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37 protocols using polybead microspheres

1

Microscopic Observation of Nematode Ovulation

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Nomarski DIC and epifluorescence microscopy was performed using a Nikon 80i compound microscope equipped with a CoolSNAP HQ2 monochrome camera (Roper Scientific, CA). Images were captured with a 60× Plan Apo objective lens using Elements software (Nikon). For time-lapse observations of sheath contraction and ovulation, day 1 young adult worms were anesthetized for 20–25 min in M9 solution with 0.1% tricaine and 0.01% tetramisole (Sigma-Aldrich, St. Louis, MO) before viewing (McCarter et al., 1997 (link)). Anesthetized worms were mounted on a 2% agarose pad. For germline RNAi experiments using worms expressing the pie-1prom∷rde-1(+) transgene, day 1 young adult worms were immobilized by placing worms on 2 μl of Polybead Microspheres 0.10μm (Polysciences) on a 5% agarose pad. A small amount of petroleum jelly was placed around the coverslip to prevent desiccation. Only worms that displayed movement indicating viability on the pad were analyzed for ovulation events.
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2

Quantifying CHE-1::GFP Protein Degradation

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To estimate the protein degradation rate of CHE-1::GFP, we used Fluorescence Recovery After Photobleaching (FRAP). Animals were immobilized using Polybead microspheres (Polyscience) in M9 buffer on agarose pads covered with a cover glass. To prevent dehydration of animals, the coverslip was sealed with VALAP (vaseline, lanolin and paraffin, ratio 1:1:1). Animals were monitored at several time points during the experiment if they were still alive by checking very subtle movement and/or pumping behaviour. The GFP signal in the ASE neurons of the animals was bleached until approximately 20% of the initial signal was left. After bleaching, the GFP signal was measured every 20 or 30 min until the signal had recovered. Images were taken with the same microscope as in the CHE-1 protein quantification section. We measured for each time point the average GFP intensity in the ASE neurons and subtracted the background intensity measured nearby the ASE neurons. The degradation rate was calculated from the initial slope of the growth curve using the following exponential model: R(t) =( fb)+(x0 (fb))ebt , where x0 is the initial fluorescent intensity at the start of the recovery curve right after bleaching. b and f represent the CHE-1 protein degradation and production rate, which are fitted on the individual measured recovery curves, to obtain the average CHE-1 protein degradation rate.
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3

Mitochondrial Morphology Assessment in C. elegans

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Synchronized populations were grown to day-1 adults at 20°C, and picked unanesthetized onto 10% agarose pads with 0.05 μm Polybead microspheres (Polysciences) for immobilization. Imaging was performed on a Ti2 CSU-W1 confocal microscope (Nikon) with 488-nm illumination of eGFP through a Plan-Apochromat 100x/1.45 objective. Qualitative assessment of mitochondrial morphology was made by blinded analysis, scoring worms based on three categories: tubular (interconnected mitochondrial network), intermediate (combination of interconnected network and isolated smaller mitochondria) or fragmented (mostly fragmented mitochondria). Differences between strains were tested for significance with Chi-square analysis (GraphPad Prism).
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4

Measuring Intestinal Mucus Thickness

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Thickness of the mucus layer was measured on live tissue as described (15 (link)). Briefly, intestinal tissue was flushed with cold Krebs buffer to remove luminal content and unattached mucus. The muscle layer was removed by microdissection and the intestine was mounted in a horizontal chamber system and maintained at 37 °C with basolateral Krebs-glucose buffer perfusion and apical Krebs-mannitol buffer. For visualization of the mucus surface black 10-μm polystyrene Polybead microspheres (Polysciences, Germany) were added apically. The surface was observed by a stereomicroscope and mucus thickness measured using a glass micropipette connected to a micrometer. For the inner colonic mucus layer, mucus thickness was measured every 15 min at five different locations for up to 45 min to calculate the mucus growth rate.
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5

Immunofluorescence Staining of Cerebral Organoids

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hHOs were transferred to microcentrifuge tubes (Eppendorf) using a cut 1000 μL pipette tip to avoid disruption to the organoids and fixed in 4% paraformaldehyde solution. Fixation was followed by washes in PBS-Glycine (20 mM) and incubation in blocking/permeabilization solution containing 10% Donkey Normal Serum, 0.5% Triton X-100, 0.5% bovine serum albumin (BSA) in PBS on a thermal mixer (Thermo Scientific) at minimum speed at 4 °C overnight. hHOs were then washed 3 times in PBS and incubated with primary antibodies (Suppl. Table 1) in Antibody Solution (1% Donkey Normal Serum, 0.5% Triton X-100, 0.5% BSA in PBS) on a thermal mixer at minimum speed at 4 °C for 24 h. Primary antibody exposure was followed by 3 washes in PBS and incubation with secondary antibodies (Supplementary Table 1) in Antibody Solution on a thermal mixer at minimum speed at 4 °C for 24 h in the dark. T-tubules staining was conducted using Wheat Germ Agglutinin (WGA) lectins conjugated with FITC (Millipore Sigma). The stained hHOs were washed 3 times in PBS before being mounted on glass microscope slides (Fisher Scientific) using Vectashield Vibrance Antifade Mounting Medium (Vector Laboratories). 90 µm Polybead Microspheres (Polyscience, Inc.) were placed between the slide and the coverslip (No. 1.5) to preserve the 3D structure of the organoids.
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6

