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Amoeba

Amoebas are single-celled eukaryotic organisms belonging to the Protozoa kingdom.
They are charecterized by their ability to change shape and move using pseudopodia, or temporary extensions of their cytoplasm.
Amoebas play a vital role in many ecosystems, acting as predators, decomposers, and symbionts.
Their diverse morphologies and behaviors make them an important subject of study in fields such as cell biology, ecology, and evolutionary biology.
Researchers can leverage PubCompare.ai to optimize their amoeba research protocols, identifying the best procedures from scientific literature and enhancing reproducibility and accuracy in their studies.

Most cited protocols related to «Amoeba»

1
Multi-scale Computational Workflow for Protein Structure Refinement
The ab initio reference calculations were carried out in a workflow involving several software packages. The initial high-dimensional dihedral grid of structures was generated from restrained simulated annealing simulations using the AMOEBA protein force field as implemented in TINKER.80 The recursive search over the two-dimensional dihedral grids was performed using a Python program that interfaces with the Q-Chem 4.1 quantum chemistry package81 -82 and uses the Work Queue distributed computing library83 to manage a large number of Q-Chem calculations running in parallel. The calculations of final optimized structures, energies and gradients were performed in Psi4.84 Frequencies were obtained in Psi4 via numerical differentiation of the analytic gradients.
The parameterization calculations were performed using ForceBalance via an interface to GROMACS 4.6.5,85 and contained two fundamental types of MM calculations – single-point energy / gradient evaluations, and frequency calculations. In the frequency calculations, the MM energy was fully minimized using the L-BFGS algorithm prior to calculating the Hessian. ForceBalance also uses the Work Queue library to evaluate individual targets in parallel, providing a significant speed-up compared to running all of the MM calculations sequentially.
The validation calculations were performed using multiple software packages. The equilibrium sampling simulations initialized from the crystal structure were carried out using GROMACS 4.6.5 running on standard Linux HPC hardware. The analyses of the equilibrium simulations to calculate RMSD from the crystal structure and NMR scalar couplings / chemical shifts were carried out using the GROMACS analysis tools, the MDTraj trajectory analysis package,86 (link) and the ShiftX2 chemical shift prediction software87 (link).
The temperature replica exchange simulations were set up using the ParmEd software package88 to convert the GROMACS topology files to AMBER format, carried out using the GPU-accelerated version of AMBER1489 running on the OLCF Titan supercomputer, and analyzed using the cpptraj90 (link) and MDTraj91 (link) software packages. The simulations of the denatured state ensemble were carried out on the Open Science Grid (OSG), a distributed computing network that utilizes donated idle CPU cycles from research computing facilities.92
Wang L.P., McKiernan K.A., Gomes J., Beauchamp K.A., Head-Gordon T., Rice J.E., Swope W.C., Martínez T.J, & Pande V.S. (2017). Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. The journal of physical chemistry. B, 121(16), 4023-4039.
Publication 2017
Amber Amoeba cDNA Library Proteins Python
2
Microscopic analysis of P. vivax parasites
Thick and thin smears were routinely made for the pre- and post-CF11 filtration from each of the P. vivax isolates collected, prior to ex vivo drug sensitivity testing at the Shoklo Malaria Research Unit (SMRU), Mae Sod, Thailand. The pre- and post-CF11 filtration, thick and thin smears from 30 randomly selected isolates collected during 2008 were examined as follows. Parasitaemias were determined from the number of IRBC per ten 100× oil immersion fields (200 RBC per field) on the thin film. The percentage of early (ring-like parasites with a single chromatin dot) and mature (amoeboid-like cytoplasm or presence of haemozoin) asexual stages was determined from examining 200 parasites in the thick smears under 100× oil immersion. Due to their very low numbers in the pre- and post-filtration smears schizonts (parasites with 3 or more chromatin dots and haemozoin) were combined with the mature stage count. Gametocyte counts were too low for statistical comparison.
