The annotation and analysis of complex 3D plant organs using 3DCoordX

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. It enables rapid spatial annotation of cells even in highly curved biological shapes. With the help of 3DCoordX we obtained new insight by analyzing cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis thaliana. Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia polymorpha and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia gibba. Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

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Predictions of cellular growth patterns by a feedback model

Journal of Theoretical Biology ◽

10.1016/0022-5193(77)90069-8 ◽

1977 ◽

Vol 68 (3) ◽

pp. 415-435 ◽

Cited By ~ 7

Author(s):

S.V. Ho ◽

M.L. Shuler

Keyword(s):

Growth Patterns ◽

Cellular Growth ◽

Feedback Model

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Author response: A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule

10.7554/elife.63262.sa2 ◽

2020 ◽

Author(s):

Athul Vijayan ◽

Rachele Tofanelli ◽

Sören Strauss ◽

Lorenzo Cerrone ◽

Adrian Wolny ◽

...

Keyword(s):

Growth Patterns ◽

Cellular Growth ◽

Author Response

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A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

10.1101/2020.09.25.313312 ◽

2020 ◽

Author(s):

Yassin Refahi ◽

Argyris Zardilis ◽

Gaël Michelin ◽

Raymond Wightman ◽

Bruno Leggio ◽

...

Keyword(s):

Flower Development ◽

Computational Models ◽

Fundamental Problem ◽

Expression Patterns ◽

Growth Control ◽

Cell Lineage ◽

Time Lapse ◽

Growth Patterns ◽

Cellular Growth ◽

Early Flower

Abstract The link between gene regulation and morphogenesis of multicellular organisms is a fundamental problem in biology. We address this question in the floral meristem of Arabidopsis, which generates new tissues and organs through complex changes in growth patterns. Starting from high-resolution time-lapse images, we generated a comprehensive 4-D atlas of early flower development including cell lineage, cellular growth rates and the expression patterns of 28 regulatory genes. This information was introduced in MorphoNet, a web-based open-access platform. The application of mechanistic computational models indicated that the molecular network based on the literature only explained a minority of the expression patterns. This was substantially improved by adding single regulatory hypotheses for individual genes. We next used the integrated information to correlate growth with the combinatorial expression of multiple genes. This led us to propose a set of hypotheses for the action of individual genes in morphogenesis, not visible by simply correlating gene expression and growth. This identified the central transcription factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated, multiscale view of flower development, this atlas should represent a fundamental step towards mechanistic multiscale-scale models of flower development.

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Plasmodiophora brassicae-Triggered Cell Enlargement and Loss of Cellular Integrity in Root Systems Are Mediated by Pectin Demethylation

Frontiers in Plant Science ◽

10.3389/fpls.2021.711838 ◽

2021 ◽

Vol 12 ◽

Author(s):

Karolina Stefanowicz ◽

Monika Szymanska-Chargot ◽

William Truman ◽

Piotr Walerowski ◽

Marcin Olszak ◽

...

Keyword(s):

Extracellular Matrix ◽

Cell Wall ◽

Life Cycle ◽

Plasmodiophora Brassicae ◽

Growth Patterns ◽

Cellular Reprogramming ◽

Cellular Growth ◽

Gall Formation ◽

Clubroot Disease ◽

Cellular Environment

Gall formation on the belowground parts of plants infected with Plasmodiophora brassicae is the result of extensive host cellular reprogramming. The development of these structures is a consequence of increased cell proliferation followed by massive enlargement of cells colonized with the pathogen. Drastic changes in cellular growth patterns create local deformities in the roots and hypocotyl giving rise to mechanical tensions within the tissue of these organs. Host cell wall extensibility and recomposition accompany the growth of the gall and influence pathogen spread and also pathogen life cycle progression. Demethylation of pectin within the extracellular matrix may play an important role in P. brassicae-driven hypertrophy of host underground organs. Through proteomic analysis of the cell wall, we identified proteins accumulating in the galls developing on the underground parts of Arabidopsis thaliana plants infected with P. brassicae. One of the key proteins identified was the pectin methylesterase (PME18); we further characterized its expression and conducted functional and anatomic studies in the knockout mutant and used Raman spectroscopy to study the status of pectin in P. brassicae-infected galls. We found that late stages of gall formation are accompanied with increased levels of PME18. We have also shown that the massive enlargement of cells colonized with P. brassicae coincides with decreases in pectin methylation. In pme18-2 knockout mutants, P. brassicae could still induce demethylation; however, the galls in this line were smaller and cellular expansion was less pronounced. Alteration in pectin demethylation in the host resulted in changes in pathogen distribution and slowed down disease progression. To conclude, P. brassicae-driven host organ hypertrophy observed during clubroot disease is accompanied by pectin demethylation in the extracellular matrix. The pathogen hijacks endogenous host mechanisms involved in cell wall loosening to create an optimal cellular environment for completion of its life cycle and eventual release of resting spores facilitated by degradation of demethylated pectin polymers.

