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Dictyostelium discoideum

Dictyostelium discoideum is a species of slime mold that has become a valuable model organism for studying cell biology, development, and signaling pathways.
This soil-dwelling amoeba undergoes a unique life cycle, transitioning from a single-celled organism to a multicellular fruiting body in response to starvation.
Researchers utilize D. discoideum to investigate fundamental cellular processes such as chemotaxis, phagocytosis, and morphogenesis.
With its rapid growth, genetic tractability, and well-characterized behaviors, this organism offers an efficient system to elucidate conserved mechanisms across eukaryotes.
Exploring D. discoideum can provide insights into human disease pathways and lead to advancements in regenerative medicine and drug discovery.

Most cited protocols related to «Dictyostelium discoideum»

1
Cell Type Ontology Development
Cited 33 times
The ontology includes the major cell types from the major model organisms (for example, human, mouse, Drosophila, Caenorhabditis, zebrafish, Dictyostelium discoideum, Arabidopsis, fungi and prokaryotes). These cell types have been collated from our own knowledge, from major textbooks (for example [20 -22 ]), from the embryo and anatomy ontologies available on the OBO site [7 ], and from colleagues (who are thanked in the acknowledgements). The ontology currently holds some 680 cell types, together with their synonyms and, in most cases, text definitions.
The ontology was constructed using the open source Java tool OBO-Edit (previously known as DAG-Edit) [23 ], which is convenient for building ontologies that are consistent with the GO formalism. The resulting ontology is available in both the GO 'flat-file' format [24 ] and the newly defined 'OBO format' [25 ], and can easily be viewed using the OBO-Edit or the COBrA open source Java tool [26 ].
Bard J., Rhee S.Y, & Ashburner M. (2005). An ontology for cell types. Genome Biology, 6(2), R21.
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Publication 2005
Arabidopsis Caenorhabditis Cells Cobra Dictyostelium discoideum Drosophila Embryo Fungi Homo sapiens Mus Prokaryotic Cells Zebrafish
2
Compiling Public Genome and Proteome Datasets
Cited 14 times
From the UCSC genome database, we obtained ce6, priPac1, hg19 and monDom5. We downloaded the Arabidopsis thaliana and Dictyostelium discoideum genomes from the NCBI. We obtained PfalciparumGenomic_PlasmoDB-6.4.fasta from PlasmoDB and Physcomitrella_patens.1_1.fasta from JGI.
From UniProt Release 2010_08, we obtained all plant proteins (739 022 unique sequences) and all vertebrate proteins (592 943 unique sequences: including mammals, rodents and human).
, & Frith M.C. (2010). A new repeat-masking method enables specific detection of homologous sequences. Nucleic Acids Research, 39(4), e23.
Publication 2010
Arabidopsis thalianas Dictyostelium discoideum Genome Homo sapiens Mammals Physcomitrella Plant Proteins Proteins Rodent Vertebrates
3
Dictyostelium Cell Migration Dynamics
Cited 7 times

Dictyostelium discoideum cells, WT (AX3), adenylyl cyclase A null, and myosin II null (both aca− and myoII− are in an AX3 background) were prepared as described previously [8] (link). Unless otherwise specified, WT and aca− cells were developed for 5 hours. MyoII− cells were developed for 6 hours. Since myoII− cells do not divide in suspension culture, they were harvested directly from plate cultures. In electrostatic repulsion experiments, cells were washed and run in 10−3 diluted phosphate buffer (see [8] (link)). All cells, except in cliff experiments, were cytoplasmically dyed with CellTracker Green CDMFA (Invitrogen) [8] (link). Acrylic resin micro-cliffs were fabricated using multiphoton absorption polymerization [36] (link) (See text S1 for more information). For cliff experiments, phase-contrast images were obtained with a 10× objective every 1.55 seconds. For footprint and polarization experiments, fluorescence, phase contrast and internal reflection microscopy (IRM) images were captured with a 40× objective every 2 or 4 seconds. For electrostatic repulsion experiments, fluorescence images were obtained on a Leica TCS SP2 confocal microscope with a 100× objective every 2 seconds. For the remaining experiments, fluorescence images were obtained on the same confocal microscope with a 40× objective every 4 seconds.
