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Dictyostelium

Dictyostelium: A genus of cellular slime molds belonging to the order Dictyosteliales.
These soil-dwelling amoebae undergo a remarkable life cycle, transitioning from a unicellular state to a multicellular fruiting body in response to starvation.
Dictyostelium species serve as important model organisms for studying cell signaling, chemotaxis, and the evolutionary origin of multicellularity.
Researchers leverage Dictyostelium to investigate fundamental biological processes with relevance to human health and disease.

Most cited protocols related to «Dictyostelium»

Gene fragments were amplified by polymerase chain reaction (PCR)2 with a 4:1 mixture of the Taq and Pfu DNA polymerases (Promega, Madison, WI). All oligonucleotide primers used in this study are listed in Table 1. The integrating Dictyostelium vector EXP4(+) [18] (link) was used as starting material. An XbaI and a HindIII site upstream of the actin15 promoter were first successively destroyed by filling in the overhanging sites after digestion with the Klenow fragment of polymerase I, followed by religation, resulting in vector EXP4(-XH). This also generated a unique Nhe1 site replacing the HindIII site.
A long multiple cloning site (MCS) was generated by deleting the existing polylinker by BglII/XhoI digestion of the vector and by ligating a duplex of primers MCS1 and MCS2 that carries compatible sticky ends into the BglII and XhoI sites. The resulting vector, EXP5(+) was used as the backbone for all subsequent constructs containing TAP and/or EGFP/EYFP fragments (Table 2).
The N-terminal TAP fragment (NTAP) was amplified from the plasmid pBS1761 [11] (link) using primers NTAP1 and NTAP2 and ligated into the BamHI and HindIII sites of EXP5(+), yielding pDV-NTAP. The C-terminal TAP fragment (CTAP) was amplified from plasmid pBS1479 [10] (link) using primers CTAP1 and CTAP2 and ligated into the ClaI and XhoI sites of EXP5(+), yielding vector pDV-CTAP. Enhanced yellow- and green fluorescent protein genes (YFP) and (GFP) were amplified from the vectors pEYFP-N1 and pEGFP-C3 (Clontech, Mountain View, CA), respectively. For N-terminal location of YFP, primers tapYFP1 and tapYFP2 were used and insertion occurred in the HindIII and SpeI sites of EXP5(+), yielding pDV-NYFP. For C-terminal location of YFP or GFP, primers tapYFP3 and tapYFP4 were used and insertion occurred into the EcoRI and ClaI sites of EXP5(+), yielding pDV-CYFP or pDV-CGFP. All constructs were validated by sequencing across the entire tag and MCS and are listed in Table 2.
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Publication 2007
Cloning Vectors Deoxyribonuclease EcoRI Dictyostelium Digestion DNA Polymerase I Genes Oligonucleotide Primers Pfu DNA polymerase Plasmids Polymerase Chain Reaction Promega SLC9A1 protein, human Vertebral Column
Phagosomes created by phagocytosing 759-nm-diameter latex beads were observed using differential interference contrast microscopy (Barak et al., 2013 (link), Barak et al., 2014 (link)). For further details, see sections 3 and 4 of Supplemental Experimental Procedures. Phagosome motion was visualized inside agar-flattened Dictyostelium cells (section 5, Supplemental Experimental Procedures). Purification and in vitro motility of latex bead phagosomes has been described (Barak et al., 2014 (link)). Further details can be found in Supplemental Experimental Procedures (section 6). Phagosomes were prepared using silica beads or latex beads from J774, RAW264.7, or Dictyostelium cells. Purity of latex bead phagosomes was confirmed using markers against endosomal, cytosolic, and membrane proteins (Supplemental Experimental Procedures, section 6; Figure S2). Confocal imaging was used to detect proteins on the phagosome membrane. EPs/LPs were treated with filipin and imaged under epifluorescence illumination. Further details can be found in Supplemental Experimental Procedures, section 7 (for phagosomes from J774 and RAW cells) and section 9 (for phagosomes from Dictyostelium). Measurement of fluorescence intensity on phagosomes is described in Supplemental Experimental Procedures, section 8. Statistical hypothesis testing was done using Student’s t test. Two-tailed p values (95% confidence) were calculated. Error bars are SD or SEM, as indicated.
