Biology subjects

de Vries, L. E.

Publications and source records attributed to de Vries, L. E..

9 recordsLinked to original sources

bioRxiv2026

A silent intergenic locus for efficient and versatile transgene expression in Plasmodium falciparum

Genetically modified Plasmodium falciparum parasites expressing transgenes such as fluorescent markers are crucial tools for malaria research. However, current reporter lines often rely on integrated transgene constructs that disrupt the coding sequence of a native gene, potentially affecting progression in the life cycle of the tool parasite line. We identified six candidate Silent Intergenic Loci (SILs): putatively editable intergenic regions without transcriptional activity, where gene insertions occurred in P. falciparum after its divergence from Plasmodium berghei and Plasmodium vivax. We characterised the largest candidate SIL on chromosome 12, SIL12, by integration of a constitutively expressed cytosolic mScarlet reporter. The resulting PfRed12 parasites progressed normally throughout the life cycle, from asexual blood-stage replication to mosquito stages and subsequent liver infection. Importantly, they infected both Anopheles stephensi and Anopheles coluzzii mosquitoes. PfRed12 parasites displayed bright fluorescence in both blood and mosquito stages, making them well suited for live visualisation of parasite transmission. In addition, we used two CRISPR-Cas9 target sites in the mScarlet cassette, one of which we purposely added, to perform efficient re-editing of the transgene. As a proof of concept, we re-edited PfRed12 parasites and integrated an apicoplast metabolic bypass construct, an inducible gametocyte producer construct, and two mNeonGreen reporter constructs. Together, our findings demonstrate that SIL12 permits stable transgene expression without compromising parasite development throughout the life cycle. We established PfRed12 as a new reporter line to study blood- and mosquito-stage development and as a versatile parental line for further genetic engineering.

microbiology↗

bioRxiv2025

OocystMeter, a machine-learning algorithm to count and measure Plasmodium oocysts, reveals clustering patterns in the Anopheles midgut

We present OocystMeter, a machine learning-based software developed to automate the segmentation of malaria oocysts from images of mosquito midguts stained with mercurochrome. Existing bioimage analysis tools, including machine learning-based ones, often struggle with the unique staining patterns, complex midgut backgrounds, and variable morphology of oocysts, making the determination of oocyst size and numbers cumbersome. To overcome these challenges, we curated a high-quality dataset comprised of 11,178 Plasmodium falciparum oocysts in Anopheles gambiae midguts annotated by expert parasitologists. Using this dataset, we fine-tuned a Mask R-CNN object detection model to achieve segmentation accuracy comparable to human parasitologists (Spearmans correlation of 0.998 for oocyst counts and 0.978 for size measurements). Applying this tool in conjunction with spatial analysis, we uncovered a non-random, clustered spatial distribution of oocysts independent of the midguts anatomical regions or geometric axes, particularly in infections with fewer than 75 oocysts/midgut. Our workflow significantly accelerates malaria oocyst intensity and size analysis, reduces human bias, and provides spatial coordinates for advanced parasitology studies. OocystMeter is freely available at https://github.com/duopeng/OocystMeter, and as a web tool at http://Oocystmeter.org/, offering a valuable resource for researchers investigating the oocyst stage of malaria development.

bioinformatics↗

bioRxiv2025

Reduced triacylglycerols and lipid droplets are associated with resilience to Alzheimers disease

IntroductionWhile it has become clear that alterations in lipid metabolism are associated with AD, it is unclear how they contribute to both cognitive decline and the pathophysiology of AD. MethodsWe performed lipidomics and activity-based protein profiling in the frontal cortex of control, AD and resilient donors, i.e. individuals with AD pathology without cognitive decline. Subsequently we integrated these data using multi-omics factor analysis and correlated the multi-omics profiles to disease and clinical parameters. ResultsThe most pronounced alterations in lipids were in the {omega}6-derived oxylipins, which were particularly increased in the AD patients. Both triacylglycerols (TAGs) and lipid droplets were more abundant in the AD donors compared to the resilient donors. Enzyme activities showed a similar direction in the AD and resilient donors, including decreased activity of ABHD6. Multi-omics factor analysis showed that increased oxylipins, loss of inhibitory cells, synaptic genes and genes related to the inflammatory response were associated with A{beta} plaque load in both AD and resilient donors. ConclusionOur multi-omics data show a response associated with A{beta} load shared among AD and resilient donors and, for the first time, reduced lipid droplets in resilient donors.

