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380 results for “co-culture”
Deep reinforcement learning for the control of microbial co-cultures in bioreactors
<p>Data for the figures in the paper:<br> <a href="https://www.biorxiv.org/content/10.1101/457366v2">https://www.biorxiv.org/content/10.1101/457366v2</a><br> (in press PLoS Comp Biol.)</p> <p>Abstract:<br> Multi-species microbial communities are widespread in natural ecosystems. When employed for biomanufacturing, engineered synthetic communities have shown increased productivity in comparison with monocultures and allow for the reduction of metabolic load by compartmentalising bioprocesses between multiple sub-populations. Despite these benefits, co-cultures are rarely used in practice because control over the constituent species of an assembled community has proven challenging. Here we demonstrate, in silico, the efficacy of an approach from artificial intelligence – reinforcement learning – for the control of co-cultures within continuous bioreactors. We confirm that feedback via reinforcement learning can be used to maintain populations at target levels, and that model-free performance with bang-bang control can outperform a traditional proportional integral controller with continuous control, when faced with infrequent sampling. Further, we demonstrate that a satisfactory control policy can be learned in one twenty-four hour experiment by running five bioreactors in parallel. Finally, we show that reinforcement learning can directly optimise the output of a co-culture bioprocess. Overall, reinforcement learning is a promising technique for the control of microbial communities.</p>
RNA sequencing of macrophages co-cultured with MSCs and RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCs
<p>RNA sequencing of macrophages co-cultured with MSCS Table 5</p> <p>RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCS Table 8</p>
Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript
<p>Supplementary videos for preprint manuscript: </p> <p><em>Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture</em><br> Liuba Dvinskikh, Hugh Sparks, Liliana Brito, Kenneth T MacLeod, Sian E Harding, Christopher Dunsby<br> bioRxiv 2023.01.28.526043; doi: https://doi.org/10.1101/2023.01.28.526043</p> <p>All videos have been rendered with JPEG compression.</p> <p>Shortened video captions (Please see supplementary information document for full caption)<br> <strong>Video 1:</strong> 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients. <br> <strong>Video 2:</strong> Widefield transillumination timelapse of hiPSC-CM and adult-CM <br> <strong>Video 3:</strong> Widefield fluorescence timelapse of hiPSC-CM and adult CM with synchronized spontaneous calcium transients. <br> <strong>Video 4a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 4b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 5a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 5b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture without NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 6a</strong>: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture undergoing synchronized spontaneous transients in a sample treated with NBleb. <br> <strong>Video 6b:</strong> Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture with NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 7a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 7b: </strong>Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture without NBleb. </p> <p> </p>
The raw microarray data and the differential expression analysis results from "Manipulating the growth environment through co-culture to enhance stress tolerance and viability of probiotic strains in the gastrointestinal tract".
<p>The signal data for each spot were subsequently quantified by using Feature Extraction software (Agilent Technologies).M1.txt to M5.txt: monoculture; C1.txt to C5.txt: co-culture; P1.txt to P5.txt: pH-controlled monoculture. The differential expression analysis results were obtained by using limma.</p>
Targeted DNA-seq analysis was performed on sorted population of CD45+/CD34+ HSPCs from control or FLI-1 modified mRNA treated mPB after co-culture with vascular niche cells
<p>Human mPB HSPCs were harvested isolated and transduced with either control or FLI-1 modified mRNA. HSPCs were introduced into co-culture with vascular niche ECs. Cultures were harvested and CD45+/CD34+ HSPCs were resoerted and processed for trageted DNA-seq analysis. Contains raw FASTQ sequencing files, unfiltered VCFs, and curated results in an excel.</p>
Analysis of Metabolomics Data to Assess Interactions in Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum
<p>This dataset refers to the metabolomics results from Metabolome Annotation QWorkflow on a co-culture of two microalgae: <em>Skeletonema marinoi </em>and <em>Prymnesium parvum</em>. The metabolomics data was acquired from endometabolome and exometabolome in both positive and negative MS modes. These will be referred as conditions. The files ms2_spectra_condition.mzML files have the MS2 combined from different MS2 files found on Zenodo with DOI: 10.5281/zenodo.10143233. The MS1 files are available on Zenodo as well with the DOI: 10.5281/zenodo.10143127</p> <p>The first section is about the results from the MS1 analysis. For the code used to generate these files, please refer to the code: <a href="https://github.com/zmahnoor14/MAW/tree/main/co-culture">https://github.com/zmahnoor14/MAW/tree/main/co-culture</a> </p> <ol> <li>Feature_info_condition.csv refers to the list of features with IDS, m/z, rt and intensity values. <ul> <li>The feature list is used to link the MS1 features to the features extracted from MS2 spectra.</li> </ul> </li> <li>Feature_list_condition.csv refers to the list of mzML origin file (samples) and the intensity of the features in those samples.</li> </ol> <p>The second section relates to the MS2 results. For source code please refer to: <a href="https://github.com/zmahnoor14/MAW/tree/main/Docker">https://github.com/zmahnoor14/MAW/tree/main/Docker</a></p> <ol> <li>SL_MAW_Coculture.csv contains list of metabolic features that were annotated and found to be present in the suspect list of either of the two organisms or both. The suspect lists for Skeletonema marinoi can be found at 10.5281/zenodo.5772755, and for Prymnesium parvum can be found at 10.5281/zenodo.7864506. </li> <li>unique_MAW_SMILES_coculture.csv file contains all information on unique SMILES.</li> <li>onlyDAF.csv contains differentially abundant features in either of the conditions: <em>S. marinoi </em>co-culture, <em>S. marinoi</em> mono-culture and similar conditions for <em>P. parvum</em>.</li> <li>condition_mergedResults-with-one-Candidates_sig_feat_for_only_inclusion.csv files contain all MS2 features and annotations together with the information on whether these features were found in the inclusion list (List provided for generating MS2 spectra in orbitrap), and whether these features were differential.</li> </ol>
Tandem Mass Spectrometry Data (LCMS-2) from Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum
<p>The mzML files in this dataset are the Liquid Chromatography Tandem Mass Spectrometry (LCMS-2) data files, derived from the RAW MS-2 files using GNPS file convertor. These files contain unprocessed features fragmented features from the MS-1 data files available as <10.5281/zenodo.10143127> acquired from the monocultures (single species: <em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em> separately) and co-culture conditions of (<em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em>). These files are used for structure annotations. </p> <p>The results of metabolomics annotation are available on Zenodo with DOI: 10.5281/zenodo.10143554</p>
Liquid Chromatography Mass Spectrometry Data (LCMS-1) from Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum
<p>The mzML files in this dataset are the Liquid Chromatography Mass Spectrometry Data (LCMS-1) data files, derived from the RAW MS files using GNPS file convertor. These files contain unprocessed features acquired from the monocultures (single species: <em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em> separately) and co-culture conditions of (<em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em>). The microalgae were grown in co-culture chambers, so the naming convention A, and B refer to the two sides of the chamber. So, 1a and 1b are <em>S. marinoi</em> monocultures, but 11a and 11b refer to s. marinoi and <em>P. parvum</em> respectively.</p> <p>The results of metabolomics data analysis are available on Zenodo with DOI: 10.5281/zenodo.10143554</p>
Transcriptome Analysis from a co-culture of Skeletonema marinoi and Prymnesium parvum