Parametric analysis of non-paired data was calculated using one-way analysis of variance. Non-parametric analysis of the paired data was performed using Wilcoxon or Friedman's tests and post-hoc analysis using Dunn's test (GraphPad Prism 5.01).
The clinical IRBC samples examined in this study were collected under the following ethical guidelines in the approved protocol OXTREC 027-05 (University of Oxford, Centre for Clinical Vaccinology and Tropical Medicine, UK)
Sriprawat K., Kaewpongsri S., Suwanarusk R., Leimanis M.L., Lek-Uthai U., Phyo A.P., Snounou G., Russell B., Renia L, & Nosten F. (2009). Effective and cheap removal of leukocytes and platelets from Plasmodium vivax infected blood. Malaria Journal, 8, 115.
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Publication 2009
Amoeba Chromatin Cytoplasm Filtration hemozoin Hypersensitivity Immersion Malaria Oil Fields Parasites prisma Schizonts
3
Polarizable Atomic Multipole Force Field
The interaction energy among atoms is expressed as:
U=Ubond+Uangle+Ub−a+Uoop+Utorsion+UvdW+Ueleperm+Ueleind
where the first five terms describe the short-range valence interactions: bond stretching, angle bending, bond-angle cross term, out-of-plane bending, and torsional rotation. The last three terms are the nonbonded interactions: van der Waals, permanent electrostatic, and induced electrostatic contributions. The individual terms for these interactions have been described in detail in a previous publication.61 (link) Some additional methodology, introduced to treat electrostatic polarization in molecular systems beyond water, will be detailed below. Polarization effects in AMOEBA are treated via Thole’s interactive induction model that utilizes distributed atomic polarizability.62 ,63 According to this interactive induction scheme, induced dipoles produced at the atomic centers mutually polarize all other sites. A damping function is used at short range to eliminate the polarization catastrophe and results in correct anisotropy of molecular response (i.e., diagonal components of the molecular polarizability tensor) starting from isotropic atomic polarizabilities. Thole damping is achieved by screening of pairwise atomic multipole interactions, and is equivalent to replacing a point multipole moment with a smeared charge distribution.13 The damping function for charges is given by
ρ=3a4πexp(−au3)
where u = rij/(αiαj)1/6 is the effective distance as a function of interatomic distance rij and the atomic polarizabilities of atom i (αi) and j (αj). The coefficient a is the dimensionless width of the smeared charge distribution and controls the damping strength. The corresponding damping functions for charge, dipole and quadrupole interactions were reported previously.18 The Thole model is able to reproduce the molecular polarizability tensors of numerous small molecules with reasonable accuracy using only element-based isotropic atomic polarizabilities and a single value for the damping factor.62 In our water study, it was discovered that the dependence of molecular polarizability on the damping coefficient is weak, but the polarization energy is much more sensitive to the strength of damping. After fitting the interaction energies of a series of small water clusters, we have chosen a universal damping factor of a = 0.39, rather than the value of 0.572 suggested by Thole. We adopt the atomic polarizabilities (Å3) as originally given by Thole, i.e., 1.334 for carbon, 0.496 for hydrogen, 1.073 for nitrogen and 0.837 for oxygen. The only exception is for aromatic carbon and hydrogen atoms, where we found the use of larger values greatly improves the molecular polarizability tensor of benzene and polycyclic aromatics. The AMOEBA values for atomic polarizability are given in Table 1. In addition, for metal dications we have found it necessary to use stronger damping (a < 0.39) to better represent the electric field around the ions.21 (link),61 (link),64 (link)
Ren P., Wu C, & Ponder J.W. (2011). Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. Journal of chemical theory and computation, 7(10), 3143-3161.
Publication 2011
A-factor (Streptomyces) Amoeba Anisotropy Benzene Carbon Debility Electricity Electrostatics factor A Hydrogen Iodine Ions Metals Nitrogen Nuclear Energy Oxygen
4
Visualizing Epitope-Tagged Mitosomal Proteins