neuroscience↗

bioRxiv2024

Mapping Plasmodium transitions and interactions in the Anopheles female

The human malaria parasite, Plasmodium falciparum, relies exclusively on Anopheles mosquitoes for transmission. Once ingested during blood feeding, most parasites die in the mosquito midgut lumen or during epithelium traversal1. How surviving ookinetes interact with midgut cells and form oocysts is poorly known, yet these steps are essential to initiate a remarkable growth process culminating in the production of thousands of infectious sporozoites2. Here, using single-cell RNA sequencing of both parasites and mosquito cells across different developmental stages and metabolic conditions, we unveil key transitions and mosquito-parasite interactions occurring in the midgut. Functional analyses uncover processes regulating oocyst growth and identify the transcription factor PfSIP2 as essential for sporozoite infection of human hepatocytes. Combining shared mosquito-parasite barcode analysis with confocal microscopy, we reveal that parasites preferentially interact with midgut progenitor cells during epithelial crossing, potentially using their basal location as an exit landmark. Additionally, we show tight connections between extracellular late oocysts and surrounding muscle cells that may ensure parasites adherence to the midgut. We confirm our major findings in several mosquito-parasite combinations, including field-derived parasites. Our study provides fundamental insight into the molecular events characterizing previously inaccessible biological transitions and mosquito-parasite interactions, and identifies candidates for transmission-blocking strategies.

microbiology↗

bioRxiv2021

Preclinical characterization and target validation of the antimalarial pantothenamide MMV693183

Drug resistance and a dire lack of transmission-blocking antimalarials hamper malaria elimination. Here, we present the pantothenamide MMV693183 as a first-in-class acetyl-CoA synthetase (ACS) inhibitor to enter preclinical development. Our studies demonstrated attractive drug-like properties and in vivo efficacy in a humanized mouse model of Plasmodium falciparum infection. The compound showed exceptional in vitro activity against P. falciparum and P. vivax clinical isolates, and potently blocked P. falciparum transmission to Anopheles mosquitoes. Genetic and biochemical studies identified ACS as the target of the MMV693183-derived antimetabolite, CoA-MMV693183. MMV693183 was well adsorbed after oral administration in mice, rats and dogs. Pharmacokinetic - pharmacodynamic modelling predicted that a single 30 mg oral dose is sufficient to cure a malaria infection in humans. In conclusion, the ACS-targeting compound MMV693183 represents a promising addition to the portfolio of antimalarials in (pre)clinical development with a novel mode of action for the treatment of malaria and blocking transmission.

microbiology↗

bioRxiv2021

A prioritized and validated resource of mitochondrial proteins in Plasmodium identifies leads to unique biology

Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by anti-malarial drugs. Most mitochondrial proteins are imported into this organelle and our picture of the Plasmodium mitochondrial proteome remains incomplete. Many data sources contain information about mitochondrial localization, including proteome and gene expression profiles, orthology to mitochondrial proteins from other species, co-evolutionary relationships, and amino acid sequences, each with different coverage and reliability. To obtain a comprehensive, prioritized list of Plasmodium falciparum mitochondrial proteins, we rigorously analyzed and integrated eight datasets using Bayesian statistics into a predictive score per protein for mitochondrial localization. At a corrected false discovery rate of 25%, we identified 445 proteins with a sensitivity of 87% and a specificity of 97%. They include proteins that have not been identified as mitochondrial in other eukaryotes but have characterized homologs in bacteria that are involved in metabolism or translation. Mitochondrial localization of seven Plasmodium berghei orthologs was confirmed by epitope labeling and co-localization with a mitochondrial marker protein. One of these belongs to a newly identified apicomplexan mitochondrial protein family that in P. falciparum has four members. With the experimentally validated mitochondrial proteins and the complete ranked P. falciparum proteome, which we have named PlasmoMitoCarta, we present a resource to study unique proteins of Plasmodium mitochondria.