<p>This Zenodo entry refers to a study using metabolomics and transcriptomic data analysis to analyse chemical interactions between two microalgae: <em>Skeletonema marinoi</em> and <em>Prymnesium parvum</em></p> <p>p_parvum_Eukaryota_augustus_gene_prediction.faa file contains the predicted protein sequences from the transcriptome of <em>Prymnesium parvum</em> using Augustus. This list is generated from a non-restrictive Busco Analysis.</p> <p>s_costatum_Stramenopiles_augustus_gene_prediction.faa file contains the predicted protein sequences from the transcriptome of <em>Skeletonema marinoi </em>using Augustus. This list is generated from a restrictive Busco Analysis.</p> <p>The files p_parvum_deseq2_results_all.csv and s_marinoi_deseq2_results_all.csv contain differential gene expression analysis, while p_parvum_deseq2_result_sorted_regulated_with_proteins.csv and s_marinoi_deseq2_result_sorted_regulated_with_proteins.csv contain only upregulated protein sequences in co-culture conditions.</p> <p>The genes_read.R script is used to generate the p_parvum_deseq2_result_sorted_regulated_with_proteins.csv and s_marinoi_deseq2_result_sorted_regulated_with_proteins.csv. The code for analysis from RAW reads to differential gene expression analysis is available on: <a href="https://github.com/Bioinformatics-Core-Facility-Jena/SE20220705_97">https://github.com/Bioinformatics-Core-Facility-Jena/SE20220705_97</a>. The RAW files are available on BioProject: PRJNA1006530</p> <p> </p> <p> </p>
Raw NMR FID data of sesquiterpenes from co-culture of Phellinus orientoasiaticus and Xylodon flaviporus
<p>This is a NMR FID data of sesquiterpenoids isolated from co-culture of Phellinus orientoasiaticus and Xylodon flaviporus.</p> <p>Isolation and structural elucidation of these compounds will be reported in the article titled "Cyclohumulanoid Sesquiterpenes Induced by the Non-competitive Co-culture of Two Basidiomycetous Fungi, <em>Phellinus orientoasiaticus</em> and <em>Xylodon flaviporus</em>", which is currently under review.</p>
Multicolor flow cytometry of monocultures and co-cultures of Bacteroides species
<p>Dataset of FCS (Flow Cytometry Standard) files, along with meta-data, related to a flow cytometry analysis of monocultures and co-cultures of <em>Bacteroides </em>species under several different conditions. </p> <p><strong>Data Collection. </strong>This<strong> </strong>dataset accompanies a journal artcle which was published in <em>Frontiers in Microbiology</em> (<a href="https://doi.org/10.3389/fmicb.2022.910390">https://doi.org/10.3389/fmicb.2022.910390</a>). The "Methods and Materials" section in this article fully describes the biological nature of these samples and how the samples were processed for flow analysis and analyzed with flow cytometry. </p> <p><strong>Data Organization. </strong>Dataset includes 1832 samples. See mapping.xlsx and mapping_key.xlsx for list of samples and their meta-data. Folders are formatted as {run_data}_{time_point} and contains only samples belonging to either a run performed on 2018/07/17 or 2018/07/21 for time points of either 0, 24, 48, 72, or 102 hours. </p> <p><strong>Data Analysis. </strong>Code used for manipulating and analyzing these samples is publicly available (<a href="https://github.com/firasmidani/BacteroidesFlowCytometry">https://github.com/firasmidani/BacteroidesFlowCytometry</a>).</p> <p><strong>Data Integrity</strong>. "hardac-hashes.txt" stores the MD5 hashes of the original folders created by the authors prior to uploading data to Zenodo.</p>
3D co-culture of pleura
<p>Pleural mesothelial cells are the predominant cell type in the pleural cavity, but their role in the pathogenesis of pleural diseases needs to be further elucidated. 3D organotypic models are a encouraging approach for an <em>in vivo</em> understanding of molecular disease development. The aim of the present study was to develop a 3D organotypic model of the pleural mesothelium. Specimens of human <em>pleura parietalis</em> were obtained from patients undergoing surgery at the University Hospital Leipzig, Germany. 3D co-culture model of pleura was established from human pleural mesothelial cells and fibroblasts. The model was compared to human pleura tissue by phase-contrast and light microscopy, immunochemistry and -fluorescence as well as solute permeation test. Histological assessment of the 3D co-culture model displayed the presence of both cell types mimicking the morphology of the human pleura. Vimentin and Cytokeratin, PHD1 showed a similar expression pattern in pleural biopsies and 3D model. Expression of Ki-67 indicates the presence of proliferating cells. Tight junctional marker ZO-1 was found localized at contact zones between mesothelial cells. Each of these markers were expressed in both the 3D co-culture model and human biopsies. Permeability of 3D organotypic co-culture model of pleura was found to be higher for 70 kDa-Dextran and no significant difference was seen in the permeability for small dextran (4kDa). In summary, the presented 3D organoid of pleura functions as a robust assay for pleural research serving as a precise reproduction of the <em>in vivo</em> morphology and microenvironment.</p>
Remotely controlled 3D-engineered scaffolds for biomimetic in vitro investigations on brain cell co-cultures
Open the record for dataset details and reuse information.
