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1. Boolink: a graphical interface for open access Boolean network simulations and use in guard cell CO2 signaling

   https://doi.org/10.1093/plphys/kiab344  

   Karanam, Aravind ; He, David ; Hsu, Po-Kai ; Schulze, Sebastian ; Dubeaux, Guillaume ; Karmakar, Richa ; Schroeder, Julian I ; Rappel, Wouter-Jan ( July 2021 , Plant Physiology)

   Abstract Signaling networks are at the heart of almost all biological processes. Most of these networks contain large number of components, and often either the connections between these components are not known or the rate equations that govern the dynamics of soluble signaling components are not quantified. This uncertainty in network topology and parameters can make it challenging to formulate detailed mathematical models. Boolean networks, in which all components are either on or off, have emerged as viable alternatives to detailed mathematical models that contain rate constants and other parameters. Therefore, open-source platforms of Boolean models for community use are desirable. Here, we present Boolink, a freely available graphical user interface that allows users to easily construct and analyze existing Boolean networks. Boolink can be applied to any Boolean network. We demonstrate its application using a previously published network for abscisic acid (ABA)-driven stomatal closure in Arabidopsis spp. (Arabidopsis thaliana). We also show how Boolink can be used to generate testable predictions by extending the network to include CO2 regulation of stomatal movements. Predictions of the model were experimentally tested, and the model was iteratively modified based on experiments showing that ABA effectively closes Arabidopsis stomata at near-zero CO2 concentrations (1.5-ppm CO2). Thus, Boolink enables public generation and the use of existing Boolean models, including the prior developed ABA signaling model with added CO2 signaling components. 

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2. Anatomical adjustments of the tree hydraulic pathway decrease canopy conductance under long-term elevated CO2

   https://doi.org/10.1093/plphys/kiac482  

   Gattmann, Marielle ; McAdam, Scott A ; Birami, Benjamin ; Link, Roman ; Nadal-Sala, Daniel ; Schuldt, Bernhard ; Yakir, Dan ; Ruehr, Nadine K ( October 2022 , Plant Physiology)

   The cause of reduced leaf-level transpiration under elevated CO2 remains largely elusive. Here, we assessed stomatal, hydraulic, and morphological adjustments in a long-term experiment on Aleppo pine (Pinus halepensis) seedlings germinated and grown for 22–40 months under elevated (eCO2; c. 860 ppm) or ambient (aCO2; c. 410 ppm) CO2. We assessed if eCO2-triggered reductions in canopy conductance (gc) alter the response to soil or atmospheric drought and are reversible or lasting due to anatomical adjustments by exposing eCO2 seedlings to decreasing [CO2]. To quantify underlying mechanisms, we analyzed leaf abscisic acid (ABA) level, stomatal and leaf morphology, xylem structure, hydraulic efficiency, and hydraulic safety. Effects of eCO2 manifested in a strong reduction in leaf-level gc (−55%) not caused by ABA and not reversible under low CO2 (c. 200 ppm). Stomatal development and size were unchanged, while stomatal density increased (+18%). An increased vein-to-epidermis distance (+65%) suggested a larger leaf resistance to water flow. This was supported by anatomical adjustments of branch xylem having smaller conduits (−8%) and lower conduit lumen fraction (−11%), which resulted in a lower specific conductivity (−19%) and leaf-specific conductivity (−34%). These adaptations to CO2 did not change stomatal sensitivity to soil or atmospheric drought, consistent with similar xylem safety thresholds. In summary, we found reductions of gc under elevated CO2 to be reflected in anatomical adjustments and decreases in hydraulic conductivity. As these water savings were largely annulled by increases in leaf biomass, we do not expect alleviation of drought stress in a high CO2 atmosphere.

    

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3. Consistent responses of vegetation gas exchange to elevated atmospheric CO 2 emerge from heuristic and optimization models

   https://doi.org/10.5194/bg-19-4387-2022  

   Manzoni, Stefano ; Fatichi, Simone ; Feng, Xue ; Katul, Gabriel G. ; Way, Danielle ; Vico, Giulia ( January 2022 , Biogeosciences)

   Abstract. Elevated atmospheric CO2 concentration is expectedto increase leaf CO2 assimilation rates, thus promoting plant growthand increasing leaf area. It also decreases stomatal conductance, allowingwater savings, which have been hypothesized to drive large-scale greening,in particular in arid and semiarid climates. However, the increase in leafarea could reduce the benefits of elevated CO2 concentration through soilwater depletion. The net effect of elevated CO2 on leaf- andcanopy-level gas exchange remains uncertain. To address this question, wecompare the outcomes of a heuristic model based on the Partitioning ofEquilibrium Transpiration and Assimilation (PETA) hypothesis and three modelvariants based on stomatal optimization theory. Predicted relative changes in leaf-and canopy-level gas exchange rates are used as a metric of plant responsesto changes in atmospheric CO2 concentration. Both model approaches predictreductions in leaf-level transpiration rate due to decreased stomatalconductance under elevated CO2, but negligible (PETA) or no(optimization) changes in canopy-level transpiration due to the compensatoryeffect of increased leaf area. Leaf- and canopy-level CO2 assimilationis predicted to increase, with an amplification of the CO2fertilization effect at the canopy level due to the enhanced leaf area. Theexpected increase in vapour pressure deficit (VPD) under warmer conditions isgenerally predicted to decrease the sensitivity of gas exchange toatmospheric CO2 concentration in both models. The consistentpredictions by different models that canopy-level transpiration varieslittle under elevated CO2 due to combined stomatal conductancereduction and leaf area increase highlight the coordination ofphysiological and morphological characteristics in vegetation to maximizeresource use (here water) under altered climatic conditions. 

