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865 results for “Germination”
Germinal Center and Cultured B cell expression libraries
<p>Comparison of gene expression profiles between in vitro mitogen-activated spleen B lymphocytes and FACS-sorted Germinal Center B lymphocytes isolated from intestinal PeyerPatches of C57BL/6 mice. In order to explore gene expression signatures that may be orchestrating somatic hypermutation (SHM, also known as affinity maturation) during antigen-induced B lymphocyte differentiation in Germinal Centers (GC), we profiled whole transcriptome gene expression of ex vivo, commensal microflora-activated GC B-cells that exhibit efficient SHM, with in vitro activated B-cell blasts, which fail to undergo SHM. In In particular, we examine our hypothesis that differential expression or the DNA endonucleases apex1 and apex2 regulate SHM. Using Templated Oligo Sequencing (TempO-Seq®) in conjunction with conventional intracellular FACS staining and B lymphocyte cell sorting, we compare gene expression profiles of in vitro mitogen-activated (LPS and anti-IgD-dextran), short-term (48h) cultured B cell blasts with Germinal Center B-cells isolated from intestinal Peyer Patches (PP, identified by surface staining B220+, CD95+, GL7+), compared to each other and to naive PP B-cells (B220+, CD95-, GL7-). We find that unique, distinct transcriptional signatures dominate the DNA repair processes in GC B-cells or in vitro B-cell blast, shedding light on genomic processes that orchestrate efficient affinity maturation of B-cells during GC differentiation. We use Templated Oligo Sequencing (TempO-Seq), a RNA motif-specific short tandem Oligo DNA hybridization technique to quantitatively measure whole transcriptome mRNA in conjunction with conventional surface membrane, fixable live/dead discriminator dye, and intracytoplasmic fluorescence antibody staining followed by FACS to isolate B cell populations of interest.</p>
Code, scripts and data for: Seasonality and competition select for variable germination behavior in perennials
<p class="MsoNoSpacing"><span>The occurrence of within-population variation in germination behavior and associated traits such as seed size has long fascinated evolutionary ecologists. In annuals, unpredictable environments are known to select for bet-hedging strategies causing variation in dormancy duration and germination strategies. Variation in germination timing and associated traits is also commonly observed in perennials and often tracks gradients of environmental predictability. Although bet-hedging is thought to occur less frequently in long-lived organisms, these observations suggest a role of bet-hedging strategies in perennials occupying unpredictable environments. We use complementary analytical and evolutionary simulation models of within-individual variation in germination behavior in seasonal environments to show how bet-hedging interacts with fluctuating selection, life-history traits, and competitive asymmetries among germination strategies. We reveal substantial scope for bet-hedging to produce variation in germination behavior in long-lived plants, when "false starts" to the growing season results in either competitive advantages or increased mortality risk for alternative germination strategies. Additionally, we find that lowering adult survival may, in contrast to classic bet-hedging theory, result in less spreading of germination by decreasing density-dependent competition. These models extend insights from bet-hedging theory to perennials and explore how competitive communities may be affected by ongoing changes in climate and seasonality patterns.</span></p>
Data from: Bet hedging is not sufficient to explain germination patterns of a winter annual plant
<div> <div> <div> <p>Bet hedging consists of life history strategies that buffer against environmental variability by trading off immediate and long-term fitness. Delayed germination in annual plants is a classic example of bet hedging and is often invoked to explain low germination fractions. We examined whether bet hedging explains low and variable germination fractions among 20 populations of the winter annual plant <em>Clarkia</em> <em>xantiana</em> ssp. <em>xantiana</em> that experience substantial variation in reproductive success among years. Leveraging 15 years of demographic monitoring and 3 years of field germination experiments, we assessed the fitness consequences of seed banks and compared optimal germination fractions from a density-independent bet-hedging model to observed germination fractions. We did not find consistent evidence of bet hedging or the expected trade-off between arithmetic and geometric mean fitness, though delayed germination increased long-term fitness in 7 of 20 populations. Optimal germination fractions were 2 to 5 times higher than observed germination fractions, and among-population variation in germination fractions was not correlated with risks across the life cycle. Our comprehensive test suggests that bet hedging is insufficient to explain the observed germination patterns. Understanding variation in germination strategies will likely require integrating bet hedging with complementary forces shaping the evolution of delayed germination.</p> </div> </div> </div>
