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173 results for “plant organs”
Quantitative and qualitative aspects of dissolved organic carbon leached from plant biomass in Taylor Slough, Shark River and Florida Bay (FCE) for samples collected in July 2004
Plant biomass was collected from Taylor Slough, Shark River and Florida Bay in Everglades National Park. Samples were taken to the lab and incubated with Milli-Q water in the dark for a period of 36 days. NaN3 was added to half the bottles to test the role of microbial activity on the leaching rates and composition of leachate. Every three days the water was decanted and replaced with fresh Milli-Q water. The decanted samples were filtered and analyzed for DOC concentration, sugar content, and total phenol content.
Soil organic matter and plant carbon allocated to nitrogen acquisition simulated by the FUN-BioCROP model
<p>This data package contains the model input, results, and validation data from Juice et al (citation below). The FUN-BioCROP model (Fixation and Uptake of Nitrogen- Bioenergy Carbon, Rhizosphere, Organisms, and Protection) advances the field of bioenergy modeling by integrating new empirical paradigms of the role of belowground processes in shaping coupled carbon (C) and nitrogen (N) cycles. It was developed by modifying the FUN-CORPSE model (Fixation and Uptake of Nitrogen- Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment, Sulman et al. 2017 Ecology Letters) for use in bioenergy systems by including mechanistic tillage, organic matter addition, nitrogen fertilization, harvest, and feedstock-specific parameters, and to be driven by DayCent plant productivity and biomass data.</p>
Nicotiana benthamiana as a model organism for plant biology study
<p><em>Nicotiana benthamiana</em> is an amenable model organism for plant biology study. Several functional genomics tools, including viral vectors, RNAi, ethylmethanesulfonate (EMS) mutagenesis, CRISPR-mediated genome editing, and agroinfiltration, are available in the <em>N. benthamiana</em> experimental system. These tools can be applied to research in genomics, biochemistry, metabolomics, cell biology and pathology as well as other topics in plant biology.</p> <p>*This is an updated graphical abstract for commnetary article "Dude, where is my mutant? <em>Nicotiana benthamiana</em> meets forward genetics" (Derevnina et al., 2019, New Phytologist 221(2):607-610).</p>
Measurement of Fuel load (organic biomass) Quantities of Organic Soils, Understory Plants and Trees at Sites within the Bonanza Creek LTER Regional Site Network in Interior Alaska, 2019
This dataset contains fuel load measurements for a subset of the BNZ LTER's RSN sites (n = 28). The data for each site separted by 16 fuel types (or plant functional types) including organic soil layers (fibric, mesic), vascular understory (evergreen shrub, short deciduous shrub, graminoid, forb, tall deciduous shrub, tree seedling/sapling, dead-downed wood), nonvascular understory (feather moss, Sphagnum moss, colonizer moss, lichen) and trees (evergreen tree, deciduous tree).
Soils Organic Matter: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem
Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.
Fiddler crab impacts from observational study 2020-21: Aboveground & diatom biomass, plant height, percent N, burrow & mussel density, belowground biomass, and organic matter
The fiddler crab, Minuca pugnax, expanded its range into the Gulf of Maine recently and was first observed in the Plum Island Estuary in 2014. In 2020 and 2021, we investigated the impact of this burrowing crab on benthic microalgal biomass, sediment properties and the above- and belowground biomass of the cordgrass, Spartina alterniflora. To accomplish this, we conducted a control-impact study in plots with and without fiddler crabs in three marshes in the PIE-LTER: Sawyer, Clubhead, and Metcalf. In its historical range (i.e., south of Cape Cod), M. pugnax, enhances Spartina aboveground biomass. In contrast, we found that, on average, when fiddler crabs were present, aboveground biomass was 40% lower in the PIE-LTER. We also found that belowground biomass was 30% lower and benthic microalgal biomass was 45% lower when fiddler crabs were present, which is in line with our expectations. Because fiddler crabs reduced the biomass of foundational primary producers in its expanded range, our results imply that M. pugnax can influence other saltmarsh functions such as carbon storage and accretion as they expand north. More broadly, our results suggest that as species expand or shift their range with climate change, not only can they have profound impacts in their new ranges, but that those impacts can be the inverse of what is seen in their historical ranges.
