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148 results for “Chlamydomonas”
Plasmid Maps for a Nuclear Transformation Vector in Chlamydomonas reinhardtii for the Expression and Secretion of the Plastic-Degrading Enzyme (PHL7)
<p><strong>pJP32PHL7 Vector:</strong></p> <ul> <li> <p><strong>Size:</strong> 5692 bp</p> </li> <li> <p><strong>Key Features:</strong></p> <ul> <li><strong>HSP70 Promoter:</strong> A heat shock protein promoter fused with the <em>rbcS2</em> promoter to drive expression of downstream genes.</li> <li><strong>Ble Resistance Gene:</strong> Confers resistance to bleomycin, useful for selection in <em>Chlamydomonas reinhardtii</em>.</li> <li><strong>PHL7 Gene:</strong> Encodes the plastic-degrading enzyme PHL7, inserted downstream of the <em>F2A</em> site for expression in the host.</li> <li><strong>Intron Sequences:</strong> Contains multiple <em>rbcS2</em> introns for enhancing expression in <em>Chlamydomonas</em>.</li> <li><strong>Selectable Marker (AmpR):</strong> Confers ampicillin resistance for selection in <em>E. coli</em>.</li> <li><strong>Replication Origin:</strong> Includes <em>ori</em> and <em>F1 ori</em> for replication in <em>E. coli</em>.</li> </ul> <p> </p> </li> <li> <p><strong>Applications:</strong> This vector is designed for nuclear transformation in <em>Chlamydomonas reinhardtii</em>, enabling the expression and secretion of the plastic-degrading enzyme (PHL7) under the control of a hybrid <em>HSP70</em>rbcS2 promoter.</p> </li> </ul> <p><strong>pJP32PHL7dg Vector:</strong></p> <ul> <li> <p><strong>Size:</strong> 5692 bp</p> </li> <li> <p><strong>Key Features:</strong></p> <ul> <li><strong>HSP70 Promoter:</strong> Retains the HSP70 and <em>rbcS2</em> fusion promoter for gene expression.</li> <li><strong>LacZ Alpha Fragment:</strong> Includes a LacZ alpha fragment for blue/white screening.</li> <li><strong>PHL7 Gene:</strong> Encodes the plastic-degrading enzyme PHL7, linked downstream of the <em>F2A</em> site, allowing for expression in the host.</li> <li><strong>Ble Resistance Gene:</strong> Also confers bleomycin resistance for selection in <em>Chlamydomonas</em>.</li> <li><strong>Selectable Marker (AmpR):</strong> Confers ampicillin resistance for selection in <em>E. coli</em>.</li> <li><strong>Intron Sequences:</strong> Contains <em>rbcS2</em> introns for optimizing gene expression in the host organism.</li> </ul> <p> </p> </li> <li> <p><strong>Applications:</strong> The pJP32PHL7dg vector is similarly designed for nuclear transformation in <em>Chlamydomonas reinhardtii.</em> It also facilitates the expression and secretion of the plastic-degrading enzyme PHL7, driven by the hybrid <em>HSP70</em>rbcS2 promoter, but without glycosilation sites.</p> </li> </ul>
Phenotypic differences between interfertile Chlamydomonas species- measurements, Cellprofiler
<p>This repository contains 2D morphology measurements from timelapse microscopy data of two interfertile <i>Chlamydomonas</i> algal species. 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>, and summarized here. Cells were collected from agar plates and suspended in water, then left to sit overnight to encourage gamete formation. During this time, non-motile cells settled, allowing for the enrichment of motile cells in the supernatant. These enriched cells were then loaded onto agar microchambers (100 micron diameter and 40 micron depth) for imaging. We collected videos on a Nikon Ti2-E microscope equipped with a Photometrics Kinetix digital scMos camera. We performed differential interference contrast (DIC) imaging using a Plan Apo 10× 0.45 Air objective. We collected videos with a 5.1 ms exposure with acquisition every 50 ms for three minutes. We placed a red light filter [IR longpass, 610 nm (ThorLabs)] in the light path to maintain swimming behavior of cells. The procedure was standardized and repeated four times to ensure consistency. Measurements collected with Cellprofiler of timelapse data of <i>C. reinhardtii </i>or C<i>. smithii </i>cells in agar microchamber wells are shared here.