DRM isolation from purified phagosomes was done as described previously (Goyette et al., 2012 (link)). Further details can be found in in section 11 of Supplemental Experimental Procedures. Lipids were extracted from phagosomes using a methanol-chloroform mixture for thin-layer chromatography (TLC) experiments. Silica TLC plates were used to separate the lipids with an appropriate solvent system, followed by visualization on a Bio-Rad instrument. Further details can be found in section 12 of Supplemental Experimental Procedures. MβCD prepared in buffer (30 mM Tris and 4 mM EGTA [pH 8.0]) was incubated with LPs (22°C, 15 min) at final concentrations ranging from 10 mM to 30 mM. Further details can be found in section 13 of Supplemental Experimental Procedures. LPG purified from Leishmania donovani (Turco et al., 1987 (link)) was obtained as a gift. The stock solution (in ddH2O) was diluted appropriately. LPs were incubated with LPG (22°C, 15 min) before observation (Dermine et al., 2005 (link)). Further details can be found in section 13 of Supplemental Experimental Procedures. Bead motility with dynein using an ATP releasate from Dictyostelium cells has been described elsewhere (Soppina et al., 2009b (link)). Further details can be found in section 14 of Supplemental Experimental Procedures. See Supplemental Experimental Procedures, section 12 for details of lipidomics measurements. PC and free cholesterol was measured on lipids obtained from EPs and LPs purified from RAW264.7 cells.
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Publication 2016
Agar Buffers Cells Chloroform Cholesterol Cytosol Dictyostelium Dynein ATPase Egtazic Acid Endosomes Filipin Fluorescence isolation Latex Leishmania donovani Light Lipids Membrane Proteins Methanol Microscopy, Differential Interference Contrast Motility, Cell Phagosomes RAW 264.7 Cells Silicon Dioxide Solvents Student Thin Layer Chromatography Tromethamine
The GFP-NE81 fusion plasmid pIS191 containing the complete coding sequence of DDB_G0289429 (Schulz et al., 2009b (link)) was used as a starting point for all further constructs. For expression of NE81 in E. coli, the complete coding sequence was cloned into pMALc2 (NEB, Frankfurt, Germany). Protein expression at room temperature and purification by amylose affinity chromatography was performed according to the manufacturer's instructions. The fusion protein was used for custom immunization of two rabbits (BioGenes, Berlin, Germany). Antisera were affinity-purified according to the manufacturer's instructions (GE Healthcare, München, Germany) using NHS-activated Sepharose with coupled MBP-NE81.
To generate the GFP-NE81ΔCLIM vector, pIS191 was used as a template for PCR amplification of the complete NE81 sequence, excluding the C-terminal CLIM motif, using SalI-linker primer TAAATTGTCGACTAATGGATATGTCAAAAAAGAAAAGTAAAC-3′ and BamHI linker primer 5′-GCGCGGATCCTTAATTTGATTTACCAGCTGAAGAAGG-3′. The PCR product was cloned into the N-terminal GFP-fusion vector pIS77 (Schulz et al., 2009a (link)) to yield pAK35 (G418 resistance).
The GFP-NE81ΔCLIM-S122A vector was generated after PCR amplification of two fragments of the NE81 sequence. The following primer combinations were used: fragment1 (385 base pairs): SalI-linker primer (see above), 5′-GTTGAGCTGCTCTATTTGGTGCTAATGGTG-3′; fragment2 (1808 base pairs): 5′-CACAAATAGGTACACCATTAGCACCAAATAG-3′; BamHI-linker primer; the exchanged bases yielding the S122A point mutation are underlined. The amplified fragments were used as templates for an overlap extension PCR using the SalI- and BamHI-linker primers. The PCR product was cloned into the N-terminal GFP-fusion vector pIS77 (Schulz et al., 2009a (link)) to yield pPB14-29.
To generate the GFP-NLS-CP224ΔC, two complementary oligonucleotides were annealed (5′-TAAATTGTCGACAAC GTAAGAGAAAGAGATCAAAAGAGCTCAATTTA-3′, 5′-TAAATTGAGCTCTT­TTGATCTCTTTCTCTTA CGTTGTCGACAATTTA-3′) and cloned with SalI and SacI into the GFP-CP224ΔC vector (Hestermann and Gräf, 2004 (link)) to yield pPB45-7.
The homologous recombination vector, containing a blasticidin S resistance cassette flanked by genomic fragments of the NE81 gene, was constructed in pLPBLP (Faix et al., 2004 (link)). Suitable linker primers were used to amplify genomic Dictyostelium DNA fragments by PCR. The 5′ SaII/HindIII fragment consisted of 820 base pairs of 5′ noncoding sequence starting at base position −852, and the 3′ PstI/BamHI fragment comprised 679 base pairs of coding sequence ending at base position 2353 of the genomic sequence. The resulting knockout plasmid (pAK43) was digested with PvuII prior to transformation into Dictyostelium cells.
