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148 results for “Chlamydomonas”
Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii
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Cell size, chlorophyll fluorescence and cadmium bioaccumulation between wild-type and mutant strains of Chlamydomonas reinhardtii upon exposure to cadmium
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Data from: Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies
Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas.
Data from: Dynamic curvature regulation accounts for the symmetric and asymmetric beats of Chlamydomonas flagella
Cilia and flagella are model systems for studying how mechanical forces control morphology. The periodic bending motion of cilia and flagella is thought to arise from mechanical feedback: dynein motors generate sliding forces that bend the flagellum, and bending leads to deformations and stresses, which feed back and regulate the motors. Three alternative feedback mechanisms have been proposed: regulation by the sliding forces, regulation by the curvature of the flagellum, and regulation by the normal forces that deform the cross-section of the flagellum. In this work, we combined theoretical and experimental approaches to show that the curvature control mechanism is the one that accords best with the bending waveforms of Chlamydomonas flagella. We make the surprising prediction that the motors respond to the time derivative of curvature, rather than curvature itself, hinting at an adaptation mechanism controlling the flagellar beat.
Data from: Positive size-speed relationships in gametes and vegetative cells of Chlamydomonas reinhardtii; implications for the evolution of sperm.
It is commonly held that differences in gametes of the two sexes (anisogamy) evolved from ancestors whose gametes were similar in size and behaviour (isogamy). Underlying many hypotheses explaining anisogamy are assumed relationships between cell size and speed in the ancestral isogamous population. Using the isogamous alga Chlamydomonas reinhardtii, we explored size-speed distributions in vegetative and gamete cells of ten cell lines, and clonal data from within two cell lines. We applied an independent speed selection approach to gamete populations of C. reinhardtii, monitoring correlated responses in size following selection for high speed. We demonstrate positive size-speed relationships in clones, cell lines and artificially selected speed selection lines. We found different size-speed relationships in the two cell types of C. reinhardtii even though they overlap in size, suggesting that cell composition and/or programs of gene expression are capable of altering this relationship, and that the relationship is evolvable. The positive genetic size-speed correlation means that the division of parent vegetative cells into numerous gametes trades off against not only size but also speed, a trade-off that has not received previous attention. Our results support re-evaluating the role of speed selection in the evolution of anisogamy.
Raw data of: Settling selection of <i>Chlamydomonas reinhardtii</i> for samarium uptake.
<p>Data are the raw results of the investigation entitled, Settling selection of <em>Chlamydomonas reinhardtii</em> for samarium uptake.</p> <p>This study uses an experimentally evolved <em>C. reinhardtii </em>(Martínez-Alesón García et al., 2021), selected under Samarium and acid pH conditions. We carry out further selection procedures to increase Sm sequestration. Control, ancestral, and selected populations of <em>C. reinhardtii </em>were characterized using a Coulter Counter multisizer 4, FlowCam 3.0, using Transmission electron microscopy<em> </em>(TEM), ray spectroscopy (Energy Dispersive X-ray (EDX)) and with an Imaging PAM fluorimeter. The populations studies were a <em>C. reinhardtii</em> wild-type control (control strain), Sm-uptake candidate strain (CSm0 strain) resulting from mixing thirteen Sm-adapted strains (refer to Martínez-Alesón García et al., 2021), and newly established strains label for the selection cycle as CSm1, CSm2, CSm3, and CSm4 strains.</p> <p><strong><em>Files:</em></strong></p> <ul> <li>Coulter Counter particles distributions of all strains: <ul> <li><a href="../api/records/8392917/draft/files/Coulter%20Counter%20raw%20data.zip/content" target="_blank" rel="noopener noreferrer">Coulter Counter raw data.zip</a> Data from Control, CSm0, CSm1, CSm2, CSm3, and CSm4 strains grown in BG11 medium under laboratory conditions for 15 days.</li> </ul> </li> <li>Microscopic images: <ul> <li><a href="../api/records/8392917/draft/files/Flow%20Cam%20raw%20images%20and%20files.zip/content" target="_blank" rel="noopener noreferrer">Flow Cam raw images and files.zip</a> FlowCam 3.0 Microphotographs and files were generated for all strains grown in BG11 medium under laboratory conditions for 15 days. </li> <li><a href="8392917" target="_blank" rel="noopener noreferrer">Optic Microscopy microphotographs.zip</a> Optic Microscopy Microphotographs measure morphological traits with ImageJ in CSm0 and CSm4 strains.</li> <li><a href="8392917" target="_blank" rel="noopener noreferrer">TEM Images.zip</a> Transmission electron microscopy<em> </em>(TEM) pictures were obtained with an electron microscope, JEOL-JEM 1400 (Jeol Ltd., Tokyo, Japan) from control and CSm4 strains.</li> </ul> </li> <li>Data files generated from microscopy images:<br> <ul> <li><a href="../api/records/8392917/draft/files/ImageJ%20analyses%20Raw%20data.xlsx/content" target="_blank" rel="noopener noreferrer">ImageJ analyses Raw data.xlsx</a>: ImageJ analyses files.</li> <li><a href="../api/records/8392917/draft/files/TEM-EDX%20analyses.zip/content" target="_blank" rel="noopener noreferrer">TEM-EDX analyses.zip</a> Ray spectroscopy (Energy Dispersive X-ray (EDX)) spectrums obtained from TEM cuts.</li> </ul> </li> <li><a href="../api/records/8392917/draft/files/PAM%20raw%20data.zip/content" target="_blank" rel="noopener noreferrer">PAM raw data.zip</a> PAM fluorescence Raw data of </li> </ul>
SI Reduction of phosphoribulokinase amount and re-routing me-tabolism in Chlamydomonas reinhardtii CP12 mutants.
