Small pieces (5 × 5 mm) of tissue from inoculated cotyledon and leaf segments were cut and immersed in 200 µL distilled water amended with Tween 20 (0.05%; Sigma-Aldrich, St. Louis, MO) in a 1.5-mL microcentrifuge tube. The tubes were vortexed on a mini-shaker (Vortex-Genie; Fisher Scientific, Waltham, MA) for 5–10 s to dislodge the sporangia from cotyledon or leaf surfaces. Sporangia in the suspension were counted using a hemocytometer under a bright-field microscope (BH-2). Sporangia counts were converted into sporangia densities (total number of sporangia/area of the cotyledon or leaf segment sampled). Sporangia counting was performed every two days from 4 dpi to 10 dpi. For each time point, eight pieces of cotyledon or leaf segments were sampled. This experiment was repeated three times.
Vortex genie
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Vortex Genie is a laboratory equipment used for mixing and agitating samples. It provides a consistent, high-speed vortex action to thoroughly mix and resuspend samples in various containers.
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Lab products found in correlation
7 protocols using vortex genie
1
Quantification of Sporangia Density
2
Diagnosing Periprosthetic Joint Infection
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The Musculoskeletal Infection Society (MSIS) criteria includes cultures to
diagnose PJI (Parvizi and Gehrke, 2014). Tissue samples were
suspended in 3 mL of LBK and vortexed (Vortex-Genie, Fisher Scientific,
Waltham, MA) for 1 min, followed by sonication for 5 min (Branson 2800
sonication bath) at 40 kHz and a power density of 0.22 W cm . Each
sample was incubated for 2 weeks with agitation (200 rpm) at 37 C
and plated overnight at 37 C. For bioluminescence (BLI), plates
were imaged using a GloMax multi-detection reader system (Promega, Madison,
WI).
diagnose PJI (Parvizi and Gehrke, 2014). Tissue samples were
suspended in 3 mL of LBK and vortexed (Vortex-Genie, Fisher Scientific,
Waltham, MA) for 1 min, followed by sonication for 5 min (Branson 2800
sonication bath) at 40 kHz and a power density of 0.22 W cm . Each
sample was incubated for 2 weeks with agitation (200 rpm) at 37 C
and plated overnight at 37 C. For bioluminescence (BLI), plates
were imaged using a GloMax multi-detection reader system (Promega, Madison,
WI).
3
Screening for Nematophagous Microbes in Soil
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In screening for nematophagous microbes we used the ‘Sargent’ potato field soil listed in Castillo et al., which has a strong likelihood of containing beneficial microbes26 (link). A two-part ‘Sargent’ soil and one-part molecular water slurry was prepared. This slurry functioned as a liquid suspension of microorganisms present within the Sargent field soil. The water and soil mixtures were contained in a 50 ml VWR Falcon tube and were homogenized for 2 hours on a Fisher Vortex Genie at maximum speed. The slurry was then centrifuged at 2440 RPM in a Sorvall Super T21 benchtop centrifuge for 10 minutes at room temperature (28.8 °C ± 2 °C) to pellet any remaining soil debris. Subsequently, the slurry was aspirated from the Falcon tube, and serially diluted to prepare 10−6, 10−7 and 10−8 dilutions. Aliquots of 50 ul and 100 ul of each slurry dilution were plated onto high population (>1,000) C. elegans culture plates (described in 4.1.2) to monitor for microbial pathogenesis (Supplementary Fig. S1 ). The studies were repeated three times using three replicates for each solution/dilution in order to locate as many nematophagous microbial candidates as possible. For a full description of this methodology and soils tested in preliminary experimentation, see Supplementary Note S1 .
4
Quantifying Biofilm Formation on Materials
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PP samples were incubated in LB-medium inoculated with P. aeruginosa as described. As a reference material, sterile glass slides, with a size of 22 × 22 mm were used. Three samples of each material were tested. After an incubation period of 24 h, planktonic cells were washed away by submerging the samples three times in physiological saline (0.9% NaCl). The biofilm/attached cells were detached from the surface by vigorous vortexing for at least 1 min (Vortex Genie, Fisher Scientific, USA) in 10 mL physiological saline (0.9% NaCl). To verify whether the biofilm has completely detached from the surface, we used the SEM to scan the surface of the vortexed samples for remaining bacteria. No bacteria were present on the surface, only residues that had formed due to previous adhesion (Figure S4 ). A serial dilution series was performed, and 100 µL of each dilution was plated onto fresh LB agar plates. The plates were incubated overnight at 37 °C. After incubation, colonies were counted and the colony-forming units per mm2 were calculated.
5
Quantifying Antibacterial Activity of PlactiveTM
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To test the antibacterial activity of PlactiveTM in terms of the viable colonies, the colony-forming unit assay was performed as a direct quantification method. Biofilms were grown on 3D printed Plactive™ and Giantarm™ PLA samples as described in the scanning electron microscopy (SEM) section. Afterward, planktonic cells were washed away by submerging the samples three times in physiological saline (0.9% NaCl). The biofilm was detached from the surface by vigorous vortexing for at least 1 min (Vortex Genie, Fisher Scientific, USA) in 10 mL physiological saline (0.9% NaCl). A serial dilution series was performed, and 100 µL of each dilution was plated onto fresh LB agar plates. The plates were incubated overnight at 37 °C. After incubation, colonies were counted and the colony-forming units were calculated.
6
Captan Residue Quantification in Apples
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Ampoules of 100µg/mL captan in acetonitrile standard solution were purchased from Restek. A standard curve was created using 10µL, 25µL, 50µL, 75µL, 100µL, and 125µL of the captan standard measured by micropipette. The volumes of standard were added to the centrifuge containing blended untreated control apples, vortexed for 30 sec using a Fisher Vortex Genie, centrifuged at 5000 rpm for 2.5 min, and extracted using the same conditions and procedure before being injected into the GC/MS.
7
Microbial Hydrophobicity Quantification
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The Microbial Adhesion to Hydrocarbons (MATH) test was employed to determine the hydrophobicity of spores examined in this study [28] . A 3ml spore suspension in distilled water with an OD600 0.4-0.6 was prepared in a McCartney bottle. OD measurements were made using an Ultrospec 1100 pro UV/Visible spectrophotometer, (Biochrom, Cambridgeshire, UK). A 300µl aliquot of hexadecane was then added to the suspension and vortex mixed (VortexGenie, Fisher Scientific, UK) for 1 min at room temperature. The mixture was incubated for 15 min at room temperature, allowing the layers to separate, with hexadane and hydrophobic components of the suspension rising to form to form the top layer, while the aqueous layer settled below with the hydrophilic components of the suspension. After this, the OD of the aqueous (bottom) layer was measured. The resulting decrease in the OD of the aqueous layer, compared to the the OD before the addition of hexadecane, was recorded.
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