For expression in human cells, the AT-rich NE81 sequence was codon-optimized for expression in mammalian cells by gene synthesis (DNA2.0, Menlo Park, CA) and cloned into pEGFP-C2 (BD Biosciences, Heidelberg, Germany).
Publication 2012
Amylose antibiotic G 418 AT Rich Sequence Base Sequence blasticidin S Cells Chromatography Chromatography, Affinity Cloning Vectors Codon Dictyostelium DNA2 protein, human Escherichia coli Genes Genome Homologous Recombination Homo sapiens Immune Sera Mammals Oligonucleotide Primers Oligonucleotides Open Reading Frames Oryctolagus cuniculus Plasmids Point Mutation Proteins Sepharose Synthetic Genes Vaccination
The deformation of the substratum was measured in three dimensions by cross-correlating each instantaneous fluorescence z-stack obtained with the confocal microscope (see 2.3) with a reference z-stack in which the substratum is not deformed (see Figure 1). In each experiment, the undeformed image was obtained by waiting for the cell to move out of the field of view, which takes approximately 10 minutes as Dictyostelium cells are highly motile. The comparison between the deformed and undeformed (reference) conditions was performed by dividing each instantaneous and reference z-stacks into 3D interrogation boxes and optimizing the 3D cross-correlation between each pair of interrogation boxes. Sub-pixel resolution was attained by tri-quadratic polynomial interpolation of the image correlation function. The image correlation codes were validated against the 3D single-particle tracking codes developed by Hur et al.[5] (link), showing very good agreement. Figure S2 in file Supporting Information (File S1) shows a representative example of the 3D cross-correlation function between interrogation boxes from the deformed and undeformed images. The signal-to-noise ratio of the measurement is defined as the ratio between the maximum value of the cross-correlation and the second highest local maximum. The measurement floor estimates the lowest deformation that could be accurately measured by our method. It was defined from the standard deviation of the deformation measured far away from the cell, where this deformation should be equal to zero. The horizontal size of the interrogation boxes was chosen to balance resolution, which decreased with box size, measurement floor, which decreased with box size, and signal-to-noise ratio, which increased with box size (see Table 1). We chose the smallest box size that provided a signal-to-noise ratio greater than 2.5 which resulted in a box with 24×24 pixels in the x and y directions, and led to a Nyquist spatial resolution of 2.1 µm. Further increases in box size led to higher signal to noise ratios but did not decrease the measurement floor appreciably. Typical values of deformations exerted by the cells ranged between 30 and 50 times the measurement floor. In addition to these considerations, phototoxic effects need to be taken into account when choosing the vertical size of the interrogation boxes, , because the level of laser radiation transmitted to the cells increases with the number of slices per z-stack. In our experiments, was the minimum box height that allowed for meaningful deformation measurements. Thus, we acquired z-stacks having between 8 and 12 slices, which enabled us to record time lapse sequences of stacks with a time resolution of 4 seconds and durations of up to 30 minutes with no apparent phototoxic effects.
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Publication 2013
Cells Dictyostelium Fluorescence Microscopy, Confocal Neoplasm Metastasis Photosensitizing Effect
Dictyostelium cells were cultured in the carbon-coated glass-bottom dish. After the medium was removed, a small aliquot (~10 μl) of 1 μM FM1-43 (Life Technologies) or 0.05 mg/ml of a GFP-actin expression vector10 (link) was applied on the cells. Otherwise, the cell suspension was mixed with these molecules and then placed on the surface of the carbon-coated coverslip. After the cells settled down on the surface of the coverslip, a laser beam was applied at a small point on the cells for 10 msec. For the Cos-1 cells, the medium was exchanged with serum-free medium (OPTI-MEM1, Life Technologies) and then most of the medium was removed, leaving 10–20 μl of residual medium. Finally, 0.5 μl of a solution containing 0.5 mg/ml of an EGFP-expression vector was mixed. A laser beam was applied in the same way as for the Dictyostelium cells.
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Publication 2016
Actins Carbon Cells Cloning Vectors COS-1 Cells Dictyostelium FM1 43 Hyperostosis, Diffuse Idiopathic Skeletal Serum

