Plant Physiological Analysis to Overcome Limitations to Plant Phenotyping.

Plant physiological status is the interaction between the plant genome and the prevailing growth conditions. Accurate characterization of plant physiology is, therefore, fundamental to effective plant phenotyping studies; particularly those focused on identifying traits associated with improved yield, lower input requirements, and climate resilience. Here, we outline the approaches used to assess plant physiology and how these techniques of direct empirical observations of processes such as photosynthetic CO2 assimilation, stomatal conductance, photosystem II electron transport, or the effectiveness of protective energy dissipation mechanisms are unsuited to high-throughput phenotyping applications. Novel optical sensors, remote/proximal sensing (multi- and hyperspectral reflectance, infrared thermography, sun-induced fluorescence), LiDAR, and automated analyses of below-ground development offer the possibility to infer plant physiological status and growth. However, there are limitations to such 'indirect' approaches to gauging plant physiology. These methodologies that are appropriate for the rapid high temporal screening of a number of crop varieties over a wide spatial scale do still require 'calibration' or 'validation' with direct empirical measurement of plant physiological status. The use of deep-learning and artificial intelligence approaches may enable the effective synthesis of large multivariate datasets to more accurately quantify physiological characters rapidly in high numbers of replicate plants. Advances in automated data collection and subsequent data processing represent an opportunity for plant phenotyping efforts to fully integrate fundamental physiological data into vital efforts to ensure food and agro-economic sustainability.

Leaf-level coordination principles propagate to the ecosystem scale.

Fundamental axes of variation in plant traits result from trade-offs between costs and benefits of resource-use strategies at the leaf scale. However, it is unclear whether similar trade-offs propagate to the ecosystem level. Here, we test whether trait correlation patterns predicted by three well-known leaf- and plant-level coordination theories - the leaf economics spectrum, the global spectrum of plant form and function, and the least-cost hypothesis - are also observed between community mean traits and ecosystem processes. We combined ecosystem functional properties from FLUXNET sites, vegetation properties, and community mean plant traits into three corresponding principal component analyses. We find that the leaf economics spectrum (90 sites), the global spectrum of plant form and function (89 sites), and the least-cost hypothesis (82 sites) all propagate at the ecosystem level. However, we also find evidence of additional scale-emergent properties. Evaluating the coordination of ecosystem functional properties may aid the development of more realistic global dynamic vegetation models with critical empirical data, reducing the uncertainty of climate change projections.

Molecular origin of the two-step mechanism of gellan aggregation.

Among hydrocolloids, gellan is one of the most studied polysaccharides due to its ability to form mechanically stable gels. Despite its long-standing use, the gellan aggregation mechanism is still not understood because of the lack of atomistic information. Here, we fill this gap by developing a new gellan force field. Our simulations offer the first microscopic overview of gellan aggregation, detecting the coil to single-helix transition at dilute conditions and the formation of higher-order aggregates at high concentration through a two-step process: first, the formation of double helices and then their assembly into superstructures. For both steps, we also assess the role of monovalent and divalent cations, complementing simulations with rheology and atomic force microscopy experiments and highlighting the leading role of divalent cations. These results pave the way for future use of gellan-based systems in a variety of applications, from food science to art restoration.

Testing Removal of Carbon Dioxide, Ozone, and Atmospheric Particles by Urban Parks in Italy.

Cities are responsible for more than 80% of global greenhouse gas emissions. Sequestration of air pollutants is one of the main ecosystem services that urban forests provide to the citizens. The atmospheric concentration of several pollutants such as carbon dioxide (CO2), tropospheric ozone (O3), and particulate matter (PM) can be reduced by urban trees through processes of adsorption and deposition. We predict the quantity of CO2, O3, and PM removed by urban tree species with the multilayer canopy model AIRTREE in two representative urban parks in Italy: Park of Castel di Guido, a 3673 ha reforested area located northwest of Rome, and Park of Valentino, a 42 ha urban park in downtown Turin. We estimated a total annual removal of 1005 and 500 kg of carbon per hectare, 8.1 and 1.42 kg of ozone per hectare, and 8.4 and 8 kg of PM10 per hectare. We highlighted differences in pollutant sequestration between urban areas and between species, shedding light on the importance to perform extensive in situ measurements and modeling analysis of tree characteristics to provide realistic estimates of urban parks to deliver ecosystem services.