bioinformatics↗

bioRxiv2020

Conjugative dissemination of plasmids in rapid sand filters: a trojan horse strategy to enhance pesticide degradation in groundwater treatment

The supply of clean water for human consumption is being challenged by the appearance of pesticide pollutants in groundwater ecosystems. Biological rapid sand filtration is a commonly employed method for the removal of organic and inorganic impurities in water which relies on the degradative properties of microorganisms for the removal of diverse contaminants, including pesticides. Although sustainable and relatively inexpensive, the bioremediation capabilities of rapid sand filters vary greatly across waterworks. Bioaugmentation efforts with degradation-proficient bacteria have proven difficult due to the inability of the exogenous microbes to stably colonize the sand filters. Pesticide degrading genes, however, are often encoded naturally by plasmids--extrachromosomal DNA elements that can transfer between bacteria--yet their ability to spread within rapid sand filters have remained unknown. To evaluate the potential use of plasmids for the dissemination of pesticide degrading genes, we examined the permissiveness of rapid sand filter communities towards four environmental transmissible plasmids; RP4, RSF1010, pKJK5 and TOL (pWWO), using a dual-fluorescent bioreporter platform combined with FACS and 16S rRNA gene amplicon sequencing. Our results reveal that plasmids can transfer at high frequencies and across distantly related taxa from rapid sand filter communities, emphasizing their suitability for introducing pesticide degrading determinants in the microbiomes of underperforming water purification plants.

microbiology↗

bioRxiv2018

Characterization of P. falciparum dipeptidyl aminopeptidase 3 specificity identifies different amino acid preferences between peptide-based substrates and inhibitors.

Malarial dipeptidyl aminopeptidases (DPAPs) are cysteine proteases important for parasite development thus making them attractive drug targets. In order to develop inhibitors specific to the parasite enzymes it is necessary to map the determinants of substrate specificity of the parasite enzymes and its mammalian homologue cathepsin C (CatC). Here, we screened peptide-based libraries of substrates and covalent inhibitors to characterize the differences in specificity between parasite DPAPs and CatC, and used this information to develop highly selective DPAP1 and DPAP3 inhibitors. Interestingly, while the primary amino acid specificity of a protease is often used to develop potent inhibitors, we show that equally potent and highly specific inhibitors can be developed based on the sequences of non-optimal peptide substrates. Importantly, analysis of previously published data about the specificity of other proteases also unveiled significant discrepancies in the amino acid preference between substrates and inhibitors. In this article, we also discuss important structural and theoretical reasons that might account for these discrepancies. Overall, this study illustrates that focusing the development of protease inhibitors solely on substrate specificity might overlook important structural features that can be exploited to develop highly potent and selective compounds.

biochemistry↗

bioRxiv2017

Plasmodium falciparum dipeptidyl aminopeptidase 3 activity is important for efficient erythrocyte invasion.

Parasite egress from infected erythrocytes and invasion of new erythrocytes are essential for the exponential asexual replication of the malaria parasite, and both processes are regulated and mediated by proteases. The putative cysteine protease dipeptidyl aminopeptidase 3 (DPAP3) was previously suggested to be essential for parasite egress, but little is known about its biological function. Here, we demonstrate that DPAP3 has proteolytic activity, but contrary to previously studied DPAPs, removal of its prodomain is not required for activation. Interestingly, P. falciparum DPAP3 localizes to merozoite apical organelles from which it is secreted immediately before egress. Using a conditional knock out approach coupled to complementation studies with wild type or mutant DPAP3, we show that DPAP3 activity is critical for efficient RBC invasion and overall parasite replication, and demonstrate that it does not play a role in parasite egress. Overall, this study establishes DPAP3 as a key regulator of erythrocyte invasion.

microbiology↗