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865 results for “germination”
Subalpine tree seed availability and germination at Niwot Ridge, 2015 - ongoing.
These data were collected to assess how seed availability and site limitations affect conifer germination across species distributions. Our study focused on areas above alpine treeline where subalpine tree species must migrate to track movement of suitable climate, but we also included sites in the core and at the lower ecotone of subalpine forests. We monitored seed availability and germination of new seedlings for four subalpine tree species from 2015-present at Niwot Ridge, Colorado, USA. Seed availability was collected in 66-95 seed traps in 14-17 sites (6-12 traps per site; see data for count per site), depending on year. In the lab, seeds were counted by species. In the field, new germinants were counted by species 3-5 weeks after snow disappearance (i.e., peak germination) and again in late September from 2015 to 2018 only. Only one census of new germinants was conducted from 2019 to 2023. New germinants from prior years were censused in subsequent summers.
Tree regeneration after fire: Effects of burn severity, seedling germination analysis
This study examines the effects of burn severity on patterns of post-fire tree establishment in the boreal forest. We collected data from 5 separate field experiments examining seedling establishment across different severity levels in 4 burns in central Yukon Territory, Canada, and interior Alaska, USA. The experimental studies focus on the germination, survival, and growth responses of four common tree species, trembling aspen (Populus tremuloides), lodgepole pine (Pinus contorta), white spruce (Picea glauca) and black spruce (Picea mariana). Data on the soil organic layer (depth, moisture, bulk density, pH) were also collected at each site. This file contains data on seedlings that germinated in the severity plots, for seeded and un-seeded (control) subplots. Data from the control subplots has been standardized by area (seedlings/subplot, where the subplot area=0.28 m2), and could be used to estimate natural rates of seedling establishment. Control values are the same for black and white spruce, as these species could not be distinguished.
Tree regeneration after fire: Effects of burn severity, germinated seedlings analysis
This study examines the effects of burn severity on patterns of post-fire tree establishment in the boreal forest. We collected data from 5 separate field experiments examining seedling establishment across different severity levels in 4 burns in central Yukon Territory, Canada, and interior Alaska, USA. The experimental studies focus on the germination, survival, and growth responses of four common tree species, trembling aspen (Populus tremuloides), lodgepole pine (Pinus contorta), white spruce (Picea glauca) and black spruce (Picea mariana). Data on the soil organic layer (depth, moisture, bulk density, pH) were also collected at each site. This file contains data on total aboveground dry biomass of germinated seedlings harvested in late August, 2002. Seedlings are separated into those found in seeded subplots (target), non-seeded control plots (ctl), or partially-seeded control plots (seed-ctl, where plots were seeded in Sept 2000 but not June 2000). Cohorts indicate the year in which the seedlings were first observed. All seedlings of a species*cohort within a subplot were weighed together, and the average weight/seedling calculated. Note that a plot entry is included in the file only where a seedling was present.
Germination and early establishment of dryland grasses and shrubs on wind-eroded soils from the Jornada Basin LTER Scrape site, 2018-2019
In this dataset, we report germination and seedling growth of contrasting perennial grass (Bouteloua eriopoda, Sporobolus airoides, and Aristida purpurea) and shrub (Prosopis glandulosa, Atriplex canescens, and Larrea tridentata) functional groups grown on non-winnowed and winnowed soils collected from the Jornada Basin LTER Scrape Site at the Jornada Experimental Range (JER) in southern New Mexico, U.S.A. The soil physical and chemical properties of winnowed and non-winnowed soils were evaluated, and soil water retention curves were obtained for the two soil types. A controlled pot experiment was conducted under the well-watered greenhouse conditions at the University of Arizona campus, Tucson, AZ in 2018 and 2019 to test if topsoil "winnowing" by wind erosion would differentially affect grass and shrub seedling establishment to promote shrub recruitment over that of grass. Data include soil water retention curves, soil chemistry, nutrients, and texture, seedling germination, and seedling growth and biomass. This study is complete and the data are published in the article below. Niu, F., Pierce, N. A., Archer, S. R., & Okin, G. S. (2021). Germination and early establishment of dryland grasses and shrubs on intact and wind-eroded soils under greenhouse conditions. Plant and Soil, 1-16. DOI: 10.1007/s11104-021-05005-9