<p>Supplementary material associated with the manuscript<strong>: </strong>Reduction of phosphoribulokinase amount and re-routing me-tabolism in Chlamydomonas reinhardtii CP12 mutants</p>
Data from: The experimental evolution of herbicide-resistance in Chlamydomonas reinhardtii results in a positive correlation between fitness in the presence and absence of herbicides
Pleiotropic fitness trade-offs will be key determinants of the evolutionary dynamics of selection for pesticide resistance. However, for herbicide resistance, empirical support for a fitness cost of resistance is mixed, and it is therefore also questionable what further ecological trade-offs can be assumed to apply to herbicide resistance. Here, we test the existence of trade-offs by experimentally evolving herbicide resistance in Chlamydomonas reinhardtii. Although fitness costs are detected for all herbicides, we find that, counterintuitively, the most resistant populations also have the lowest fitness costs as measured by growth rate in the ancestral environment. Furthermore, after controlling for differences in the evolutionary dynamics of resistance to different herbicides, we also detect significant positive correlations between resistance, fitness in the ancestral environment and cross-resistance to other herbicides. We attribute this to the highest levels of nontarget-site resistance being achieved by fixing mutations that more broadly affect cellular physiology, which results in both more cross-resistance and less overall antagonistic pleiotropy on maximum growth rate. Consequently, the lack of classical ecological trade-offs could present a major challenge for herbicide resistance management.
Data from: Dynamic curvature regulation accounts for the symmetric and asymmetric beats of Chlamydomonas flagella
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Data from: The experimental evolution of herbicide-resistance in Chlamydomonas reinhardtii results in a positive correlation between fitness in the presence and absence of herbicides
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Data from: Positive size-speed relationships in gametes and vegetative cells of Chlamydomonas reinhardtii; implications for the evolution of sperm.
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Data from: Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii
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Data from: Flow cytometric methods for indirect analysis and quantification of gametogenesis in Chlamydomonas reinhardtii (Chlorophyceae)
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Data from: Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii
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Data from: Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies
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Data from: Spontaneous mutation accumulation in multiple strains of the green alga, Chlamydomonas reinhardtii
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Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery
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Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii
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Selecting for Chlamydomonas reinhardtii fitness in the KSC Veggie Unit
The Space Algae Experiment Verification Test completed a competitive growth selection on mutagenized microalgae in a series of batch cultures that were passaged for three growth cycles. The experiment was conducted with ground control conditions similar to those actually used in spaceflight. Cultures were limited in growth rate due to gas permeable membranes to provide oxygen and carbon dioxide exchange and a lack of agitation to mix the cells throughout the liquid media. Two strains were grown and three biological replicates were completed for each strain. Specific variables (factors) tested were: 1) The effect of UVC mutagenesis was tested by sampling the algae cultures prior to mutagenesis. 2) The sensitivity of different strains was tested by conducting the experiment with a wild-type and cell wall mutant (cw15) strain. 3) The effect of competitive growth was tested by sampling each biological replicate experiment at the end of each growth cycle. 4) The effect of live culture storage in the dark was tested by sampling each growth cycle twice. At the time of passage a sample of cells was pelleted and frozen. The cultures were then stored in the dark in a Cargo Transport Bag (CTB) to simulate storage on the ISS and return of cultures. This factor tested whether cultures could be stored alive in the dark or if samples needed to be fixed at the time of passage in order to get an accurate representation of the genetic variation in each cycle of growth. Paired-end whole genome sequencing was completed for 38 samples: 2 strains pre mutagenesis and 2 strains X 3 biological replicates X 3 growth cycles X 2 storage conditions.
Transcriptomics analysis of the Chlamydomonas reinhardtii diurnal cycle.
GEO Series GSE112394. Chlamydomonas reinhardtii. 16 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)
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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.