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17 protocols using dm5500b compound microscope

1

Observing Worm Locomotion Dynamics

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Animals were prepared for observation by immobilization in a 5 µL drop of 15 mM levamisole on a 4% agar pad. Worms were observed under 40×, 63×, and 100× objective lens using a Leica DM5500B compound microscope equipped with differential interference contrast optics and epifluorescence. Images were captured using a Hamamatsu C4742-95 digital camera controlled with Leica LAS © software.
To make a video of grinder turnover during L4 lethargus, we immobilized the animals against agarose pads using polystyrene nanoparticles (Kim, E., et al., 2013 (link)). Images were captured at 3.75 frames per second using an Imaging Source DMK 31BU03 camera on a Leica DM 2500 P upright microscope at 63× and analyzed using IC Capture 2.2 software (Imaging Source). To make the video, one out of every 36 images was used and played at 30 frames per second.
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2

Fungal Morphology Characterization on PDA

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Colony characteristics of cultures on a ½-potato dextrose agar (PDA; Difco Laboratories, Franklin Lakes, NJ, USA) medium were photographed after 14 d of incubation at 25 °C. The fungal morphology was recorded from colonies grown in the dark for 14 d at 25 °C on PDA. Fungal structures were examined in lactic acid on slide mounts under a Leica DM5500B compound microscope (Wetzlar, Germany) with Nomarski differential interference contrast illumination, and images were captured with a Leica DFC 500 camera. Measurements of at least 30 conidia and other fungal structures were taken at 1000× magnification. Novel species were registered in MycoBank [33 ].
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3

Studying Adult Insect Structures

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Basic methods for studying adult structures, and terms used, are given in Maddison (1993) . Body length was measured from the front of the labrum to the elytral apex. Genitalia have been mounted in Euparal between two small coverslips attached to archival-quality heavyweight watercolor paper.
Photographs of body parts were taken with a Leica Z6 Apo lens and DMC4500 camera, and of male genitalia with a Leica DM5500B compound microscope and DMC425C camera. A stack of images from different focal positions was then merged using the PMax procedure in Zerene Systems’s Zerene Stacker; the final images thus potentially have some artifacts caused by the merging algorithm.
Specimens examined are housed in the following collections: Essig Museum Entomological Collection, University of California, Berkeley (EMEC), James R. LaBonte collection, Dallas, Oregon (JRLC) and Oregon State Arthropod Collection, Oregon State University, Corvallis (OSAC).
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4

Visualizing Arabidopsis Protein Localization

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Plasmids of N- and C-terminal YFP protein fusions were co-transformed into Arabidopsis protoplasts as described above and then incubated in a 23 °C growth chamber overnight in the dark. The YFP fluorescence was monitored using a Leica DM 5500B Compound Microscope with Leica DFC290 Color Digital Camera. FM4-64 (Invitrogen, T3166) was used as a counter stain for the plasma membrane marker.
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5

Microscopy and Measurement Protocols for Solenysa reflexlis

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Specimens were examined and measured by using a Leica MZ16A stereo microscope. Further details, such as epigynes, were studied with a Leica DM5500B compound microscope. Digital images were taken with a Leica DFC 500 camera and as a composite of multiple focus images assembled using the software package Leica Application Suite. Epigynes were cleared in methyl salicylate (Holm 1979 ) for examination under the microscope and temporarily mounted as described by Grandjean (1949) and Coddington (1983) . SEM images were taken by using a Hitachi S-3400N scanning electron microscope at China Agriculture University. For SEM examination, the PageBreakspecimens were prepared as described by Álvarez-Padilla and Hormiga (2008) . The non-chitinous abdominal tissue was digested with Sigma Pancreatin LP 1750 enzyme complex to expose the internal structures for examination. Due to the unavailability of specimen, no SEM image provided for the male palp of Solenysareflexlis.
All measurements are given in millimeters. The leg measurements are given in the following sequence: Total (femur, patella+tibia, metatarsus, tarsus). Terminology for the genital characters follows Tu and Hormiga (2011) . The specimens examined here have been deposited in the Department of Zoology, National Science Museum, Tokyo, Japan (NSMT) and in College of Life Sciences, Capital Normal University, Beijing (China).
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6

