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148 results for “Chlamydomonas”
Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia
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Developmental changes in ciliary composition during gametogenesis in Chlamydomonas
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Chlamydomonas cilia proteins
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The effects of sex on extinction dynamics of Chlamydomonas reinhardtii depend on the rate of environmental change
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Dataset of phototactic response kinetics of Chlamydomonas reinhardtii
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Compartmentalized sesquiterpenoid biosynthesis and functionalization in the Chlamydomonas reinhardtii plastid
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Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii
We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits.
Fluorescence microscopy of Chlamydomonas reinhardtii for mCherry detection: secretion peptides strains.
<p><strong>Overview</strong></p> <p>Life-cell imaging was performed with a confocal fluorescence microscopy to observe mCherry in the secretion vacuoles. mCherry fluorescence compartmentalization was observed by a Confocal Zeiss LSM 780-NLO, using an argon laser 543 nm to excite mCherry and a spectral detector set approximately to 610-650 nm range. For chlorophyll, we used a laser at 405 nm for excitation, and spectral detector set to 680 nm region. All pictures were taken with the same system configuration and analyzed by Fiji, an ImageJ distribution software. Cells images were acquired in bundles of 0.4 μm afar photos per channel in the z-axis. </p> <p> </p> <p><strong>Files info:</strong></p> <p>Each file is the raw image obtained from fluorescent microscopy.</p> <p> </p> <p><strong>Organization</strong></p> <p>Construct_name.czi - Ex: "pAH04mCherry.czi"</p> <p>pAH04mCherry -> construct without signal peptide</p> <p>pJP22mCherry -> construct with signal peptide from arylsulfatase 1 (<em>Chlamydomonas </em><em>reinhardtii</em>)</p> <p>pJP26mCherry -> construct with signal peptide from binding protein 1 (<em>C. </em><em>reinhardtii</em>)</p> <p>pJP28mCherry -> construct with signal peptide from carbonic anhydrase 1 (<em>C. </em><em>reinhardtii</em>)</p> <p>pJP29 mCherry -> construct with signal peptide from ice-binding protein 1 (Artic <em>Chlamydomonas sp</em>)</p> <p>pJP30-35mCherry -> construct with signal peptide from in silico identified list (DOI 10.5281/zenodo.556792).</p> <p>Wildtype cc1690 -> parental strain used for transformation.</p> <p> </p> <p>For more information on the constructs, check our paper. </p> <p> </p> <p><strong>Consider citing our work. </strong></p> <p>Molino JVD, de Carvalho JCM, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. https://doi.org/10.1371/journal. pone.0192433</p> <p> </p>
Phenotypic differences between interfertile Chlamydomonas species - Cell Wall Analysis
<p>This repository contains raw .TIF image data of Chlamydomonas reinhardtii (cc-124) and Chlamydomonas smithii (cc-1373) stained with Calcofluor White with Evan's blue, fixed in 4% PFA, and imaged on a spinning disk confocal microscope. The protocol to generate this data is described in the associated publication, <a href="https://doi.org/10.57844/arcadia-35f0-3e16">"Phenotypic differences between interfertile <i>Chlamydomonas</i> species". </a><br><br>Cells grown in TAP media were collected through centrifugation at 2,000 RPM for 1 minute. Cells were suspended in TAP media with the noted concentration of Calcofluor White (CFW) stain (Sigma-Aldrich, SKU 18909) for 10 minutes while rotating at ambient temperature. Afterward, cells were washed twice in fresh TAP media. For initial protocol development, cells were immediately imaged after washes. For the datasets quantified in this pub, cells were fixed in freshly made 4% paraformaldehyde in PBS for 15 minutes at ambient temperature while protected from light. Fixed cells were washed twice in PBS and stored at 4 C until imaged. <br><br>We acquired micrographs with a Yokogawa CSU W1-SoRa scanner unit attached to a Nikon Ti2-E confocal microscope. We used a Plan Apo λ 40× air objective to collect images using standard DAPI channel settings. We acquired images at the medial focal plane of the cells in the field of view.<br><br>File Name Description: <br>[well position]_[strain number]_[Treatment]_[prep]_[microscope]_[secondary magnification]_[image number]<br><br>The code to analyze these images is available on GitHub</p>
Chlamydomonas pacifica Lipid Transcription Factors
<p>Contains the plasmid sequence for <span>pJPCHx1_CpaDpWRI1, pJPCHx1_CpaAtWRI1, pJPCHx1_CpaMYB6, pJPCHx1_CpabZIP1, pJPCHx1_CpaSPL12, pJPCHx1_CpaPSR1, pJPCHx1_CpaCHT7, pJPCHx1_CpaNRR1, and pJPCHx1_CpaLRL1.</span></p>
FIGURE 5 in Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses
FIGURE 5. Secondary structures of ITS-1 rDNA sequences among the species of Chlamydomonas, A. C. schloesseri, B. C. incerta, and C. C. reinhardtii. CBCs and HCBCs are marked in black and grey, respectively.