Current and future impacts of drought and ozone stress on Northern Hemisphere forests.

Rising ozone (O3 ) concentrations, coupled with an increase in drought frequency due to climate change, pose a threat to plant growth and productivity which could negatively affect carbon sequestration capacity of Northern Hemisphere (NH) forests. Using long-term observations of O3 mixing ratios and soil water content (SWC), we implemented empirical drought and O3 stress parameterizations in a coupled stomatal conductance-photosynthesis model to assess their impacts on plant gas exchange at three FLUXNET sites: Castelporziano, Blodgett and Hyytiälä. Model performance was evaluated by comparing model estimates of gross primary productivity (GPP) and latent heat fluxes (LE) against present-day observations. CMIP5 GCM model output data were then used to investigate the potential impact of the two stressors on forests by the middle (2041-2050) and end (2091-2100) of the 21st century. We found drought stress was the more significant as it reduced model overestimation of GPP and LE by ~11%-25% compared to 1%-11% from O3 stress. However, the best model fit to observations at all the study sites was obtained with O3 and drought stress combined, such that the two stressors counteract the impact of each other. With the inclusion of drought and O3 stress, GPP at CPZ, BLO and HYY is projected to increase by 7%, 5% and 8%, respectively, by mid-century and by 14%, 11% and 14% by 2091-2100 as atmospheric CO2 increases. Estimates were up to 21% and 4% higher when drought and O3 stress were neglected respectively. Drought stress will have a substantial impact on plant gas exchange and productivity, off-setting and possibly negating CO2 fertilization gains in future, suggesting projected increases in the frequency and severity of droughts in the NH will play a significant role in forest productivity and carbon budgets in future.

Effects of Fiber Density and Strain Rate on the Mechanical Properties of Electrospun Polycaprolactone Nanofiber Mats.

This study examines the effects of electrospun polycaprolactone (PCL) fiber density and strain rate on nanofiber mat mechanical properties. An automated track collection system was employed to control fiber number per mat and promote uniform individual fiber properties regardless of the duration of collection. Fiber density is correlated to the mechanical properties of the nanofiber mats. Young's modulus was reduced as fiber density increased, from 14,901 MPa for samples electrospun for 30 s (717 fibers +/- 345) to 3,615 MPa for samples electrospun for 40 min (8,310 fibers +/- 1,904). Ultimate tensile strength (UTS) increased with increasing fiber density, where samples electrospun for 30 s resulted in a UTS of 594 MPa while samples electrospun for 40 min demonstrated a UTS of 1,250 MPa. An average toughness of 0.239 GJ/m3 was seen in the 30 s group, whereas a toughness of 0.515 GJ/m3 was observed at 40 min. The ultimate tensile strain for samples electrospun for 30 s was observed to be 0.39 and 0.48 for samples electrospun for 40 min. The relationships between UTS, Young's modulus, toughness, and ultimate tensile strain with increasing fiber density are the result of fiber-fiber interactions which leads to network mesh interactions.

Water use strategy affects avoidance of ozone stress by stomatal closure in Mediterranean trees-A modelling analysis.

Both ozone (O3 ) and drought can limit carbon fixation by forest trees. To cope with drought stress, plants have isohydric or anisohydric water use strategies. Ozone enters plant tissues through stomata. Therefore, stomatal closure can be interpreted as avoidance to O3 stress. Here, we applied an optimization model of stomata involving water, CO2 , and O3 flux to test whether isohydric and anisohydric strategies may affect avoidance of O3 stress by stomatal closure in four Mediterranean tree species during drought. The data suggest that stomatal closure represents a response to avoid damage to the photosynthetic mechanisms under elevated O3 depending on plant water use strategy. Under high-O3 and well-watered conditions, isohydric species limited O3 fluxes by stomatal closure, whereas anisohydric species activated a tolerance response and did not actively close stomata. Under both O3 and drought stress, however, anisohydric species enhanced the capacity of avoidance by closing stomata to cope with the severe oxidative stress. In the late growing season, regardless of the water use strategy, the efficiency of O3 stress avoidance decreased with leaf ageing. As a result, carbon assimilation rate was decreased by O3 while stomata did not close enough to limit transpirational water losses.

Ozone and particle fluxes in a Mediterranean forest predicted by the AIRTREE model.