Germination in three R/FR light environments (El Verde)
Experiments were conducted in the Tabonuco forest at Luquillo Experimental Forest to determine the germination success of a number of species in different light environments. Species tested included: Byrsonima spicata, Calophyllum brasiliense, Carapa sp., Choven venosa, Guarea guidonia, Manilkara bidentata, Ochroma pyramidale and an unidentified species known locally as Jobo. Seeds were collected as they fell and placed on moist towling in horticulture trays at four sites. Seeds were kept moist and germination was recorded daily for 81 days and three times weekly for an additional 75 days. Light environments included a site exposed to full sun (FS) and sites with 55%, 75% and 80% cover. Instantaneous light measurements were made with a Licor 1800 spectroradiometer to determine the Red (660 nm) to Far-red (730 nm) ratio (R/FR) (Lee, 1987). Analysis of light data indicated that the four sites chosen provided three significantly different R/FR ratio environments, and that germination of some species was affected by the light environment (Smith, H. & Whitelam, G.C. 1990). Three species failed to germinate in any of the four light environments. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Code and data for SylvanSeeds, a seed germination database for temperate deciduous forests
<p>This is a version of record of the manuscript's data and code as accepted by the Journal of Vegetation Science.</p>
Changes in gene expression during germination reveal pea genotypes with either 'quiescence' or 'escape' mechanisms of waterlogging tolerance
<p>Waterlogging causes germination failure in pea (<em>Pisum sativum</em> L.). Three genotypes (BM-3, NL-2 and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Among the most differentially regulated genes, upregulated gene tyrosine protein kinase responsible for metabolic regulation and downregulated LOX5 involved in fat metabolism indicated energy preservation in tolerant Kaspa, while in the other tolerant NL-2 subtilase family protein and PNC2 involved in protein and fat metabolism respectively showed upregulated expression suggesting energy utilization during waterlogging. By contrast, in sensitive genotype BM-3 high upregulation was recorded for the kunitz-type trypsin/protease inhibitor whose role is blocking the activity of protein metabolism leading to excessive lipid metabolism causing membrane leakage and subsequent seed damage. Pathway analyses based on gene ontologies showed seed storage protein metabolism as upregulated in tolerant genotypes and downregulated in the sensitive genotype. Understanding the tolerance mechanism provides a platform to breed for adaptation to waterlogging stress at germination in pea. </p>
Changes in gene expression during germination reveal pea genotypes with either 'quiescence' or 'escape' mechanisms of waterlogging tolerance
<p>Waterlogging causes germination failure in pea (<em>Pisum sativum</em> L.). Three genotypes (BM-3, NL-2 and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Among the most differentially regulated genes, upregulated gene tyrosine protein kinase responsible for metabolic regulation and downregulated LOX5 involved in fat metabolism indicated energy preservation in tolerant Kaspa, while in the other tolerant NL-2 subtilase family protein and PNC2 involved in protein and fat metabolism respectively showed upregulated expression suggesting energy utilization during waterlogging. By contrast, in sensitive genotype BM-3 high upregulation was recorded for the kunitz-type trypsin/protease inhibitor whose role is blocking the activity of protein metabolism leading to excessive lipid metabolism causing membrane leakage and subsequent seed damage. Pathway analyses based on gene ontologies showed seed storage protein metabolism as upregulated in tolerant genotypes and downregulated in the sensitive genotype. Understanding the tolerance mechanism provides a platform to breed for adaptation to waterlogging stress at germination in pea. </p>
SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses
<p>These are the<strong> processed</strong> BCR repertoire bulk sequencing data described in <a href="https://doi.org/10.1038/s41586-021-03738-2">Turner & O'Halloran et al., Nature, 2021</a> (Fig 3b-d; Extended Data Fig 3; Extended Data Table 6). The corresponding <strong>raw</strong> sequencing reads are available on SRA under <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA731610">BioProject PRJNA731610</a>.</p> <p><strong>Summary</strong>: Bulk-sorted total plasmablasts from PBMCs and germinal centre B cells at 4 weeks after primary immunization from 3 vaccinees who had no prior history of infection with SARS-CoV-2. </p> <p><strong>Code: </strong>Code along with Docker container for reproducing the NGS data-based figures and analyses in the published paper can be <a href="https://github.com/julianqz/wustl_published/tree/main/nature_2021">found on GitHub</a>.</p> <p><strong>Metadata file</strong>: WU368_turner_et_al_nature_2021_meta.tsv</p> <p>Abbreviations:</p> <ul> <li>LN = lymph node</li> <li>PB = plasmablast</li> <li>GC = germinal centre</li> <li>mAb = monoclonal antibody</li> </ul> <p><strong>BCR data file</strong>: WU368_turner_et_al_nature_2021_bcr.tsv.gz</p> <p>In addition to the processed bulk sequences, also included are the heavy chains of 37 mAbs that had been validated to be spike-binding and that were used together with the bulk sequences for clonal lineage inference. The mAbs are annotated as "mab" in the "seq_type" column.</p> <p><strong>BCR data column descriptions</strong></p> <p>The columns largely follow the <a href="https://changeo.readthedocs.io/en/stable/standard.html">AIRR-C Rearrangement format</a>. The main deviation is that CDR3s are used, as opposed to IMGT-defined "junctions". Non-standard columns are noted below.</p> <ul> <li>v_call_genotyped: V gene annotation reassigned after individualized genotyping by <a href="https://tigger.readthedocs.io/en/stable/">TIgGER</a></li> <li>germline_[vdj]_call: clonal consensus germline sequence reconstructed via <a href="https://changeo.readthedocs.io/en/stable/methods/germlines.html">`CreateGermlines.py --cloned` using Change-O</a></li> <li>isotype: IGH[ADEGM]</li> <li>cdr3: CDR3 nucleotide sequence</li> <li>cdr3_length: CDR3 nucleotide sequence length</li> <li>cdr3_aa: CDR3 amino acid sequence</li> <li>collapse_count: number of duplicate IMGT-aligned V(D)J sequences that were collapsed by <a href="https://alakazam.readthedocs.io/en/stable/topics/collapseDuplicates/">`alakazam::collapseDuplicates`</a></li> <li>donor: vaccinee</li> <li>sample: sample ID (arbitrary)</li> <li>timepoint: time point at which sample was collected</li> <li>tissue: tissue from which sample was collected</li> <li>sorting: FACS sorting</li> <li>seq_type: sequence type (mAb or bulk)</li> <li>nuc_RS_19_312: number of replacement and silent mutations between IMGT-numbered nucleotide positions 19-312 along IGHV sequences, calculated by <a href="https://shazam.readthedocs.io/en/stable/topics/calcObservedMutations/">`shazam::calcObservedMutations`</a></li> <li>nuc_denom_19_312: number of informative nucleotide positions for counting mutations, excluding non-A/T/G/C positions (such as "N", "-", ".")</li> <li>nuc_RS_freq_19_312: nucleotide-level mutation frequency (= nuc_RS_19_312 / nuc_denom_19_312)</li> </ul>
Germination of crop species in response to whole-soil inoculants that originate from conventional vs organic farming systems
<p>Dataset of manuscript entitled “Germination of crop species in response to whole-soil inoculants that originate from conventional vs organic farming systems”. This manuscript includes the results of WP2 from the SOFT project (ref. 890874).</p>
Tree seedling germination, precipitation index, and SWE data for subalpine forest, 1940-2010
Annual germination dates for over 450 Engelmann spruce and over 500 subalpine fir seedlings collected across a complex topographic-moisture gradient were compared to climate variability in the Colorado Front Range. This dataset contains the SPEI (standardized-evaporation precipitation index) and snow-water equivalent (SWE) data from 1940 to 2010 used in the study as well as the number of seedlings establishing each year from 1940 to 2010 by species.
Alpine plant seed microbiomes, germination, and plant-soil feedbacks, Niwot Ridge and Green Lakes Valley, 2018.
Seed and soil microbiomes strongly affect plant performance, and these effects can scale-up to influence plant community structure. However, seed and soil microbial community composition are variable across landscapes, and different microbial communities can differentially influence multiple plant metrics (biomass, germination rate), and community stabilizing mechanisms. We measured how microbiomes inside seeds and in soils varied among alpine plant species and communities that differed in plant species richness and density. Across 10 common alpine plant species, we found a total of 318 bacterial and 128 fungal operational taxonomic units (OTUs) associated with seeds, with fungal richness affected by plant species identity more than sampling location. However, seed microbes had only marginally significant effects on plant germination success and timing. In contrast, soil microbes associated with two different plant species had significant effects on plant biomass, and their effect depended both on the plant species and the location the soils were sampled from.