</p><h4>Reference</h4><p><a href="https://doi.org/10.57844/arcadia-35f0-3e16">Essock-Burns T, Garcia III G, MacQuarrie CD, Mets DG, York R. (2023). Phenotypic differences between interfertile <i>Chlamydomonas </i>species</a></p><h4>Notes</h4><p>Directory and subdirectories containing csv files of measurements of algal cells segmented from images.<br><br>Directory structure: experiments_csv/{experiment}/{video_length}/objects/{species}/{microchamber AKA "pool ID"}/measurements/measurementschlamy.csv</p><p>"Cr" indicates <i>Chlamydomonas reinhardtii</i></p><p>"Cs" indicates <i>Chlamydomonas smithii</i></p>
Phenotypic differences between interfertile Chlamydomonas species- focus-filtered timelapse data and measurements
<p>This repository contains focus-filtered timelapse microscopy data of two interfertile <i>Chlamydomonas</i> algal species. 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>, and summarized here. Cells were collected from agar plates and suspended in water, then left to sit overnight to encourage gamete formation. During this time, non-motile cells settled, allowing for the enrichment of motile cells in the supernatant. These enriched cells were then loaded onto agar microchambers (100 micron diameter and 40 micron depth) for imaging. We collected videos on a Nikon Ti2-E microscope equipped with a Photometrics Kinetix digital scMos camera. We performed differential interference contrast (DIC) imaging using a Plan Apo 10× 0.45 Air objective. We collected videos with a 5.1 ms exposure with acquisition every 50 ms for three minutes. We placed a red light filter [IR longpass, 610 nm (ThorLabs)] in the light path to maintain swimming behavior of cells. The procedure was standardized and repeated four times to ensure consistency. Focus-filtered timelapse data of <i>C. reinhardtii </i>or C<i>. smithii </i>cells in agar microchamber wells are shared here. The code for focus-filtering and collection of measurements can be found in the <a href="https://github.com/Arcadia-Science/chlamy-comparison">associated Github repository</a>.</p><h4>Reference</h4><p><a href="https://doi.org/10.57844/arcadia-35f0-3e16">Essock-Burns T, Garcia III G, MacQuarrie CD, Mets DG, York R. (2023). Phenotypic differences between interfertile <i>Chlamydomonas </i>species</a></p><h4>Notes</h4><p>In addition to the raw data, the dataset includes sample images that are intermediates in the image processing pipeline, as well as 2D morphology measurements of the cells in a csv file.</p><p>"Cr" indicates <i>Chlamydomonas reinhardtii</i></p><p>"Cs" indicates <i>Chlamydomonas smithii</i></p><p>Frame rate: 20 frames per second (fps)</p><p>Pixel size: 0.6398 microns/pixel</p>
Competitive growth experiments with a high-lipid Chlamydomonas reinhardtii mutant strain and its wild-type to predict industrial and ecological risks
<p>Key microalgal species are currently being exploited as biomanufacturing platforms using mass cultivation systems. The opportunities to enhance productivity levels or produce non-native compounds are increasing as genetic manipulation and metabolic engineering tools are rapidly advancing. Regardless of the end product, there are both environmental and industrial risks associated to open pond cultivation of mutant microalgal strains. A mutant escape could be detrimental to local biodiversity and increase the risk of algal blooms. Similarly, if the cultivation pond is invaded by a wild-type microalgae or the mutant reverts to wild-type phenotypes, productivity could be impacted. To investigate these potential risks, a response surface methodology was applied to determine the competitive outcome of two <em>Chlamydomonas reinhardtii</em> strains, a wild-type (CC-124) and a high-lipid accumulating