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89 results for “Experimental mechanics”
Data from: Genetics of adaptation: experimental test of a biotic mechanism driving divergence in traits and genes
The genes underlying adaptations are becoming known, yet the causes of selection on genes -- a key step in the study of the genetics of adaptation -- remains uncertain. We address this issue experimentally in a threespine stickleback species pair showing exaggerated divergence in bony defensive armor in association with competition-driven character displacement. We used semi-natural ponds to test the role of a native predator in causing divergent evolution of armor and two known underlying genes. Predator presence/absence altered selection on dorsal spines and allele frequencies at the Msx2a gene across a generation. Evolutionary trajectories of alleles at a second gene, Pitx1, and the pelvic spine trait it controls, were more variable. Our experiment demonstrates how manipulation of putative selective agents help to identify causes of evolutionary divergence at key genes, rule out phenotypic plasticity as a sole determinant of phenotypic differences, and eliminate reliance on fitness surrogates. Divergence of predation regimes in sympatric stickleback is associated with coevolution in response to resource competition, implying a cascade of biotic interactions driving species divergence. We suggest that as divergence proceeds, an increasing number of biotic interactions generate divergent selection, causing more evolution in turn. In this way, biotic adaptation perpetuates species divergence through time during adaptive radiation in an expanding number of traits and genes.
Data from: Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms
Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 hours post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to pCO2-acidified seawater to identify genes correlated with initial shell deposition. By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important role of dynein motor proteins as transporters of cellular components during the initial shell formation process. This work provides a foundation for further studies on how genetic variation in these identified genes could affect fitness of oyster populations subjected to future environmental changes, such as ocean acidification.
Data from: Can plants evolve tolerance mechanisms to heterospecific pollen effects? An experimental test of the adaptive potential in Clarkia species
Flowering plants do not occur alone and often grow in mixed-species communities where pollinator sharing is high and interactions via pollinators can occur at pre- and post-pollination stages. While the causes and consequences of pre-pollination interactions have been well studied little is known about post-pollination interactions via heterospecific pollen (HP) receipt, and even less about the evolutionary implications of these interactions. In particular, the degree to which plants can evolve tolerance mechanisms to the negative effects of HP receipt has received little attention. Here, we aim to fill this gap in our understanding of post-pollination interactions by experimentally testing whether two co-flowering Clarkia species can evolve HP tolerance, and whether tolerance to specific HP 'genotypes' (fine-scale local adaptation to HP) occurs. We find that Clarkia species vary in their tolerance to HP effects. Furthermore, conspecific pollen performance and the magnitude of HP effects were related to the recipient's history of exposure to HP in C. xantiana but not in C. speciosa. Specifically, better conspecific pollen performance and smaller HP effects were observed in populations of C. xantiana plants with previous exposure to HP compared to populations without such exposure. These results suggest that plants may have the potential to evolve tolerance mechanisms to HP effects but that these may occur not from the female (stigma, style) but from the male (pollen) perspective, a possibility that is often overlooked. We find no evidence for fine-scale local adaptation to HP receipt. Studies that evaluate the adaptive potential of plants to the negative effects of HP receipt are an important first step in understanding the evolutionary consequences of plant–plant post-pollination interactions. Such knowledge is in turn crucial for deciphering the role of plant–pollinator interactions in driving floral evolution and the composition of co-flowering communities.
Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution
Natural selection acts on multiple traits simultaneously. How mechanisms underlying such traits enable or constrain their response to simultaneous selection is poorly understood. We show how antagonism and synergism among three traits at the developmental level enable or constrain evolutionary change in response to simultaneous selection on two focal traits at the phenotypic level. After 10 generations of 25% simultaneous directional selection on all four combinations of body size and development time in Manduca sexta (Sphingidae), the changes in the three developmental traits predict 93% of the response of development time and 100% of the response of body size. When the two focal traits were under synergistic selection, the response to simultaneous selection was enabled by juvenile hormone and ecdysteroids and constrained by growth rate. When the two focal traits were under antagonistic selection, the response to selection was due primarily to change in growth rate and constrained by the two hormonal traits. The approach used here reduces the complexity of the developmental and endocrine mechanisms to three proxy traits. This generates explicit predictions for the evolutionary response to selection that are based on biologically informed mechanisms. This approach has broad applicability to a diverse range of taxa, including algae, plants, amphibians, mammals, and insects.
Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations
<p>Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups of experimentally evolved D. melanogaster populations with different aging and longevity patterns. Our metabolomic analysis found that aging alters mitochondrial metabolism through increased consumption of NAD<sup>+</sup> and increased usage of the TCA cycle. Combining our genomic and metabolomic data produced a list of biologically relevant candidate genes. Among these candidates, we found significant enrichment for genes and pathways associated with neurological development and function, and carbohydrate metabolism. While we do not explicitly find enrichment for aging canonical genes, neurological dysregulation and carbohydrate metabolism are both known to be associated with accelerated aging and reduced longevity. Taken together, our results provide plausible genetic mechanisms for what might be driving longevity differences in this experimental system. More broadly, our findings demonstrate the value of combining multiple types of omic data with experimental evolution when attempting to dissect mechanisms underlying complex and highly polygenic traits such as aging.</p>
Screening and mechanism of novel angiotensin-I-converting enzyme inhibitory peptides in X. sorbifolium seed meal: A computer-assisted experimental study method
<p>本文档是补充材料</p>
Pre-analytical validity of arterial blood gas samples: A prospective experimental study on changes derived from time delay and mechanical stress
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Experimental and theoretical data generated to study mechanism of water intrusion into flexible ZIF-8
<p><span>Open access to experimental data generated by the project </span><a href="https://www.electro-intrusion.eu/en"><span>Electro-Intrusion</span></a><span> (101017858, Horizon 2020, European Union) along with the research on the thermal behaviour of hydrophobic porous materials to be used in intrusion-extrusion applications. Research pertaining to Task 2.1 (WP2).</span></p> <p><span>Underlying data for the publication Amayuelas, E. et al. Mechanism of Water Intrusion into Flexible ZIF-8: Liquid Is Not Vapor. Nanoletters 2023, 23, 5430-5436. <a title="DOI URL" href="https://doi.org/10.1021/acs.nanolett.3c00235">https://doi.org/10.1021/acs.nanolett.3c00235</a>. Data related to Figures 1 and 2 in the article.</span></p>
SP datasets for experimental study on the redox mechanism of geobattery and related electrical signals
<p><strong>The uploaded datasets are from the paper "Redox mechanism of geobattery and related electrical signals using a novel real-time self-potential monitoring experimental platform", which has been published at the <em>Journal of Central South University</em>. The laboratory data is available to all readers, and you can cite it by "Xie, J., Cui, Y., Zhang, L., et al. 2024. Redox mechanism of geobattery and related electrical signals using a novel real-time self-potential monitoring experimental platform. Journal of Central South University, 2024, 31(11): 1-19.".</strong></p> <p><strong>Note that there is a wrong description about the title of the journal paper in the "read me" file. Please ignore this issue. </strong></p> <p> </p>
Data from: Genetics of adaptation: experimental test of a biotic mechanism driving divergence in traits and genes
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Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations
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Data from: Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms
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Data from: Can plants evolve tolerance mechanisms to heterospecific pollen effects? An experimental test of the adaptive potential in Clarkia species
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Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution
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Data from: An experimental study of the putative mechanism of a synthetic autonomous rotary DNA nanomotor
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Defining the mechanism of systemic NK cell dysfunction associated with melanoma lung metastasis in spontaneous and experimental models
GEO Series GSE248264. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Experimental evolution identifies adaptive aneuploidy as a mechanism of fluconazole resistance in Candida auris
GEO Series GSE136768. Candidozyma auris. 6 samples. Type: Expression profiling by high throughput sequencing.
Molecular mechanisms of the Xiao-chai-hu-tang on chronic stress-induced colorectal cancer growth based on an integrated network pharmacology and RNA sequencing approach with experimental validation
GEO Series GSE276601. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Leveraging Integrated RNA Sequencing to Decipher Adrenomedullin’s Protective Mechanisms in Experimental Bronchopulmonary Dysplasia
GEO Series GSE264612. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
The elucidation of the anti-inflammatory mechanism of EMO in rheumatoid arthritis through an integrative approach combining bioinformatics and experimental verification
GEO Series GSE232679. Rattus norvegicus. 6 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.