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Oxidative stress and its role in cancer: a molecular perspective

Ciencia e Innovación en Salud ◽

10.17081/innosa.97 ◽

2020 ◽

Author(s):

Georgina Crespo ◽

Luis Alejandro Di Toro ◽

Valbuena Desiree ◽

Jose Luis Perez Vicuña ◽

María Paula Díaz ◽

...

Keyword(s):

Oxidative Stress ◽

Free Radicals ◽

Cancer Biology ◽

Therapeutic Potential ◽

Typical Feature ◽

Cellular Growth ◽

System Capacity ◽

Antioxidant Systems ◽

Cellular Processes ◽

Underlying Mechanisms

Cancer development is a product of cellular growth and proliferation caused by DNA mutations, nevertheless, other processes are able to favor tumoral progression, such as the activity of reactive oxygen species (ROS) produced within cells as a result of different metabolic reactions. Oxidative stress is defined as an imbalance between free radicals and highly reactive metabolites synthesis and the antioxidant system capacity to eliminate these molecules. In this sense, the overproduction of free radicals is a typical feature of neoplastic cells that allows the promotion of cellular processes related to survival, proliferation, invasion, and metastasis. Furthermore, underlying mechanisms involved in malignant transformation can modify the antioxidant systems in charge of ROS elimination. However, cancer has the particularity of presenting a dual behavior in which both antioxidant or prooxidant activity within tumoral cells can predominate depending on the stage of the disease. As a consequence, many therapeutic efforts have been directed into the stimulation or inhibition of oxidant and antioxidant components in the tumor microenvironment. The aim of this review is to describe the role of oxidative stress in cancer biology and its therapeutic potential.

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The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 in Arabidopsis thaliana

10.1101/470732 ◽

2018 ◽

Author(s):

Sebastian Scholz ◽

Janys Pleßmann ◽

Regina Hüttl ◽

Katrin Wassmer ◽

Balaji Enugutti ◽

...

Keyword(s):

Transcription Factor ◽

Protein Kinase ◽

Seed Coat ◽

Stress Responses ◽

Biological Data ◽

Growth Patterns ◽

Cellular Growth ◽

Distinct Cell ◽

Cell Layers ◽

Planar Growth

AbstractTissue morphogenesis critically depends on the coordination of cellular growth patterns. In plants, many organs consist of clonally distinct cell layers, such as the epidermis, whose cells undergo divisions that are oriented along the plane of the layer. The developmental control of such planar growth is poorly understood. We have previously identified the Arabidopsis AGCVIII-class protein kinase UNICORN (UCN) as a central regulator of this process. Plants lacking UCN activity show spontaneous formation of ectopic multicellular protrusions in integuments and malformed petals indicating that UCN suppresses uncontrolled growth in those tissues. In the current model UCN regulates planar growth of integuments in part by directly repressing the putative transcription factor ABERRANT TESTA SHAPE (ATS). Here we report on the identification of 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) as a novel factor involved in UCN-mediated growth control. PDK1 constitutes a basic component of signaling mediated by AGC protein kinases throughout eukaryotes. Arabidopsis PDK1 is implied in stress responses and growth promotion. Here we show that loss-of-function mutations in PDK1 suppress aberrant growth in integuments and petals of ucn mutants. Additional genetic, in vitro, and cell biological data support the view that UCN functions by repressing PDK1. Furthermore, our data indicate that PDK1 is indirectly required for deregulated growth caused by ATS overexpression. Our findings support a model proposing that UCN suppresses ectopic growth in integuments through two independent processes: the attenuation of the protein kinase PDK1 in the cytoplasm and the repression of the transcription factor ATS in the nucleus.Author SummaryPlant organs, such as petals or roots, are composites of distinct cell layers. As a rule, cells making up a layer, for example the epidermis, the outermost layer of a tissue, divide “within the plane” of the layer. This cellular behavior results in the two-dimensional sheet-like or planar growth of the cell layer. The mechanism orchestrating such a growth pattern is poorly understood. In particular, it is unclear how uncontrolled and “out-of-plane” growth is avoided. Here we provide insight into this process. Our data indicate that higher than normal activity of a central regulator of growth and stress responses results in wavy and malformed petals and in protrusion-like aberrant outgrowths in the tissue that will develop into the seed coat. It is therefore important to keep this factor in check to allow proper formation of those tissues. We further show that a protein called UNICORN attenuates the activity of this regulator thereby ensuring the sheet-like growth of young petals or the developing seed coat.

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Regulation of Photosynthetic Carbohydrate Metabolism by a Raf-Like Kinase in the Liverwort Marchantia polymorpha

Plant and Cell Physiology ◽

10.1093/pcp/pcz232 ◽

2019 ◽

Vol 61 (3) ◽

pp. 631-643

Author(s):

Eri Koide ◽

Noriyuki Suetsugu ◽

Megumi Iwano ◽

Eiji Gotoh ◽

Yuko Nomura ◽

...