Data for: Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia)
<p>Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4–11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.</p>
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
<p><span>The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen <em>Verticillium dahliae</em>,<em> </em>known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for <em>V. dahliae </em>are also present in other <em>Verticillium</em> species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the <em>Verticillium</em> genus.</span></p>
scmcclelland/joint-mediation-study: Data, Analysis, and Figure Scripts for "Soil organic carbon sequestration jointly-mediated by plants and microbes after compost application"
<p>This repository contains data, analysis, and figure scripts to create findings from the manuscript "Soil organic carbon sequestration jointly-mediated by plants and microbes after compost application" currently under minor revisions.</p> <p>This release includes updated code, primarily improvements to figures, and a new script for a supplementary map figure.</p>
Data from: Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both
<p>Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ~1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae —primarily the oaks (genus <em>Quercus</em>; ~435 sp). The association of oak gall wasps with oaks is ancient (~50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified the strong signal of host plant shifting among oak gall wasps that has been found in other phytophagous insect systems. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich. We collected 86 species of Nearctic oak gall wasps from 10 of the 14 major clades of Nearctic oaks and sequenced >1000 Ultra Conserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic wasp clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Though formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.</p>
Text-fig. 7. Stereomicroscope microphotographs of plant remains sieved out of a sediment bulk sample (C3X) from bed GLA10 of Govone. a: Tetraclinis salicornioides (UNGER) KVAČEK, shoot fragment, MGPT-PU141083). b: Toddalia latisiliquata (R.LUDW.) H.-J. GREGOR, seed, MGPT-PU141084. c: Toddalia rhenana H.-J.GREGOR, seed, MGPT-PU141085. d: Eurya stigmosa (R.LUDW.) MAI, small seed with piths filled by organic remains and sediment, MGPT-PU141086. e: Eurya stigmosa (R.LUDW.) MAI, fragmentary seed, MGPT-PU141087. f: Visnea germanica MENZEL, fruit from two opposite sides, MGPT-PU141088. g: Symplocos casparyi R.LUDW., endocarp in lateral view from two opposite sides, MGPT-PU141089. Scale bar 1 mm. in Remains Of A Subtropical Humid Forest In A Messinian Evaporitebearing Succession At Govone, Northwestern Italy - Preliminary Results
Text-fig. 7. Stereomicroscope microphotographs of plant remains sieved out of a sediment bulk sample (C3X) from bed GLA10 of Govone. a: Tetraclinis salicornioides (UNGER) KVAČEK, shoot fragment, MGPT-PU141083). b: Toddalia latisiliquata (R.LUDW.) H.-J. GREGOR, seed, MGPT-PU141084. c: Toddalia rhenana H.-J.GREGOR, seed, MGPT-PU141085. d: Eurya stigmosa (R.LUDW.) MAI, small seed with piths filled by organic remains and sediment, MGPT-PU141086. e: Eurya stigmosa (R.LUDW.) MAI, fragmentary seed, MGPT-PU141087. f: Visnea germanica MENZEL, fruit from two opposite sides, MGPT-PU141088. g: Symplocos casparyi R.LUDW., endocarp in lateral view from two opposite sides, MGPT-PU141089. Scale bar 1 mm.
Supporting data sets for "Estimating Carbon Fixation of Plant Organs for Afforestation Monitoring using a Process-based Ecosystem Model and Ecophysiological Parameter Optimization". (the survey of tree breast diameter and tree height in 11-year old Eucommia ulmoides plantation, values of simulation results used in figures and tables.)