FIGURE 1 in Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses
FIGURE 1. Morphology and phenotypic plasticity of Chlamydomonas schloesseri sp. nov. A–J. vegetative cells, arrow in F. marked the eyespot; K–O. different sporangia; scale bar = 10 μm.
FIGURE 8 in Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses
FIGURE 8. Comparison of the amino acid composition of the rbcL gene among the species of Chlamydomonas. The IUPAC symbols were used for the amino acids.
FIGURE 4 in Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses
FIGURE 4. Molecular phylogeny of Chlamydomonas and representatives belonging to the Tetrabaenaceae and Goniaceae based on rbcL and ITS rDNA sequence comparisons. The phylogenetic trees shown were inferred using the maximum likelihood method based on the data sets (29 taxa: 915 aligned positions for ITS, 1128 for rbcL) using PAUP 4.0b10. For the analyses the best model was calculated by Modeltest 3.7. The setting of the best model was given as follows: (ITS) GTR+I+G (base frequencies: A 0.2634, C 0.2225, G 0.2192, T 0.2949; rate matrix A-C 1.2503, A-G 2.1014, A-U 2.0643, C-G 0.3957, C-U 3.3009, G-U 1.0000) with the proportion of invariable sites (I = 0.2682) and gamma shape parameter (G = 0.6858); (rbcL) GTR+I+G (base frequencies: A 0.2777, C 0.1688, G 0.2048, T 0.3487; rate matrix A-C 0.2771, A-G 3.5238, A-U 4.0693, C-G 0.6646, C-U 7.4921, G-U 1.0000) with the proportion of invariable sites (I = 0.5523) and gamma shape parameter (G = 0.6480). The branches in bold are highly supported in all analyses (Bayesian values> 0.95 calculated with PHASE and MrBayes; bootstrap values> 70% calculated with PAUP using maximum likelihood, neighbor-joining, maximum parsimony and RAxML using maximum likelihood). The Goniaceae are only weakly supported in bootstrap and Bayesian analyses, which is indicated by an asterisk.
FIGURE 7 in Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses
FIGURE 7. Comparison of the conserved region of ITS-2 among the species of Chlamydomonas. Extraction of this region and translation into a number code for its usage as barcode (extracted bases highlighted with an asterisk). Number code for each base pair: 1 = A-U; 2 = U-A; 3 = G-C; 4 = C-G; 5 = G•U; 6 = U•G; 7 = mismatch.
FIGURE 6 in Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses
FIGURE 6. Secondary structures of ITS-2 rDNA sequences among the species of Chlamydomonas, A. C. schloesseri, B. C. incerta, and C. C. reinhardtii. CBCs and HCBCs are marked in black and grey, respectively.
