Biology subjects

Andre, B.

Publications and source records attributed to Andre, B..

6 recordsLinked to original sources

bioRxiv2026

A genetically-encoded cysteine biosensor to monitor cysteine dynamics across life domains

Cysteine is a central metabolite in cellular redox regulation and iron-sulfur cluster assembly. Despite its critical role, monitoring cysteine dynamics in living systems has remained a challenge due to the lack of tools that avoid cysteine oxidation and/or do not destroy the cell in the process. Here, we report the development of Cystector (from Cysteine Detector), a genetically encoded, ratiometric green fluorescent biosensor for cysteine that exhibits an exceptional selectivity, minimal pH sensitivity in the physiological range, and a dynamic range of up to 4500%. Furthermore, the sensor retains functionality in the presence of physiological glutathione concentrations. We demonstrate the live-cell functionality of Cystector by monitoring intracellular and extracellular cysteine dynamics in different organisms. In E. coli, we show how cystine reduction in Escherichia coli is dependent on glutathione and glutaredoxins, and that the reduced cysteine is then exported into the extracellular environment. In yeast, we demonstrate how energy metabolism and oxidative stress determine cysteine homeostasis. In mammalian cells, we show how Cystector effectively monitors cysteine depletion in response to treatments such as H2O2, erastin2, and glutamate. Finally, we demonstrate, via a mitochondrially targeted variant, that Cystector can be used to monitor subcellular cysteine dynamics. These results together establish Cystector as a robust tool to unravel cysteine metabolism and transport in live cells across life domains.

molecular biology↗

bioRxiv2025

Vsb1, Ypq1 and Ypq2 control dynamic cationic amino acid storage in the yeast vacuole

Although the yeast vacuole plays a crucial role in storing and mobilizing cationic amino acids (CAA), CAA transport at the vacuolar membrane remains poorly understood. Here, by combining analysis of CAA pools, uptake and permeabilization assays, we establish Vsb1 as the principal vacuolar lysine transporter, enabling its strong accumulation in the vacuole while mitigating its toxicity. We further show that, although Ypq1 can mediate proton-independent vacuolar lysine import, it mainly functions as a lysine exporter necessary for lysine mobilization under conditions of lysine scarcity and downregulated as lysine stores are exhausted. Using quantitative models based on dynamic metabolic labeling, we further show that, surprisingly, in growing cells, CAA rapidly exchange between vacuolar and cytosolic compartments, a process involving the export activity of Ypq1 and its paralogue Ypq2, specific for lysine and arginine, respectively. Together, our findings reveal the unexpectedly complex function of Vsb1 and Ypq1/2 as the key transporters mediating dynamic vacuolar CAA storage. 40-word summaryZaremba et al. characterize Vsb1 as the main yeast vacuolar lysine importer and Ypq1/2 as bi- directional vacuolar transporters of lysine and arginine. Their study highlights the role of vacuolar transporters in regulating cationic amino acid homeostasis under fluctuating nutrient availability.

cell biology↗

bioRxiv2025

Improving eDNA filtration and purification for qPCR detection of Schistosoma mansoni in lakes Albert and Victoria

BackgroundSchistosomiasis, a parasitic disease caused by Schistosoma trematodes, remains a significant public health burden in sub-Saharan Africa, particularly in regions with limited access to clean water, sanitation and hygiene. Effective disease control strategies rely on large-scale surveillance to accurately identify and target high-risk populations. However, traditional methods such as malacological surveys and stool/urine microscopy in humans often lack sensitivity and scalability. Environmental DNA (eDNA) is emerging as a promising tool for non-invasive surveillance of aquatic pathogens, offering enhanced sensitivity and feasibility for large-scale monitoring. MethodsThis study evaluated the efficacy of eDNA-based detection of Schistosoma mansoni in water samples from Lake Albert and Lake Victoria, Uganda. Three eDNA filtration techniques: open membrane, Waterra capsule and Sylphium capsule filters, were compared for DNA yield and detection efficiency. SYBR Green quantitative polymerase chain reaction (qPCR) targeting the mitochondrial cytochrome oxidase subunit I (COI) gene was performed to quantify S. mansoni eDNA, following in silico and in vitro optimisation of primers. Conventional malacological surveys were conducted in parallel to validate eDNA findings, and statistical analyses examined the influence of environmental factors (turbidity and total dissolved solids (TDS)) on eDNA yield and detection rates. ResultsThe SYBR Green S. mansoni qPCR assay had a practical limit of detection (LOD), defined as amplification in >95% of 33 technical replicates, of 100 copies per reaction. The assay amplified in 82% of reactions with 10 DNA copies and 76% with a single copy. The theoretical LOD, determined via amplification probabilities in RStudio, was 83 copies per reaction, which was also the calculated limit of quantification (LOQ). Schistosoma mansoni eDNA was detected in 58.1% (25/43) of filters from Lake Albert and 19.2% (10/52) from Lake Victoria. The Waterra capsule filter yielded the highest eDNA concentrations, while the Sylphium-coupled capsule filter exhibited comparable detection efficiency. Among the DNA purification methods tested, the Sylphium precipitation-based protocol produced significantly higher eDNA yield than column-based kits (DNeasy Blood and Tissue and Zymo Research). Despite significant variation in eDNA recovery across filtration methods, qPCR detection rates were consistent. No significant correlation was observed between turbidity and S. mansoni eDNA detectability. ConclusionOur findings highlight the potential of eDNA as a sensitive, scalable tool for schistosomiasis surveillance. While Waterra filters and Sylphium extraction maximised DNA yield, lower-yield filtration methods still enabled S. mansoni detection in high-transmission settings. These findings support the adaptability of eDNA approaches across varying resource contexts. Future work should prioritise protocol standardisation, ecological validation, and development of field-ready diagnostics such as LAMP to enable broader implementation in endemic regions.