E. histolytica transformants expressing epitope-tagged mitosomal proteins were previously established [5] (link). Approximately 5×105 trophozoites were resuspended in 2 ml BI-S-33 medium and seeded onto a molybdenum disk (Nissin EM Co., JAPAN) in a well of a 24-well plate. After 15-min incubation at 35.5°C, the molybdenum disk that amoebas adhered to was removed and immediately immersed in liquid propane at −175°C. The disk was further fixed and sectioned as previously described [21] (link). The disk was reacted with primary antibody diluted at 1∶2000 (anti-Cpn60 antiserum) and 1∶500 (anti-HA monoclonal antibody) in phosphate-buffered saline containing 1.5% bovine serum albumin for overnight at 4°C. The samples were then reacted with colloidal gold-conjugated anti-rabbit or anti-mouse secondary antibody (1∶20) for 1 h at room temperature. Samples were examined by electron microscopy at Tokaii Microscopy., Inc (Nagoya, JAPAN).
Mi-ichi F., Makiuchi T., Furukawa A., Sato D, & Nozaki T. (2011). Sulfate Activation in Mitosomes Plays an Important Role in the Proliferation of Entamoeba histolytica. PLoS Neglected Tropical Diseases, 5(8), e1263.
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Publication 2011
Amoeba Antibodies, Anti-Idiotypic Electron Microscopy Epitopes Gold Colloid Immune Sera Immunoglobulins Microscopy Molybdenum Mus Phosphates Propane Proteins Rabbits Saline Solution Serum Albumin, Bovine Trophozoite
5
Ewald Summation for Multipole Potentials
The energy gradient due to permanent multipole moments, including force and torque components, was derived by Smith for a standard Ewald summation.68 We have previously reported the AMOEBA Ewald force, torque and virial arising from dipole induction in water systems.18 Note the pairwise direct (non-Ewald) formula can be obtained by replacing the real-space screening factor B(r) with the corresponding function of 1/r,18 ,68 and vice versa. The torque components are converted to atomic forces on the relevant frame-defining atoms in our implementation. It is also possible to derive the analytical forces corresponding to the torques directly via an infinitesimal rotation,69 (link) or by taking the derivative of the rotation matrix.70 When evaluating the energy derivative directly, the additional chain rule terms due to the local frame rotation matrices are equivalent to the forces converted by means of the torque implementation. In the appendix, we provide a derivation of the polarization energy gradient, with a focus on terms arising from intramolecular polarization.
The Ewald real-space interactions need to be modified to accommodate short-range scaling of electrostatics and damping of dipole induction as mentioned above. To scale the interaction between an atom pair, a term (fscale − 1) U′ is added to the total Ewald energy, where U′ is the full (non-Ewald) interaction between the pair, and the scaling factor, fscale, ranges from 0 to 1. Analogous approaches are used in computing forces, fields and torques.
Particle-mesh Ewald (PME) for point multipoles69 (link) has been implemented in the TINKER and AMBER/PMEMD software packages. PME significantly improves the computational efficiency as its cost scales as NlogN, where N is the number of particles. The addition of dipole and quadrupole moments to the PME method roughly doubles the computational expense versus point charge only models. Calculation of induced dipoles can be time consuming with the simple iterative solution method, depending upon the level of SCF convergence required. Alternative fast predictive induced dipole schemes have been suggested.71 ,72 Acceleration via extended Lagrangian methods has been reported for induced dipole polarization,73 –75 and is under investigation for the AMOEBA model.
A standard Ewald summation implies the use of “tin-foil” boundary conditions, corresponding to a system immersed in a conducting dielectric environment (i.e., ε=∞). It is possible to include a boundary correction to the Ewald energy if other environments, such as insulating boundary conditions, are desired. For a cubic box, the correction term is a function of the total cell dipole moment, while for other system shapes the analytical form is difficult to derive.76 ,77 Note the energy obtained via Ewald summation is equivalent to the energy obtained using an infinitely long atom-based cutoff for the same periodic system. However, group-based cutoff are often applied to preserve local charge neutrality. When using group cutoffs, the energy asymptotically approaches a different value from atom cutoffs as the cutoff length increases. The difference between the two energies is exactly equal to the above boundary correction term. This suggests care must be taken if cutoff methods are applied to a system containing multipoles since the dipole and higher order moments are intrinsically group based.
Ren P., Wu C, & Ponder J.W. (2011). Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. Journal of chemical theory and computation, 7(10), 3143-3161.
Publication 2011
Acceleration Amber Amoeba Complement Factor B Cuboid Bone Electrostatics Physiology, Cell Reading Frames Torque

