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222 results for “photosynthesis”
Continued adaptation of C4 photosynthesis after an initial burst of changes in the Andropogoneae grasses
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Data from: Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution
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Data from: Low photosynthesis of treeline white spruce is associated with limited soil nitrogen availability in the Western Brooks Range, Alaska
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Data from: The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages
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Table of C4 model equations used to explore the effect of irradiance, CO2 and temperature on C4 photosynthesis
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Elevated CO2 alleviates adverse effects of drought on plant water relations and photosynthesis: a global meta-analysis
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Data for Drought-Net rainfall shelters did not cause non-drought effects on photosynthesis for California central coast plants.
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Leaf net photosynthesis in CO2 x N x water treatment combinations:BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Data from: In silico study of the role of cell growth factors in photosynthesis using a virtual leaf tissue generator coupled to a microscale photosynthesis gas exchange model
Computational tools that allow in silico analysis of the role of cell growth and division on photosynthesis are scarce. We present a freely available tool that combines a virtual leaf tissue generator and a two-dimensional microscale model of gas transport during C3 photosynthesis. A total of 270 mesophyll geometries were generated with varying degree of growth anisotropy, growth extent and extent of schizogenous airspace formation in the palisade mesophyll. The anatomical properties of the virtual leaf tissue and microscopic cross sections of actual leaf tissue of tomato (Solanum lycopersicum L.) were statistically compared. Model equations for transport of CO2 in the liquid phase of the leaf tissue were discretized over the geometries. The virtual leaf tissue generator produced a leaf anatomy of tomato that was statistically similar to real tomato leaf tissue. The response of photosynthesis to intercellular CO2 predicted by a model that used the virtual leaf tissue geometry compared well with measured values. The results indicate that the light-saturated rate of photosynthesis was influenced by interactive effects of extent and directionality of cell growth and degree of airspace formation through the exposed surface of mesophyll per leaf area. The tool could be used further in investigations of improving photosynthesis and gas exchange in relation to cell growth and leaf anatomy.
Data from: Altered leaf elemental composition with climate change is linked to reductions in photosynthesis, growth and survival in a semiarid shrubland
Climate change will increase heat and drought stress in many dryland areas, which could reduce soil nutrient availability for plants and aggravate nutrient limitation of primary productivity. Any negative impacts of climate change on foliar nutrient contents would be expected to negatively affect the photosynthetic capacity, water use efficiency and overall fitness of dryland vegetation. We conducted a four-year manipulative experiment using open top chambers and rainout shelters to assess the impacts of warming (~2ºC, W), rainfall reduction (~30%, RR) and their combination (W+RR) on the nutrient status and ecophysiological performance of six native shrub species of contrasting phylogeny in a semiarid ecosystem. Leaf nutrient status and gas exchange were assessed yearly, whereas biomass production and survival were measured at the end of the study. Warming (W and W+RR) advanced shoot growth phenology and reduced foliar macro- (N, P, K) and micronutrient (Cu, Fe, Zn) concentrations (by 8-18% and 14-56%, respectively), net photosynthetic rate (32%), aboveground biomass production (28-39%) and survival (23-46%). Decreased photosynthesis and growth in W and W+RR plants was primarily linked to enhanced nutritional constraints on carbon fixation. Poor leaf nutrient status in W and W+RR plants partly decoupled carbon assimilation from water flux and led to drastic reductions in water use efficiency (WUEi; ~41%) across species. The RR treatment moderately decreased foliar macro- and micronutrients (6-17%, except for Zn) and biomass production (22%). The interactive impacts of warming and rainfall reduction (W+RR treatment) on plant performance were generally smaller than expected from additive single‐factor effects. Synthesis: Large decreases in plant nutrient pool size and productivity combined with increased mortality during hotter droughts will reduce vegetation cover and nutrient retention capacity, thereby disrupting biogeochemical processes and accelerating dryland degradation with impending climate change. Increased macro- and micronutrient co-limitation of photosynthesis with forecasted climate change conditions may offset any gains in WUEi and productivity derived from anthropogenic CO2 elevation, thereby increasing dryland vegetation vulnerability to drought stress in a warmer and drier climate. The generalized reduction in leaf nutrient contents with warming compromises plant nutritional quality for herbivores, with potential cascading negative effects across trophic levels.