mutant (CC-4333), grown in mixotrophic conditions, with differing levels of nitrogen and initial wild-type to mutant ratios. Results of the growth experiments show that mutant cells have double the exponential growth rate of the wild-type in monoculture. However, due to a slower transition from lag phase to exponential phase, mutant cells are outcompeted by the wild-type in every co-culture treatment. This suggests that, under the conditions tested, outdoor cultivation of the <em>C. reinhardtii</em> cell wall-deficient mutant strains does not carry a significant environmental risk to its wild-type in an escape scenario. Furthermore, lipid results show the mutant strain accumulates over 200% more TAGs per cell, at 50 mg/L NH<sub>4</sub>Cl, compared to the wild-type, therefore, the fragility of the mutant strain could impact on overall industrial productivity.</p>
In silico identified signal peptides of Chlamydomonas reinhardtii
<p><strong>Overview</strong></p> <p><em>Chlamydomonas reinhardtii </em>theoretical signal peptides identified by<em> </em>SignalP 4.0 in a protein data set described below:</p> <ul> <li>Protein data set came from "The Genome Portal of the Department of Energy Joint Genome Institute" (http://genome.jgi.doe.gov/)</li> <li>Protein sequences were evaluated in SignalP 4.0 Server (http://www.cbs.dtu.dk/services/SignalP/)</li> </ul> <p> </p> <p><strong>File used</strong></p> <p>Chlre4_best_proteins.fasta.gz -> Protein dataset version used for analysis</p> <p> </p> <p><strong>Workflow</strong> </p> <p> ______Chlre4_best_proteins.fasta.gz_______</p> <p> | |</p> <p> Chlre4_best_proteins_fasta_protein_woSP.fasta Chlre4_best_proteins_signalPeptide.fasta</p> <p> |</p> <p> ___Chlre4_best_proteins_signalPeptide_unique.fasta___</p> <p> | |</p> <p> Chlre4_best_proteins_signalPeptide_unique.aln Signal Peptide Anotation from aligned.xlsx</p> <p> </p> <p><strong>Info</strong></p> <p>Chlre4_best_proteins_fasta_protein_woSP.fasta -> Mature protein sequences from proteins identified without signal peptide</p> <p>Chlre4_best_proteins_signalPeptide.fasta -> Identified signal peptide</p> <p>Chlre4_best_proteins_signalPeptide_unique.fasta -> Unique identified signal peptide</p> <p>Chlre4_best_proteins_signalPeptide_unique.aln -> Align signal peptides (UGENE)</p> <p>Signal Peptide Annotation from aligned.xlsx -> Signal peptide list, highlighted in orange theoretical tested.</p> <p> </p> <p><strong>Citations</strong></p> <p>For use of signal peptide dataset, please cite:</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>and </p> <p><strong>SignalP 4.0: discriminating signal peptides from transmembrane regions</strong><br> Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen<br> <em>Nature Methods</em>, <strong>8</strong>:785-786, <strong>2011</strong><br> <br> doi: 10.1038/nmeth.1701<br> PMID: 21959131<br> Supplementary materials: nmeth.1701-S1.pd</p> <p>and </p> <p><strong>The genome portal of the Department of Energy Joint Genome Institute: 2014 updates</strong></p> <p>H. Nordberg, M. Cantor, S. Dusheyko, S. Hua, A. Poliakov, I. Shabalov, T. Smirnova, I. V. Grigoriev, I. Dubchak, ,</p> <p>Nucleic Acids Res. 42, 26–31. <strong>2014</strong> </p> <p>doi:10.1093/nar/gkt1069.</p> <p> </p>
Phenotypic differences between interfertile Chlamydomonas species- timelapse microscopy data, part 2