Most recents protocols related to «Amoeba»

1
Dictyostelium Strains Suppress Soft Rot Pathogens
Not available on PMC !

Example 1

119 Dicty strains were screened for their ability to feed on Dickeya (Dd) or Pectobacterium (Pcc) at 10° C. This assay was performed by inoculating Dd or Pcc on a low nutrient medium (SM2 agar) that supports both bacterial and Dicty growth. Dicty spores from individual strains were then inoculated on top of the bacterial growth and incubated at 10° C. to mimic potato storage temperatures. Dicty strains that successfully fed on Dd or Pcc created visible clearings in the lawn of bacterial growth and ultimately produced sporangia (fruiting bodies) that rose from the agar surface. An example of the phenotype that was considered successful clearing of bacteria is shown in FIG. 3A. From this initial screen, 36 Dicty strains that were capable of feeding on both Dd and Pcc at 10° C. were identified (FIG. 1B).

Of the 36 strains capable of feeding on both Dd and Pcc, 34 came from the Group 4 Dictyostelids (FIG. 1). This group includes D. discoideum, D. giganteum, D. minutum, D. mucoroides, D. purpureum, and D. sphaerocephalum (72). The results indicate that this group is particularly enriched in Dd and Pcc-feeding strains.

A further experiment was performed to identify Dicty species capable of feeding on biofilms of Dd and Pcc. Microporous polycarbonate membranes (MPMs) are widely reported to support biofilm formation of numerous Enterobacteriaceae species (2, 63, 70, 71). It was determined if Dd and Pcc formed biofilms on MPMs and determined if Dicty strains were capable of feeding on these biofilms. Membranes were placed on top of SM2 agar to provide Dd and Pcc with nutrients for growth. Bacteria were then inoculated on the surface of the MPMs and growth was monitored over the course of 1 week by washing bacteria off the membranes and performing dilution plating for colony counting. Growth of both bacterial strains plateaued around 4 dpi (FIG. 2).

From these results, it was determined that the best time to collect inoculated MPMs for biofilm analysis was at 2 dpi. Scanning electron microscopy (SEM) is commonly used to confirm biofilm formation by detecting extracellular polymeric substance (EPS) that forms the biofilm matrix (2). Samples of Dd and Pcc after 2 days of growth on MPMs in the presence and absence of Dicty are analyzed using SEM.

19 Dicty strains identified as active were tested for their ability to feed on Dd and Pcc growing on MPMs. These experiments were performed by establishing Dd and Pcc growth on MPMs overlaid on SM2 agar at 37° C. for 24 hr. Dicty spores were then applied to the center of bacterial growth in a 5 uL drop containing 1000 spores. Bacteria and Dicty were incubated at 10° C. for 2 weeks before remaining bacteria were washed off and colonies were counted. Representative images of Dicty growing on Dd and Pcc on MPMs are shown in FIG. 3A.

No Dicty strains produced a statistically significant reduction in Dd viability compared to the non-treated control. However, treating Dd lawns with Cohen 36, Cohen 9, WS-15, WS-20, and WS-69 consistently reduced the number of viable bacteria by approximately 100,000-fold compared to the non-treated control (FIG. 3B). Cohen 9 was the only Dicty strain that produced a statistically significant reduction in viability of Pcc compared to the non-treated control (FIG. 3C). Other Dicty strains capable of reducing the number of viable Pcc by at least 100,000-fold were Cohen 35, Cohen 36, WS-647, and WS-69 (FIG. 3C).