FIGURE 3 in Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses
FIGURE 3. Molecular phylogeny of Chlamydomonas and representatives belonging to the Tetrabaenaceae, Goniaceae and Volvocaceae based on SSU and ITS rDNA sequence comparisons. The phylogenetic trees shown were inferred using the maximum likelihood method based on the data sets (2688 aligned positions of 75 taxa) using PAUP 4.0b10. For the analyses the best model was calculated by Modeltest 3.7. The setting of the best model was given as follows: GTR+I+G (base frequencies: A 0.2516, C 0.2232, G 0.2514, T 0.2738; rate matrix A-C 1.3107, A-G 2.3565, A-U 2.4706, C-G 0.4123, C-U 4.2284, G-U 1.0000) with the proportion of invariable sites (I = 0.6048) and gamma shape parameter (G = 0.3904). The branches in bold are highly supported in all analyses (Bayesian values> 0.95 calculated with PHASE and MrBayes; bootstrap values> 70% calculated with PAUP using maximum likelihood, neighbor-joining, maximum parsimony and RAxML using maximum likelihood). The Goniaceae are only moderated supported in bootstrap and Bayesian analyses, which is indicated by an asterisk.
FIGURE 2 in Chlamydomonas schloesseri sp. nov. (Chlamydophyceae, Chlorophyta) revealed by morphology, autolysin cross experiments, and multiple gene analyses
FIGURE 2. Lysis of sporangium cell wall under influence of the VLE autolysin in Chlamydomonas schloesseri (SAG 2485); scale bar = 10 μm.
Cell size, chlorophyll fluorescence and cadmium bioaccumulation between wild-type and mutant strains of Chlamydomonas reinhardtii upon exposure to cadmium
<p>Heavy metal contamination presents a constant threat to biological systems. Simultaneously, heavy metals have become one of the major contaminants in the aquatic ecosystem. In this regard, the investigation of heavy metal-tolerance genes in algae is relevant. <i>Chlamydomonas reinhardtii</i> is a unicellular green alga, and an excellent model organism used in heavy metal studies. In <i>C. reinhardtii</i>, a novel gene designated as Cia7, was hypothesized to play a role in heavy metal homeostasis due to CIA7's conserved cysteine-residue motif. This study compared two strains of <i>C. reinhardtii</i>, cc4425, the wild-type possessing the functional CIA7 protein and cc5013, the mutant strain possessing the disrupted cia7- gene. The hypothesis was that the expression of Cia7 contributes to an increased cadmium (Cd)-tolerance in <i>C. reinhardtii</i>. The Cd-tolerance would be described by physiological markers of microalgae health, and by intracellular accumulation of the metal. Methods: The objectives of this study were (1) to compare chlorophyll fluorescence and cell size in cc4425 and cc5013 exposed to Cd<sup>2+</sup>, and (2) to compare Cd<sup>2+</sup> bioaccumulation in cc4425 and cc5013 strains in different growth media. Flow cytometry, and inductively coupled plasma optical emission spectrometry (ICP-OES) analysis were performed. Results: There was no significant statistical difference in Cd<sup>2+</sup> bioaccumulation between the two strains, cc4425 and cc5013, regardless of growth media. However, a statistically significant difference in Cd<sup>2+</sup> bioaccumulation (p<0.0001) was determined between the media (with acetate and without acetate). The cia7- mutant, cc5013 was found to be more susceptible to a Cd<sup>2+</sup>-induced decrease in chlorophyll fluorescence and had a reduced cell size compared to cc4425, the wild-type strain. Conclusions: These observed differences between the strains suggest that CIA7's biological activity could play a direct or indirect role in increasing Cd tolerance in <i>C. reinhardtii</i>.</p>
A PETase enzyme synthesised in the chloroplast of the microalga Chlamydomonas reinhardtii is active against PET and polystyrene
<p>The list contains:</p> <p>1) raw data for chromatographies: HiprepSPHP and SEC</p> <p>2) raw data for UV-vis Spectrum</p> <p>3) raw data for all MS/MS spectra manuscript + supplementary</p> <p>4) raw data for AFM </p> <p>5) report data from HPLC</p>
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