Most recents protocols related to «Dictyostelium»

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The expression of RasCQ62L in pten− cells maintained for an additional 16-28 hours resulted in cells that underwent a catastrophic fragmentation and death (FIG. 6). It was verified that 98% of the induced cells were dead by Trypan Blue staining and their failure to form foci on re-plating. The surviving 2% of cells were not flattened, indicating that they lost expression of RasCQ62L. This observed mode of cell death has not been elucidated before in either Dictyostelium or in mammalian cells. This mechanism was named “sparagmosis” from the Greek sparasso, meaning “tear, rend, or pull to pieces.” Other pairwise combinations of perturbations that generated flattened cells such as expression of RasCQ62L in RAM mutants or expression of Rap1AG12V in pten− also led to similar cell death by fragmentation.

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Patent 2024
Cell Death Cells Dictyostelium Mammals PTEN protein, human Signal Transduction Tears Trypan Blue
Dictyostelium AX4 (axenic) amoebae were grown at 22°C on a rotary shaker (180 rpm) in HL5 media containing 100 mg/mL of streptavidin and 100 units/mL penicillin. Initially, the IC50 for thymoquinone was determined by seeding amoebae at 5x 104 cells/ml with 0.25, 0.5, 1, 2.5, 5.0, 7.5, and 10 μM) for 0, 24, 48, and 72 hours to determine working concentrations of thymoquinone. Viability of amoeba was determined by Trypan blue stating of the amoeba for all time points. For subsequent proliferation studies, thymoquinone was prepared in HL5 and added to 5x 104 cells/mL at 0, 2.5, 5, and 7.5μM. Cell counts and trypan blue staining for viability was obtained by hemocytometer at 24, 48, and 72hr in accordance with previously published studies [10 (link)].
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Publication 2023
Amoeba Cells Dictyostelium Penicillins Streptavidin thymoquinone Trypan Blue
To express Pvio acaA from its own promoter, a 5833 bp segment containing the Pv-acaA promoter, coding and terminator regions was amplified from gDNA in two fragments, A and B, using primer set Pv-aca-P51K (with KpnI site) and Pv-aca-C31 for A and Pv-aca-C51 and Pv-aca-31C (with ClaI site) for B. The fragments were cloned into pCR-BluntII-TOPO for sequence validation. Using an acaA internal BamHI site, fragment A was isolated from its TOPO plasmid using KpnI and BamHI and ligated into the KpnI/BamHI digested plasmid that contained fragment B, thus reconstructing the entire 5.8 kb acaA genomic segment. This segment was excised with KpnI/ClaI and ligated into KpnI/ClaI digested vector pHygTm(plus)/pG7 (http://dictybase.org/db/cgi-bin/dictyBase/SC/plasmid_details.pl?id=453), which contains a hygromycin resistance cassette, yielding vector pPv-acaA-Exp.
To express Pvio acrA from its own promoter, a segment containing the acrA coding region, part of its promoter and the terminator were amplified from gDNA using primers Pv-ACB-P51X/Pv-ACB-31S. The fragment was digested with SpeI/SacII and cloned into pBluescript SK+ for sequence validation, yielding plasmid pBs-PvAcrA. The remaining part of the promoter region was excised with XbaI/SmaI from pPv-acrA-LacZ (see above) and ligated into the XbaI/SmaI digested vector pHygTm(plus)/pG7, which was subsequently digested with SmaI and SpeI. The PvAcrA fragment from pBs-PvAcrA was excised with SpeI/HpaI and ligated into the SpeI/SmaI digested vector, yielding pPv-acrA-Exp, which now harboured a 6.4 kb region encompassing the acrA promoter, coding region and terminator. pPv-acrA-Exp was introduced into both acrAˉ and acaAˉ/acrAˉ cells by electroporation and pPv-acaA-Exp into acaAˉ/acrAˉ only. Transformants were incubated with autoclaved Klebsiella aerogenes in 10% HL5 with 30 μg/ml of hygromycin in petri dishes for 48 h, and next distributed with E. coli on 1/5th SM plates supplemented with 30 µg/ml of hygromycin. The plasmids and knock-out cell lines prepared for the study are in the Dictyostelium Stock Center http://dictybase.org/StockCenter/StockCenter.html.
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Publication 2023
7-anilinocoumarin-4-acetic acid Cell Lines Cells Cloning Vectors Dictyostelium Electroporation Enterobacter aerogenes Escherichia coli Genome HMN (Hereditary Motor Neuropathy) Proximal Type I hygromycin A Hyperostosis, Diffuse Idiopathic Skeletal LacZ Genes Oligonucleotide Primers Plasmids Terminator Regions, Genetic Topotecan
Detailed methods are provided in the online version of this paper and include the following:

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EXPERIMENTAL MODEL AND SUBJECT DETAILS

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Dictyostelium transformation

Lattice light-sheet microscopy

Deconvolution and registration

Cell segmentation

Fluorescence projection

Annotation

PIP3 domain segmentation

PIP3 domain grading

Fluorescence measurements

PIP3 domain geometry

3D maximum intensity projections

Surfaces

Modelling

Base closure

Quantification and statistical analysis

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Publication 2023
Cells Dictyostelium Fluorescence Light Microscopy
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.
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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

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More about "Dictyostelium"

Dictyostelium, a genus of cellular slime molds, has captivated researchers worldwide with its remarkable life cycle and potential as a model organism.
These soil-dwelling amoebae, also known as social amoebae or cellular slime molds, undergo a fascinating transition from a unicellular state to a multicellular fruiting body, in response to starvation.
Dictyostelium species serve as invaluable tools for studying fundamental biological processes, such as cell signaling, chemotaxis, and the evolutionary origin of multicellularity.
Researchers leveraging Dictyostelium have made groundbreaking discoveries with direct relevance to human health and disease.
To optimize Dictyostelium research, scientists often employ specialized media and reagents, such as HL5 medium, HL5c medium, and protease inhibitor cocktails.
These components provide the necessary nutrients and environmental conditions for culturing and maintaining these unique organisms.
The application of advanced techniques, like gene electroporation using the Gene Pulser Xcell, allows researchers to manipulate Dictyostelium genetically, unlocking new avenues of investigation.
Similarly, the use of specific antibodies, such as the Anti-phospho-RPS6KB1 antibodies, enables the study of signaling pathways and cellular processes within these model organisms.
By harnessing the power of Dictyostelium, researchers can gain insights into a wide range of biological phenomena, from cell motility and differentiation to the evolution of multicellularity.
This knowledge can then be translated to enhance our understanding of human biology and inform the development of novel therapeutic approaches.
Dictyostelim's versitility as a model organism, coupled with the availability of specialized tools and reagents, make it an invaluable resource for the scientific community.
Explore the full potential of Dictyostelium research and unlock new frontiers in the pursuit of scientific discovery.