A5017299073- Plant Molecular Biology Research
- Plant nutrient uptake and metabolism
- Single-cell and spatial transcriptomics
- Plant Genetic and Mutation Studies
- DNA Repair Mechanisms
- Chromosomal and Genetic Variations
- Polysaccharides and Plant Cell Walls
- Photosynthetic Processes and Mechanisms
- Plant Reproductive Biology
- Microtubule and mitosis dynamics
- Aluminum toxicity and tolerance in plants and animals
- Plant tissue culture and regeneration
- Genomics and Phylogenetic Studies
- Arsenic contamination and mitigation
- Plant Water Relations and Carbon Dynamics
- ICT Impact and Policies
- Ubiquitin and proteasome pathways
- Plant Stress Responses and Tolerance
- Plant Gene Expression Analysis
- Immunotherapy and Immune Responses
- Extracellular vesicles in disease
- Gene expression and cancer classification
- Advanced biosensing and bioanalysis techniques
- CRISPR and Genetic Engineering
- Economic Growth and Development
VIB-UGent Center for Plant Systems Biology
2014-2025
VIB Single Cell Core
2023-2025
Ghent University
2014-2025
Guangzhou University
2023
Institute of Molecular Biology and Biotechnology
2023
National Botanical Research Institute
2023
Council of Scientific and Industrial Research
2023
Weatherford College
2023
University of Lausanne
2023
VIB-VUB Center for Structural Biology
2023
Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these are gaining traction in molecular developmental biology for elucidating transcriptional changes across cell types a specific tissue or organ, upon treatments, response to biotic abiotic stresses, between genotypes. Despite rapidly accelerating use technologies, collective standardized experimental analytical procedures support acquisition...
Abstract Whereas our knowledge about the diverse pathways aiding DNA repair upon genome damage is steadily increasing, little known molecular players that adjust plant cell cycle in response to stress. By a meta-analysis of stress microarray data sets, three family members SIAMESE/SIAMESE-RELATED (SIM/SMR) class cyclin-dependent kinase inhibitors were discovered react strongly genotoxicity. Transcriptional reporter constructs corroborated specific and strong activation SIM/SMR genes...
Somatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates but especially prominent higher plants, where it has been postulated to be essential for cell growth fate maintenance. However, a comprehensive understanding of the physiological significance plant endopolyploidy remained elusive. Here, we modeled experimentally verified high-resolution DNA endoploidy map developing Arabidopsis thaliana root, revealing remarkable spatiotemporal control levels...
Significance Plants show remarkable regenerative abilities, allowing them to recover from wounds and organ loss. This capacity is controlled in part by auxin, the most promiscuous plant hormone controlling organogenesis tissue patterning. We that stem cell death diverges auxin flow, much like rocks a stream, resulting an accumulation tissues surrounding wound. demonstrate within these tissues, wound-induced expression of plant-specific transcription factor ERF115 works synergistically with...
The effects of brassinosteroid signaling on shoot and root development have been characterized in great detail but a simple consistent positive or negative impact basic cellular parameter was not identified. In this study, we combined digital 3D single-cell shape analysis mRNA sequencing to characterize meristems mature segments brassinosteroid-blind mutants wild type. resultant datasets demonstrate that affects neither cell volume nor proliferation capacity. Instead, is essential for the...
Abstract Plant roots possess remarkable regenerative potential owing to their ability replenish damaged or lost stem cells. ETHYLENE RESPONSE FACTOR 115 (ERF115), one of the key molecular elements linked this potential, plays a predominant role in activation cell divisions. However, downstream operating machinery driving wound-activated division is largely unknown. Here, we biochemically and genetically identified GRAS-domain transcription factor SCARECROW-LIKE 5 (SCL5) as an interaction...
Non-small cell lung cancer (NSCLC) is known for high relapse rates despite resection in early stages. Here, we present the results of a phase I clinical trial which dendritic (DC) vaccine targeting patient-individual neoantigens evaluated patients with resected NSCLC. Vaccine manufacturing feasible six 10 enrolled patients. Toxicity limited to grade 1-2 adverse events. Systemic T responses are observed five out vaccinated patients, remaining detectable up 19 months post vaccination....
In Arabidopsis thaliana, brassinosteroid (BR) signaling and stomatal development are connected through the SHAGGY/GSK3-like kinase BR INSENSITIVE2 (BIN2). BIN2 is a key negative regulator of but it plays dual role in development. promotes or restricts asymmetric cell division (ACD) depending on its subcellular localization, which regulated by lineage-specific scaffold protein POLAR. BRs inactivate BIN2, how they govern remains unclear. Mapping single-cell transcriptome lineages after...
Aluminum (Al) toxicity and inorganic phosphate (Pi) limitation are widespread chronic abiotic mutually enhancing stresses that profoundly affect crop yield. Both strongly inhibit root growth, resulting from a progressive exhaustion of the stem cell niche. Here, we report on casein kinase 2 (CK2) inhibitor identified by its capability to maintain functional niche in Arabidopsis thaliana under Al toxic conditions. CK2 operates through phosphorylation cycle checkpoint activator SUPPRESSOR OF...
