Biology subjects

de Groot, A.

Publications and source records attributed to de Groot, A..

3 recordsLinked to original sources

bioRxiv2024

PIMENTA: PIpeline for MEtabarcoding through Nanopore Technology used for Authentication

DNA metabarcoding has become a cost-effective method to assess species composition of mixed samples. Developments such as advances in sequencing technology and increased species coverage of reference databases can be leveraged to gain more insights from metabarcoding experiments, given suitable tools. To this end, we introduce PIMENTA, a new pipeline that streamlines the analysis of Nanopore DNA metabarcoding sequencing data. PIMENTA consists of four phases: pre-processing, clustering per sample, reclustering of all samples, and taxonomic identification. PIMENTA expands a workflow created by Voorhuijzen-Harink et al. Multiple updates have been made, including parallelization of the analysis of multiple samples with the use of high-performance computing (HPC), implementation of a local taxonomy database, and expansion of the taxonomic results summary. Settings have been optimized to process higher quality nanopore reads, for an increased accuracy of taxonomic identification. We evaluated the pipeline with mock samples of zooplankton species, incorporating COI, 18SV4, and 18SV9 marker sequences. The performance and runtime have been benchmarked against two other existing pipelines. PIMENTA was able to quickly identify species with a high resolution and minimal misidentifications.

bioinformatics↗

bioRxiv2022

NRF2 activation induces NADH-reductive stress providing a metabolic vulnerability in lung cancer

Multiple cancers regulate oxidative stress by activating the transcription factor NRF2 through mutation of its negative regulator KEAP1. NRF2 has been studied extensively in KEAP1-mutant cancers, however the role of this pathway in cancers with wildtype KEAP1 remains poorly understood. To answer this question, we induced NRF2 via pharmacological inactivation of KEAP1 in a panel of 50+ non-small lung cancer cell lines. Unexpectedly, marked decreases in viability were observed in >13% of the cell lines--an effect that was completely rescued by NRF2 ablation. Genome-wide and targeted CRISPR screens revealed that NRF2 induces NADH-reductive stress, through the upregulation of the NAD+-consuming enzyme ALDH3A1. Leveraging these findings, we show that cells treated with KEAP1 inhibitors or those with endogenous KEAP1 mutations are selectively vulnerable to Complex I inhibition, which impairs NADH oxidation capacity and potentiates reductive stress. Thus, we identify reductive stress as a metabolic vulnerability in NRF2-activated lung cancers.

molecular biology↗

bioRxiv2019

NINscope: a versatile miniscope for multi-region circuit investigations

Miniaturized fluorescence microscopes (miniscopes) have been instrumental to monitor neural activity during unrestrained behavior and their open-source versions have helped to distribute them at an affordable cost. Generally, the footprint and weight of open-source miniscopes is sacrificed for added functionality. Here, we present NINscope: a light-weight, small footprint, open-source miniscope that incorporates a high-sensitivity image sensor, an inertial measurement unit (IMU), and an LED driver for an external optogenetic probe. We highlight the advantages of NINscope by performing the first simultaneous cellular resolution (dual scope) recordings from cerebellum and cerebral cortex in unrestrained mice, revealing that the activity of both regions generally precedes the onset of behavioral acceleration. We further demonstrate the optogenetic stimulation capabilities of NINscope and show that cerebral cortical activity can be driven strongly by cerebellar stimulation. To validate the performance of our miniscope to image from deep-brain regions, we recorded in the dorsal striatum and, using the IMU to assess turning movements, replicate previous studies that show encoding of action space in this subcortical region. Finally, we combine optogenetic stimulation of distinct cortical regions projecting to the dorsal striatum, to probe functional connectivity. In combination with cross-platform control software, NINscope is a versatile addition to the expanding toolbox of open-source miniscopes and will aid multi-region circuit investigations during unrestrained behavior.

neuroscience↗