Advancing plant science through precision 3D bioprinting: new tools for research and biotech applications.

The integration of 3D bioprinting into plant science and biotechnology is revolutionizing research and applications. While many high-throughput techniques have advanced plant biology, replicating the complex 3D organization and cellular environments of plant tissues remains a significant challenge. Traditional 2D culture systems fall short of capturing the necessary spatial context for accurate studies of cell behavior, gene expression, and tissue development.

Advancing our understanding of root development: Technologies and insights from diverse studies.

Understanding root development is critical for enhancing plant growth and health, and advanced technologies are essential for unraveling the complexities of these processes. In this review, we highlight select technological innovations in the study of root development, with a focus on the transformative impact of single-cell gene expression analysis. We provide a high-level overview of recent advancements, illustrating how single-cell RNA sequencing (scRNA-seq) has become a pivotal tool in plant biology.

Global-to-Local Dependencies in Phosphorus Mass Flows and Markets: Pathways to Improving System Resiliency in Response to Exogenous Shocks.

Uneven global distribution of phosphate rock deposits and the supply chains to transport phosphorus (P) make P fertilizers vulnerable to exogenous shocks, including commodity market shocks; extreme weather events or natural disasters; and geopolitical instability, such as trade disputes, disruption of shipping routes, and war. Understanding bidirectional risk transmission (global-to-local and local-to-global) in P supply and consumption chains is thus essential. Ignoring P system interdependencies and associated risks could have major impacts on critical infrastructure operations and increase the vulnerability of global food systems.

Insights into multilevel spatial regulation within the root stem cell niche.

All differentiated root cells derive from stem cells spatially organized within the stem cell niche (SCN), a microenvironment located within the root tip. Here, we compiled recent advances in the understanding of how the SCN drives the establishment and maintenance of cell types. The quiescent center (QC) is widely recognized as the primary driver of cell fate determination, but it is recently considered a convergence center of multiple signals.

Phosphate starvation: response mechanisms and solutions.

Phosphorus is essential to plant growth and agricultural crop yields, yet the challenges associated with phosphorus fertilization in agriculture, such as aquatic runoff pollution and poor phosphorus bioavailability, are increasingly difficult to manage. Comprehensively understanding the dynamics of phosphorus uptake and signaling mechanisms will inform the development of strategies to address these issues. This review describes regulatory mechanisms used by specific tissues in the root apical meristem to sense and take up phosphate from the rhizosphere.

Functional annotation of proteins for signaling network inference in non-model species.

Molecular biology aims to understand cellular responses and regulatory dynamics in complex biological systems. However, these studies remain challenging in non-model species due to poor functional annotation of regulatory proteins. To overcome this limitation, we develop a multi-layer neural network that determines protein functionality directly from the protein sequence.

A Data-Driven Signaling Network Inference Approach for Phosphoproteomics.

Proteins are rapidly and dynamically post-transcriptionally modified as cells respond to changes in their environment. For example, protein phosphorylation is mediated by kinases while dephosphorylation is mediated by phosphatases. Quantifying and predicting interactions between kinases, phosphatases, and target proteins over time will aid the study of signaling cascades under a variety of environmental conditions.

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

The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence.

Establishing a reproducible approach to study cellular functions of plant cells with 3D bioprinting.

Capturing cell-to-cell signals in a three-dimensional (3D) environment is key to studying cellular functions. A major challenge in the current culturing methods is the lack of accurately capturing multicellular 3D environments. In this study, we established a framework for 3D bioprinting plant cells to study cell viability, cell division, and cell identity.

POPEYE intercellular localization mediates cell-specific iron deficiency responses.

Plants must tightly regulate iron (Fe) sensing, acquisition, transport, mobilization, and storage to ensure sufficient levels of this essential micronutrient. POPEYE (PYE) is an iron responsive transcription factor that positively regulates the iron deficiency response, while also repressing genes essential for maintaining iron homeostasis. However, little is known about how PYE plays such contradictory roles.

RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic spp. in Strawberry.

Two hemibiotrophic pathogens, (Ca) and . (Cg), cause anthracnose fruit rot and anthracnose crown rot in strawberry ( × Duchesne), respectively. Both Ca and Cg can initially infect through a brief biotrophic phase, which is associated with the production of intracellular primary hyphae that can infect host cells without causing cell death and establishing hemibiotrophic infection (HBI) or quiescent (latent infections) in leaf tissues.

Quantifying Intercellular Movement and Protein Stoichiometry for Computational Modeling.

Analyzing protein movement dynamics and their regulation has shown to be important in the study of cell fate decisions. Such analyses can be performed with scanning fluorescence correlation spectroscopy (scanning FCS), a versatile imaging methodology that has been applied in the animal kingdom and recently adapted to the plant kingdom. Specifically, scanning FCS allows for qualitatively capturing protein movement across barriers, such as the active transport through plasmodesmata, the analysis of protein movement rates, and the quantification of the stoichiometry of protein complexes, composed of one or more different proteins.

Tissue Regeneration with Hydrogel Encapsulation: A Review of Developments in Plants and Animals.

Hydrogel encapsulation has been widely utilized in the study of fundamental cellular mechanisms and has been shown to provide a better representation of the complex microenvironment in natural biological conditions of mammalian cells. In this review, we provide a background into the adoption of hydrogel encapsulation methods in the study of mammalian cells, highlight some key findings that may aid with the adoption of similar methods for the study of plant cells, including the potential challenges and considerations, and discuss key findings of studies that have utilized these methods in plant sciences.

Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis.

Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets and unravel the molecular signaling events of BR response in Arabidopsis. We profile the levels of 26,669 transcripts, 9,533 protein groups, and 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths of time.

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

Grafting has been adopted for a wide range of crops to enhance productivity and resilience; for example, grafting of Solanaceous crops couples disease-resistant rootstocks with scions that produce high-quality fruit. However, incompatibility severely limits the application of grafting and graft incompatibility remains poorly understood. In grafts, immediate incompatibility results in rapid death, but delayed incompatibility can take months or even years to manifest, creating a significant economic burden for perennial crop production.

Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification.

Gene expression data analysis and the prediction of causal relationships within gene regulatory networks (GRNs) have guided the identification of key regulatory factors and unraveled the dynamic properties of biological systems. However, drawing accurate and unbiased conclusions requires a comprehensive understanding of relevant tools, computational methods, and their workflows. The topics covered in this chapter encompass the entire workflow for GRN inference including: (1) experimental design; (2) RNA sequencing data processing; (3) differentially expressed gene (DEG) selection; (4) clustering prior to inference; (5) network inference techniques; and (6) network visualization and analysis.

Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots.

Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem cell-specific transcription factors BRAVO and WOX5 co-localize in the quiescent centre (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture.

A hybrid model connecting regulatory interactions with stem cell divisions in the root.

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 WUSCHEL-RELATED HOMEOBOX 5 (WOX5) and SHORTROOT (SHR), regulate divisions in the root stem cell niche.

Down-regulation of Fra a 1.02 in strawberry fruits causes transcriptomic and metabolic changes compatible with an altered defense response.

The strawberry Fra a 1 proteins belong to the class 10 Pathogenesis-Related (PR-10) superfamily. In strawberry, a large number of members have been identified, but only a limited number is expressed in the fruits. In this organ, Fra a 1.

BAM1/2 receptor kinase signaling drives CLE peptide-mediated formative cell divisions in roots.

Cell division is often regulated by extracellular signaling networks to ensure correct patterning during development. In , the SHORT-ROOT (SHR)/SCARECROW (SCR) transcription factor dimer activates ; () to drive formative divisions during root ground tissue development. Here, we show plasma-membrane-localized BARELY ANY MERISTEM1/2 (BAM1/2) family receptor kinases are required for -dependent formative divisions and expression, but not -dependent ground tissue specification.