scholarly journals Cell Type-Specific Imaging of Calcium Signaling in Arabidopsis thaliana Seedling Roots Using GCaMP3

2020 ◽  
Vol 21 (17) ◽  
pp. 6385
Author(s):  
William Krogman ◽  
J. Alan Sparks ◽  
Elison B. Blancaflor
Keyword(s):  
Arabidopsis Thaliana ◽  
Cell Types ◽  
Root Cell ◽  
Cauliflower Mosaic Virus ◽  
Cell Type ◽  
Root Cells ◽  
Cell Tissue ◽  
Seedling Roots ◽  
Cell Type Specific

Cytoplasmic calcium ([Ca2+]cyt) is a well-characterized second messenger in eukaryotic cells. An elevation in [Ca2+]cyt levels is one of the earliest responses in plant cells after exposure to a range of environmental stimuli. Advances in understanding the role of [Ca2+]cyt in plant development has been facilitated by the use of genetically-encoded reporters such as GCaMP. Most of these studies have relied on promoters such as Cauliflower Mosaic Virus (35S) and Ubiquitin10 (UBQ10) to drive expression of GCaMP in all cell/tissue types. Plant organs such as roots consist of various cell types that likely exhibit unique [Ca2+]cyt responses to exogenous and endogenous signals. However, few studies have addressed this question. Here, we introduce a set of Arabidopsis thaliana lines expressing GCaMP3 in five root cell types including the columella, endodermis, cortex, epidermis, and trichoblasts. We found similarities and differences in the [Ca2+]cyt signature among these root cell types when exposed to adenosine tri-phosphate (ATP), glutamate, aluminum, and salt, which are known to trigger [Ca2+]cyt increases in root cells. These cell type-targeted GCaMP3 lines provide a new resource that should enable more in depth studies that address how a particular environmental stimulus is linked to specific root developmental pathways via [Ca2+]cyt.

scholarly journals Revisiting the role of IRF3 in inflammation and immunity by conditional and specifically targeted gene ablation in mice

2018 ◽  
Vol 115 (20) ◽  
pp. 5253-5258 ◽  
Author(s):  
Hideyuki Yanai ◽  
Shiho Chiba ◽  
Sho Hangai ◽  
Kohei Kometani ◽  
Asuka Inoue ◽  
...  
Keyword(s):  
Immune Cell ◽  
Cell Types ◽  
Type I ◽  
Type I Ifn ◽  
Cell Type ◽  
Gene Ablation ◽  
Cell Type Specific

IFN regulatory factor 3 (IRF3) is a transcription regulator of cellular responses in many cell types that is known to be essential for innate immunity. To confirm IRF3’s broad role in immunity and to more fully discern its role in various cellular subsets, we engineered Irf3-floxed mice to allow for the cell type-specific ablation of Irf3. Analysis of these mice confirmed the general requirement of IRF3 for the evocation of type I IFN responses in vitro and in vivo. Furthermore, immune cell ontogeny and frequencies of immune cell types were unaffected when Irf3 was selectively inactivated in either T cells or B cells in the mice. Interestingly, in a model of lipopolysaccharide-induced septic shock, selective Irf3 deficiency in myeloid cells led to reduced levels of type I IFN in the sera and increased survival of these mice, indicating the myeloid-specific, pathogenic role of the Toll-like receptor 4–IRF3 type I IFN axis in this model of sepsis. Thus, Irf3-floxed mice can serve as useful tool for further exploring the cell type-specific functions of this transcription factor.

scholarly journals Prediction of condition-specific regulatory maps in Arabidopsis using integrated genomic data

2019 ◽  
Author(s):  
Qi Song ◽  
Jiyoung Lee ◽  
Shamima Akter ◽  
Ruth Grene ◽  
Song Li
Keyword(s):  
Stress Responses ◽  
Abiotic Stresses ◽  
Individual Cell ◽  
Genomic Data ◽  
Cell Types ◽  
Root Cell ◽  
Specific Gene ◽  
Open Chromatin ◽  
Cell Type ◽  
Cell Type Specific