It was observed that Dicty strains Cohen 9, Cohen 36, and WS-69 were capable of feeding on both Dd and Pcc when these bacteria were cultured on SM2 agar and MPMs (FIGS. 1 and 3). These strains were also particularly effective feeders as all three reduced the number of viable Dd and Pcc on MPMs at 10° C. by 100,000-fold compared to the non-treated control (FIGS. 3B and 3C).

To determine if these strains could suppress soft rot development on seed potato tubers, tubers were tab-inoculated with Dd or Pcc and treated with spores from each Dicty strain. Seed potatoes were surface-sterilized and punctured using a sterile screw to a depth of 1.5 mm. Overnight cultures of Dd and Pcc were suspended in 10 mM potassium phosphate buffer, diluted to an OD600 of approximately 0.003, and administered as a 5 μL drop into the wound. Next, 5 of a Dicty spore suspension (100,000 spores) was added to the wound. Inoculated seed potatoes were placed in a plastic container with moist paper towels and were misted with water twice a day to maintain a high humidity. After 3 days at room temperature, seed potatoes were sliced in half and the area of macerated tissue was quantified using ImageJ.

All three strains reduced the severity of soft rot caused by Dd and Pcc (FIG. 4). Cohen 36 was the most effective strain on both Dd and Pcc: reducing the area of tissue maceration by 60% and 35%, respectively (FIG. 4B). Treating seed potatoes with WS-69 reduced the area of tissue maceration by 50% and 30% for Dd and Pcc, respectively (FIG. 4B). Finally, Cohen 9 was the least effective, but still able to reduce tissue maceration caused by Dd and Pcc by 25% and 20%, respectively (FIG. 4B).

FIG. 7 shows that three Dicty isolates control Dd and Pcc in seed tubers (at 25° C.). Two sets of data from different weeks were normalized to the Dickeya or Pectobacterium only bacterial control. The average area of macerated potato tissue measured in mm2 was set as “1” or “100%”. The average of all the other treatments including Dicty were divided by bacteria only control and multiplied by 100 to obtain a percentage. Each set contained 5 tubers per treatment.

Dicty should be capable of sporulating at temperatures as cold as 10° C. on a potato surface if they are applied as a one-time pre-planting or post-harvest treatment. Sporulation was assessed by inoculating small potato discs (5×6 mm) with 10 μL of Dd or Pcc suspensions at an OD600 of 3×10−5 and Dicty spores at a concentration of 1×107 spores/mL. Potato discs were kept in a covered 96-well plate for two weeks at 10° C. followed by visual inspection for son using a dissecting microscope. Representative images of a strain producing many sori (WS-517) and a strain producing few sori (WS-69) are shown in FIG. 5. Of the 11 strains evaluated, only Cohen 9 and WS-20 were unable to sporulate in the presence of both pathogens (Table 1).

TABLE 1
Assessment of Dicty sporulation at 10° C. on potato
in the presence of Dd or Pcc. A (✓) indicates sori
have been observed while a ( [Figure (not displayed)]  ) means they have not.
Dicty strainDdPcc
Cohen 9✓[Figure (not displayed)]
Cohen 36✓✓
WS-69✓✓
WS-517✓✓
WS-588✓✓
WS-606✓✓
WS-15✓✓
WS-20[Figure (not displayed)] ✓
DC-7✓✓
DC-61✓✓
WS-116d✓✓

Example 2

This example describes the use of a high throughput screening assay to identify Dicty strains from Alaska (e.g., BAC10A, BAF6A, BAC3A, NW2, KB4A (ATCC® MYA-4262™) SO8B, SO3A, BAF9B, IC2A (ATCC® MYA-4259™), AK1A1 (ATCC® MYA-4272™) PBF4B (ATCC® MYA-4263), PBF8B, BSB1A, SO5B (ATCC® MYA-4249), PBF3C, PBF6B, NW2B, NW10B (ATCC® MYA-4271™), PBF9A, IC5A (ATCC® MYA-4256TH), ABC8A (ATCC® MYA-4260), NW16B, ABC10B, ABB6B (ATCC® MYA-4261), BA4A (ATCC® MYA-4252), AKK5A, AKK52C, HP4 (ATCC® MYA-4286), HP8 (ATCC® MYA-4284), or NW9A) that feed on Dd and Pcc at 10° C. on potatoes.