Mitochondrial Morphology Assessment in C. elegans

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Synchronized populations were grown to day-1 adults at 20°C, and picked unanesthetized onto 10% agarose pads with 0.05 μm Polybead microspheres (Polysciences) for immobilization. Imaging was performed on a Ti2 CSU-W1 confocal microscope (Nikon) with 488-nm illumination of eGFP through a Plan-Apochromat 100x/1.45 objective. Qualitative assessment of mitochondrial morphology was made by blinded analysis, scoring worms based on three categories: tubular (interconnected mitochondrial network), intermediate (combination of interconnected network and isolated smaller mitochondria) or fragmented (mostly fragmented mitochondria). Differences between strains were tested for significance with Chi-square analysis (GraphPad Prism).
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7

Light-Induced Inactivation of Axonal Domains

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Light-induced inactivation using the miniSOG(103L) fusion protein was performed on an Olympus FV1000MPE microscope under a 20× 1.00 N.A. water immersion objective. Adult transgenic animals expressing Pglr-3∷miniSOG(103L)-VAMP2-mCherry or Pglr-3∷miniSOG(103L)-mCherry (untagged control) were immobilized on a thin 5% agar pad with 20 nM sodium azide diluted in Polybead® Microspheres (Polysciences, Inc). The identification of the RIA axonal domains was aided by the expression of mCherry. Axonal domains were illuminated using a 488nm laser for 6-8 minutes. After illumination, the animals were recovered under the standard cultivation condition for 5 minutes before examination of the locomotory behavior. The angles of head undulations were measured using the WormLab System (http://www.mbfbioscience.com/wormlab-imaging-system) and the ventral direction was defined as positive. The average angle of all the head undulations was determined for each worms and multiple worms were examined for each genotype.
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8

Measuring CHE-1::GFP Protein Degradation

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To estimate the protein degradation rate of CHE-1::GFP, we used Fluorescence Recovery After Photobleaching (FRAP). Animals were immobilized using Polybead microspheres (Polyscience) in M9 buffer on agarose pads covered with a cover glass. To prevent dehydration of animals, the coverslip was sealed with VALAP (vaseline, lanolin and paraffin, ratio 1:1:1). Animals were monitored at several time points during the experiment if they were still alive by checking very subtle movement and/or pumping behaviour. The GFP signal in the ASE neurons of the animals was bleached until approximately 20% of the initial signal was left. After bleaching, the GFP signal was measured every 20 or 30 minutes until the signal had recovered. Images were taken with the same microscope as in the CHE-1 protein quantification section. We measured for each time point the average GFP intensity in the ASE neurons and subtracted the background intensity measured nearby the ASE neurons. The degradation rate was calculated from the initial slope of the growth curve using the following exponential model:
, where 𝑥 ! is the initial fluorescent intensity at the start of the recovery curve right after bleaching. 𝑏 and 𝑓 represent the CHE-1 protein degradation and production rate, which are fitted on the individual measured recovery curves, to obtain the average CHE-1 protein degradation rate.
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9

Synchronizing Hermaphrodite Worm Ovulation

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Animals were synchronized using an “egg prep” procedure. Gravid hermaphrodites were lysed using an alkaline hypochlorite solution, and then the embryos were washed in M9 buffer (22 mM KH2PO4, 42 mM NaHPO4, 86 mM NaCl, and 1 mM MgSO4; Hope, 1999 ). Animals were grown at 23°C for ∼50–54 h. Adults were immobilized on a 5% agarose slide with a 1:1:1.5 ratio of water, M9 buffer, and 0.05-μm Polybead microspheres (Polysciences). First ovulations were imaged using a Nikon Eclipse 80i microscope with a 60× oil-immersion lens, a charge-coupled device camera, and SPOT R3 software. Ovulations were imaged at a rate of 1 Hz and analyzed using ImageJ.
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10

Preparation and Characterization of Organic Droplets

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Dodecane (Aldrich, GR) was used to prepare organic droplets. Into a 1.0 M potassium chloride solution, a small amount of Dodecane (1 -20 vol %) was added and sonicated for 20 min. The solution contained 0.2 mM Triton X-100 as a surfactant to stabilize fine emulsion droplets smaller than ten micrometers. Hexadecyltrimethylammonium bromide (CTAB) and sodium lauryl sulfate (SDS) were also used as surfactants at a concentration of 2.0 mM to examine the effect of ionic charge on the electromagnetophoretic behavior of droplets. To confirm any electromagnetophoretic migration in the magnetic circuit system, a polystyrene particle with a 10-μm diameter (Polybead ® Microspheres, Polysciences Inc.) was used. All reagents were of analytical reagent grade and used as purchased. Water was purified by a Milli-Q system (Merck Millipore).
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