Driscoll M.K., McCann C., Kopace R., Homan T., Fourkas J.T., Parent C, & Losert W. (2012). Cell Shape Dynamics: From Waves to Migration. PLoS Computational Biology, 8(3), e1002392.
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Publication 2012
5-chloromethylfluorescein diacetate Acrylic Resins Adenylate Cyclase Buffers Cells Dictyostelium discoideum Disgust Electrostatics Fluorescence Microscopy Microscopy, Confocal Microscopy, Phase-Contrast Myosin Type II Neoplasm Metastasis Phosphates Polymerization Reflex
4
Identification and Phylogenetic Analysis of Fungal ABC Transporters
Cited 6 times
To identify gene loci encoding ABC proteins in the fungal genomes, multiple blastp and tblastn searches against selected genomes were performed either at the National Center for Biotechnology Information website or at the website of the Broad Institute. Sequences of S. cerevisiae and A. nidulans ABC proteins representing all known subfamilies were used as queries, so that two searches per subfamily (except for ABC-A, for which no S. cerevisiae members are known) were performed. All hits producing E-values below 10-4 were further analyzed. For the genome sequences deposited at the Broad Institute, produced data sets were additionally checked against the list of sequences containing PFAM protein domains 'ABC transporter', 'ABC-2 type transporter', and 'ABC transporter transmembrane region'.
Phylogenetic analysis was performed with the program package MEGA4 [107 (link)] using neighbor-joining, minimum evolution and maximum parsimony algorithms and bootstrapping with 500 replicates. First, ABC proteins of each species were separated into subfamilies by their comparison with S. cerevisiae, A. nidulans, Homo sapiens, Arabidopsis thaliana, and Dictyostelium discoideum transporters. Afterwards, members of each subfamily and, in the case of ABC-B transporters, also full-length and half-size proteins were analyzed separately. Although the topologies of the phylogenetic trees produced with the different algorithms showed some minor differences, the same major groups of ABC proteins were recognized with all three algorithms.
Kovalchuk A, & Driessen A.J. (2010). Phylogenetic analysis of fungal ABC transporters. BMC Genomics, 11, 177.
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Publication 2010
Arabidopsis thalianas ATP-Binding Cassette Transporters Biological Evolution Dictyostelium discoideum Fungal Proteins Genetic Loci Genome Genome, Fungal Homo sapiens Membrane Transport Proteins Protein Domain Proteins Saccharomyces cerevisiae
5
Evolution of Multicellular Gene Families
Cited 5 times
We chose several gene families that are particularly interesting in the context of the evolution of multicellularity. For each gene family, we inferred the presence and absence of the gene or protein domains in chosen taxa using the HMMER45 (link) package, mutual Blast and phylogenetic analyses based on maximum likelihood trees inferred by RAxML42 (link). Analysed taxa include three bilaterians (Homo sapiens, Strongylocentrotus purpuratus and Drosophila melanogaster), three non-bilaterian metazoans (Nematostella vectensis, Trichoplax adhaerens and Amphimedon queenslandica), the choanoflagellate M. brevicollis, the filasterean C. owczarzaki, three fungi (Rhizopus oryzae, Laccaria bicolor and Neurospora crassa), and the amoebozoan Dictyostelium discoideum. We also searched, if necessary, further basal eukaryotes whose genomes have been sequenced, in order to know the origin of gene families that could predate the split between amoebozoans and opisthokonts.
