variables when collecting multi-session stop-signal task data, as our results have convincingly shown that stopping speeds are far from trait-like under identical experimental conditions. This session-by-session approach will help future research in which neural signatures of reactive stopping need to be extracted in a time-precise manner, because time-locking stop-related neural activity to session-specific SSRTs is expected to capture the signature more precisely as opposed to an across-session SSRT.

animal behavior and cognition↗

bioRxiv2021

Physiological relevance, localization and substrate specificity of the alternative (type II) mitochondrial NADH dehydrogenases of Ogataea parapolymorpha

Mitochondria from Ogataea parapolymorpha harbor a branched electron-transport chain containing a proton-pumping Complex I NADH dehydrogenase and three alternative (type II) NADH dehydrogenases (NDH2s). To investigate the physiological role, localization and substrate specificity of these enzymes, growth of various NADH dehydrogenase mutants was quantitatively characterized in shake-flask and chemostat cultures, followed by oxygen-uptake experiments with isolated mitochondria. Furthermore, NAD(P)H:quinone oxidoreduction of the three NDH2s were individually assessed. Our findings show that the O. parapolymorpha respiratory chain contains an internal NADH-accepting NDH2 (Ndh2-1/OpNdi1), at least one external NAD(P)H-accepting enzyme and likely additional mechanisms for respiration-linked oxidation of cytosolic NADH. Metabolic regulation appears to prevent competition between OpNdi1 and Complex I for mitochondrial NADH. With the exception of OpNdi1, the respiratory chain of O. parapolymorpha exhibits metabolic redundancy and tolerates deletion of multiple NADH-dehydrogenase genes without compromising fully respiratory metabolism. ImportanceTo achieve high productivity and yields in microbial bioprocesses, efficient use of the energy substrate is essential. Organisms with branched respiratory chains can respire via the energy-efficient proton-pumping Complex I, or make use of alternative NADH dehydrogenases (NDH2s). The yeast Ogataea parapolymorpha contains three uncharacterized, putative NDH2s which were investigated in this work. We show that O. parapolymorpha contains at least one internal NDH2, which provides an alternative to Complex I for mitochondrial NADH oxidation, albeit at a lower efficiency. The use of this NDH2 appeared to be limited to carbon excess conditions and the O. parapolymorpha respiratory chain tolerated multiple deletions without compromising respiratory metabolism, highlighting opportunities for metabolic (redox) engineering. By providing a more comprehensive understanding of the physiological role of NDH2s, including insights into their metabolic capacity, orientation and substrate specificity this study also extends our fundamental understanding of respiration in organisms with branched respiratory chains.

microbiology↗

bioRxiv2018

Allele-specific genome editing using CRISPR-Cas9 causes off-target mutations in diploid yeast

Targeted DNA double-strand breaks (DSBs) with CRISPR-Cas9 have revolutionized genetic modification by enabling efficient genome editing in a broad range of eukaryotic systems. Accurate gene editing is possible with near-perfect efficiency in haploid or (predominantly) homozygous genomes. However, genomes exhibiting polyploidy and/or high degrees of heterozygosity are less amenable to genetic modification. Here, we report an up to 99-fold lower gene editing efficiency when editing individual heterozygous loci in the yeast genome. Moreover, Cas9-mediated introduction of a DSB resulted in large scale loss of heterozygosity affecting DNA regions up to 360 kb that resulted in introduction of nearly 1700 off-target mutations, due to replacement of sequences on the targeted chromosome by corresponding sequences from its non-targeted homolog. The observed patterns of loss of heterozygosity were consistent with homology directed repair. The extent and frequency of loss of heterozygosity represent a novel mutagenic side-effect of Cas9-mediated genome editing, which would have to be taken into account in eukaryotic gene editing. In addition to contributing to the limited genetic amenability of heterozygous yeasts, Cas9-mediated loss of heterozygosity could be particularly deleterious for human gene therapy, as loss of heterozygous functional copies of anti-proliferative and pro-apoptotic genes is a known path to cancer.

molecular biology↗