Anacyclus clavatus seed germination data
<p>This Dataset include four different files to produce all results of the manuscript "<strong>Fruit wings accelerate germination in <em>Anacyclus clavatus</em> (Asteraceae)</strong>".</p> <p> </p>
Data from: Selection on early survival does not explain germination rate clines in Mimulus cardinalis
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Data from: Effects of manakin gut passage on germination of a neotropical melastome shrub (Melastomataceae)
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Physical seed damage, not rodent’s saliva, accelerates seed germination of trees in a subtropical forest
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Data from: Annual species’ experimental germination responses to light and temperature do not correspond with their microhabitat associations in the field
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Code, scripts and data for: Seasonality and competition select for variable germination behavior in perennials
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Endozoochory by black rhinoceroses enhances germination of a key arid savanna tree species
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Variable seed bed microsite conditions and light influence germination in Australian winter annuals
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Data from: Bet hedging is not sufficient to explain germination patterns of a winter annual plant
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Germination response to winter temperatures changes with seed shape and length of temperature exposure
In many regions, the climate is changing faster during winter than during any other season, and a loss of snow cover combined with increased temperature variability can expose overwintering organisms to harmful conditions. Understanding how species respond to these changes during critical developmental times, such as seed germination, helps us assess ecological implications of winter climate change. To address this concern, we measured the breaking of seed dormancy and cold tolerance of temperate grassland species in the lab and field. In the lab, we ran germination trials testing the tolerance of 17 species to an extreme cold event. In the field, we deployed seeds of two species within a snow manipulation experiment at three locations and measured germination success biweekly from seeds subjected to ambient and reduced snow cover from winter into spring. From lab trials, cold tolerance varied among species, with seed germination decreasing <10% to 100% following extreme cold events. Cold tolerance was related to seed traits, specifically less round seeds, seeds that required cold stratification, and seeds that mature later in the season tended to be more impacted by extreme cold temperatures. This variation in seed cold tolerance may contribute to altered community composition with continued winter climate change. In the field, germination increased through late winter, coinciding with the accumulation of days where temperatures were favorable for cold stratification. Through spring, germination success decreased as warm temperatures accumulated. Collectively, species-specific seed cold tolerances and mortality rates may contribute to compositional changes in grasslands under continued winter climate change.
Measures of germination and seedling survival for Prosartes lanuginosa, Maianthemum racemosa, and Melampyrum lineareae in the French Broad Watershed, 2009-2011
We asked how performance and population dynamics of the temperate forest herb Prosartes lanuginosa differed between recently logged (20-40 years ago) and old (>90 years) logged forests in the Southern Appalachians, USA. We conducted a seed sowing experiment to determine whether germination and establishment differed with stand age. Germination and performance of individual seedlings was monitored over three years across 20 forest stands.
SGS-LTER CO2 Elevation Study: Amount of seedlings germinated from surface soil of Open Top Chamber plots on the Central Plains Experimental Range, Nunn, Colorado, USA 1997 - 2001
This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/82454. At the end of the Open Top Chamber study, surface soil was removed from each of the 9 plots, and placed in flats in a greenhouse; mist irrigated frequently, and germinated seedlings were identified by species, to get an idea of the available seed bank after 5 years. There was a great amount of variability; overall there was an increase in seeds in the chambered plots. This research was conducted at the Central Plains Experimental Range, near Nunn, CO; lat.40degrees 40 minutes N; long. 104 degrees 45 minutes W in the shortgrass steppe region of NE Colorado, USA and as a collaboration between SGS-LTER and USDA-ARS researchers.
