Biology subjects

De Meyer, M.

Publications and source records attributed to De Meyer, M..

9 recordsLinked to original sources

bioRxiv2026

Altitude-mediated niche partitioning between Dacus bivittatus and Dacus punctatifrons along an elevational transect in the Uluguru Mountains, Tanzania

Understanding how fruit fly species partition resources along environmental gradients is important for predicting pest pressure under changing climatic conditions. The population ecology of Dacus bivittatus (Bigot) and Dacus punctatifrons (Karsch) (Diptera: Tephritidae) was examined across six sites spanning 526-1,650 m above sea level in the Uluguru Mountains, Tanzania, over eight years (2004-2012). A total of 2,200 weekly trap records were aggregated into 292 site-month observations and standardised as flies per trap per day (FTD). Dacus bivittatus showed strong seasonal structuring (H = 43.03, p < 0.001), with abundance peaking during the cool dry season (June-August), whereas D. punctatifrons showed no clear seasonal pattern. Both species declined significantly with increasing altitude ({rho} = -0.308 and -0.769, respectively; p < 0.001), but the decline was steeper for D. punctatifrons. Species dominance shifted along the gradient: D. punctatifrons dominated warm lowland conditions (>24 {degrees}C), whereas D. bivittatus prevailed at elevations above approximately 569 m. Seasonal niche overlap declined markedly with altitude, indicating increasing temporal segregation between the species in cooler environments. These findings demonstrate that altitude structures ecological divergence between two closely related fruit fly pests and provide a basis for site-specific monitoring and climate-sensitive pest forecasting in tropical mountain agroecosystems.

ecology↗

bioRxiv2025

Virotrap Reveals Salmonella SopB as A Ubiquitinated Cargo for Host ESCRT-0

The pathogenic bacterium Salmonella survives and replicates in host cells within a Salmonella-containing vacuole (SCV), a membranous niche it actively remodels via secreted effectors. The phosphoinositide phosphatase SopB is a key effector implicated in SCV biogenesis, yet its host protein interactome has remained incompletely defined. Using the mass spectrometry-based interactomics technology Virotrap, we identify a novel set of SopB-associated host proteins, including the ESCRT-0 subunit HGS and other membrane remodeling proteins. We demonstrate that SopB directly interacts with HGS via its ubiquitin-binding domains, and show that SopB promotes ESCRT-0 recruitment to the SCV, yet ultimately counteracts its anti-replicative effect. As the ESCRT machinery plays a central role in cargo sorting and membrane remodeling, we propose a new SopB-dependent strategy by which Salmonella hijacks host endosomal trafficking to build its intracellular niche.

microbiology↗

bioRxiv2024

Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is challenged by their extreme low abundance. Here, we describe an optimized bioinformatical framework to enhance the confident identification of bacterial immunopeptides. Immunopeptidomics data of cell cultures infected with Listeria monocytogenes were searched by four different search engines, PEAKS, Comet, Sage and MSFragger, followed by data-driven rescoring with MS2Rescore. Compared to individual search engine results, this integrated workflow boosted immunopeptide identification by an average of 27% and led to the high-confidence detection of 18 additional bacterial peptides (+27%) matching 15 different Listeria proteins (+36%). Despite the strong agreement between the search engines, a small number of spectra (< 1%) had ambiguous matches to multiple peptides and were excluded to ensure high-confident identifications. Finally, we demonstrate our workflow with sensitive timsTOF SCP data acquisition and find that rescoring, now with inclusion of ion mobility features, identifies 76% more peptides compared to Q Exactive HF acquisition. Together, our results demonstrate how integration of multiple search engine results along with data-driven rescoring maximizes immunopeptide identification, boosting the detection of high-confidence bacterial epitopes for vaccine development.

molecular biology↗

bioRxiv2023

Evidence that recent climatic changes have expanded the potential geographic range of the Mediterranean fruit fly