Data from: Annual species' experimental germination responses to light and temperature do not correspond with their microhabitat associations in the field
<p>Annual species have evolved sets of germination cues that are thought to be predictive of the post-germination environment. In naturally patchy environments, germination microsites often vary considerably in the amount of light they receive and in the diurnal temperature fluctuations they experience. However, whether species' differential germination responses to light and temperature are associated with their spatial patterns of occurrence remains largely untested.</p> <p>We surveyed species' occurrences in annual plant communities in 150 quadrats across gradients of canopy cover and litter cover. Nineteen species recorded in this survey were then included in a germination experiment that manipulated (1) Light vs. Dark (12h light or continuous dark) approximating seeds near the soil surface versus those covered by litter and (2) Cold vs. Warm temperature regimes (7/18 °C and 7/24 °C) approximating diurnal fluctuations experienced in shaded versus sun-exposed microsites, respectively.</p> <p>In the germination experiment, six species had highest germination probabilities in the Light treatment (regardless of temperature), five in <em>Cold</em> + <em>Light</em>, one in <em>Warm</em> + <em>Light</em>, two were indifferent to the treatments, and four did not germinate at all. Binomial linear mixed-effects models showed that species' maximum responses to light and temperature did not explain their spatial distributions along canopy cover and litter cover gradients, contrary to theoretical expectations of germination being a strong driver of species' occurrences.</p> <p>Despite variation in species' responses to experimental treatments, no association was found with their field microsite associations. Germination strategies in our system were wider than expected for Mediterranean systems. Our results support that germination cues are not strong drivers of microhabitat associations in this system.</p>
Fig. 2 in Effect of the seed maturation stage and pre-germination treatments on emergence of Erythrina crista-galli L.
Fig. 2 TC, T1-T5. Seedling emergency (E%) in relation to the number of days after sowing (DAS). TC. control; T1. sanded and soaked in water for 48 h; T2. sanded and soaked in water for 24 h; T3. soaked in water outside of heating at the initial temperature of 60 °C until reaching ambient temperature; T4. only sanded; T5. immature seeds.
Figs. 1A-E in Germination and acclimatization of Melocactus sergipensis Taylor & Meiado
Figs. 1A-E. Development of the morphology of Melocactus sergipensis seedlings. A. Micropillary hilum region (MH); B. Hypocotyl (Hyp), Integument (Int) and Primordial radicle (Prad); C. Hilum (H), Cotyledon (Cot) and hypocotyl (Hyp); D. Areola (Are) and Trichoma (Ti); E. Cotyledon (Cot), Epicotyl (Ep), Hypocotyl (Hyp), Root (Rad). Source: Bravo Filho (2016). Bars: Figs. 1A-D = 1mm; Fig. 1E = 1 cm.
Fig. 1 in Effect of the seed maturation stage and pre-germination treatments on emergence of Erythrina crista-galli L.
Fig. 1 TC, T1-T5. Erythrina crista-galli. Seeds in different maturation stages and submitted to pre-germination treatments. TC. control; T1. sanded (seeds subjected to abrasion with 60-grit sandpaper, on the opposite side of the hilum) and soaked in water for 48 h; T2. sanded and soaked in water for 24 h; T3. soaked in water outside of heating at the initial temperature of 60 °C until reaching ambient temperature; T4. only sanded; T5. immature seeds.
Fig. 3 in Asymbiotic germination, multiplication and development of Alatiglossum fuscopetalum (Orchidaceae) as affected by culture medium, sucrose and growth regulators
Fig. 3. Growth index of Alatiglossum fuscopetalum on Murashige and Skoog (MS and ½MS), Knudson (KN), and Vacin and Went (VW) media, 90 days after the onset of seed germination. Histobars with the same letters are not significantly different according to the Tukey's test at the 5% probability level.
Fig. 2 in Asymbiotic germination, multiplication and development of Alatiglossum fuscopetalum (Orchidaceae) as affected by culture medium, sucrose and growth regulators
Fig. 2. Germination percentages of Alatiglossum fuscopetalum seeds on Murashige and Skoog (MS and ½MS), Knudson (KN), and Vacin and Went (VW) media. Histobars with the same letters are not significantly different according to the Tukey's test at the 5% probability level.
Figs. 1 A-D in Asymbiotic germination, multiplication and development of Alatiglossum fuscopetalum (Orchidaceae) as affected by culture medium, sucrose and growth regulators
Figs. 1 A-D. Protocorm developmental stages of Alatiglossum fuscopetalum from seed germination in vitro. A. Stage 1 swollen green embryos (protocorm phase); B. Stage 2 protocorm bearing one leaf; C. Stage 3 protocorm bearing two leaves; D. Stage 4 protocorm with leaves and one root (seedling stage). Bars = 1 mm.
Fig. 6 in Immediate Allelopathic Effect Of Two Invasive Heracleum Species On Acceptor-Germination
Fig. 6. CCU content accordingly ryegrass germination in leachates of H. sosnovskyi and H. mantegazzianum (p<0,05; mean±SE).
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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.
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DANDI Archive for NWB datasets
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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
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