Results from 11 Dicty strains screened against Dd at 10° C. are presented in FIG. 6. Data was analyzed for significance using a one-way analysis of variance (ANOVA; alpha =0.05) with Tukey's honest significant difference (HSD) test to compare means between the treatments and the No Dicty control. A reduction in Dd proliferation when potato discs were treated with Dicty strains Cohen 9, Cohen 36, WS-15, Maryland 18a, BAF6A, NW2, and SO3A.

The Alaskan Dicty strains, and those identified in Example 1, are further tested against coinfections of Dd and Pcc. It is useful to identify Dicty strains that can suppress Dd and Pcc coinfections as these two pathogens have been isolated together from diseased potatoes (15). The ability of Dicty strains with different feeding preferences (Dd vs. Pcc) to complement each other when administered as a cotreatment is assayed.

US11864559B2. Therapeutic amoeba and uses thereof (2024-01-09). AmebaGone, LLC [US]. Inventors: Marcin Filutowicz [US], Ryan Kessens [US], Amy Jancewicz [US].
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Patent 2024
A-A-1 antibiotic Agar Amoeba Bacteria Biofilms Buffers Coinfection Cold Temperature Combined Modality Therapy Dickeya Dictyosteliida Enterobacteriaceae Extracellular Polymeric Substance Matrix Extracellular Polymeric Substances High-Throughput Screening Assays Human Body Humidity Microscopy neuro-oncological ventral antigen 2, human Nutrients Pathogenicity Pectobacterium Phenotype Plant Tubers polycarbonate potassium phosphate Scanning Electron Microscopy Solanum tuberosum Sporangia Spores Sterility, Reproductive Strains Technique, Dilution Tissue, Membrane Tissues Wounds
2
Cultivation of Amoeba proteus and Tetrahymena
Amoeba proteus was cultured in plastic boxes (300 mm×220 mm×50 mm) filled with KCM medium (9.39 µM KCl, 32.5 µM MgSO4·7H2O, 54.4 µM CaCl2·2H2O) at 25°C and fed Tetrahymena pyriformis twice a week. T. pyriformis was cultured in 2% (w/v) Bacto Proteose Peptone medium (Becton, Dickinson and Company, USA) for 3 days. A. proteus was starved for at least 3 days before the experiments.
Taniguchi A., Nishigami Y., Kajiura-Kobayashi H., Takao D., Tamaoki D., Nakagaki T., Nonaka S, & Sonobe S. (2023). Light-sheet microscopy reveals dorsoventral asymmetric membrane dynamics of Amoeba proteus during pressure-driven locomotion. Biology Open, 12(2), bio059671.
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Publication 2023
Amoeba Bacto-peptone proteose-peptone Proteus Sulfate, Magnesium Tetrahymena pyriformis
3
Quantitative Immunoblot Analysis of Amoebae
Amoebae lysed in RIPA buffer containing protease inhibitors (Sigma), were sonicated, and centrifuged at 14,000 rpm for 20 min at 4°C. Supernatant protein concentrations were calculated, and samples electrophoresed on 10% SDS-polyacrylamide gels. Proteins were electroblotted onto PVDF membranes (Millipore) and blocked in PBST (PBS containing 0.1% Tween 20)/5% milk. Membranes were incubated with antibodies directed against DdGSTA2 or DdGSTA3 [10 (link)] (1:2000 each), discoidin I, alpha-tubulin, and csA/gp80 proteins (0.5ug/mL each, obtained from the Developmental Hybridoma Bank). Immunoblots were washed in PBST (PBS/0.1% Tween 20) were incubated with species-specific peroxidase-labeled secondary antibodies, developed either by chemiluminescent or colorimetric (3–3, diamino benzidine) methods. Blots were scanned or imaged using a BioRad Versadoc 3000 system, and densitometry and quantitation was performed with ImageJ software.
Alsaffar N., Fang Y, & Walters E. (2023). Thymoquinone effect on the Dictyostelium discoideum model correlates with functional roles for glutathione S-transferases in eukaryotic proliferation, chemotaxis, and development. PLOS ONE, 18(3), e0282399.
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Publication 2023
alpha-Tubulin Amoeba Antibodies benzidine Buffers Colorimetry Densitometry Discoidin-I Hybridomas IL6R protein, human Immunoblotting Milk, Cow's Peroxidase polyacrylamide gels polyvinylidene fluoride Protease Inhibitors Proteins Radioimmunoprecipitation Assay Tissue, Membrane Tween 20
4
Quantifying Oxidative Stress in Dictyostelium
The production of ROS was measured using DCFDA (2’-7’dichlorofluorescin diacetate) dye (1μg/ml, Sigma). Control and treated D. discoideum amoebae (1×106 cells/ml) were starved in 1X KK2 buffer in the presence of thymoquinone for six hours, then gently washed with PBS followed by the addition of DCFDA, and incubated for 30 min at 22°C with gentle shaking. DAPI was added to aggregated cells and fluorescence was captured using a Nikon ES400 microscope [28 (link)]. Quantitation of DCFDA staining was performed by measuring intensity values of comparable sized clusters of aggregated cells for three independent samples and performing statistical evaluation of relative intensity using averages of five clusters/group, followed by the Student’s t-test.
Alsaffar N., Fang Y, & Walters E. (2023). Thymoquinone effect on the Dictyostelium discoideum model correlates with functional roles for glutathione S-transferases in eukaryotic proliferation, chemotaxis, and development. PLOS ONE, 18(3), e0282399.
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Publication 2023
Amoeba Buffers Cells DAPI diacetyldichlorofluorescein dichlorofluorescin Fluorescence Microscopy Student thymoquinone
5
Thymoquinone Cytotoxicity in Dictyostelium
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)].
Alsaffar N., Fang Y, & Walters E. (2023). Thymoquinone effect on the Dictyostelium discoideum model correlates with functional roles for glutathione S-transferases in eukaryotic proliferation, chemotaxis, and development. PLOS ONE, 18(3), e0282399.
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Publication 2023
Amoeba Cells Dictyostelium Penicillins Streptavidin thymoquinone Trypan Blue