Mediterranean forests are among the most threatened ecosystems by the concurrent effects of climate change and atmospheric pollution. In this work we parameterized the AIRTREE multi-layer model to predict CO2, water, ozone, and fine particles exchanges between leaves and the atmosphere. AIRTREE consists of four different modules: (1) a canopy environmental module determines the leaf temperature and radiative fluxes at different levels from above to the bottom of the canopy; (2) a hydrological module predicts soil water flow and water availability to the plant's photosynthetic apparatus; (3) a photosynthesis module estimates the net photosynthesis and stomatal conductance, and (4) a deposition module estimates ozone and PM deposition sinks as a function of the resistances to gas diffusion in the atmosphere, and within the canopy and leaf boundary layer. We describe the AIRTREE model framework, accuracy and sensitivity by comparing modeling results against long-term continuous Eddy Covariance measurements of ozone, water, and CO2 fluxes in a Mediterranean Holm oak forest, and we discuss potential application of AIRTREE for ozone-risk assessment in view of availability of a large observational database from ecosystems distributed worldwide.

Nanoscale morphology and electronic coupling at the interface between indium tin oxide and organic molecular materials.

The correlation between nanoscale morphology and charge injection rates at the interface between an organic semiconductor layer and a transparent metal oxide electrode was investigated by integrating molecular dynamics simulations with electronic structure calculations. The simulation approach proposed has been applied to the analysis of the hole injection mechanism at the interface between an amorphous layer of tris[(3-phenyl-1H-benzimidazol-1-yl-2(3H)-ylidene)-1,2-phenylene]Ir (DPBIC), a hole transport and emitter molecule, and the surface of indium tin oxide (ITO), a material commonly used as anode in OLEDs. The link between interface morphology and charge injection was investigated by implementing a two-step, top-down simulation approach. Namely, nanoscale molecular aggregation phenomena at the organic/electrode interface were first assessed by molecular dynamics simulations, mimicking different processing conditions, and followed by density functional theory calculations of the electronic coupling between molecular levels and the manifold of electrode states involved in the charge injection process. The correlation between structural parameters and electronic coupling suggests a significant role of specific molecule/electrode configurations on charge transport processes at the interface, resulting in a broad distribution of charge injection rates, and highlights the link between molecular structure, nanoscale aggregation and processing in the realization of heterointerfaces for efficient charge injection in organic electronic devices.

Mechanical Considerations for Electrospun Nanofibers in Tendon and Ligament Repair.

Electrospun nanofibers possess unique qualities such as nanodiameter, high surface area to volume ratio, biomimetic architecture, and tunable chemical and electrical properties. Numerous studies have demonstrated the potential of nanofibrous architecture to direct cell morphology, migration, and more complex biological processes such as differentiation and extracellular matrix (ECM) deposition through topographical guidance cues. These advantages have created great interest in electrospun fibers for biomedical applications, including tendon and ligament repair. Electrospun nanofibers, despite their nanoscale size, generally exhibit poor mechanical properties compared to larger conventionally manufactured polymer fiber materials. This invites the question of what role electrospun polymer nanofibers can play in tendon and ligament repair applications that have both biological and mechanical requirements. At first glance, the strength and stiffness of electrospun nanofiber grafts appear to be too low to fill the rigorous loading conditions of these tissues. However, there are a number of strategies to enhance and tune the mechanical properties of electrospun nanofiber grafts. As researchers design the next-generation electrospun tendon and ligament grafts, it is critical to consider numerous physiologically relevant mechanical criteria and to evaluate graft mechanical performance in conditions and loading environments that reflect in vivo conditions and surgical fixation methods.

Validity of Weyl fermion picture for transition metals monopnictides TaAs, TaP, NbAs, and NbP from ab initio studies.

We investigate electronic and optical properties of the topological Weyl semimetals TaAs, TaP, NbAs and NbP crystallizing in bct geometry by means of the ab initio density functional theory with spin-orbit interaction within the independent-particle approximation. The small energetical overlap of Ta5d or Nb4d derived conduction and valence bands leads to electron and/or hole pockets near the Fermi energy at the 24 Weyl nodes. The nodes give rise to two-(three-)dimensional Dirac cones for the W1 (W2) Weyl type. The band dispersion and occupation near the Weyl nodes determine the infrared optical properties. They are dominated by interband transitions, which lead to a deviation from the expected constant values of the imaginary part of the dielectric function. The resulting polarization anisotropy is also visible in the real part of the optical conductivity, whose lineshape deviates from the expected linearity. The details of the Weyl nodes are discussed in relation to recent ARPES results for TaAs and NbP, and compared with measured optical spectra for TaAs. The spectral features of the anisotropic and tilted Weyl fermions are restricted to low excitation energies above absorption onsets due to the band occupation.