Elevation filters seed traits and germination strategies in the eastern Tibetan Plateau
<p><span><span><span><span><span><span><span><span><span><span><span>Seeds are the colonizing propagules for many plants and may therefore contribute to the filtering of species during the process of colonization and community assembly. Environmental filtering of seed traits may occur among species and influence community composition, or within species and influence the environmental breadth that a given species inhabits. To test for evidence of such filtering of seed traits, we measured morphological and germination traits of seeds of 408 angiosperm species collected across an elevational gradient in the eastern Tibetan Plateau grasslands. We tested for elevational filtering of traits at the species level, as well as within 22 of those species that occurred at different elevations, in order to test whether within-species variation reflected among-species patterns. Elevational patterning occurred in both seed morphology and seed germination. Seeds were smaller, more elongated, and had a higher surface area:volume ratio and shorter germination times at higher elevation. Seed morphology was associated with germination such that more elongated and smaller seeds with a higher surface area:volume ratio germinated faster, leading to earlier germination in seeds from high elevation. Within species, elevational variation in seed traits was observed in several species, but species differed in how those traits were distributed across elevation. These results suggest that taxonomic differences in seed traits may contribute to elevational variation in the species composition of plant communities, but that seed traits may be variably selected by elevation within species.</span></span></span></span></span></span></span></span></span></span></span></p>
Populations of arable weed species show intra-specific variability in germination base temperature but not in early growth rate
<p>Key plant traits affecting growth performance can differ among and within species, influencing competitive plant community dynamics. We determined the intra-specific variability of germination base temperature among 13 arable weed species and the seedlings' early post-emergence relative growth rate among 21 species in climate chamber and green house experiments. Intra-specific variability was quantified with two seed populations (originating from contrasting climate in Germany & France) for the germination base temperature of 6 species and for the early growth rate of 16 species. Inter-specific variability for both traits was always higher than intra-specific variability. Within a given species, we found that germination base temperatures were higher in seeds stemming from colder climate populations. Seedling relative growth rates did not differ between seed populations. Models simulating weed growth should reflect these differences in germination traits among populations, especially when they are used for weed community assembly studies in a local to regional extent.</p>
Germination and epiphytic seed fungi on Festuca roemeri and Danthonia californica
<p>Demographic studies measure drivers of plant fecundity such as seed production and survival, but few address environmental drivers of seed viability, such as germination and dormancy. Variation in climate and seed type may both directly and indirectly alter seed germination via altered fungal pathogen abundance.</p> <p>We examined seed germination and microbial communities of seeds of <i>Danthonia californica</i>, which are either chasmogamous (external, wind-pollinated) or cleistogamous (internal, self-fertilized) and <i>Festuca roemeri</i>, which are solely chasmogamous. Seed populations were sourced across environmental gradients. We tested germination and characterized seed fungal community structure, using high-throughput sequencing.</p> <p>For <i>F. roemeri</i>, maternal plant significantly influenced germination as did climate and pathogens; germination increased in wetter, cooler sites. For <i>D. californica</i>, the main drivers of germination were maternal plant, seed type and pathogens; on average, more chasmogamous seeds germinated. Fungal composition depended on seed type, with fewer fungi associated with cleistogamous seeds. Seed fungal composition varied with climate, plant density and mean proportion of seeds germinated.</p> <p>Putative pathogens that were negatively correlated with germination were more abundant for both <i>Danthonia</i> and <i>Festuca</i> chasmogamous seeds than <i>Danthonia</i> cleistogamous seeds. In <i>D. californica</i>, cleistogamous and chasmogamous<i> </i>seeds contain vastly different fungal communities.</p>
Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice
<p>To investigate the genetic architecture underlying cold tolerance during germination in rice (<i>Oryza sativa</i>), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch's Lab at Cornell University and consists of 7,098 SNPs (Morales et al. 2020, under review). After genotyping 257 rice accessions with the 7K array (C7AIR), poor-performing SNP markers (SNPs of call rate <90%; minor allele frequency <5%; or heterozygosity >20%) were removed from the dataset. For our study, a subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis. The dataset representing the genotype data of 5,185 SNP markers by 257 rice accessions is presented here.</p>
Data from: Species-specific variation in germination rates contributes to spatial coexistence more than adult plant water use in four closely-related annual flowering plants
1. Spatial partitioning is a classic hypothesis to explain plant species coexistence, but evidence linking local environmental variation to spatial sorting, demography, and species' traits is sparse. If co-occurring species' performance is optimized differently along environmental gradients because of trait variation, then spatial variation might facilitate coexistence. 2. We used a system of four naturally co-occurring species of Clarkia (Onagraceae) to ask if distribution patchiness corresponds to variation in two environmental variables that contribute to hydrological variation. We then reciprocally sowed Clarkia into each patch type and measured demographic rates in the absence of congeneric competition. Species sorted in patches along one or both gradients, and in three of the four species, germination rate in the "home" patch was higher than all other patches. 3. Spatially variable germination resulted in the same three species exhibiting the highest population growth rates in their home patches. 4. Species' trait values related to plant water use, as well as indicators of water stress in home patches, differed among species and corresponded to home patch attributes. However, post-germination survival did not vary among species or between patch types, and fecundity did not vary spatially. 5. Synthesis Our research demonstrates the likelihood that within-community spatial heterogeneity affects plant species coexistence, and presents novel evidence that differential performance in space is explained by what happens in the germination stage. Despite the seemingly obvious link between adult plant water-use and variation in the environment, our results distinguish the germination stage as important for spatially variable population performance.
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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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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.