Suga H., Chen Z., de Mendoza A., Sebé-Pedrós A., Brown M.W., Kramer E., Carr M., Kerner P., Vervoort M., Sánchez-Pons N., Torruella G., Derelle R., Manning G., Lang B.F., Russ C., Haas B.J., Roger A.J., Nusbaum C, & Ruiz-Trillo I. (2013). The Capsaspora genome reveals a complex unicellular prehistory of animals. Nature Communications, 4, 2325.
Publication 2013
Biological Evolution Choanoflagellata Dictyostelium discoideum Drosophila melanogaster Eukaryota Fungi Genes Genome Homo sapiens Klippel-Feil Syndrome Laccaria bicolor Multiple Birth Offspring Neurospora crassa Predate Protein Domain Rhizopus oryzae Strongylocentrotus purpuratus Trees Trichoplax

Most recents protocols related to «Dictyostelium discoideum»

1
Dictyostelium discoideum Cell Growth Dynamics
AX2 axenic cells of Dictyostelium discoideum were grown in HL5 medium with glucose (Formedium, Norfolk, UK) at 22 °C in tubes with shaking conditions (180 rpm for oxygenation). Exponentially growing cells were harvested, counted and deposited in 6-well plates, with a initial surface cell density ρ0 between 5 × 103 and 2 × 105 cells/cm2. Cells were submerged below liquid growth medium with height ranging from h = 0.5  to 3 mm. The temperature was kept constant at 22 °C.
We observed the growth and aggregation of cells under this free liquid film for days. We also performed experiments where the liquid film is topped with a thin layer of oil (low viscosity paraffin oil, ref. 294365H, VWR Chemicals). Because the product of solubility and diffusion coefficient of oxygen in oil is high, the presence of oil does not appreciably reduce the availability of oxygen and the final mean aggregate size is close (within 10%) to that observed without oil.
The growth and aggregation of Dd cells were observed in transmission with three types of microscope: (i) a TE2000-E inverted microscope (Nikon) controlled with Micromanager (version 2.0 gamma) and equipped with a motorized stage, a 4X Plan Fluor objective lens (Nikon) and a Zyla camera (Andor) using brightfield for most of the timelapse experiments lasting up to several days (Figs. 1a–c, 2b, c, Supplementary Figs. 4–5, and Supplementary Movies 1, 3, and 5), (ii) a binocular MZ16 (Leica) controlled with LAS X software (version 3.4.2 Leica) and equipped with a TL3000 Ergo transmitted light base (Leica) operated in the one-sided darkfield illumination mode and a Leica LC/DMC camera (Leica) for large field experiments (Fig. 1e, Supplementary Figs. 1–2 and Supplementary Movie 4) and finally (iii) a confocal microscope (Leica SP5) controlled with the LAS software (version 3.4 Leica) and equipped with a 10X objective lens for larger magnification experiments (Supplementary Fig. 3A–C and Supplementary Movie 2) and with a Tile Scan to create large field reconstituted mosaic images (Fig. 2a).
Carrère A., d’Alessandro J., Cochet-Escartin O., Hesnard J., Ghazi N., Rivière C., Anjard C., Detcheverry F, & Rieu J.P. (2023). Microphase separation of living cells. Nature Communications, 14, 796.
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Publication 2023
Cell Aggregation Cell Respiration Cells Culture Media Dictyostelium discoideum Diffusion Gamma Rays Glucose Lens, Crystalline Light Microscopy Microscopy, Confocal Oxygen paraffin oils Radionuclide Imaging Viscosity
2
Culturing Dictyostelium discoideum Cells
Dictyostelium discoideum (AX2) and all mutant cells were cultured at 22 °C in a plastic dish containing HL5 medium (1.3% bacteriological peptone, 0.75% yeast extract, 85.5 mM d-glucose, 3.5 mM Na2HPO4, and 3.5 mM KH2PO4; pH 6.3)30 (link). For the wound experiments, the cells were suspended in HL5 medium supplemented with 3 mM CaCl2.
