Biology subjects

Bogaerts, A.

Publications and source records attributed to Bogaerts, A..

5 recordsLinked to original sources

bioRxiv2026

Long-term stomatal and leaf trait dynamics in invasive knotweeds in Europe - insights from 160 years of herbarium records

O_LIStomata and leaf traits are key regulators of plant water use efficiency and are expected to have changed in response to rising atmospheric CO2 concentrations and climate warming over the past centuries. However, long-term data documenting such changes are rare. C_LIO_LIWe leveraged herbarium collections to track changes in stomatal characteristics and leaf traits in 656 individuals of invasive Japanese knotweed and its hybrid Bohemian knotweed collected across their European range and spanning 160 years of invasive spread. C_LIO_LIWe found that several functional traits including stomatal density and maximum anatomical stomatal conductance did not show significant changes over time but that plants adjusted their stomatal size and shape over time, and that these changes were associated with increased atmospheric CO2 levels. Interestingly, Reynoutria japonica showed increases in stomatal size and stomatal elongation, while the hybrid R. x bohemica showed a reduction in stomatal size. Traits also varied systematically with climates of origin. Plants from warmer origins with higher evaporative demands during the growing season had thicker leaves, lower SLA, smaller stomata and higher stomatal density, indicating more conservative water-use strategies. Stomatal density and gas exchange capacity co-varied with leaf structural traits, and there was a trade-off between stomatal size and number. Overall, "fast" leaf economic traits were associated with "slow" physiological traits. C_LIO_LIOur results suggest that stomatal anatomical plasticity may enhance climate resilience by maintaining a stable maximum gas exchange capacity across environmental gradients. Herbarium collections provide a unique resource for reconstructing plant responses to historical environmental changes and understanding intraspecific trait variation. C_LI

ecology↗

bioRxiv2026

Using herbarium genomics to understand the history of a global plant invasion

Invasive plants are dynamic eco-evolutionary systems characterized by rapid spread and evolutionary change. Herbarium genomics offers a powerful way to study these processes across broad spatial and temporal scales. We generated low-coverage shotgun-sequencing data from 152 herbarium specimens of the invasive Japanese knotweed species complex (Reynoutria), collected across its native range in Japan and China, and its introduced ranges in Europe and North America, spanning 200 years of global spread. Introduced populations of R. japonica, R. japonica var. compacta and R. sachalinensis showed reduced genetic diversity compared to native populations and were genetically most similar to Japanese specimens, indicating Japan as the source of all three introductions. European and North American R. japonica were genetically highly similar and closely related to local R. x bohemica hybrids, suggesting that these hybrids originated post-introduction, through hybridization and subsequent introgression from the R. japonica parent. A few R. x bohemica hybrids in the UK and France shared a multilocus lineage with R. sachalinensis, indicating an independent but ecologically less successful hybridization event involving introgression from R. sachalinensis. A genetically distinct R. x bohemica from Japan was closely related to a Japanese R. sachalinensis specimen, suggesting that hybridization also occurs in the native range. Introduced R. japonica has remained genetically uniform for [~]200 years reflecting long-term founder effects. The dominance of a single R. japonica lineage supports the general-purpose genotype hypothesis and the importance of vegetative reproduction in its spread. Herbarium genomics thus uncovers the origin and global spread of Japanese knotweed, providing direct molecular evidence of long-term plant invasions.

evolutionary biology↗

bioRxiv2024

Effect of cysteine oxidation in SARS-CoV-2 Spike protein on its conformational changes: insights from atomistic simulations

