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71 results for “dynamic lighting”
Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged fairywren
<p>The existence of distinct traits in island versus mainland populations offers opportunities to gain insights into how eco-evolutionary processes operate under natural conditions. We used two island colonization events in the white-winged fairywren (<i>Malurus </i><i>leucopterus</i>) to investigate the genomic and demographic origin of melanic plumage. This avian species is distributed across most of Australia, and males of the mainland subspecies (<i>M. l. leuconotus</i>) exhibit a blue nuptial plumage in contrast to males of two island subspecies – <i>M. l. leucopterus </i>on Dirk Hartog Island<i> </i>and <i>M. l. edouardi</i>on Barrow Island – that exhibit a black nuptial plumage. We used reduced-representation sequencing to explore differentiation and demographic history in this species and found clear patterns of divergence between mainland and island populations, with additional substructuring on the mainland. Divergence between the mainland and Dirk Hartog was approximately 10 times more recent than the split between the mainland and Barrow Island, supporting two independent colonizations. In both cases, estimated gene flow between the mainland and the islands was low, contributing to signals of divergence among subspecies. Our results present demographic reconstructions of mainland-island dynamics and associated plumage variation in white-winged fairywrens, with broader implications regarding our understanding of convergent evolution in insular populations.</p>
Data from: Dynamic antagonism between phytochromes and PIF-family bHLHs induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis
Plants respond to shade-modulated light-signals, via the phytochrome (phy) system, by adaptive changes, collectively termed the shade avoidance syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors, PIF1, 3, 4 and 5, in relaying this information to the transcriptional network, we compared the genome-wide expression profiles of wild-type and quadruple pif (pifq) mutants in response to shade. The data identify a subset of genes, enriched in transcription-factor-encoding loci, that respond rapidly (within 1 h), in a PIF-dependent manner, to the shade signal, and that contain promoter-located G-box-sequence motifs (CACGTG), known to be preferred PIF binding sites. These genes are thus potential direct targets of phy-PIF signaling that function in the primary transcriptional circuitry controlling downstream response-elaboration. A second subset of PIF-dependent, early-response genes, lacking G-box motifs, are enriched for auxin-responsive loci, suggestive of being indirect targets of phy-PIF signaling involved in the rapid cell-expansion known to be induced by shade. A meta-analysis comparing deetiolation- and shade-responsive transcriptomes identifies a further subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals at the inception of deetiolation and shade-avoidance, respectively. Collectively, these data define a core set of transcriptional and hormonal (auxin, cytokinin) processes that appear to be dynamically poised to react rapidly to changes in the light environment via perturbations in the mutually antagonistic actions of the phys and PIFs. Data from comparative analysis of the quadruple pifq and all triple pif-mutant combinations in response to light and shade, confirm that the PIF-quartet members act with overlapping redundancy on seedling morphogenesis and transcriptional regulation, but that the individual PIFs contribute differentially to these responses.
Data from: Managing seagrass resilience under cumulative dredging affecting light: predicting risk using dynamic Bayesian networks
Coastal development is contributing to ongoing declines of ecosystems globally. Consequently, understanding the risks posed to these systems, and how they respond to successive disturbances, is paramount for their improved management. We study the cumulative impacts of maintenance dredging on seagrass ecosystems as a canonical example. Maintenance dredging causes disturbances lasting weeks to months, often repeated at yearly intervals. We present a risk-based modelling framework for time varying complex systems centred around a dynamic Bayesian network (DBN). Our approach estimates the impact of a hazard on a system's response in terms of resistance, recovery and persistence, commonly used to characterise the resilience of a system. We consider whole-of-system interactions including light reduction due to dredging (the hazard), the duration, frequency and start time of dredging, and ecosystem characteristics such as the life-history traits expressed by genera and local environmental conditions. The impact on resilience of dredging disturbances is evaluated using a validated seagrass ecosystem DBN for meadows of the genera Amphibolis (Jurien Bay, WA, Australia), Halophila (Hay Point, Qld, Australia) and Zostera (Gladstone, Qld, Australia). Although impacts varied by combinations of dredging parameters and the seagrass meadows being studied, in general, 3 months of duration or more, or repeat dredging every 3 or more years, were key thresholds beyond which resilience can be compromised. Additionally, managing light reduction to less than 50% can significantly decrease one or more of loss, recovery time and risk of local extinction, especially in the presence of cumulative stressors. Synthesis and applications. Our risk-based approach enables managers to develop thresholds by predicting the impact of different configurations of anthropogenic disturbances being managed. Many real-world maintenance dredging requirements fall within these parameters, and our results show that such dredging can be successfully managed to maintain healthy seagrass meadows in the absence of other disturbances. We evaluated opportunities for risk mitigation using time windows; periods during which the impact of dredging stress did not impair resilience.
