Biology subjects

Van den Broeck, L.

Publications and source records attributed to Van den Broeck, L..

8 recordsLinked to original sources

bioRxiv2024

Large scale comparative wheat phosphoproteome profiling pinpoints temperature-associated molecular signatures

Elevated temperatures resulting from climate change adversely affect natural and crop ecosystems, necessitating the development of heat-tolerant crops. We established a framework to precisely identify wheat protein-phosphorylated sites associated with varying temperature sensitivities. We identified specific kinases primarily associated with a specific temperature, but our results also suggest a striking overlap between cold and heat signaling. We furthermore demonstrated that the phosphorylation state of a specific set of proteins creates a unique signature for heat stress tolerance. These findings can potentially aid in the identification of targets for breeding or genome editing to enhance sub/supra optimal temperature tolerance.

plant biology↗

bioRxiv2024

Cell-material interactions in 3D bioprinted plant cells

3D bioprinting is an additive manufacturing technology with promise towards facilitating tissue engineering and single-cell investigations of cellular development and microenvironment responses. 3D bioprinting is still a new technology in the field of plant biology so its optimization with plant cells is still widely needed. Here, we present a study in which 3D bioprinting parameters, such as needle gauge, extrusion pressure, and scaffold type, were all tested in 3D bioprinted Tobacco BY-2 cells to evaluate how cell viability is responsive to each parameter. As a result, this study revealed an optimal range of extrusion pressures and needle gauges that resulted in an optimum cell viability. Furthermore, this study applied the identified optimal 3D bioprinting parameters to a different cell line, Arabidopsis root protoplasts, and stress condition, phosphate starvation, to confirm that the identified parameters were optimal in a different species, cell type, and cellular microenvironment. This suggested that phosphate-starved bioprinted Arabidopsis cells were less viable by 7 days, which was consistent with whole root phosphate starvation responses. As a result, the 3D bioprinter optimization yielded optimal cell viabilities in both BY-2 and Arabidopsis cells and facilitated an applied investigation into phosphate starvation stress.

cell biology↗

bioRxiv2023

Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation

Nitrogen (N) is an essential macronutrient and its bioavailability plays a major role in how plant development is tuned to environmental nutrient status. To find novel factors in early root system architecture responses to N conditions, we performed Arabidopsis thaliana root transcriptome profiling of a short-term time course in limiting and sufficient N conditions. Using this data, we inferred transcriptional regulatory networks in each condition, which revealed the N-condition specific responses of jasmonate regulation; transcriptional factor (TF) ERF107 plays a more generalized role in lateral root development while TF LBD13 is specific to N-limiting conditions. Further, we used a single cell LR cell-type specific transcriptome dataset to model and analyze the roles of TFs LBD13, ERF107, and PDF2 in early stages of LR development. Linking the N time course transcriptomics, LR mutant phenotypes, and cell-type specific single cell profiling, these approaches provide multiple lines of evidence to find and test the roles of TFs that are involved in early root patterning responses to N conditions.

plant biology↗

bioRxiv2022

Establishing a reproducible approach for the controllable deposition and maintenance of plants cells with 3D bioprinting

Capturing cell-to-cell and cell-to-environment signals in a defined 3 dimensional (3D) microenvironment is key to study cellular functions, including cellular reprogramming towards tissue regeneration. A major challenge in current culturing methods is that these methods cannot accurately capture this multicellular 3D microenvironment. In this study, we established the framework of 3D bioprinting with plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis root cells and soybean meristematic cells. To analyze the large image datasets generated during these long-term viability studies, we developed an open source high-throughput image analysis pipeline. Furthermore, we showed the cell cycle re-entry of the isolated Arabidopsis and soybean cells leading to the formation of microcalli. Finally, we showed that the identity of isolated cells of Arabidopsis roots expressing endodermal markers maintained longer periods of time. The framework established in this study paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle re-entry towards tissue regeneration.