Keyword(s):

Starch Synthesis ◽

Photosynthetic Electron Transport ◽

Growth Defect ◽

Marchantia Polymorpha ◽

Common Amino Acid ◽

Cellular Processes ◽

Biochemical Analyses ◽

Activity Dependent ◽

Photosynthetic Activities ◽

Do So

Abstract To optimize growth and development, plants monitor photosynthetic activities and appropriately regulate various cellular processes. However, signaling mechanisms that coordinate plant growth with photosynthesis remain poorly understood. To identify factors that are involved in signaling related to photosynthetic stimuli, we performed a phosphoproteomic analysis with Marchantia polymorpha, an extant bryophyte species in the basal lineage of land plants. Among proteins whose phosphorylation status changed differentially between dark-treated plants and those after light irradiation but failed to do so in the presence of a photosynthesis inhibitor, we identified a B4-group Raf-like kinase, named PHOTOSYNTHESIS-RELATED RAF (MpPRAF). Biochemical analyses confirmed photosynthesis-activity-dependent changes in the phosphorylation status of MpPRAF. Mutations in the MpPRAF gene resulted in growth retardation. Measurement of carbohydrates demonstrated both hyper-accumulation of starch and reduction of sucrose in Mppraf mutants. Neither inhibition of starch synthesis nor exogenous supply of sucrose alleviated the growth defect, suggesting serious impairment of Mppraf mutants in both the synthesis of sucrose and the repression of its catabolism. As a result of the compromised photosynthate metabolism, photosynthetic electron transport was downregulated in Mppraf mutants. A mutated MpPRAF with a common amino acid substitution for inactivating kinase activity was unable to rescue the Mppraf mutant defects. Our results provide evidence that MpPRAF is a photosynthesis signaling kinase that regulates sucrose metabolism.

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Glutamatergic Receptor Trafficking and Delivery: Role of the Exocyst Complex

Cells ◽

10.3390/cells9112402 ◽

2020 ◽

Vol 9 (11) ◽

pp. 2402

Author(s):

Matías Lira ◽

Rodrigo G. Mira ◽

Francisco J. Carvajal ◽

Pedro Zamorano ◽

Nibaldo C. Inestrosa ◽

...

Keyword(s):

Plasma Membrane ◽

Long Term Potentiation ◽

Receptor Trafficking ◽

Cellular Growth ◽

Recycling Endosomes ◽

Neuronal Communication ◽

Cellular Processes ◽

Exocyst Complex ◽

Term Potentiation ◽

Membrane Compartments

Cells comprise several intracellular membrane compartments that allow them to function properly. One of these functions is cargo movement, typically proteins and membranes within cells. These cargoes ride microtubules through vesicles from Golgi and recycling endosomes to the plasma membrane in order to be delivered and exocytosed. In neurons, synaptic functions employ this cargo trafficking to maintain inter-neuronal communication optimally. One of the complexes that oversee vesicle trafficking and tethering is the exocyst. The exocyst is a protein complex containing eight subunits first identified in yeast and then characterized in multicellular organisms. This complex is related to several cellular processes, including cellular growth, division, migration, and morphogenesis, among others. It has been associated with glutamatergic receptor trafficking and tethering into the synapse, providing the molecular machinery to deliver receptor-containing vesicles into the plasma membrane in a constitutive manner. In this review, we discuss the evidence so far published regarding receptor trafficking and the exocyst complex in both basal and stimulated levels, comparing constitutive trafficking and long-term potentiation-related trafficking.

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Role of microRNAs in Chronic Lymphocytic Leukemia Pathogenesis

Current Medicinal Chemistry ◽

10.2174/0929867326666190911114842 ◽

2020 ◽

Vol 27 (2) ◽

pp. 282-297 ◽

Cited By ~ 8

Author(s):

Ehsan Javandoost ◽

Ehsan Firoozi-Majd ◽

Hosein Rostamian ◽

Mohammad Khakpoor- Koosheh ◽

Hamid Reza Mirzaei

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Chromosomal Abnormalities ◽

Lymphoblastic Leukemia ◽

Lymphocytic Leukemia ◽

Cellular Growth ◽

Western World ◽

Lymphoid Tissues ◽

Cellular Processes ◽

Trisomy 12 ◽

Underlying Mechanisms

MicroRNAs (miRNAs) are a group of small endogenous non-coding RNAs involved in many cancers and various cellular processes such as cellular growth, DNA methylation, apoptosis, and differentiation. 13q14.3 chromosomal region contains miR-15 and miR-16 and deletion of this region is a commonly reported aberration in Chronic Lymphoblastic Leukemia (CLL), suggesting miRNAs involvement in CLL pathogenesis. MicroRNAs are known as oncogenes and tumor suppressors in CLL which may also serve as markers of onset and progression of the disease. The most prevalent form of leukemia diagnosed in adults in the western world, chronic lymphocytic leukemia, accounts for one-third of all leukemias. CLL is characterized by the presence of B Cell Malignant Clones in secondary lymphoid tissues, peripheral blood and bone marrow. The precise etiology of CLL is remained to be known, however, a number of Chromosomal Abnormalities such as deletions of 13q14.3, 11q and 17p and trisomy 12 have been detected. In this review, we offer our prospect on how miRNAs are involved in the CLL pathogenesis and disease progression. Further understanding of the underlying mechanisms and regulation of CLL pathogenesis has underscored the need for further research regarding their role in this disease.

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