Tanvir M.I, & Yumura S. (2023). Effects of wounds in the cell membrane on cell division. Scientific Reports, 13, 1941.
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Publication 2023
Cells Dictyostelium discoideum Glucose Hyperostosis, Diffuse Idiopathic Skeletal Peptones Wounds Yeast, Dried
3
Phylogenetic Analysis of P2X Receptor Genes
Protein gene model FASTAs and genome gffs were downloaded from public databases or publication-related data repositories (Supplementary Tables S1 and S2). FASTA sequences were filtered to retain only the longest isoform per gene based on header or gff information. Genome completeness was evaluated using BUSCO (5.3.0)88 (link) and its Metazoa database. Target genomes were selected based on genome quality and phylogenetic representation relative to Clytia and across animals, and also on previous studies in specific species. Final 17 species included were Viridiplantae Ostreococcus tari, Amoebozoa Dictyostelium discoideum, Fungi Allomyces macrogynus, Choanoflagellata Monosiga brevicollis, Porifera Amphimedon queenslandica, Ctenophora Mnemiopsis leidyi, Placozoa Trichoplax adhaerens, Cnidaria Myxozoa Thelohanellus kitauei, Cnidaria Cubozoa Morbakka virulenta, Cnidaria Hexacorallia Nematostella vectensis, Cnidaria Hexacorallia Acropora millepora, Cnidaria Scyphozoa Rhopilema esculentum, Cnidaria Hydrozoa Clytia hemisphaerica, Mollusca Lottia gigantea, Arthropoda Limulus polyphemus, Cephalochordata Branchiostoma floridae, Chordata Homo sapiens. A reference gene set FASTA was built using human HUGO Gene Nomenclature Committee-identified P2XR sequences (HUGO:https://www.genenames.org/) and published sequences for Dictyostelium discoidia. Local BLASTp databases were built for individual target and reference genomes (Blast + 2.6.0) (Supplementary Data). Reference sequences were BLASTed against each genome using BLASTp (e-value threshold e-1). All initial hits in target genomes were BLASTed against the reference genome. Initial hits having a top hit to a reference gene in a reference genome were retained and formed the candidate gene set. Candidate sequences were combined with reference sequences. The combined sequences were aligned in MAFFT (7.515)89 (link) and the alignment trimmed in ClipKit (1.4.1)90 (link). Maximum-likelihood-based phylogenetic trees were built using the trimmed alignments and IQTree (2.1.4) tree-building software, including use of ultrafast bootstraps. Alignments and trees were evaluated by hand in Geneious (2023.0.4) (geneious:https://www.geneious.com), FigTree (1.4.4) (https://github.com/rambaut/figtree), and iTOL (6.7.3)91 (link). Partial sequences were identified in alignments and removed from the combined set of sequences to produce a final gene set. The final gene set was aligned, trimmed, and trees built as before for final analysis. The final tree was evaluated in iTOL91 (link) and branches with less than 95% ultrafast bootstrap support were collapsed. Scripts for all steps post-genome evaluation are provided as a Python Juypter notebook.
Lee E.E., O’Malley-Krohn I., Edsinger E., Wu S, & Malamy J. (2023). Epithelial wound healing in Clytia hemisphaerica provides insights into extracellular ATP signaling mechanisms and P2XR evolution. Scientific Reports, 13, 18819.