The species distributions migration poleward and into higher altitudes in a warming climate is especially concerning for economically important insect pest species, as their introduction can potentially occur in places previously considered unsuitable for year-round survival. We explore the expansion of the climatically suitable areas for a horticultural pest, the Mediterranean fruit fly (medfly) Ceratitis capitata (Diptera, Tephritidae), with an emphasis on Europe and California. We reviewed and refined a published CLIMEX model for C. capitata, taking into consideration new records in marginal locations, with a particular focus on Europe. To assess the model fit and to aid in interpreting the meaning of the new European distribution records, we used a time series climate dataset to explore the temporal patterns of climate suitability for C. capitata from 1970 to 2019. At selected bellwether sites in Europe, we found statistically significant trends in increasing climate suitability, as well as a substantial northward expansion in the modelled potential range. In California, we also found a significant trend of northward and altitudinal expansion of areas suitable for C. capitata establishment. These results provide further evidence of climate change impacts on species distributions and the need for innovative responses to increased invasion threats.

ecology↗

bioRxiv2023

Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics

Protein-protein interactions play an important biological role in every aspect of cellular homeostasis and functioning. Proximity labeling mass spectrometry-based proteomics overcomes challenges typically associated with other methods, and has quickly become the current state-of-the-art in the field. Nevertheless, tight control of proximity labeling enzymatic activity and expression levels is crucial to accurately identify protein interactors. Here, we leverage a T2A self-cleaving peptide and a non-cleaving mutant to accommodate the protein-of-interest in the experimental and control TurboID setup. To allow easy and streamlined plasmid assembly, we built a Golden Gate modular cloning system to generate plasmids for transient expression and stable integration. To highlight our T2A Split-link design, we applied it to identify protein interactions of the glucocorticoid receptor and SARS-CoV-2 nucleocapsid and NSP7 proteins by TurboID proximity labeling. Our results demonstrate that our T2A split-link provides an opportune control that builds upon previously established control requirements in the field. MotivationIn proximity labeling proteomics protein-protein interactions are identified by in vivo biotinylation. However, the current lack of a universally applicable negative control for differential analysis affects accurate mapping of the interactome. To bridge this gap, we conceptualized a system based on the T2A self-cleaving peptide to match expression levels between control and bait protein setups while using the same bait protein. In addition, we implemented a versatile modular cloning system to build mammalian expression vectors for, but not limited to, proximity labeling assays.

biochemistry↗

bioRxiv2023

Diversity and abundance of pestiferous fruit flies (Diptera: Tephritidae) infesting cucurbit crops in Morogoro, eastern-central Tanzania

Fruit flies represent a significant threat to cucurbit production. They inflict about 30% to 100% losses on cucurbit crops. The aim of this study was to characterize the community of fruit flies infesting cucurbit crops in Morogoro, Tanzania. We investigate the diversity and abundance of fruit fly species infesting cucumber, watermelon, and squash across the two agroecological zones of the Morogoro using three attractants (Cue Lure, Zingerone and Biolure). The attractants were deployed for 16 weeks from June to November 2020. In total, 12017 fruit fly specimens were collected. Of these, 77.23% were collected from the mountainous and the remaining 22.77% from the plateau zone. All specimens belonged to the genera Dacus, Zeugodacus and Bactrocera. Zeugodacus cucurbitae was the most abundant species (77.6%) while the remaining species constituted 22.4%. The mountainous zone harboured a significantly higher number of fruit fly species than the plateau zone. The abundance of fruit flies was significantly influenced by altitudes and seasons. The study characterized the community of fruit flies in Morogoro and confirms the prevalence of Z. cucurbitae, D. bivittatus and D. punctatifrons as prominent species in this region. Therefore, management programs should focus on containing these species regardless of the agroecological zones and seasons.

ecology↗

bioRxiv2023

Host use preference of fruit flies (Diptera: Tephritidae) among selected cucurbitaceous vegetables in Morogoro, Eastern-Central Tanzania