Abstract The ataxia-telangiectasia mutated (ATM) and ATM Rad3-related (ATR) kinases coordinate the DNA damage response. roles described for Arabidopsis thaliana ATR are assumed to be conserved over other plant species, but molecular evidence is scarce. Here, we demonstrate that functions of only partially between maize (Zea mays). In both play a key role in repair cell cycle checkpoint activation, whereas plants do not suffer from absence under control growth conditions, mutant accumulate...
Despite the broad use of single-cell/nucleus RNA sequencing in plant research, accurate cluster annotation less-studied species remains a major challenge due to lack validated marker genes. Here, we generated single-cell atlas soil-grown wheat roots and annotated identities by transferring annotations from publicly available datasets wheat, rice, maize, Arabidopsis. The predictions our orthology-based approach were next using untargeted spatial transcriptomics. These results allowed us...
Summary Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is crucial first step toward engineering improved resilience. However, the molecular to are complex as they depend multiple factors, including severity of drought, profiled organ, its developmental stage or even cell types therein. Thus, deciphering transcriptional especially challenging. In this study, we investigated tissue‐specific...
Abstract During secondary growth, the vascular cambium produces conductive xylem and phloem cells, while phellogen (cork cambium) deposits phellem (cork) as outermost protective barrier. Although most of tissues are made up parenchyma which also produced by both cambia, their diversity function poorly understood. Here we combined single-cell RNA sequencing analysis with lineage tracing to recreate developmental trajectories cell types in Arabidopsis root undergoing growth. By analysing 93...
Cadmium (Cd) exposure causes an oxidative challenge and inhibits cell cycle progression, ultimately impacting plant growth. Stress-induced effects on the are often a consequence of activation DNA damage response (DDR). The main aim this study was to investigate role transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) three downstream cyclin-dependent kinase inhibitors SIAMESE-RELATED (SMR) family in Cd-induced DDR leaves Arabidopsis thaliana. Effects Cd growth, regulation expression...
The anaphase promoting complex/cyclosome (APC/C) controls unidirectional progression through the cell cycle by marking key proteins for proteasomal turnover. Its activity is temporally regulated docking of different activating subunits, known in plants as CELL DIVISION PROTEIN20 (CDC20) and CYCLE SWITCH52 (CCS52). Despite importance APC/C during proliferation, number identified targets plant limited. Here, we used growth meristem phenotypes Arabidopsis (Arabidopsis thaliana)...
The endocycle represents a modified mitotic cell cycle that in plants is often coupled to enlargement and differentiation. Endocycle onset controlled by activity of the Anaphase Promoting Complex/Cyclosome (APC/C), multisubunit E3 ubiquitin ligase targeting cell-cycle factors for destruction. CELL CYCLE SWITCH52 (CCS52) proteins represent rate-limiting activator subunits APC/C. In Arabidopsis (Arabidopsis thaliana), mutations either CCS52A1 or CCS52A2 activators result delayed onset, whereas...
Abstract We introduce scywalker , an innovative and scalable package developed to comprehensively analyze long-read nanopore sequencing data of full-length single-cell or single-nuclei cDNA. Existing analysis tools showed severe limitations in handling current sizes. novel methods for cell barcode demultiplexing isoform calling quantification incorporated these easily deployable package. Scywalker streamlines the entire process, from sequenced fragments FASTQ format demultiplexed pseudobulk...
Galls induced by plant-parasitic nematodes involve a hyperactivation of the plant mitotic and endocycle machinery for their profit. Dedifferentiation host root cells includes drastic cellular molecular readjustments. In such background, potential DNA damage in genome gall is evident. We investigated whether checkpoint activation followed repair occurred, or was eventually circumvented, nematode-induced galls. display transcriptional kinase WEE1, correlated with its protein localization...
The WEE1 and ATM AND RAD3-RELATED (ATR) kinases are important regulators of the plant intra-S-phase checkpoint; consequently, WEE1KO ATRKO roots hypersensitive to replication-inhibitory drugs. Here, we report on a loss-of-function mutant allele FASCIATA1 (FAS1) subunit chromatin assembly factor 1 (CAF-1) complex that suppresses phenotype WEE1- or ATR-deficient Arabidopsis (Arabidopsis thaliana) plants. We demonstrate lack FAS1 activity results in activation an ATAXIA TELANGIECTASIA MUTATED...
Abstract During the process of secondary growth, vascular cambium produces conductive xylem and phloem cells, while phellogen (cork cambium) deposit phellem (cork) as outermost protective barrier. Although most tissues is made up by parenchyma cells which are also produced both cambia, their diversity function poorly understood. Here we combined single-cell RNA sequencing analysis with lineage tracing to recreate developmental trajectories cell types in Arabidopsis root undergoing growth. By...