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Publication 2023
Allomyces macrogynus Amoebozoa Animals Arthropods Branchiostoma floridae Cephalochordata Choanoflagellata Chordata Cnidaria Ctenophora Cubozoa Dictyostelium Dictyostelium discoideum FCER2 protein, human Fungi Gene Products, Protein Genes Genes, vif Genome Homo sapiens Hydrozoa Klippel-Feil Syndrome Limulus polyphemus Metazoa Mnemiopsis Mollusca Myxozoa Placozoa Plants Porifera Protein Isoforms Python Scyphozoa Trees Trichoplax
4
Comparative Fungal Protein Domain Analysis
One hundred seventy-nine Fungi species as well as five reference species from other Eukaryotic clades (Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, and Dictyostelium discoideum) were included in the study. The “Simple Modular Architecture Research Tool” (50 (link)) was used to assign annotated domains to all encoded proteins in their genomes. Orthology relations between the genes in these species were retrieved from EggNOG version 5.0 (51 ). For all matched domain pairs between a reference species and a given Fungi species of interest, pairwise global sequence alignments were performed with EMBOSS-needleall (52 (link)) using the Needleman–Wunsch alignment algorithm (53 (link)). The domain pairs were filtered for at least 40% sequence identity, and only the highest-scoring alignment pair was considered in case multiple domains of the same type were annotated for any of the two orthologous sequences.
Huang Q., Szklarczyk D., Wang M., Simonovic M, & von Mering C. (2023). PaxDb 5.0: Curated Protein Quantification Data Suggests Adaptive Proteome Changes in Yeasts. Molecular & Cellular Proteomics : MCP, 22(10), 100640.
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Publication 2023
Caenorhabditis elegans Dictyostelium discoideum Drosophila melanogaster Eukaryota Fungi Genes Genome Homo sapiens Plasmodium falciparum Protein Domain Sequence Alignment
5
GFP-Sac1 Pulldown in Dictyostelium
Dictyostelium discoideum strains (Sup. Tab. 3) expressing either pDM317-GFP-Sac1 or pDM317-GFP63 were grown at 22 °C in HL5-C medium (ForMedium) supplemented with geneticin (G418, 5 μg/ml). Electroporation of D. discoideum was performed according to Paschke et al. 2018 with modification64 (link). The cell number was determined (Countess II F2, Thermo Fisher Invitrogen), and 3 ∙ 107 cells were used for each sample. Pulldowns were performed in biological independent triplicates (n = 3). Cells were pelleted and washed once in cold Soerensen-Sorbitol. Cell pellets were snap frozen in liquid nitrogen and lysed with glass beads in 500 µl GFP pulldown buffer (20 mM HEPES pH 7.4, 150 mM KOAc, 5% glycerol, 1% GDN, Roche Complete Protease Inhibitor Cocktail EDTA free, Roche) using a FastPrep (MP biomedicals). The supernatant was cleared at 21,000 g for 10 min and incubated for 10 min rotating at 4 °C together with 12.5 µl pre-equilibrated GFP-Trap beads (Chromotek). Beads were washed four times with GFP pulldown buffer at 2500 g for 2 min at 4 °C. Afterwards, they were washed two times with wash buffer (20 mM HEPES pH 7.4, 150 mM KOAc, 5% glycerol) at 2500 g for 2 min at 4 °C. Beads were further treated following the iST Sample Preparation Kit (PreOmics) protocol. Dried peptides were resuspended in 10 µl LC-Load, and 4 µl were used to perform reversed-phase chromatography as described above. Data were analyzed using MaxQuant (V2.2.0.0, https://www.maxquant.org/maxquant/)65 (link),66 (link) with the corresponding FASTA database. Contaminants were identified based on the MaxQuant contaminants.fasta file. The resulting data were analyzed using Perseus (V2.0.7.0, www.maxquant.org/perseus)58 (link). Significance lines in the volcano plot of the Perseus software package corresponding to a given FDR were determined by a permutation-based method.59 (link) The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE60 (link) partner repository.
Schäfer J.H., Körner C., Esch B.M., Limar S., Parey K., Walter S., Januliene D., Moeller A, & Fröhlich F. (2023). Structure of the ceramide-bound SPOTS complex. Nature Communications, 14, 6196.