<p>This repository contains timelapse microscopy data of two interfertile <i>Chlamydomonas</i> algal species. 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>, and summarized here. Cells were collected from agar plates and suspended in water, then left to sit overnight to encourage gamete formation. During this time, non-motile cells settled, allowing for the enrichment of motile cells in the supernatant. These enriched cells were then loaded onto agar microchambers (100 micron diameter and 40 micron depth) for imaging. We collected videos on a Nikon Ti2-E microscope equipped with a Photometrics Kinetix digital scMos camera. We performed differential interference contrast (DIC) imaging using a Plan Apo 10× 0.45 Air objective. We collected videos with a 5.1 ms exposure with acquisition every 50 ms for three minutes. We placed a red light filter [IR longpass, 610 nm (ThorLabs)] in the light path to maintain swimming behavior of cells. The procedure was standardized and repeated four times to ensure consistency. Timelapse data of <i>C. reinhardtii </i>or C<i>. smithii </i>cells in agar microchamber wells from experiments "3" and "4" are shared here.</p><h4>Reference</h4><p><a href="https://doi.org/10.57844/arcadia-35f0-3e16">Essock-Burns T, Garcia III G, MacQuarrie CD, Mets DG, York R. (2023). Phenotypic differences between interfertile <i>Chlamydomonas </i>species</a></p><h4>Notes</h4><p>Experiment 3, performed on 230519: DIC timelapse data of <i>Chlamydomonas</i> cells swimming in agar microchamber wells. In some of the wells, external fluid movement modified the cell motility patterns.</p><p>Experiment 4, performed on 230523: DIC timelapse data of <i>Chlamydomonas </i>cells swimming in agar microchamber wells.</p><p>"Cr" indicates <i>Chlamydomonas reinhardtii</i></p><p>"Cs" indicates <i>Chlamydomonas smithii</i></p><p>Timelapse frames: 3601 frames</p><p>Frame rate: 20 frames per second (fps)</p><p>Pixel size: 0.6398 microns/pixel</p>
Phenotypic differences between interfertile Chlamydomonas species- timelapse microscopy data, part 1
<p>This repository contains timelapse microscopy data of two interfertile <i>Chlamydomonas</i> algal species. 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>, and summarized here. Cells were collected from agar plates and suspended in water, then left to sit overnight to encourage gamete formation. During this time, non-motile cells settled, allowing for the enrichment of motile cells in the supernatant. These enriched cells were then loaded onto agar microchambers (100 micron diameter and 40 micron depth) for imaging. We collected videos on a Nikon Ti2-E microscope equipped with a Photometrics Kinetix digital scMos camera. We performed differential interference contrast (DIC) imaging using a Plan Apo 10× 0.45 Air objective. We collected videos with a 5.1 ms exposure with acquisition every 50 ms for three minutes. We placed a red light filter [IR longpass, 610 nm (ThorLabs)] in the light path to maintain swimming behavior of cells. The procedure was standardized and repeated four times to ensure consistency. Timelapse data of <i>C. reinhardtii </i>or C<i>. smithii </i>cells in agar microchamber wells from experiments "1" and "2" are shared here.</p><h4>Reference</h4><p><a href="https://doi.org/10.57844/arcadia-35f0-3e16">Essock-Burns T, Garcia III G, MacQuarrie CD, Mets DG, York R. (2023). Phenotypic differences between interfertile <i>Chlamydomonas </i>species</a></p><h4>Notes</h4><p>Experiment 1, performed on 230509: This experiment was meant to include DIC timelapse data, but a DIC polarizer was not inserted during the data collection. The resulting data was effectively brightfield data.</p><p>Experiment 2, performed on 230516: DIC timelapse data of <i>Chlamydomonas</i> cells swimming in agar microchamber wells.</p><p>"Cr" indicates <i>Chlamydomonas reinhardtii</i></p><p>"Cs" indicates <i>Chlamydomonas smithii</i></p><p>Timelapse frames: 3601 frames</p><p>Frame rate: 20 frames per second (fps)</p><p>Pixel size: 0.6398 microns/pixel<br> </p>
Characterization of the nuclear proteome of Chlamydomonas in response to salt stress
<p><strong>Supplementary Files and Figures for the manuscript </strong></p> <p><strong>"Characterization of the nuclear proteome of Chlamydomonas in response to salt stressCharacterization of the nuclear proteome of Chlamydomonas in response to salt stress"</strong></p>
Dataset for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."