AbstractRecent advances in genomic technologies have generated large-scale protein-DNA interaction data and open chromatic regions for multiple plant species. To predict condition specific gene regulatory networks using these data, we developed the Condition Specific Regulatory network inference engine (ConSReg), which combines heterogeneous genomic data using sparse linear model followed by feature selection and stability selection to select key regulatory genes. Using Arabidopsis as a model system, we constructed maps of gene regulation under more than 50 experimental conditions including abiotic stresses, cell type-specific expression, and stress responses in individual cell types. Our results show that ConSReg accurately predicted gene expressions (average auROC of 0.84) across multiple testing datasets. We found that, (1) including open chromatin information from ATAC-seq data significantly improves the performance of ConSReg across all tested datasets; (2) choice of negative training samples and length of promoter regions are two key factors that affect model performance. We applied ConSReg to Arabidopsis single cell RNA-seq data of two root cell types (endodermis and cortex) and identified five regulators in two root cell types. Four out of the five regulators have additional experimental evidence to support their roles in regulating gene expression in Arabidopsis roots. By comparing regulatory maps in abiotic stress responses and cell type-specific experiments, we revealed that transcription factors that regulate tissue levels abiotic stresses tend to also regulate stress responses in individual cell types in plants.

scholarly journals Dynamics of gene expression in single root cells ofA. thaliana

2018 ◽  
Author(s):  
Ken Jean-Baptiste ◽  
José L. McFaline-Figueroa ◽  
Cristina M. Alexandre ◽  
Michael W. Dorrity ◽  
Lauren Saunders ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Developmental Trajectories ◽  
Cell Types ◽  
Cell Type ◽  
Specific Expression ◽  
Root Cells ◽  
Cell Lineages ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

ABSTRACTSingle-cell RNA-seq can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of cell lineages. Here, we apply this approach toA. thalianaroot cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single-cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. We assess and interpret changes in total RNA expression along developmental trajectories and show that trajectory branch points mark developmental decisions. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single-cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution.

scholarly journals Jasmonate biosynthesis arising from altered cell walls is prompted by turgor-driven mechanical compression

2021 ◽  
Vol 7 (7) ◽  
pp. eabf0356
Author(s):  
Stefan Mielke ◽  
Marlene Zimmer ◽  
Mukesh Kumar Meena ◽  
René Dreos ◽  
Hagen Stellmach ◽  
...  
Keyword(s):  
Cell Walls ◽  
Turgor Pressure ◽  
Mechanical Compression ◽  
Wild Type ◽  
Cell Type ◽  
Cortex Cell ◽  
Seedling Roots ◽  
Cell Type Specific ◽  
Altered Cell

Despite the vital roles of jasmonoyl-isoleucine (JA-Ile) in governing plant growth and environmental acclimation, it remains unclear what intracellular processes lead to its induction. Here, we provide compelling genetic evidence that mechanical and osmotic regulation of turgor pressure represents a key elicitor of JA-Ile biosynthesis. After identifying cell wall mutant alleles in KORRIGAN1 (KOR1) with elevated JA-Ile in seedling roots, we found that ectopic JA-Ile resulted from cell nonautonomous signals deriving from enlarged cortex cells compressing inner tissues and stimulating JA-Ile production. Restoring cortex cell size by cell type–specific KOR1 complementation, by isolating a genetic kor1 suppressor, and by lowering turgor pressure with hyperosmotic treatments abolished JA-Ile signaling. Conversely, hypoosmotic treatment activated JA-Ile signaling in wild-type plants. Furthermore, constitutive JA-Ile levels guided mutant roots toward greater water availability. Collectively, these findings enhance our understanding on JA-Ile biosynthesis initiation and reveal a previously undescribed role of JA-Ile in orchestrating environmental resilience.

scholarly journals Jasmonate biosynthesis arising from altered cell walls is prompted by turgor-driven mechanical compression and guides root hydrotropism

2020 ◽  
Author(s):  
Stefan Mielke ◽  
Marlene Zimmer ◽  
Mukesh Kumar Meena ◽  
René Dreos ◽  
Hagen Stellmach ◽  
...  
Keyword(s):  
Cell Walls ◽  
Turgor Pressure ◽  
Mechanical Compression ◽  
Cell Type ◽  
Cortex Cell ◽  
Key Factor ◽  
Seedling Roots ◽  
Cell Type Specific ◽  
Altered Cell

ABSTRACTDespite the vital roles of jasmonoyl-isoleucine (JA-Ile) in governing plant growth and environmental acclimation, it remains unclear what intracellular processes lead to its induction. Here, we provide compelling genetic evidence that mechanical and osmotic regulation of turgor pressure represents a key factor in eliciting JA-Ile biosynthesis. After identifying cell wall mutant alleles in KORRIGAN1 (KOR1) with elevated JA-Ile in seedling roots, we found that ectopic JA-Ile resulted from cell non-autonomous signals deriving from enlarged cortex cells compressing inner tissues and stimulating JA-Ile production. Restoring cortex cell size by cell-type-specific KOR1 complementation, by isolating a genetic kor1 suppressor, and by lowering turgor pressure with hyperosmotic treatments, abolished JA-Ile signalling. Strikingly, heightened JA-Ile levels guided kor1 roots towards greater water availability, uncovering a previously unrecognized JA-Ile function in root hydrotropism. Collectively, these findings enhance our understanding of JA-Ile biosynthesis initiation, and reveal a novel role of JA-Ile in orchestrating environmental resilience.