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More about "Amoeba"

Amoebae are fascinating single-celled eukaryotic organisms that belong to the Protozoa kingdom.
These microscopic creatures are characterized by their remarkable ability to change shape and move using temporary extensions called pseudopodia, which are made of cytoplasm.
Amoebas play a crucial role in many ecosystems, serving as predators, decomposers, and symbionts.
Their diverse morphologies and behaviors make them an important subject of study in fields such as cell biology, ecology, and evolutionary biology.
Researchers can leverage powerful tools like the EnSpire Multimode Plate Reader, EVOS FL Cell Imaging System AMF4300, and EnSpire microplate reader to enhance their amoeba research protocols.
These versatile protozoans can be cultured in the lab using growth media like Fetal Bovine Serum (FBS) and antibiotics like Gentamicin.
Genetic analysis of amoebas can be performed using DNA extraction kits like the QIAamp DNA Mini Kit and QIAamp DNA Blood Mini Kit, while microscopic imaging can be done with instruments like the LSM 780 and EVOS M5000 Imaging System.
By optimizing research procedures and leveraging the latest technologies, scientists can unravel the intriguing mysteries of amoebas and their role in the natural world.
PubCompare.ai provides a valuable platform to identify the best experimental protocols from scientific literature, pre-prints, and patents, helping to improve the reproducibility and accuracy of amoeba studies.