Although it is a central question in biology, how cell shape controls intracellular dynamics largely remains an open question. Here, we show that the shape of Arabidopsis pavement cells creates a ...stress pattern that controls microtubule orientation, which then guides cell wall reinforcement. Live-imaging, combined with modeling of cell mechanics, shows that microtubules align along the maximal tensile stress direction within the cells, and atomic force microscopy demonstrates that this leads to reinforcement of the cell wall parallel to the microtubules. This feedback loop is regulated: cell-shape derived stresses could be overridden by imposed tissue level stresses, showing how competition between subcellular and supracellular cues control microtubule behavior. Furthermore, at the microtubule level, we identified an amplification mechanism in which mechanical stress promotes the microtubule response to stress by increasing severing activity. These multiscale feedbacks likely contribute to the robustness of microtubule behavior in plant epidermis. DOI: http://dx.doi.org/10.7554/eLife.01967.001.
The spectral analysis and data products in Data Release 16 (DR16; 2019 December) from the high-resolution near-infrared Apache Point Observatory Galactic Evolution Experiment (APOGEE)-2/Sloan Digital ...Sky Survey (SDSS)-IV survey are described. Compared to the previous APOGEE data release (DR14; 2017 July), APOGEE DR16 includes about 200,000 new stellar spectra, of which 100,000 are from a new southern APOGEE instrument mounted on the 2.5 m du Pont telescope at Las Campanas Observatory in Chile. DR16 includes all data taken up to 2018 August, including data released in previous data releases. All of the data have been re-reduced and re-analyzed using the latest pipelines, resulting in a total of 473,307 spectra of 437,445 stars. Changes to the analysis methods for this release include, but are not limited to, the use of MARCS model atmospheres for calculation of the entire main grid of synthetic spectra used in the analysis, a new method for filling "holes" in the grids due to unconverged model atmospheres, and a new scheme for continuum normalization. Abundances of the neutron-capture element Ce are included for the first time. A new scheme for estimating uncertainties of the derived quantities using stars with multiple observations has been applied, and calibrated values of surface gravities for dwarf stars are now supplied. Compared to DR14, the radial velocities derived for this release more closely match those in the Gaia DR2 database, and a clear improvement in the spectral analysis of the coolest giants can be seen. The reduced spectra as well as the result of the analysis can be downloaded using links provided on the SDSS DR16 web page.
Thoughtful use of simplifying assumptions is crucial to make systems biology models tractable while still representative of the underlying biology. A useful simplification can elucidate the core ...dynamics of a system. A poorly chosen assumption can, however, either render a model too complicated for making conclusions or it can prevent an otherwise accurate model from describing experimentally observed dynamics. Here, we perform a computational investigation of sequential multi-step pathway models that contain fewer pathway steps than the system they are designed to emulate. We demonstrate when such models will fail to reproduce data and how detrimental truncation of a pathway leads to detectable signatures in model dynamics and its optimised parameters. An alternative assumption is suggested for simplifying such pathways. Rather than assuming a truncated number of pathway steps, we propose to use the assumption that the rates of information propagation along the pathway is homogeneous and, instead, letting the length of the pathway be a free parameter. We first focus on linear pathways that are sequential and have first-order kinetics, and we show how this assumption results in a three-parameter model that consistently outperforms its truncated rival and a delay differential equation alternative in recapitulating observed dynamics. We then show how the proposed assumption allows for similarly terse and effective models of non-linear pathways. Our results provide a foundation for well-informed decision making during model simplifications.
Fast directional growth is a necessity for the young seedling; after germination, it needs to quickly penetrate the soil to begin its autotrophic life. In most dicot plants, this rapid escape is due ...to the anisotropic elongation of the hypocotyl, the columnar organ between the root and the shoot meristems. Anisotropic growth is common in plant organs and is canonically attributed to cell wall anisotropy produced by oriented cellulose fibers. Recently, a mechanism based on asymmetric pectin-based cell wall elasticity has been proposed. Here we present a harmonizing model for anisotropic growth control in the dark-grown
hypocotyl: basic anisotropic information is provided by cellulose orientation) and additive anisotropic information is provided by pectin-based elastic asymmetry in the epidermis. We quantitatively show that hypocotyl elongation is anisotropic starting at germination. We present experimental evidence for pectin biochemical differences and wall mechanics providing important growth regulation in the hypocotyl. Lastly, our in silico modelling experiments indicate an additive collaboration between pectin biochemistry and cellulose orientation in promoting anisotropic growth.
