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91 results for “light environment”
Data from: Roles of pathogens on replacement of tree seedlings in heterogeneous light environments in a temperate forest: a reciprocal seed sowing experiment
1. In forest communities, the Janzen–Connell (J-C) hypothesis proposes that species diversity is maintained by non-competitive distance- and/or density-dependent seedling mortality caused by host-specific natural enemies. However, the effects of pathogen associations from nearby conspecifics vs. heterospecifics remain unknown in spatially heterogeneous light environments. 2. Seeds of hardwood species Cornus controversa (Cornus) and Prunus grayana (Prunus) were sown beneath 6–7 Cornus and Prunus adults in both the forest understory (FU) and in gaps (Gap) created by felling all woody vegetation near the focal adults. Seedling growth, mortality, killing agents (e.g. pathogens that cause damping-off and leaf diseases), and root infection by arbuscular mycorrhizal fungi (AMF) were investigated. 3. We found strong habitat effects on the expression of soil fungi beneath both tree species. Seedling mortality caused by soil-borne damping-off pathogens was greater in FU than in Gap, and AMF infection, which enhanced relative seedling growth rate, was greater in Gap than in FU. Seedling mortality caused by damping-off pathogens did not differ between Cornus and Prunus seedlings beneath the adults of conspecific or heterospecific adults in both FU and Gap, suggesting little distance-dependence or host preference in the fungus. 4. Beneath the adults of Cornus and Prunus, the most prevalent leaf diseases were zonate leaf blight and angular leaf spot caused by the airborne pathogenic fungi Haradamyces foliicola and Phaeoisariopsis pruni-grayanae, respectively. Although these pathogens attacked the seedlings of both species, conspecific seedlings (i.e. home) showed more severe leaf damage, earlier leaf shedding and/or less defensive behaviour (cell wall defence) relative to heterospecific seedlings (i.e. away), suggesting negative distance-dependent attack (i.e. host preference) for these leaf diseases. As a result, greater seedling mortality was observed for conspecific seedlings under both FU and Gap treatments. 5. Synthesis. In the temperate forest, the J-C hypothesis is largely mediated through the strong negative influence of airborne leaf diseases rather than through soil-borne damping-off pathogens. We found that airborne diseases demonstrated distance-dependent host preferences, which led to greater conspecific seedling damage regardless of environmental light conditions.
Data from: The role of transcriptomes linked with responses to light environment on seedling mortality in a subtropical forest, China
Differences in seedling survival in trees have a lasting imprint on seedling, juvenile and adult community structure. Identifying the drivers of these differences, therefore, is a critical research objective that ultimately requires knowledge regarding how organismal function interacts with the local environment to influence survival rates. In tree communities, differences in light use strategies are frequently invoked to explain differences in seedling demographic performance through growth and survival trade-offs. For example, shade-tolerant species grow slowly and have higher survival rates, whereas shade-intolerant species grow quickly but have lower survival rates. Thus, functional traits related to photosynthesis should be strong predictors of demographic rates, but results in the literature are mixed indicating that additional or alternative information regarding organismal function should be considered. Here, we provide a community-wide inventory of transcriptomes in a subtropical tree community. This information is utilized to determine the degree to which species share homologous genes related to gene ontologies for light use and harvesting. These species similarities are used in neighbourhood generalized linear mixed-effects models of seedling survival that evaluated seedling survival as a function of the transcriptomic, functional trait and phylogenetic composition of the local neighbourhood. The results show neighbourhood similarity in three of the 15 gene ontologies evaluated are significantly related to survival rates based on neighbourhood composition. For two of these ontologies, survival rates increase when neighbours are similar in their gene tree composition indicating the importance of abiotic filtering and performance hierarchies. Synthesis. The present work takes a novel approach by sequencing the transcriptomes of naturally co-occurring tree species in a subtropical forest in China. The results show that the transcriptomic similarity of species is a significant predictor of differential survival. The study demonstrates that exploring the functional genomic similarity of non-model species in nature has the potential to increase the breadth and depth of our understanding of how gene function influences species co-occurrence and population dynamics in communities.
Data from: Roles of pathogens on replacement of tree seedlings in heterogeneous light environments in a temperate forest: a reciprocal seed sowing experiment
In forest communities, the Janzen–Connell (J-C) hypothesis proposes that species diversity is maintained by non-competitive distance- and/or density-dependent seedling mortality caused by host-specific natural enemies. However, the effects of pathogen associations from nearby conspecifics versus heterospecifics remain unknown in spatially heterogeneous light environments. Seeds of hardwood species Cornus controversa (Cornus) and Prunus grayana (Prunus) were sown beneath 6–7 Cornus and Prunus adults in both the forest understory (FU) and in gaps (Gap) created by felling all woody vegetation near the focal adults. Seedling growth, mortality, killing agents (e.g. pathogens that cause damping-off and leaf diseases), and root infection by arbuscular mycorrhizal fungi (AMF) were investigated. We found strong habitat effects on the expression of soil fungi beneath both tree species. Seedling mortality caused by soil-borne damping-off pathogens was greater in FU than in Gap, and AMF infection, which enhanced relative seedling growth rate, was greater in Gap than in FU. Seedling mortality caused by damping-off pathogens did not differ between Cornus and Prunus seedlings beneath the adults of conspecific or heterospecific adults in both FU and Gap, suggesting little distance-dependence or host preference in the fungus. Beneath the adults of Cornus and Prunus, the most prevalent leaf diseases were zonate leaf blight and angular leaf spot caused by the airborne pathogenic fungi Haradamyces foliicola and Phaeoisariopsis pruni-grayanae, respectively. Although these pathogens attacked the seedlings of both species, conspecific seedlings (i.e. home) showed more severe leaf damage, earlier leaf shedding and/or less defensive behaviour (cell wall defence) relative to heterospecific seedlings (i.e. away), suggesting negative distance-dependent attack (i.e. host preference) for these leaf diseases. As a result, greater seedling mortality was observed for conspecific seedlings under both FU and Gap treatments. Synthesis. In the temperate forest, the J-C hypothesis is largely mediated through the strong negative influence of airborne leaf diseases rather than through soil-borne damping-off pathogens. We found that airborne diseases demonstrated distance-dependent host preferences, which led to greater conspecific seedling damage regardless of environmental light conditions.
