Biology subjects

Van Laere, K.

Publications and source records attributed to Van Laere, K..

5 recordsLinked to original sources

bioRxiv2026

A genomic and functional framework for the rapid domestication of the wild plant Chenopodium album

Global reliance on a small number of genetically uniform crops makes our food system increasingly vulnerable to pests, diseases, and climate change, highlighting the need to develop resilient local species as crops. Chenopodium album, a stress-tolerant, protein-rich wild plant whose seeds were part of prehistoric Northern European diets and whose leaves are still foraged worldwide, remains undomesticated despite its agrifood potential. We established a Danish collection of 143 accessions and combined seed metabolomics, ploidy assessment and genomics to uncover the molecular basis of key nutritional and anti-nutritional traits. Seed profiling revealed substantial variation in protein content (14-22%), comparable to or higher than major crops, and 16 distinct triterpenoid saponins, which are widespread bitter and anti-nutritional compounds. Seed production of field-grown lines reached up to 1.5 t/ha in trials conducted in Denmark, demonstrating promising yield potential. A high-quality tetraploid genome of a low-saponin line was assembled and contrasted with resequencing of a diploid high-saponin line in order to uncover the genetic basis of saponin variation in C. album. Comparative genomic, phylogenetic, and transcriptomic analyses identified structural variants and candidate genes associated with saponin biosynthesis, and functional validation confirmed the coordinated activity of a {beta}-amyrin synthase, three CYP716 cytochromes P450, and a glucuronosyltransferase that reconstitute the core C. album saponin pathway. Together, these results define the genomic and biochemical foundation of C. album, establishing a platform for its rapid domestication as a locally adapted, high-protein seed crop and a model for translating wild plant diversity into future food security.

plant biology↗

bioRxiv2024

Loss of the lysosomal lipid flippase ATP10B leads to progressive dopaminergic neurodegeneration and Parkinsonian motor deficits

BackgroundATP10B, a transmembrane lipid flippase located in late endosomes and lysosomes, facilitates the export of glucosylceramide and phosphatidylcholine by coupling this process to ATP hydrolysis. Recently, loss-of-function mutations in the ATP10B gene have been identified in Parkinsons disease patients, pointing to ATP10B as a candidate genetic risk factor. Previous studies have shown compromised lysosomal functionality upon ATP10B knockdown in human cell lines and primary cortical neurons. However, its role in vivo and specifically in the nigrostriatal dopaminergic system remains poorly understood. MethodsTo investigate the role ATP10B in PD neuropathology, we induced ATP10B knockdown specifically in substantia nigra pars compacta neurons of rats using viral vector technology. Two different microRNA-based shRNA constructs targeting distinct regions of the ATP10B mRNA were used to cross-validate the findings. Behavioral evaluation, dopamine transporter 18F-FE-PE2I positron emission tomography imaging and neuropathological examination of the nigrostriatal pathway at one year post-injection were conducted. Additionally, midbrain neuronal cultures derived from ATP10B knock-out human induced pluripotent stem cells clones were used to study the impact of ATP10B loss in dopaminergic neurons in a more translational model. ResultsATP10B knockdown in rat brain induced Parkinsonian motor deficits, and longitudinal striatal dopamine transporter 18F-FE-PE2I PET imaging revealed a progressive decrease in binding potential. Immunohistochemical analysis conducted one year post-injection confirmed the loss of dopaminergic terminals in the striatum, alongside a loss of dopaminergic neurons in the substantia nigra pars compacta. The expression of LAMP1, LAMP2a, cathepsin B and glucocerebrosidase was studied by immunofluorescence in the surviving dopaminergic neurons. A decrease in lysosomal numbers and an increase in lysosomal volume were observed more consistently in one of the knockdown constructs. The vulnerability of dopaminergic neurons to ATP10B loss-of-function was also observed in midbrain neuronal cultures derived from ATP10B knock-out human induced pluripotent stem cells clones, which showed a significant reduction in TH-positive neurons. ConclusionTaken together, our findings demonstrate that ATP10B depletion detrimentally impacts the viability of dopaminergic neurons both in vivo and in vitro. Moreover, a broader impact on the functionality of the nigrostriatal pathway was evidenced as rats with ATP10B knockdown exhibited motor impairments similar to those observed in PD patients.

neuroscience↗

bioRxiv2023

Industrial chicory genome gives insight into the molecular time table of anther development and male sterility

Industrial chicory (Cichorium intybus var. sativum) is a biannual crop mostly cultivated for extraction of inulin, a fructose polymer used as a dietary fiber. F1 hybrid breeding is a promising breeding strategy in chicory but crucially relies on stable self-incompatibility. Here, we report the assembly and annotation of a new industrial chicory reference genome. Additionally, we performed RNA-Seq on subsequent stages of flower bud development of a fertile line and two cytoplasmic male sterile (CMS) clones. Comparison of fertile and CMS flower bud transcriptomes combined with morphological microscopic analysis of anthers, provided a molecular understanding of anther development and identified key genes in a range of underlying processes, including tapetum development, sink establishment, pollen wall development and anther dehiscence. We also described the role of phytohormones in the regulation of these processes under normal fertile flower bud development. In parallel, we evaluated which processes are disturbed in CMS clones and could contribute to the male sterile phenotype. Taken together, this study provides a state-of-the-art industrial chicory reference genome, an annotated and curated candidate gene set related to anther development and male sterility as well as a detailed molecular timetable of flower bud development in fertile and CMS lines.

plant biology↗

bioRxiv2020

STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters

Introductory paragraphSince the emergence of SARS-CoV-2 causing COVID-19, the world is being shaken to its core with numerous hospitalizations and hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that productive SARS-CoV-2 infection in the lungs of mice is limited and restricted by early type I interferon responses. In contrast, we show that Syrian hamsters are highly permissive to SARS- CoV-2 and develop bronchopneumonia and a strong inflammatory response in the lungs with neutrophil infiltration and edema. Moreover, we identify an exuberant innate immune response as a key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Finally, we assess SARS-CoV- 2-induced lung pathology in hamsters by micro-CT alike used in clinical practice. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients.

microbiology↗

bioRxiv2018

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.\n\nWe produced a haploid rose line from R. chinensis Old Blush and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

genomics↗