molecular biology↗

bioRxiv2023

Ferroptosis-Protective Membrane Domains in Quiescence

Quiescence is a common cellular state, required for stem-cell maintenance and microorganismal survival under stress conditions or starvation. However, the mechanisms promoting quiescence maintenance remain poorly known. Plasma membrane components segregate into distinct microdomains, yet the role of this compartmentalization in quiescence remains unexplored. Here, we show that Flavodoxin-like proteins (FLPs), ubiquinone reductases of the yeast eisosome membrane compartment, protect quiescent cells from lipid peroxidation and ferroptosis. Eisosomes and FLPs expand specifically in respiratory-active quiescent cells, and mutants lacking either show accelerated aging, defective quiescence maintenance, and accumulate peroxidized phospholipids with monounsaturated or polyunsaturated fatty acids (PUFA). FLPs are essential for the extra-mitochondrial regeneration of the lipophilic antioxidant ubiquinol. FLPs, alongside the Gpx1/2/3 glutathione peroxidases, prevent iron-driven, PUFA-dependent ferroptotic cell death. Our work is the first description of ferroptosis-protective mechanisms in yeast and introduces plasma membrane compartmentalization as an important factor for the long-term survival of quiescent cells.

cell biology↗

bioRxiv2022

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology optimized for samples of fresh cells. Complexes of one cell paired with one barcoded bead are stabilized by a chemical linker and dispersed in a hydrogel in the liquid state. Upon gelation on ice the complexes are immobilized and physically separated without requiring nanowells or droplets. Cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcoded beads for further processing with reverse transcription and preparation for cDNA sequencing. As a proof of concept, analysis of PBMC using RevGel-seq achieves results similar to microfluidic-based technologies when using the same original sample and the same data analysis software. In addition, a clinically relevant application of RevGel-seq is presented for pancreatic islet cells. Furthermore, characterizations carried out on cardiomyocytes demonstrate that the hydrogel technology readily accommodates very large cells. Standard analyses are in the 10,000-input cell range with the current gelation device, in order to satisfy common requirements for single-cell research. A convenient stopping point after two hours has been established by freezing at the cell lysis step, with full preservation of gene expression profiles. Overall, our results show that RevGel-seq represents an accessible and efficient instrument-free alternative, enabling flexibility in terms of experimental design and timing of sample processing, while providing broad coverage of cell types.

cell biology↗

bioRxiv2020

Uptake of endogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae

Sphingolipids are abundant and essential molecules in eukaryotes that have crucial functions as signaling molecules and as membrane components. Sphingolipid biosynthesis starts in the endoplasmic reticulum with the condensation of serine and palmitoyl-CoA. Sphingolipid biosynthesis is highly regulated to maintain sphingolipid homeostasis. Even though, serine is an essential component of the sphingolipid biosynthesis pathway, its role in maintaining sphingolipid homeostasis has not been precisely studied. Here we show that serine uptake is an important factor for the regulation of sphingolipid biosynthesis in Saccharomyces cerevisiae. Using genetic experiments, we find the broad-specificity amino acid permease Gnp1 to be important for serine uptake. We confirm these results with serine uptake assays in gnp1{Delta} cells. We further show that uptake of exogenous serine by Gnp1 is important to maintain cellular serine levels and observe a specific connection between serine uptake and the first step of sphingolipid biosynthesis. Using mass spectrometry-based flux analysis, we further observed imported serine as the main source for de novo sphingolipid biosynthesis. Our results demonstrate that yeast cells preferentially use the uptake of exogenous serine to regulate sphingolipid biosynthesis. Our study can also be a starting point to analyze the role of serine uptake in mammalian sphingolipid metabolism. Author SummarySphingolipids (SPs) are membrane lipids globally required for eukaryotic life. In contrast to other lipid classes, SPs cannot be stored in the cell and therefore their levels have to be tightly regulated. Failure to maintain sphingolipid homeostasis can result in pathologies including neurodegeneration, childhood asthma and cancer. However, we are only starting to understand how SP biosynthesis is adjusted according to need. In this study, we use genetic and biochemical methods to show that the uptake of exogenous serine is necessary to maintain SP homeostasis in Saccharomyces cerevisiae. Serine is one of the precursors of long chain bases in cells, the first intermediate of SP metabolism. Our results suggest that the uptake of serine is directly coupled to SP biosynthesis at ER-plasma membrane contact sites. Overall, our study identifies serine uptake as a novel regulatory factor of SP homeostasis. While we use yeast as a discovery tool, these results also provide valuable insights into mammalian SP biology especially under pathological conditions.

genetics↗