scholarly journals The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael W. Dorrity ◽  
Cristina M. Alexandre ◽  
Morgan O. Hamm ◽  
Anna-Lena Vigil ◽  
Stanley Fields ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Single Cell ◽  
Regulatory Networks ◽  
Cell Types ◽  
Analytical Framework ◽  
Cell Type ◽  
Tissue Heterogeneity ◽  
Shared Information ◽  
Cell Type Specific ◽  
Regulatory Landscape

AbstractThe scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to Arabidopsis thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. We find that the entirety of a cell’s regulatory landscape and its transcriptome independently capture cell type identity. We leverage this shared information on cell identity to integrate accessibility and transcriptome data to characterize developmental progression, endoreduplication and cell division. We further use the combined data to characterize cell type-specific motif enrichments of transcription factor families and link the expression of family members to changing accessibility at specific loci, resolving direct and indirect effects that shape expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.

scholarly journals Cell Type-Specific Mechanisms in the Pathogenesis of Ischemic Stroke: The Role of Apoptosis Signal-Regulating Kinase 1

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
So Yeong Cheon ◽  
Eun Jung Kim ◽  
Jeong Min Kim ◽  
Bon-Nyeo Koo
Keyword(s):  
Ischemic Stroke ◽  
Brain Injury ◽  
Cerebral Ischemia ◽  
Cell Types ◽  
Ischemic Brain Injury ◽  
Cell Type ◽  
Ischemic Brain ◽  
Cell Type Specific ◽  
The Brain

Stroke has become a more common disease worldwide. Despite great efforts to develop treatment, little is known about ischemic stroke. Cerebral ischemia activates multiple cascades of cell type-specific pathomechanisms. Ischemic brain injury consists of a complex series of cellular reactions in various cell types within the central nervous system (CNS) including platelets, endothelial cells, astrocytes, neutrophils, microglia/macrophages, and neurons. Diverse cellular changes after ischemic injury are likely to induce cell death and tissue damage in the brain. Since cells in the brain exhibit different functional roles at distinct time points after injury (acute/subacute/chronic phases), it is difficult to pinpoint genuine roles of cell types after brain injury. Many experimental studies have shown the association of apoptosis signal-regulating kinase 1 (ASK1) with cellular pathomechanisms after cerebral ischemia. Blockade of ASK1, by either pharmacological or genetic manipulation, leads to reduced ischemic brain injury and subsequent neuroprotective effects. In this review, we present the cell type-specific pathophysiology of the early phase of ischemic stroke, the role of ASK1 suggested by preclinical studies, and the potential use of ASK suppression, either by pharmacologic or genetic suppression, as a promising therapeutic option for ischemic stroke recovery.

Organization and cell differentiation in lateral roots of Arabidopsis thaliana

Development ◽  
1997 ◽  
Vol 124 (1) ◽  
pp. 33-44 ◽  
Author(s):  
J.E. Malamy ◽  
P.N. Benfey
Keyword(s):  
Arabidopsis Thaliana ◽  
Cell Differentiation ◽  
Lateral Root ◽  
Lateral Roots ◽  
Cell Types ◽  
Cell Type ◽  
Root Primordia ◽  
Lateral Root Primordia ◽  
Lateral Root Development ◽  
Cell Type Specific

Lateral root formation in plants involves the stimulation of mature pericycle cells to proliferate and redifferentiate to create a new organ. The simple organization of the root of Arabidopsis thaliana allows the development of lateral root primordia to be characterized histologically. We have divided the process of lateral root development into 8 stages defined by specific anatomical characteristics and cell divisions. To identify the cell types in the developing primordium we have generated a collection of marker lines that express beta-glucuronidase in a tissue- or cell type-specific manner in the root. Using these tools we have constructed a model describing the lineage of each cell type in the lateral root. These studies show that organization and cell differentiation in the lateral root primordia precede the appearance of a lateral root meristem, with differential gene expression apparent after the first set of divisions of the pericycle.

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