Data from: The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria
C4 photosynthesis represents a most remarkable case of convergent evolution of a complex trait, which includes the reprogramming of the expression patterns of thousands of genes. Anatomical, physiological, and phylogenetic and analyses as well as computational modeling indicate that the establishment of a photorespiratory carbon pump (termed C2 photosynthesis) is a prerequisite for the evolution of C4. However, a mechanistic model explaining the tight connection between the evolution of C4 and C2 photosynthesis is currently lacking. Here we address this question through comparative transcriptomic and biochemical analyses of closely related C3, C3-C4, and C4 species, combined with Flux Balance Analysis constrained through a mechanistic model of carbon fixation. We show that C2 photosynthesis creates a misbalance in nitrogen metabolism between bundle sheath and mesophyll cells. Rebalancing nitrogen metabolism requires anaplerotic reactions that resemble at least parts of a basic C4 cycle. Our findings thus show how C2 photosynthesis represents a pre-adaptation for the C4 system, where the evolution of the C2 system establishes important C4 components as a side effect.
Data from: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave
Background: Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. However, the genomic basis of evolutionary innovation of CAM in genus Agave is largely unknown. Results: Using an approach that integrated genomics, gene co-expression networks, comparative genomics and protein structure analyses, we investigated the molecular evolution of CAM as exemplified in Agave. Comparative genomics analyses among C3, C4 and CAM species revealed that core metabolic components required for CAM have ancient genomic origins traceable to non-vascular plants while regulatory proteins required for diel re-programming of metabolism have a more recent origin shared among C3, C4 and CAM species. We showed that accelerated evolution of key functional domains in proteins responsible for primary metabolism and signaling, together with a diel re-programming of the transcription of genes involved in carbon fixation, carbohydrate processing, redox homeostasis, and circadian control is required for the evolution of CAM in Agave. Furthermore, we highlighted the potential candidates contributing to the adaptation of CAM functional modules. Conclusions: This work provides evidence of adaptive evolution of CAM related pathways. We showed that the core metabolic components required for CAM are shared by non-vascular plants, but regulatory proteins involved in re-reprogramming of carbon fixation and metabolite transportation appear more recently. We propose that the accelerated evolution of key proteins together with a diel re-programming of gene expression were required for CAM evolution from C3 ancestors in Agave.
Data from: Phylogeny and photosynthesis of the grass tribe Paniceae
PREMISE OF THE STUDY: The grass tribe Paniceae includes important food, forage, and bioenergy crops such as switchgrass, napiergrass, various millet species, and economically important weeds. Paniceae are also valuable for answering scientific and evolutionary questions about C4 photosynthetic evolution, drought tolerance, and spikelet variation. However, the phylogeny of the tribe remains incompletely resolved. METHODS: Forty-five taxa were selected from across the tribe Paniceae and outgroups for genome survey sequencing (GSS). These data were used to build a phylogenetic tree of the Paniceae based on 102 markers (78 chloroplast, 22 mitochondrial, 2 nrDNA). Ancestral state reconstruction analyses were also performed within the Paniceae using both the traditional and two subtype classification systems to test hypotheses of C4 subtype evolution. KEY RESULTS: The phylogenetic tree resolves many areas of the Paniceae with high support and provides insight into the origin and number of C4 evolution events within the tribe. The recovered phylogeny and ancestral state reconstructions support between four and seven independent origins of C4 photosynthesis within the tribe and indicate which species are potentially the closest C3 sister taxa of each of these events. CONCLUSIONS: Although the sequence of evolutionary events that produced multiple C4 subtypes within the Paniceae remains undetermined, the results presented here are consistent with only a subset of currently proposed models. The species used in this study constitute a panel of C3 and C4 grasses that are suitable for further studies on C4 photosynthesis, bioenergy, food and forage crops, and various developmental features of the Paniceae.