plant biology↗

bioRxiv2021

The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice

The architecture of the rice inflorescence is an important determinant of seed yield. The length of the inflorescence and the number of branches are among the key factors determining the amount of spikelets, and thus seeds, that will develop. Especially the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem regulates the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in rice. Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq we observed that two ALOG genes, Oryza sativa OsG1-like 1 (OsG1L1) and OsG1L2, have an expression profile similar to TAW1. Here we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes as the taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the datasets were also used for the construction of a gene regulatory network (GRN) proposing interactions between genes potentially involved in controlling inflorescence development in rice. The spatio-temporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of the homeodomain-leucine zipper transcription factor gene OsHOX14 suggest that the proposed GRN indeed serves as a valuable resource for the identification of new players involved in rice inflorescence development. One-sentence summaryOsG1L1 and OsG1L2 control panicle architecture through delaying the transition from indeterminate branch- to determinate spikelet-meristem identity.

developmental biology↗

bioRxiv2021

Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation

Graft incompatibility is a poorly understood phenomenon that presents a serious agricultural challenge. Unlike immediate incompatibility that results in rapid death, delayed incompatibility can take months or even years to manifest, creating a significant economic burden for perennial crop production. To gain insight into the genetic mechanisms underlying this phenomenon, we developed a model system with Solanum lycopersicum tomato and Capsicum annuum pepper heterografting, which expresses signs of anatomical junction failure within the first week of grafting. By generating a detailed timeline for junction formation we were able to pinpoint the cellular basis for this delayed incompatibility. Furthermore, we infer gene regulatory networks for compatible self-grafts versus incompatible heterografts based on these key anatomical events, which predict core regulators for grafting. Finally, we delve into the role of vascular development in graft formation and validate SlWOX4 as a regulator for grafting in tomato. Notably, SlWOX4 is the first gene to be functionally implicated in vegetable crop grafting.

plant biology↗

bioRxiv2020

Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions

Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WOX5 and SHR, regulate divisions in the root stem cell niche (SCN). However, how these proteins coordinately function to establish systemic behavior is not well understood. We propose a non-cell autonomous role for WOX5 in the CEI and identify a regulator, AN3/GIF1, that coordinates CEI divisions. Here we show with a multiscale hybrid model integrating ODEs and agent-based modeling that QC and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behavior, which led us to predict cell-type-specific expression dynamics of SHR, SCR, WOX5, AN3, and CYCD6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions. Thumbnail image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/404426v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@abcd10org.highwire.dtl.DTLVardef@123e110org.highwire.dtl.DTLVardef@8d175dorg.highwire.dtl.DTLVardef@f8f498_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2018

Early mannitol-triggered changes in the Arabidopsis leaf (phospho)proteome

Drought is one of the most detrimental environmental stresses to which plants are exposed. Especially mild drought is relevant to agriculture and significantly affects plant growth and development. In plant research, mannitol is often used to mimic drought stress and study the underlying responses. In growing leaf tissue of plants exposed to mannitol-induced stress, a highly-interconnected gene regulatory network is induced. However, early signaling and associated protein phosphorylation events that likely precede part of these transcriptional changes are largely unknown. Here, we performed a full proteome and phosphoproteome analysis on growing leaf tissue of Arabidopsis plants exposed to mild mannitol-induced stress and captured the fast (within the first half hour) events associated with this stress. Based on this in-depth data analysis, 167 and 172 differentially regulated proteins and phosphorylated sites were found back, respectively. Additionally, we identified H(+)-ATPASE 2 (AHA2) and CYSTEINE-RICH REPEAT SECRETORY PROTEIN 38 (CRRSP38) as novel regulators of shoot growth under osmotic stress.\n\nHighlightWe captured early changes in the Arabidopsis leaf proteome and phosphoproteome upon mild mannitol stress and identified AHA2 and CRRSP38 as novel regulators of shoot growth under osmotic stress

plant biology↗