This study investigates the effect of cysteine (Cys) oxidation on the conformational changes of the SARS-CoV-2 Spike (S) protein, a critical factor in viral attachment and entry into host cells. Using targeted molecular dynamics (TMD) simulations, we explore the conformational transitions between the down (inaccessible) and up (accessible) states of the SARS-CoV-2 S protein in both its native and oxidized forms. Our findings reveal that oxidation significantly increases the energy barrier for these transitions, as indicated by the work required to move from the down to the up conformation and vice versa. Specifically, in the oxidized system compared to the native system, the energy required to transition from the down to the up conformation increases by approximately 131 {+/-} 1 kJ.mol-1, while the energy required for the reverse transition increases by about 223 {+/-} 6 kJ.mol-1. This is due to the stabilizing effect of oxidation on the conformation of the SARS-CoV-2 S protein. Analysis of hydrogen bond and salt bridge formation before and after oxidation provides additional insights into the stabilization mechanisms, showing an increase in salt bridge formation that contributes to conformational stabilization. These results underscore the potential of targeting translational modifications to hamper viral entry or enhance susceptibility to neutralization, offering a novel perspective for antiviral strategy development against SARS-CoV-2. This study adds important knowledge to the field of viral protein dynamics and highlights the critical role of structural and computational biology in uncovering new therapeutic avenues.

biophysics↗

bioRxiv2021

The colonial legacy of herbaria

Herbarium collections shape our understanding of the worlds flora and are crucial for addressing global change and biodiversity conservation. The formation of such natural history collections, however, are not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the global North, the extent of this disparity has not been rigorously quantified to date. Here, by analyzing over 85 million specimen records and surveying herbaria across the globe, we assess the colonial legacy of botanical collections and how we may move towards a more inclusive future. We demonstrate that colonial exploitation has contributed to an inverse relationship between where plant biodiversity exists in nature and where it is housed in herbaria. Such disparities persist in herbaria across physical and digital realms despite overt colonialism having ended over half a century ago, suggesting ongoing digitization and decolonization efforts have yet to alleviate colonial-era discrepancies. We emphasize the need for acknowledging the inconvenient history of herbarium collections and the implementation of a more equitable, global paradigm for their collection, curation, and use.

ecology↗

bioRxiv2021

OrBITS: A High-throughput, time-lapse, and label-free drug screening platform for patient-derived 3D organoids

BackgroundPatient-derived organoids are invaluable for fundamental and translational cancer research and holds great promise for personalized medicine. However, the shortage of available analysis methods, which are often single-time point, severely impede the potential and routine use of organoids for basic research, clinical practise, and pharmaceutical and industrial applications. MethodsHere, we developed a high-throughput compatible and automated live-cell image analysis software that allows for kinetic monitoring of organoids, named Organoid Brightfield Identification-based Therapy Screening (OrBITS), by combining computer vision with a convolutional network machine learning approach. The OrBITS deep learning analysis approach was validated against current standard assays for kinetic imaging and automated analysis of organoids. A drug screen of standard-of-care lung and pancreatic cancer treatments was also performed with the OrBITS platform and compared to the gold standard, CellTiter-Glo 3D assay. Finally, the optimal parameters and drug response metrics were identified to improve patient stratification. ResultsOrBITS allowed for the detection and tracking of organoids in routine extracellular matrix domes, advanced Gri3D(R)-96 well plates, and high-throughput 384-well microplates, solely based on brightfield imaging. The obtained organoid Count, Mean Area, and Total Area had a strong correlation with the nuclear staining, Hoechst, following pairwise comparison over a broad range of sizes. By incorporating a fluorescent cell death marker, intra-well normalization for organoid death could be achieved, which was tested with a 10-point titration of cisplatin and validated against the current gold standard ATP-assay, CellTiter-Glo 3D. Using this approach with OrBITS, screening of chemotherapeutics and targeted therapies revealed further insight into the mechanistic action of the drugs, a feature not achievable with the CellTiter-Glo 3D assay. Finally, we advise the use of the growth rate-based normalised drug response metric to improve accuracy and consistency of organoid drug response quantification. ConclusionsOur findings validate that OrBITS, as a scalable, automated live-cell image analysis software, would facilitate the use of patient-derived organoids for drug development and therapy screening. The developed wet-lab workflow and software also has broad application potential, from providing a launching point for further brightfield-based assay development to be used for fundamental research, to guiding clinical decisions for personalized medicine.

cancer biology↗