Ozone flux in plant ecosystems: new opportunities for long-term monitoring networks to deliver ozone-risk assessments.

Ozone (O3) is a photochemically formed reactive gas responsible for a decreasing carbon assimilation in plant ecosystems. Present in the atmosphere in trace concentrations (less than 100 ppbv), this molecule is capable of inhibiting carbon assimilation in agricultural and forest ecosystems. Ozone-risk assessments are typically based on manipulative experiments. Present regulations regarding critical ozone levels are mostly based on an estimated accumulated exposure over a given threshold concentration. There is however a scientific consensus over flux estimates being more accurate, because they include plant physiology analyses and different environmental parameters that control the uptake-that is, not just the exposure-of O3. While O3 is a lot more difficult to measure than other non-reactive greenhouse gases, UV-based and chemiluminescence sensors enable precise and fast measurements and are therefore highly desirable for eddy covariance studies. Using micrometeorological techniques in association with latent heat flux measurements in the field allows for the partition of ozone fluxes into the stomatal and non-stomatal sinks along the soil-plant continuum. Long-term eddy covariance measurements represent a key opportunity in estimating carbon assimilation at high-temporal resolutions, in an effort to study the effect of climate change on photosynthetic mechanisms. Our aim in this work is to describe potential of O3 flux measurement at the canopy level for ozone-risk assessment in established long-term monitoring networks.

Electronic and optical properties of topological semimetal Cd3As2.

Using ab initio density functional theory the band structure and the dielectric function of a bct Cd3As2 crystal are calculated. We find a Dirac semimetal with two Dirac nodes k± near the Γ point on the tetragonal axis. The bands near the Fermi level exhibit a linear behavior. The resulting Dirac cones are anisotropic and the electron-hole symmetry is destroyed along the tetragonal axis. Along this axis the symmetry-protected band linearity only exists in a small energy interval. The Dirac cones seemingly found by ARPES in a wider energy range are interpreted in terms of pseudo-linear bands. The behavior as 3D graphene-like material is traced back to As p orbital pointing to Cd vacancies, in directions which vary throughout the unit cell. Because of the Dirac nodes the dielectric functions (imaginary part) show a plateau for vanishing frequencies whose finite value is proportional to the Sommerfeld fine structure constant but varies with the light polarization. The consequences of the anisotropy of the Dirac cones are highlighted for the polarization dependence of the infrared optical conductivity.

High Ca2+ Influx During Traumatic Brain Injury Leads to Caspase-1-Dependent Neuroinflammation and Cell Death.

We investigated the hypothesis that high Ca2+ influx during traumatic brain injury induces the activation of the caspase-1 enzyme, which triggers neuroinflammation and cell apoptosis in a cell culture model of neuronal stretch injury and an in vivo model of fluid percussion injury (FPI). We first established that stretch injury causes a rapid increase in the intracellular Ca2+ level, which activates interleukin-converting enzyme caspase-1. The increase in the intracellular Ca2+ level and subsequent caspase-1 activation culminates into neuroinflammation via the maturation of IL-1ß. Further, we analyzed caspase-1-mediated apoptosis by TUNEL staining and PARP western blotting. The voltage-gated sodium channel blocker, tetrodotoxin, mitigated the stretch injury-induced neuroinflammation and subsequent apoptosis by blocking Ca2+ influx during the injury. The effect of tetrodotoxin was similar to the caspase-1 inhibitor, zYVAD-fmk, in neuronal culture. To validate the in vitro results, we demonstrated an increase in caspase-1 activity, neuroinflammation and neurodegeneration in fluid percussion-injured animals. Our data suggest that neuronal injury/traumatic brain injury (TBI) can induce a high influx of Ca2+ to the cells that cause neuroinflammation and cell death by activating caspase-1, IL-1ß, and intrinsic apoptotic pathways. We conclude that excess IL-1ß production and cell death may contribute to neuronal dysfunction and cognitive impairment associated with TBI.