Mitogens trigger cell division in animals. In plants, cytokinins, a group of phytohormones derived from adenine, stimulate cell proliferation. Cytokinin signaling is initiated by membrane-associated ...histidine kinase receptors and transduced through a phosphorelay system. We show that in the
shoot apical meristem (SAM), cytokinin regulates cell division by promoting nuclear shuttling of Myb-domain protein 3R4 (MYB3R4), a transcription factor that activates mitotic gene expression. Newly synthesized MYB3R4 protein resides predominantly in the cytoplasm. At the G2-to-M transition, rapid nuclear accumulation of MYB3R4-consistent with an associated transient peak in cytokinin concentration-feeds a positive feedback loop involving importins and initiates a transcriptional cascade that drives mitosis and cytokinesis. An engineered nuclear-restricted MYB3R4 mimics the cytokinin effects of enhanced cell proliferation and meristem growth.
The data and analysis methodology used for the SDSS/APOGEE Data Releases 13 and 14 are described, highlighting differences from the DR12 analysis presented in Holtzman et al. Some improvement in the ...handling of telluric absorption and persistence is demonstrated. The derivation and calibration of stellar parameters, chemical abundances, and respective uncertainties are described, along with the ranges over which calibration was performed. Some known issues with the public data related to the calibration of the effective temperatures (DR13), surface gravity (DR13 and DR14), and C and N abundances for dwarfs (DR13 and DR14) are highlighted. We discuss how results from a data-driven technique, The Cannon, are included in DR14 and compare those with results from the APOGEE Stellar Parameters and Chemical Abundances Pipeline. We describe how using The Cannon in a mode that restricts the abundance analysis of each element to regions of the spectrum with known features from that element leads to Cannon abundances can lead to significantly different results for some elements than when all regions of the spectrum are used to derive abundances.
WUSCHEL (WUS) is a homeodomain transcription factor produced in cells of the niche/organizing center (OC) of shoot apical meristems. WUS specifies stem cell fate and also restricts its own levels by ...activating a negative regulator, CLAVATA3 (CLV3), in adjacent cells of the central zone (CZ). Here we show that the WUS protein, after being synthesized in cells of the OC, migrates into the CZ, where it activates CLV3 transcription by binding to its promoter elements. Using a computational model, we show that maintenance of the WUS gradient is essential to regulate stem cell number. Migration of a stem cell-inducing transcription factor into adjacent cells to activate a negative regulator, thereby restricting its own accumulation, is a theme that is unique to plant stem cell niches.
We report the first APOGEE metallicities and -element abundances measured for 3600 red giant stars spanning a large radial range of both the Large (LMC) and Small Magellanic Clouds, the largest Milky ...Way (MW) dwarf galaxies. Our sample is an order of magnitude larger than that of previous studies and extends to much larger radial distances. These are the first results presented that make use of the newly installed southern APOGEE instrument on the du Pont telescope at Las Campanas Observatory. Our unbiased sample of the LMC spans a large range in metallicity, from Fe/H = −0.2 to very metal-poor stars with Fe/H −2.5, the most metal-poor Magellanic Cloud (MC) stars detected to date. The LMC /Fe-Fe/H distribution is very flat over a large metallicity range but rises by ∼0.1 dex at −1.0 < Fe/H −0.5. We interpret this as a sign of the known recent increase in MC star formation activity and are able to reproduce the pattern with a chemical evolution model that includes a recent "starburst." At the metal-poor end, we capture the increase of /Fe with decreasing Fe/H and constrain the " -knee" to Fe/H −2.2 in both MCs, implying a low star formation efficiency of ∼0.01 Gyr−1. The MC knees are more metal-poor than those of less massive MW dwarf galaxies such as Fornax, Sculptor, or Sagittarius. One possible interpretation is that the MCs formed in a lower-density environment than the MW, a hypothesis that is consistent with the paradigm that the MCs fell into the MW's gravitational potential only recently.
The cytoskeleton plays a key role in establishing robust cell shape. In animals, it is well established that cell shape can also influence cytoskeletal organization. Cytoskeletal proteins are well ...conserved between animal and plant kingdoms; nevertheless, because plant cells exhibit major structural differences to animal cells, the question arises whether the plant cytoskeleton also responds to geometrical cues. Recent numerical simulations predicted that a geometry-based rule is sufficient to explain the microtubule (MT) organization observed in cells. Due to their high flexural rigidity and persistence length of the order of a few millimeters, MTs are rigid over cellular dimensions and are thus expected to align along their long axis if constrained in specific geometries. This hypothesis remains to be tested in cellulo. Here, we explore the relative contribution of geometry to the final organization of actin and MT cytoskeletons in single plant cells of Arabidopsis thaliana. We show that the cytoskeleton aligns with the long axis of the cells. We find that actin organization relies on MTs but not the opposite. We develop a model of selforganizing MTs in three dimensions, which predicts the importance of MT severing, which we confirm experimentally. This work is a first step toward assessing quantitatively how cellular geometry contributes to the control of cytoskeletal organization in living plant cells.
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