UFLUX 100m daily photosynthesis fluxes in northeastern UK 2022
<h3>UFLUX Ensemble UK100mdaily (UK 100 Daily) in northeastern UK 2022</h3> <p><strong>Overview</strong><br>The <strong>UFLUX ensemble dataset</strong> offers <strong>European fluxes at 100 m spatial resolution</strong>, generated using<strong> machine learning models</strong>. It integrates <strong>satellite-based Sentinel-1 backscatters and Sentinel-2 vegetation proxies NIRv</strong> with <strong>ERA5 climate reanalysis</strong>, and is trained against <strong>ICOS eddy covariance observations</strong>. It includes five core flux components:</p> <ul> <li> <p>Gross Primary Production (<strong>GPP</strong>) [<em>open access</em>]</p> </li> <li> <p>Ecosystem Respiration (<strong>RECO</strong>) [<em>in progress</em>]</p> </li> <li> <p>Net Ecosystem Exchange (<strong>NEE</strong>) [<em>in progress</em>]</p> </li> <li> <p>Sensible Heat Flux (<strong>H</strong>) [<em>in progress</em>]</p> </li> <li> <p>Latent Energy Flux (<strong>LE</strong>) [<em>in progress</em>]</p> </li> </ul> <p><strong>Background and Methodology</strong><br>The <strong>Unified FLUXes (UFLUX)</strong> initiative is a data-driven, machine learning-based platform designed to upscale eddy covariance (EC) flux measurements from tower sites to the global scale. It aims to answer pressing questions about how effectively terrestrial ecosystems are managed under climate change.</p> <p>Key innovations of UFLUX include:</p> <ol> <li> <p><strong>Consistent Upscaling Framework</strong>: Harmonizes flux upscaling across spatial/temporal scales and multiple flux types (GPP, RECO, etc.) using deep decision tree-based methods, better suited than conventional neural networks for EC flux data.</p> </li> <li> <p><strong>Hybrid Explainable ML</strong>: Combines black-box ML with ecological interpretability through residual learning, offering both predictive power and new scientific insight (UFLUXv2).</p> </li> <li> <p><strong>Uncertainty Quantification</strong>: Employs sampling space completeness to assess model uncertainty in a transparent, robust manner.</p> </li> <li> <p><strong>Multisource Integration</strong>: Leverages complementary strengths of vegetation proxies (e.g., NIRv, SIF) and climate data (e.g., ERA5) to represent carbon dynamics more comprehensively than single-source approaches.</p> </li> <li> <p><strong>Superior Gap-Filling</strong>: Originally developed as a global EC flux gap-filling tool, UFLUX improves accuracy by up to 30% and reduces uncertainty by as much as 70% compared to traditional methods.</p> </li> <li> <p><strong>High Performance</strong>: Achieves strong predictive accuracy, with global-scale R² > 0.8 for RECO and ≈0.9 for GPP, while being computationally efficient enough to run on a standard laptop.</p> </li> <li> <p><strong>Community Adoption</strong>: Already used by other global upscaling projects, highlighting its reliability and impact.</p> </li> </ol> <p><strong>Applications</strong><br>UFLUX is ideal for studying the interactions between land management, climate change, and carbon fluxes, particularly in improving global estimates of GPP and RECO by addressing biases in EC measurements.</p> <p><strong>Resources</strong></p> <ul> <li><strong>UFLUX Website: <a href="https://github.com/soonyenju/uflux" target="_new" rel="noopener">https://sites.google.com/view/uflux</a></strong></li> <li> <p><strong>Code Repository</strong>: <a href="https://github.com/soonyenju/uflux" target="_new" rel="noopener">https://github.com/soonyenju/uflux</a></p> </li> <li> <p><strong>Technical & Descriptive Publication</strong>: <a href="https://doi.org/10.1080/01431161.2024.2312266" target="_new" rel="noopener">https://doi.org/10.1080/01431161.2024.2312266</a></p> </li> </ul>
"Contrasting responses to increasing dissolved iron on photosynthesis and O2 availability in the gastric cavity of two Mediterranean corals." Dataset
<p>Dataset of iron levels, coral metabolic rates, PAM, Oxygen microprofiles </p>
Data supporting "Aerobic methane production in Scots pine shoots is independent of drought or photosynthesis"
<p>Data supporting our New Phytologist publication "Aerobic methane production in Scots pine shoots is independent of drought or photosynthesis"</p>
Ultrafast Charge Dynamics in Nitrogen-Rich Covalent Organic Frameworks for Hydrogen Peroxide Photosynthesis
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Photosynthesis Capacity of Isodon rubescens (Hemsley) H. Hara Leaves at different Leaf Positions
<p>The paraffin section of I. rubescens stem peeled due to ice ribbons</p>
Effects of pH/pCO2 fluctuation on photosynthesis and fatty acid composition of two marine diatoms
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Novel representation of leaf phenology improves simulation of Amazonian evergreen forest photosynthesis in a land surface model
<p>This dataset contains the LAI, Litterfall and GPP etc. of the four Amazon FLUX sites (BR-Sa1, BR-Sa3, BR-Ma2 and GF-Guy) simulated using the improved ORCHIDEE model and the corresponding FLUXNET eddy-covariance or ground-measured data. The more detial please the ReadMe.pdf in the zip.</p> <p>Data is organized with netCDF4(.nc).</p> <p><br> If you want to know more detail please contact: chenxzh73@mail.sysu.edu.cn</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.