Data from: Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle
BACKGROUND: Growth of the ocean's most abundant primary producer, the cyanobacterium Prochlorococcus, is tightly synchronized to the natural 24-hour light-dark cycle. We sought to quantify the relationship between transcriptome and proteome dynamics that underlie this obligate photoautotroph's highly choreographed response to the daily oscillation in energy supply. METHODOLOGY/PRINCIPAL FINDINGS: Using Illumina RNA-sequencing transcriptomics and mass spectrometry-based quantitative proteomics, we measured timecourses of paired mRNA-protein abundances for 312 genes every 2 hours over a light-dark cycle. These temporal expression patterns reveal strong oscillations in transcript abundance that are broadly damped at the protein level, with mRNA levels varying on average 2.3 times more than the corresponding protein. The single strongest observed protein-level oscillation is in a ribonucleotide reductase, which may reflect a defense strategy against phage infection. The peak in abundance of most proteins also lags that of their transcript by 2-8 hours, and the two are completely antiphase for some genes. While abundant antisense RNA was detected, it apparently does not account for the observed divergences between expression levels. The redirection of flux through central carbon metabolism from daytime carbon fixation to nighttime respiration is associated with quite small changes in relative enzyme abundances. CONCLUSIONS/SIGNIFICANCE: Our results indicate that expression responses to periodic stimuli that are common in natural ecosystems (such as the diel cycle) can diverge significantly between the mRNA and protein levels. Protein expression patterns that are distinct from those of cognate mRNA have implications for the interpretation of transcriptome and metatranscriptome data in terms of cellular metabolism and its biogeochemical impact.
Supporting data for "Health benefits of US light-duty vehicle electrification: roles of fleet dynamics, clean electricity, and policy timing"
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Dynamic Light Scattering for Studying Lens Aging and Cataract Formation
ClinicalTrials.gov study NCT00081991. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Dynamic Light Scattering Ocular Measurement in the Detection of Dementia
ClinicalTrials.gov study NCT06613971. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Dynamic Light Scattering Device (DLS) Study of Age-Related Changes in the Lens and Cataracts
ClinicalTrials.gov study NCT00007215. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Dynamic Light Scattering to Study Crystalline Proteins in Young Normal Lenses
ClinicalTrials.gov study NCT00304967. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Dynamic Light Scattering and Keratoscopy for Corneal Examination
ClinicalTrials.gov study NCT00050466. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Pilot Study: Dynamic Light Scattering Device for Studying Early Changes in Cataract
ClinicalTrials.gov study NCT00067483. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle
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Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged fairywren
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Data from: Managing seagrass resilience under cumulative dredging affecting light: predicting risk using dynamic Bayesian networks
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Data from: Dynamic antagonism between phytochromes and PIF-family bHLHs induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis
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LADL: Light-activated dynamic looping for endogenous gene expression control
GEO Series GSE115963. Mus musculus. 20 samples. Type: Other.
Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation
GEO Series GSE201015. Arabidopsis thaliana. 124 samples. Type: Expression profiling by high throughput sequencing.
Data from: Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica
Studies of postglacial range shifts could enhance our understanding of seaweed species' responses to climate change, and hence facilitate the conservation of natural resources. However, the distribution dynamics and phylogeographic diversification of the commercially and ecologically important kelp Saccharina japonica in the Northwest Pacific (NWP) are still poorly surveyed. In this study, we analyzed the evolutionary history of S. japonica using two mitochondrial markers and 24 nuclear microsatellites. A STRUCTURE analysis revealed two partially isolated lineages: lineage H, which is scattered along the coast of Japan; and lineage P, which occurs along the west coast of the Japan Sea. Ecological niche modeling projections to the Last Glacial Maximum (LGM) revealed that the southern coasts of the Japan Sea and the Pacific side of the Oshima and Honshu Peninsulas provided the most suitable habitats for S. japonica, implying that these regions served as ancient refugia during the LGM. Ancient isolation in different refugia may explain the observed divergence between lineages P and H. An approximate Bayesian computation analysis indicated that the two lineages experienced post‐LGM range expansion, and that postglacial secondary contact occurred in Sakhalin. Model projections into the year 2100 predicted that S. japonica will shift northwards and lose its genetic diversity center on the Oshima Peninsula in Hokkaido and Shimokita Peninsula in Honshu. The range shifts and evolutionary history of S. japonica improve our understanding of how climate change impacted the distribution range and diversity of this species and provide useful information for the conservation of natural resources under ongoing environmental change in the NWP.
Microscopic simulations of the dynamics of excitonic many-body correlations coupled to quantum light
<p>Dataset of the publication "Microscopic simulations of the dynamics of excitonic many-body correlations coupled to quantum light" H. Rose, P. R. Sharapova, and T. Meier, Proc. SPIE 12884, Ultrafast Phenomena and Nanophotonics XXVIII, 1288403 (2024). ( https://doi.org/10.1117/12.2690245 ). The zip file includes the data on which the plots shown in figures 1 and 2 are based.</p>
Ultrafast light-induced dynamics in the microsolvated biomolecular indole chromophore with water
<p>Data underlying <em>Ultrafast light-induced dynamics in the microsolvated biomolecular indole chromophore with water, </em>by Jolijn Onvlee, Sebastian Trippel, and Jochen Küpper, Nature Commun. <strong>13</strong>, 7462 (2022). <a href="https://doi.org/10.1038/s41467-022-33901-w">https://doi.org/10.1038/s41467-022-33901-w</a>, arXiv: <a href="https://arxiv.org/abs/2103.07171">arXiv:2103.07171</a></p> <p><em>Data_and_analysis.zip</em> contains the data and python scripts used to produce the figures. </p>
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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.