<p>Plasmid sequences for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."</p>
Phenotypic differences between interfertile Chlamydomonas species- high-resolution confocal z-stacks for visualizing organelle morphology
<p>This repository contains high-resolution confocal z-stacks of two interfertile <i>Chlamydomonas</i> algal species. The protocol to generate this data is described in the associated publication, "Phenotypic differences between interfertile <i>Chlamydomonas</i> species", and briefly summarized here. Cells were collected from agar plates with TAP medium and suspended in 500 µl of liquid TAP medium in a 1.5 ml eppendorf tube overnight. Cells were pelleted using a microcentrifuge at 2000 x g for 2 min and the supernatant removed. For staining mitochondria, PKMito orange was used at a 1:500 concentration and cells were moved to opaque black microcentrifuge tubes and placed on a tube rotator for 45 min. Cells were pelleted again and washed twice with fresh TAP medium. After the final wash and supernatant removal, cells were resuspended in 25 µl of 1.25% low gelling agar in TAP medium (kept at 45 C). Then 1 µl of the cell/agar mixture was mounted on a #1.5 coverslip with a small wax circle drawn to retain the droplet. Coverslips were flipped and placed on a slide and sealed with VALAP. </p><p>Images were collected on a Nikon CSU W-1 SoRA spinning disk confocal microscope equipped with an ORCA-Fusion BT digital scMOS camera. In order to apply deconvolution in the downstream processing, we needed to oversample (sample beyond Nyquist) in z resolution. To do this, we used a 100×/1.45 NA objective in 2.8× SoRa magnification mode, using ROIs of either 670 × 670 × 81 or 850 × 850 × 91. We imaged with a z-step size of 100 nm for sub-Nyquist sampling. We imaged bright-field first, then 640 nm excitation autofluorescence of chloroplasts, and then 561 nm excitation for PKmito orange dye, because the chloroplasts would bleach after 561 nm excitation. We set exposures to 300 ms with 30% and 50% laser power for 640 and 561, respectively.</p><p>We have included a set of demo data (10 images per species) that accompany the pub hosted on the Arcadia Science webpage (3Dmorpho_demo_data). In addition, we included all of the raw data we collected in this experiment (3Dmorpho_raw_data). Please use the point spread functions (PSF) from the zipped folders for each respective dataset (demo or raw). </p>
Chlamydomonas pacifica (CC-5697 or CC-5699) Genomic Data
<p>Here is a brief description of each file in this dataset: -</p> <ol> <li>"<strong>Cpacifica_genome_assembly.fasta</strong>": Genome assembly sequence data.</li> <li>"<strong>Cpacifica_protein_sequences.faa</strong>": Protein sequences for all identified proteins.</li> <li>"<strong>Cpacifica_proteins_coding_sequence.codingseq</strong>": Coding DNA sequences for all proteins.</li> <li>"<strong>Cpacifica_transcriptomic_data.gtf</strong>": Predicted transcript data.</li> </ol>
Membrane mesh and tomogram of the Chlamydomonas chloroplast
<p>Membrane mesh and tomogram of the Chlamydomonas chloroplast. These data were originally published in <a href="https://doi.org/10.7554/eLife.53740">Wietrzynski and Schaffer et al., eLife, 2020</a>. The tomograms were accessed from <a href="https://www.ebi.ac.uk/emdb/EMD-10780">EMD-10780</a>.</p>
Intelligent image-activated sorting of Chlamydomonas reinhardtii by mitochondrial localization
<p>Data for image-based cell sorting based on complex intracellular morphology taken with an imaging flow cytometer</p> <p>Includes: </p> <p>Flow cytometry images of two strains of microalgae </p> <p>6-layer CNN model used for real-time cell sorting</p> <p>meta-data for the CNN containing the parameters used for creating the CNN model</p> <p>Validation images of the image-based sorting experiments.</p>
Developmental changes in ciliary composition during gametogenesis in Chlamydomonas
<p><em>Chlamydomonas reinhardtii</em> transitions from mitotically dividing vegetative cells to sexually competent gametes of two distinct mating types following nutrient deprivation. Gametes of opposite mating type interact via their cilia, initiating an intraciliary signaling cascade and ultimately fuse forming diploid zygotes. The process of gametogenesis is genetically encoded and a previous study revealed numerous significant changes in mRNA abundance during this life cycle transition. Here we describe a proteomic analysis of cilia derived from vegetative and gametic cells of both mating types in an effort to assess the global changes that occur within the organelle during this process. We identify numerous membrane and/or matrix-associated proteins in gametic cilia that were not detected in cilia from vegetative cells. This includes the pro-protein from which the GATI-amide gametic chemotactic modulator derives, as well as receptors, a dynamin-related protein, ammonium transporters, two proteins potentially involved in the intraciliary signaling cascade-driven increase in cAMP, and multiple proteins with a variety of interaction domains. These changes in ciliary composition likely directly affect the functional properties of this organelle as the cell transitions between life cycle stages.</p>