Traumatic brain injury induced matrix metalloproteinase2 cleaves CXCL12α (stromal cell derived factor 1α) and causes neurodegeneration.

Traumatic brain injury (TBI), even at mild levels, can activate matrix metalloproteinases (MMPs) and the induction of neuroinflammation that can result in blood brain barrier breakdown and neurodegeneration. MMP2 has a significant role in neuroinflammation and neurodegeneration by modulating the chemokine CXCL12α (stromal cell derived factor SDF-1α) signaling pathway and the induction of apoptosis. SDF-1α is responsible for cell proliferation and differentiation throughout the nervous system and is also implicated in various neurodegenerative illnesses. We hypothesized that TBI leads to MMP2 activation and cleavage of the N-terminal 4 amino acid residues of CXCL12α with generation of the highly neurotoxic fragment SDF-1(5-67). Using an in vitro stretch-injury model of rat neuronal cultures and the in vivo fluid percussion injury (FPI) model in rats, we found that oxidative stress has a significant role in the activation of MMP2. This is initiated by the induction of free radical generating enzyme NADPH oxidase 1 (NOX1). Induction of NOX1 correlated well with the signatures of oxidative stress marker, 4HNE in the injured neuronal cultures and cerebral cortex of rats. Further, using MMP2 siRNA and pharmacological MMP2 inhibitor, ARP100, we established the neurodegenerative role of MMP2 in cleaving SDF-1α to a neurotoxic fragment SDF-1(5-67). By immunofluorescence, western blotting and TUNEL experiments, we show the cleaved form of SDF leads to apoptotic cell death in neurons. This work identifies a new potential therapeutic target to reduce the complications of brain damage in TBI.

Particle deposition in a peri-urban Mediterranean forest.

Urban and peri-urban forests provide a multitude of Ecosystem Services to the citizens. While the capacity of removing carbon dioxide and gaseous compounds from the atmosphere has been tested, their capacity to sequestrate particles (PM) has been poorly investigated. Mediterranean forest ecosystems are often located nearby or inside large urban areas. This is the case of the city of Rome, Italy, which hosts several urban parks and is surrounded by forested areas. In particular, the Presidential Estate of Castelporziano is a 6000 ha forested area located between the Tyrrhenian coast and the city (25 km downtown of Rome). Under the hypothesis that forests can ameliorate air quality thanks to particle deposition, we measured fluxes of PM1, 2.5 and 10 with fast optical sensors and eddy covariance technique. We found that PM1 is mainly deposited during the central hours of the day, while negligible fluxes were observed for PM 2.5 and 10. A Hybrid Single-Particle Lagrangian Integrated Trajectory model (HYSPLIT v4) simulated PM emission from traffic areas in the city of Rome and showed that a significant portion of PM is removed by vegetation in the days when the plume trajectory meets the urban forest.

Many-Body Perturbation Theory Extended to the Quantum Mechanics/Molecular Mechanics Approach: Application to Indole in Water Solution.

Optical properties of aromatic chromophores are used to probe complex biological processes, yet how the environment tunes their optical properties is far from being fully understood. Here we present a method to calculate such properties on large-scale systems, like biologically relevant molecules in aqueous solution. Our approach is based on many-body perturbation theory combined with a quantum mechanics/molecular mechanics (QM/MM) approach. We include quasiparticle and excitonic effects for the calculation of optical absorption spectra in a QM/MM scheme. We apply this scheme, together with the well-established TDDFT approach, to indole in water solution. Our calculations show that the solvent induces a red shift in the main spectral peak of indole, in quantitative agreement with the experiments, and they point to the relevance of both the electrostatic and geometrical origin of the shift.

Electronic structure of surface-supported bis(phthalocyaninato) terbium(III) single molecular magnets.

The electronic structure of isolated bis(phthalocyaninato) terbium(III) molecules, a novel single-molecular-magnet (SMM), supported on the Cu(111) surface has been characterized by density functional theory and scanning tunneling spectroscopy. These studies reveal that the interaction with the metal surface preserves both the molecular structure and the large spin magnetic moment of the metal center. The 4f electron states are not perturbed by the adsorption while a strong molecular/metal interaction can induce the suppression of the minor spin contribution delocalized over the molecular ligands. The calculations show that the inherent spin magnetic moment of the molecule is only weakly affected by the interaction with the surface and suggest that the SMM character might be preserved.