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4. Influence of plant ecophysiology on ozone dry deposition: comparing between multiplicative and photosynthesis-based dry deposition schemes and their responses to rising CO₂ level

   https://doi.org/10.5194/bg-19-1753-2022  

   Sun, Shihan ; Tai, Amos P. ; Yung, David H. ; Wong, Anthony Y. ; Ducker, Jason A. ; Holmes, Christopher D. ( January 2022 , Biogeosciences)

   Abstract. Dry deposition is a key process for surface ozone(O3) removal. Stomatal uptake is a major component of O3 drydeposition, which is parameterized differently in current land surfacemodels and chemical transport models. We developed and used a standaloneterrestrial biosphere model, driven by a unified set of prescribedmeteorology, to evaluate two widely used dry deposition modeling frameworks,Wesely (1989) and Zhang et al. (2003), with different configurations ofstomatal resistance: (1) the default multiplicative method in the Weselyscheme (W89) and Zhang et al. (2003) scheme (Z03), (2) the traditionalphotosynthesis-based Farquhar–Ball–Berry (FBB) stomatal algorithm, and (3) theMedlyn stomatal algorithm (MED) based on optimization theory. We found thatusing the FBB stomatal approach that captures ecophysiological responses toenvironmental factors, especially to water stress, can generally improve thesimulated dry deposition velocities compared with multiplicative schemes.The MED stomatal approach produces higher stomatal conductance than FBB andis likely to overestimate dry deposition velocities for major vegetationtypes, but its performance is greatly improved when spatially varying slopeparameters based on annual mean precipitation are used. Large discrepancieswere also found in stomatal responses to rising CO2 levels from 390to 550 ppm: the multiplicative stomatal method with an empirical CO2response function produces reduction (−35 %) in global stomatalconductance on average much larger than that with the photosynthesis-basedstomatal method (−14 %–19 %). Our results show the potential biases inO3 sink caused by errors in model structure especially in the Weselydry deposition scheme and the importance of using photosynthesis-basedrepresentation of stomatal resistance in dry deposition schemes under achanging climate and rising CO2 concentration. 

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5. The Arabidopsis heterotrimeric G‐protein β subunit, AGB 1, is required for guard cell calcium sensing and calcium‐induced calcium release

   https://doi.org/10.1111/tpj.14318  

   Jeon, Byeong Wook ; Acharya, Biswa R. ; Assmann, Sarah M. ( April 2019 , The Plant Journal)

   Cytosolic calcium concentration ([Ca²⁺]_cyt) and heterotrimeric G‐proteins are universal eukaryotic signaling elements. In plant guard cells, extracellular calcium (Ca_o) is as strong a stimulus for stomatal closure as the phytohormone abscisic acid (ABA), but underlying mechanisms remain elusive. Here, we report that the sole Arabidopsis heterotrimeric Gβ subunit,AGB1, is required for four guard cell Ca_oresponses: induction of stomatal closure; inhibition of stomatal opening; [Ca²⁺]_cytoscillation; and inositol 1,4,5‐trisphosphate (InsP3) production. Stomata in wild‐type Arabidopsis (Col) and in mutants of the canonical Gα subunit,GPA1, showed inhibition of stomatal opening and promotion of stomatal closure by Ca_o. By contrast, stomatal movements ofagb1mutants andagb1/gpa1double‐mutants, as well as those of theagg1agg2 Gγ double‐mutant, were insensitive to Ca_o. These behaviors contrast withABA‐regulated stomatal movements, which involveGPA1 andAGB1/AGG3 dimers, illustrating differential partitioning of G‐protein subunits among stimuli with similar ultimate impacts, which may facilitate stimulus‐specific encoding.AGB1knockouts retained reactive oxygen species andNOproduction, but lostYC3.6‐detected [Ca²⁺]_cytoscillations in response to Ca_o, initiating only a single [Ca²⁺]_cytspike. Experimentally imposed [Ca²⁺]_cytoscillations restored stomatal closure inagb1. Yeast two‐hybrid and bimolecular complementation fluorescence experiments revealed thatAGB1 interacts with phospholipase Cs (PLCs), and Ca_oinduced InsP3 production in Col but not inagb1. In sum, G‐protein signaling viaAGB1/AGG1/AGG2 is essential for Ca_o‐regulation of stomatal apertures, and stomatal movements in response to Ca_oapparently require Ca²⁺‐induced Ca²⁺release that is likely dependent on Gβγ interaction withPLCs leading to InsP3 production.

    

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