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Publication 2023
antibiotic G 418 Biopharmaceuticals Buffers Cells Chromatography, Reverse-Phase Cold Temperature Dictyostelium discoideum Edetic Acid Electroporation Freezing Geneticin Glycerin HEPES Mass Spectrometry Nitrogen Pellets, Drug Peptides Protease Inhibitors Sorbitol Strains

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1
Hl5 medium by Formedium
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The HL5 medium is a laboratory culture medium used for the cultivation and growth of various microorganisms. It provides essential nutrients and growth factors to support the optimal development of microbial cells. The composition and formulation of the HL5 medium are designed to meet the standard requirements for culturing a wide range of microorganisms in a laboratory setting.
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Hl5c medium by Formedium
Sourced in United Kingdom
The HL5c medium is a nutrient-rich culture medium used for the growth and maintenance of various cell lines in laboratory settings. It provides the necessary components to support the proliferation and viability of cells under controlled conditions.
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Ulwcd 0 by Olympus
Sourced in Japan
The ULWCD 0.30 is a high-precision objective lens designed for use in optical microscopy. It features a numerical aperture of 0.30 and is optimized for use with ultraviolet, visible, and near-infrared light wavelengths. The lens is constructed with high-quality optical components to provide excellent image quality and resolution.
4
Yeast extract by Thermo Fisher Scientific
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Yeast extract is a light-colored, water-soluble powder that is derived from the autolysis of baker's yeast. It serves as a nutrient source, providing a complex mixture of amino acids, vitamins, and other growth factors to support the cultivation of microbial cultures in various scientific and industrial applications.
5
Hl5 axenic medium by Formedium
Sourced in United Kingdom
HL5 axenic medium is a laboratory culture medium formulated for the growth and maintenance of Dictyostelium discoideum cells in an axenic environment. It provides the essential nutrients required for the cultivation of this species of cellular slime mold.
6
Ls b6516 50 by LSBio
LS-B6516-50 is a lab equipment product. It is a 50 mL centrifuge tube with a screw cap.
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Penicillin by Thermo Fisher Scientific
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Mascot by Matrix Science
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Methionine amide by Bachem
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More about "Dictyostelium discoideum"

Dictyostelium discoideum, commonly known as D. discoideum or the social amoeba, is a species of slime mold that has become a valuable model organism for studying various biological processes.
This soil-dwelling amoeba undergoes a unique life cycle, transitioning from a single-celled organism to a multicellular fruiting body in response to starvation.
Researchers utilize D. discoideum to investigate fundamental cellular processes such as chemotaxis, phagocytosis, and morphogenesis.
This organism offers an efficient system to elucidate conserved mechanisms across eukaryotes, thanks to its rapid growth, genetic tractability, and well-characterized behaviors.
D. discoideum is often cultured using specialized media such as HL5 (Hay's Lactose medium) and HL5c (HL5 with added carbohydrates), which provide the necessary nutrients for its growth and development.
Additionally, researchers may use ULWCD 0.30 (Ultra-Low Wheat Carbohydrate Diet) to study the effects of different nutrient conditions on the organism.
Exploring D. discoideum can provide valuable insights into human disease pathways and lead to advancements in regenerative medicine and drug discovery.
Researchers may also utilize Yeast extract, a common additive in D. discoideum culture media, to enhance the organism's growth and development.
For efficient laboratory work, researchers may use LS-B6516-50, a commercial product containing Penicillin, a commonly used antibiotic to prevent bacterial contamination in D. discoideum cultures.
The Mascot software, on the other hand, is a powerful tool used for the identification and quantification of proteins in D. discoideum proteomics studies.
Furthermore, Methionine amide, a modified amino acid, has been used in various studies to investigate the role of protein synthesis and metabolism in D. discoideum.
Vaseline, a petroleum-based ointment, can be used to seal the lids of Petri dishes containing D. discoideum cultures, maintaining the necessary humidity and preventing dehydration.
By leveraging the insights and resources available for D. discoideum, researchers can optimize their investigations and gain a deeper understanding of this fascinating model organism, ultimately contributing to advancements in cell biology, developmental biology, and related fields.