Green fluorescent protein-like pigments optimize the internal light environment in symbiotic reef building corals
<p>Pigments homologous to the Green Fluorescent Protein (GFP) have been proposed to fine-tune the internal light microclimate of corals, facilitating photoacclimation of photosynthetic coral symbionts (Symbiodiniaceae) to life in different reef habitats and environmental conditions. However, direct measurements of the <i>in vivo</i> light conditions inside the coral tissue supporting this conclusion are lacking. Here, we quantified the intra-tissue spectral light environment of corals expressing GFP-like proteins from widely different light regimes. We focus on (1) photoconvertible red fluorescent proteins (pcRFPs), thought to enhance photosynthesis in mesophotic habitats via wavelength conversion, and (2) chromoproteins (CPs), which provide photoprotection to the symbionts in shallow water via light absorption. Optical microsensor measurements indicated that both pigment groups strongly alter the<i> </i>coral tissue light environment. Estimates derived from light spectra measured in pcRFP-containing corals showed that fluorescence emission can contribute to >50% of orange-red light available to the photosynthetic symbionts at mesophotic depths. We further show that upregulation of pink CPs in shallow-water corals during bleaching leads to a reduction of orange light by 10-20% compared to low-CP tissue. Thus, screening by CPs has an important role in mitigating the light-enhancing effect of coral tissue scattering during bleaching. Our results provide the first experimental quantification of the importance of GFP-like proteins in fine-tuning the light microclimate of corals during photoacclimation.</p>
Data from: Light environment change induces differential expression of guppy opsins in a multi-generational evolution experiment
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Green fluorescent protein-like pigments optimize the internal light environment in symbiotic reef building corals
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Data from: Acclimatization of symbiotic corals to mesophotic light environments through wavelength transformation by fluorescent protein pigments
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Data from: Roles of pathogens on replacement of tree seedlings in heterogeneous light environments in a temperate forest: a reciprocal seed sowing experiment
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Data from: The role of transcriptomes linked with responses to light environment on seedling mortality in a subtropical forest, China
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Data from: Fluorescent protein-mediated colour polymorphism in reef corals: multi-copy genes extend the adaptation/acclimatization potential to variable light environments
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Data from: Roles of pathogens on replacement of tree seedlings in heterogeneous light environments in a temperate forest: a reciprocal seed sowing experiment
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Data from: Early life conditions and precipitation influence the performance of widespread understory herbs in variable light environments
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Data from: Male courtship decisions are influenced by light environment and female receptivity
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Data from: Variable light environments induce plastic spectral tuning by regional opsin coexpression in the African cichlid fish, Metriaclima zebra
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Adaptive response of Arabidopsis seedlings in microgravity and Mars reduced gravity environment is enhanced by red light photostimulation
The response of plants to the spaceflight environment and microgravity is still not well understood although there has been an increased emphasis on this topic. Even less is known about plants response to partial or reduced gravity levels. In the absence of the directional cues provided by the gravity vector the plant is especially perceptive to other cues such as light. Here we investigate the response of Arabidopsis thaliana 6-day-old seedlings to microgravity and the Mars partial gravity level during spaceflight as well as the effects of red light photostimulation by determining meristematic cell growth and proliferation. These experiments involve microscopic techniques together with transcriptomic studies. We demonstrate that microgravity and partial gravity trigger differential responses. The microgravity environment activates hormonal routes responsible for proliferation/growth and upregulates plastid/mitochondrial-encoded transcripts even in the dark. In contrast the Mars gravity level inhibits these routes and activates responses to stress factors to restore cell growth parameters only when red photostimulation is provided. This response is accompanied by upregulation of numerous transcription factors such as the environmental acclimation-related WRKY family. In the long term these discoveries can be applied in the design of bioregenerative life support systems and space farming.
Low red to far-red light environments alter nitrogen assimilation in corn (Zea mays)
GEO Series GSE213949. Zea mays. 9 samples. Type: Expression profiling by high throughput sequencing.
Effects of gene-by-environment interaction on the H3K4me3 profile in the light of differential susceptibility
GEO Series GSE109928. Mus musculus. 42 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Combination LIGHT overexpression and checkpoint blockade disrupts the tumor immune environment eradicating colorectal liver metastases
GEO Series GSE252597. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
Effect of Bright Light Treatment On Elders In a Long Term Care Environment
ClinicalTrials.gov study NCT01042587. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Effects of gene-by-environment interaction on the mRNA profile in the light of differential susceptibility
GEO Series GSE109929. Mus musculus. 48 samples. Type: Expression profiling by high throughput sequencing.
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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)
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.