Seven Fluorescent proteins profile in Chlamydomonas reinhardtii and R code statistic for analysis
<p><strong>Overview</strong></p> <p>Data points present in this dataset were obtained following the protocol described in dx.doi.org/10.17504/protocols.io.kfnctme. We picked transformed colonies and cultured in 400 μL TAP medium for 7 days in Deep-well plates (Corning Axygen®, No.: PDW500CS, Thermo Fisher Scientific Inc., Waltham, MA), covered with Breathe-Easy® (Sigma-Aldrich®). Cultivation was performed on a rotary shaker, set to 150 rpm, under constant illumination (50 μmol photons/m<sup>2</sup>s). Then 100 μL sample were transferred clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA) and fluorescence was measured using an Infinite® M200 PRO plate reader (Tecan, Männedorf, Switzerland). Supernatant samples were obtained by spinning Deep-well plates at 3000 × <em>g</em> for 10 min and transferring 100 μL from each well to the clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA), followed by fluorescence measurement. To compare the constructs, R Statistic version 3.3.3 was used to perform one-way ANOVA (with Tukey's test), and to test statistical hypotheses, the significance level was set at 0.05. Graphs were generated in RStudio v1.0.136. The codes are deposit herein.</p> <p><strong>Info</strong></p> <p>ANOVA_Turkey_Sub.R -> code for ANOVA analysis in R statistic 3.3.3</p> <p>Anova_Output_Summary_Guide.pdf -> Explain the ANOVA files content</p> <p>Analysis_Raw_FP.xlsx -> File with raw values organized in a spreadsheet </p> <p>pRFU_<strong>FLUORESCENT PROTEIN</strong>_+_bk.csv -> relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii </em></p> <p>sup_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.csv -> supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.csv -> whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>pRFU_<strong>FLUORESCENT PROTEIN</strong>_+_bk.doc -> ANOVA of relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>sup_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.doc -> ANOVA of supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.doc -> ANOVA of whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p> </p> <p><strong>Consider citing our work. </strong></p> <p>1. Molino JVD, de Carvalho JCM, Mayfield S. Evaluation of secretion reporters to microalgae biotechnology: blue to red fluorescent proteins. Algal Res. 2018;31: 252–261. doi:10.1016/j.algal.2018.02.018</p>
Twin colony isolate genome assemblies: Chlamydomonas 3112/3222 and WS3/WS7 and Scenedesmus ARA/ARA3
<p>Genomes and assemblies for twin isolate pairs from:</p> <p>David R. Nelson, Amphun Chaiboonchoe, Weiqi Fu, Khaled M. Hazzouri, Ziyuan Huang, Ashish Jaiswal, Sarah Daakour, Alexandra Mystikou, Marc Arnoux, Mehar Sultana, Kourosh Salehi-Ashtiani,<br>Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae,<br>iScience,<br>Volume 11,<br>2019,<br>Pages 450-465,<br>ISSN 2589-0042,<br>https://doi.org/10.1016/j.isci.2018.12.035.<br>(https://www.sciencedirect.com/science/article/pii/S2589004218302657)</p> <p>Abstract: Summary<br>The activities of microalgae support nutrient cycling that helps to sustain aquatic and terrestrial ecosystems. Most microalgal species, especially those from the subtropics, are genomically uncharacterized. Here we report the isolation and genomic characterization of 22 microalgal species from subtropical coastal regions belonging to multiple clades and three from temperate areas. Halotolerant strains including Halamphora, Dunaliella, Nannochloris, and Chloroidium comprised the majority of these isolates. The subtropical-based microalgae contained arrays of methyltransferase, pyridine nucleotide-disulfide oxidoreductase, abhydrolase, cystathionine synthase, and small-molecule transporter domains present at high relative abundance. We found that genes for sulfate transport, sulfotransferase, and glutathione S-transferase activities were especially abundant in subtropical, coastal microalgal species and halophytic species in general. Our metabolomics analyses indicate lineage- and habitat-specific sets of biomolecules implicated in niche-specific biological processes. This work effectively expands the collection of available microalgal genomes by ∼50%, and the generated resources provide perspectives for studying halophyte adaptive traits.<br>Keywords: Global Nutrient Cycle; Phycology; Genomics; Metabolomics</p> <p>https://www.sciencedirect.com/science/article/pii/S2589004218302657</p> <p> </p> <p>Files are as follows:</p> <p> </p> <p>.fa = assembly</p> <p>.tr.fa = coding sequences</p> <p>.aa.fa = predicted proteins</p> <p>.gff = annotation files</p>