<p>Supporting data sets for Miyauchi et al., Ecology and Evolution, 2019 (accepted).</p> <p>The files store: </p> <p>(1) The survey of tree breast diameter and tree height in <em>Eucommia ulmoides</em> plantation<em>.</em> The ring and stem analysis and dry weight of seven harvested sample trees in the plantation.</p> <p>(2) Values of optimization result used fig.7.</p> <p>(3) Values of prediction result used fig.8. and table 4.</p> <p>(4) Values of optimized parameters by optimization methods, parameter range and constrain.</p>
Figure 7 in High seeding rates, interrow mowing, and electrocution for weed management in organic no-till planted soybean
Figure 7. Annual, perennial, dicot, and monocot weed biomass in each weed management treatment pooled across fields. Similar letters above bars indicate no significant difference using separate Fisher's LSD tests (P> 0.05). Error bars are standard errors, and treatments are abbreviated: NC, nontreated control; SR, seeding rate; IM, interrow mower; WZ, Weed Zapper™.
Figure 6 in High seeding rates, interrow mowing, and electrocution for weed management in organic no-till planted soybean
Figure 6. Diversity indices of weed communities for all treatments. Weed by species biomass was pooled across fields.Similar letters above bars indicate no significant difference using separate Fisher's LSD tests (P> 0.05).Error bars are standard errors and treatments are abbreviated:NC,nontreated control; SR,seeding rate; IM, interrow mower;WZ,Weed Zapper™.
Figure 5 in High seeding rates, interrow mowing, and electrocution for weed management in organic no-till planted soybean
Figure 5. Weed biomass in each weed management treatment pooled across all site-years.Biomass was sampled in mid-August after all management tactics had been applied. Similar letters above bars indicate no significant difference using Fisher's LSD test (P> 0.05). Error bars are standard errors, and treatments are abbreviated: NC, nontreated control; SR, seeding rate; IM, interrow mower; WZ, Weed Zapper™.
Figure 4 in High seeding rates, interrow mowing, and electrocution for weed management in organic no-till planted soybean
Figure 4. Soybean density in August after all weed management treatments were applied. Data were pooled across all site-years. Similar letters above bars indicate no significant difference using Fisher's LSD test (P> 0.05). Error bars are standard errors, and treatments are abbreviated: NC, nontreated control; SR, seeding rate; IM, interrow mower; WZ, Weed Zapper™.
Figure 8 in High seeding rates, interrow mowing, and electrocution for weed management in organic no-till planted soybean
Figure 8. Soybean yield from each weed management treatment pooled across fields. Yield is dry weight corrected to 13% moisture. Similar letters above bars indicate no significant difference using Fisher's LSD test (P> 0.05). Error bars are standard errors, and treatments are abbreviated: NC, nontreated control; SR, seeding rate; IM, interrow mower; WZ, Weed Zapper™.
Figure 1 in High seeding rates, interrow mowing, and electrocution for weed management in organic no-till planted soybean
Figure 1. The interrow mower used in this experiment, attached to a John DeereṜ 5100R tractor with a three-point hitch. The mower is powered with a hydraulic system and was custom made by IRM X4, R-Tech Industries (Homewood, MB, Canada).
Figure 2. The model 6R30 in High seeding rates, interrow mowing, and electrocution for weed management in organic no-till planted soybean
Figure 2. The model 6R30 Weed Zapper™ used in this experiment. The generator is attached to the back of a John DeereṜ 5100R tractor with a three-point hitch. The 4.6-m electric copper boom is attached to the front of the tractor with a three-point hitch. The Weed Zapper™ was purchased from Old School Manufacturing (Sedalia, MO, USA).
Figure 3 in High seeding rates, interrow mowing, and electrocution for weed management in organic no-till planted soybean
Figure 3. Monthly temperature and precipitation in Aurora, NY, USA, in 2021 and 2022. Pink lines indicate 30-yr average.
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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)
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DANDI Archive for NWB datasets
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OpenNeuro
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