Earthworm migration improves soil quality and modifies tri-trophic interactions with rice-fish co-culture
<p><strong>Earthworm migration improves soil quality and modifies tri-trophic interactions</strong> <strong>with rice-fish co-culture</strong></p>
hiPSC-CM and co-culture calcium dynamics videos
<p>Note: This version is now redundant - updated videos are available here: <br> <br> Dvinskikh, Liuba, Sparks, Hugh, Brito, Liliana, MacLeod, Kenneth T, Harding, Sian E, & Dunsby, Chris. (2023, January 29). Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript (Version 1). Zenodo. https://doi.org/10.5281/zenodo.7580163<br> <br> ---------------------------------------------------------------------------------------------</p> <p> </p> <p> </p> <p>Supplementary videos for manuscript " Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocyte in co-culture " <br> The videos included are the following: <br> <br> Video 1: 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients.<br> Video 2: Widefield transillumination timelapse of hiPSC-CM and adult-CM co-culture.<br> Video 3: Widefield epifluorescence timelapse of hiPSC-CM and adult-CM co-culture<br> Video 4: 3D LSFM timelapse of synchronized transients in hiPSC-CM and adult-CM co-culture.<br> Video 5a: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture, without NBleb.<br> Video 5b: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture, with NBleb.<br> </p>
Supplementary Videos S1-S2 3D co-culture spheroid formation containing A498-ST cells
<p><strong>Supplementary Videos S1-S2</strong></p> <p><strong>3D co-culture spheroid formation containing A498-ST cells </strong></p> <p>Representative movies (<strong>S1</strong>, bright field and <strong>S2,</strong> fluorescence stained) recorded for 24 hours of an A498-ST 3D co-culture capturing the kinetic formation of a 3D spheroid. 3D co-cultures harbor 70% tumor cells (A498-ST, green), 20% fibroblasts (NHDFα, blue) and 10% endothelial cells (ECRF24, red). Scalebar represents 1000 µm. </p>
Fig. 2 in Global metabolome analysis of Dunaliella tertiolecta, Phaeobacter italicus R11 Co-cultures using thermal desorption - Comprehensive two-dimensional gas chromatography - Time-of-flight mass spectrometry (TD-GC×GC-TOFMS)
Fig. 2. Workflow for sample preparation and injection. Culture samples were filtered and dried (A–B). Dried filter papers were placed in clean vials (C) and then resuspended in methanol (D) before being extracted with Chloroform (E). Water was added (F) and subsequently, the chloroform layer was aliquotted into GC vials (G) for further sample preparation. Extracts were dried (H) and then derivatized using a two-step methoximation/silylation process to yield derivatized extracts (I). 9-μL aliquots of derivatized extracts were automatically transferred to microvial inserts in thermal desorption tubes for injection (J) using an initial solvent vent step to remove excess solvent and derivatisation reagents (K), followed by thermal desorption to a cooled PTV inlet and subsequent splitless injection to the GC × GC-TOFMS system. Non-volatile residues from the extracts remained in the microvial insert for subsequent disposal (L). See text for details.
Fig. 4 in Global metabolome analysis of Dunaliella tertiolecta, Phaeobacter italicus R11 Co-cultures using thermal desorption - Comprehensive two-dimensional gas chromatography - Time-of-flight mass spectrometry (TD-GC×GC-TOFMS)
Fig. 4. From left to right: results of principal component analysis of the raw data (autoscaled), similarly scaled data normalised to class-specific TUPA, and the normalised, scaled data using the selected features from the FS-CR routine. Quality control samples were not included in the feature selection routine, and are displayed as filled icons connected to their corresponding replicate with a straight line, following projection into the optimised principal component space. Confidence ellipses were drawn about each sample class for a confidence interval of 0.95. Note the convention: DUN refers to D. tertiolecta samples, CO refers to co-culture samples, and BAC refers to P. italicus R11 samples.
Human iPSC-derived liver co-culture spheroids to model liver fibrosis
<div> <p><span>The lack of adequate human <em>in vitro</em> models that recapitulate the cellular composition and response of the human liver to injury hampers the development of anti-fibrotic drugs. The goal of this study was to develop a human spheroid culture model to study liver fibrosis by using induced pluripotent stem cell (iPSC)-derived liver cells. iPSCs were independently differentiated towards hepatoblasts (iHepatoblasts), hepatic stellate cells (iHSCs), endothelial cells (iECs) and macrophages (iMΦ), before assembly into free floating spheroids by culturing cells in 96-well U-bottom plates and orbital shaking for up to 21 days to allow further maturation. Through transcriptome analysis, we show further maturation of iECs and iMΦ, the differentiation of the iHepatoblasts towards hepatocyte-like cells <span> </span>(iHeps) and the inactivation of the iHSCs by the end of the 3D culture. Moreover, these cultures display a similar expression of cell-specific marker genes (<em>CYP3A4</em>, <em>PDGFRβ</em>, <em>CD31</em> and <em>CD68</em>) and sensitivity to hepatotoxicity as spheroids made using freshly isolated primary human liver cells. Furthermore, we show the functionality of the iHeps and the iHSCs by mimicking liver fibrosis through iHep-induced iHSC activation, using acetaminophen.<span> </span><br>In conclusion, we have established a reproducible human iPSC-derived liver culture model that can be used to mimic fibrosis <em>in vitro</em> as a replacement of primary human liver derived 3D models. The model can be used to investigate pathways involved in fibrosis development and to identify new targets for chronic liver disease therapy.</span></p> </div>
Fig. 3 in Global metabolome analysis of Dunaliella tertiolecta, Phaeobacter italicus R11 Co-cultures using thermal desorption - Comprehensive two-dimensional gas chromatography - Time-of-flight mass spectrometry (TD-GC×GC-TOFMS)
Fig. 3. Example Total Ion Current (TIC) chromatograms from each sample class.
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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.
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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.
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