Supplementary videos of "Description of a novel extremophile green algae, Chlamydomonas pacifica, and its potential as a biotechnology host" Molino et al
<p><strong>Supplementary Video 1: </strong>Motility tracking of <em>C. pacifica</em> - (Raw_402_Video_1.mp4)</p> <p> </p> <p><strong>Supplementary Video 2: </strong>Motility tracking of <em>C. pacifica</em> - (Raw_402_Video_2.mp4)</p> <p> </p> <p><strong>Supplementary Video 3:</strong> Motility tracking of <em>C. pacifica</em> - (Raw_402_Video_3.mp4)</p> <p> </p> <p><strong>Supplementary Video 4:</strong> Motility tracking of <em>C. pacifica</em> - (TrackMate capture of Video_1_402.avi)</p> <p> </p> <p><strong>Supplementary Video 5: </strong>Motility tracking of <em>C. pacifica</em> - (TrackMate capture of Video_2_402.avi)</p> <p> </p> <p><strong>Supplementary Video 6:</strong> Motility tracking of <em>C. pacifica</em> - (TrackMate capture of Video_3_402.avi)</p> <p> </p> <p><strong>Supplementary Video 7:</strong> Mating video 1 - (Starting to aggregate 402 403.avi)</p> <p> </p> <p><strong>Supplementary Video 8:</strong> Mating video 2 - (Fusing_cell_wall_motility.avi)</p> <p> </p> <p> </p>
The effects of sex on extinction dynamics of Chlamydomonas reinhardtii depend on the rate of environmental change
<p>The continued existence of sex, despite many the costs it entails, still lacks an adequate explanation, as previous studies demonstrated that the effects of sex are environment-dependent: sex enhances the rate of adaptation in changing environments, but the benefits level off in benign conditions. To the best of our knowledge, the potential impact of different patterns of environmental change on the magnitude of these benefits received less attention in theoretical studies. In this paper, we begin to explore this issue by examining the effect of the rate of environmental deterioration (negatively correlated with population survival rate), on the benefits of sex.</p> <p>To investigate the interplay of sex and the rate of environmental deterioration, we carried out a long-term selection experiment with a unicellular alga (<em>Chlamydomonas</em> <em>reinhardtii</em>), by manipulating mode of reproduction (asexual, facultative or obligate sexual) and the rate of environmental deterioration (an increase of salt concentration). We monitored both the population size and extinction dynamics.</p> <p>The results revealed that the relative advantage of sex increased at the intermediate rate and plateaued at the highest rate of environmental deterioration. Obligate sexual populations had the slowest extinction rate under the intermediate rate of environmental deterioration, while facultative sexuality was favoured under the high rate-treatment.</p> <p>To the best of our knowledge, our study is the first to demonstrate that the interplay of sex and the rate of environmental deterioration affects the probability of survival, which indicates that mode of reproduction may be an important determinant of survival of the anthropogenic-induced environmental change.</p>
Chlamydomonas cilia proteins
<p>Axonemal dyneins are highly complex molecular motors that power ciliary motility. These multi-subunit enzymes are assembled at dedicated sites within the cytoplasm. At least nineteen cytosolic factors are specifically needed for the generation of dynein holoenzymes and/or their trafficking to the growing cilium. Many proteins are subject to N-terminal processing and acetylation which can generate degrons subject to the AcN-end rule and alter N-terminal electrostatics, generate new binding interfaces, and affect subunit stoichiometry through targeted degradation. Here we have used mass spectrometry of cilia samples and electrophoretically purified dynein heavy chains from <em>Chlamydomonas</em> to define their N-terminal processing; we also detail the N-terminal acetylase complexes present in this organism. We identify four classes of dynein heavy chain based on their processing pathways by two distinct acetylases one of which is dependent on methionine aminopeptidase activity. In addition, we find that one component of both the outer dynein arm intermediate/light chain subcomplex and the docking complex are processed to yield an unmodified Pro residue which may provide a setpoint to direct the cytosolic stoichiometry of other dynein complex subunits that contain N-terminal degrons. Thus, we identify an additional level of processing and complexity in the pathways leading to axonemal dynein formation in cytoplasm. </p>
Cultivation of Chlamydomonas cells
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