Fruit flies (Diptera, Tephritidae) represent a major threat to cucurbit production in Tanzania. They cause huge economic losses on cucurbit crops. Information on the infestation and yield loss caused by fruit flies on cucurbit crops is vital in designing a sound fruit fly management program. We identified the fruit fly species attacking cucurbit crops (Cucurbitales: Cucurbitaceae): cucumber (Cucumis sativus L.), watermelon (Citrullus lanatus [Thunb.] Matsum. & Nakai) and squash (Cucurbita moschata D.) in the Morogoro region and quantified their incidence and infestation per crop species. A weekly sampling of ten fruits per crop was repeated twice per plot for each zone for five consecutive weeks between March and October 2020. The number of fruit flies emerging from the collected fruits was quantified and infestation per crop species was determined. We observed significant differences in infestation between cucurbit species, across zones and seasons. Squash showed the highest infestation of Zeugodacus cucurbitae (Coquillet) in both zones followed by watermelon. Watermelon was highly infested by Dacus vertebratus (Bigot) in the plateau zone followed by squash. Squash showed the highest infestation of Dacus ciliatus Loew in the plateau zone followed by watermelon. Cucumber had the lowest infestation for all fruit fly species.

ecology↗

bioRxiv2023

Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective

By applying dual proteome profiling to Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters with its epithelial host (here, S. Typhimurium infected human HeLa cells), a detailed interdependent and holistic proteomic perspective on host-pathogen interactions over a time course of infection was obtained. Data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows, especially in identifying the downregulated bacterial proteome response during infection progression infection by permitting quantification of low abundant bacterial proteins at early times of infection at low bacterial infection load. S. Typhimurium invasion and replication specific proteomic signatures in epithelial cells revealed interdependent host/pathogen specific responses besides pointing to putative novel infection markers and signalling responses.

cell biology↗

bioRxiv2020

Constitutive Steroidal Glycoalkaloid Biosynthesis in Tomato is Regulated by the Clade IIIe Basic Helix-Loop-Helix Transcription Factors MYC1 and MYC2

Specialized metabolites are produced by plants to fend off biotic enemies. Across the plant kingdom, the biosynthesis of these defense compounds is promoted by jasmonate signaling in which clade IIIe basic helix-loop-helix (bHLH) transcription factors take on a central role. Tomato (Solanum lycopersicum) produces cholesterol-derived steroidal glycoalkaloids (SGAs) that act as phytoanticipins against a broad variety of herbivores and pathogens. The biosynthesis of SGAs from cholesterol occurs constitutively in tomato plants and can be further stimulated by jasmonates. Here, we demonstrate that the two tomato clade IIIe bHLH transcription factors, MYC1 and MYC2, redundantly and specifically control the constitutive biosynthesis of SGAs. Double myc1 myc2 loss-of-function tomato hairy roots displayed suppressed constitutive expression of cholesterol and SGA biosynthesis genes, and consequently severely reduced levels of the main tomato SGAs -tomatine and dehydrotomatine. In contrast, basal expression of genes involved in canonical jasmonate signaling or in the biosynthesis of highly jasmonate-inducible phenylpropanoid-polyamine conjugates was not affected. Furthermore, CRISPR-Cas9(VQR)-mediated genome editing of a specific cis-regulatory element, targeted by MYC1/2, in the promoter of a cholesterol biosynthesis gene led to decreased constitutive expression of this gene, but did not affect its jasmonate inducibility. Our results demonstrate that clade IIIe bHLH transcriptional regulators might have evolved to regulate the biosynthesis of specific constitutively accumulating specialized metabolites independent of jasmonate signaling. One sentence summaryThe clade IIIe basic helix-loop-helix transcription factors MYC1 and MYC2 control the constitutive biosynthesis of tomato steroidal glycoalkaloids and might do so independently of jasmonate signaling.

plant biology↗