Morphological Characterization of Fungal Isolates

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To determine morphological characteristics, isolates were grown on water agar with pieces of sterilised wheat stems placed on the surface (WSA) and incubated under a 12 h photoperiod with near ultraviolet light (NUV) (Smith 2002 ) at 23 °C. Fungal structures were mounted on glass slides in lactic acid (100 % v/v) for microscopic examination after 28 d of incubation. At least 20 measurements of selected structures were made and, means and standard deviations (SD) calculated. Ranges were expressed as (min–) mean-SD – mean+SD (–max) with values rounded to 0.5 μm. Images were captured with a Leica DFC 500 camera attached to a Leica DM5500B compound microscope with Nomarski differential interference contrast.
For colony morphology, 3-d-old cultures on 9 cm diam plates of PDA and oatmeal agar (OMA) (Oxoid) that had been grown in the dark at 23 °C were grown for a further 7 d under 12 h photoperiod with NUV light at 23 °C (Thompson et al. 2011 (link)). Colony colours (surface and reverse) were described according to the colour charts of Rayner (1970) . Nomenclatural novelties were deposited in MycoBank (Crous et al. 2004 ) (www.mycobank.org).
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7

Fungal Colony and Morphology Analysis

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Colony characteristics of cultures on ½-potato dextrose agar (PDA; Difco Laboratories, Franklin Lakes, NJ, USA.) medium were recorded after 7 d incubation at 25 °C. Fungal morphology was recorded from colonies grown in the dark for 14 d at 25 °C on PDA as well as on autoclaved pine needles on water agar. Fungal structures were examined in lactic acid on slide mounts under a Leica DM5500B compound microscope (Wetzlar, Germany) with Nomarski differential interference contrast illumination, and images were taken with a Leica DFC 500 camera. Measurements of at least 30 conidia and other fungal structures were taken at 1000× magnification. Novel species were registered in MycoBank [35 ].
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8

Microscopic Examination of Spider Genitalia

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Specimens were examined and illustrated by using a Leica M205A stereomicroscope and a Leica DM5500B compound microscope. The male palp and female epigynum were examined after they were dissected from the body. The embolic division was excised by breaking the membranous column connecting between the suprategulum and radix. For microscopic examination and illustration, the male palp and epigynum were cleared in methyl salicylate. Illustrations were made using a drawing tube.

Scanning Electron Microscopy

(SEM)
images were taken by using a LEO 1430VP at the Department of Biological Sciences at George Washington University. For SEM examination the specimens were prepared following Álvarez-Padilla and Hormiga (2008) . SEM images of the embolic division taken from the right palp were mirrored to match those taken from the left palp. All specimens examined here are deposited in the

Institute of Zoology, Chinese Academy of Sciences, Beijing, China

(IZCAS)
, and the

College of Life Sciences, Capital Normal University, China

(CNU)
. Terminology for the genital and somatic characters follows Hormiga (2000) , Tu and Hormiga (2010 (link), 2011), Saaristo and Tanasevitch (1996) and Wang et al. (2015) (link).
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9

Fungal Isolate Characterization Protocol

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Fungal isolates were cultured on four media types; PDA, oatmeal agar (OA), malt extract agar (MEA) (Boerema et al. 2004 (link); Chen et al. 2015a (link)), and carnation leaf agar (CLA). The colonies were measured at 7 d, and morphology examined after 12–14 d incubation in the same light and temperature conditions described above. Images of the colonies were captured by an Epson Perfection V700 scanner at a 300 dpi resolution. Colony colour was determined on surface and reverse using the colour charts of Rayner (1970) . Isolates were characterised microscopically from the PDA plates. Lactic acid (100 % v/v) was used as the mounting fluid. Specimens were examined using a Leica DM5500B compound microscope with a Leica DFC 500 camera fitted to capture images under Nomarski differential interference contrast illumination. Micromorphological measurements and descriptions of pycnidia, pycnidial wall cells and conidia were taken from up to 20 samples, and septation and colour recorded. Images of pycnidia were taken from CLA plates using a Leica M165C stereo microscope and Lecia DFC 500 camera. The NaOH spot test on MEA culture plates helped distinguish taxa (Boerema et al. 2004 (link)).
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10

Quantifying Neoblast Markers in Planarians

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In Figure S1D, cto+ cells were imaged using a Leica DM5500B compound microscope with optical sectioning equipped with an Optigrid structured illumination device. After a maximum projection of z-stacks, cto+ cells were counted manually in Metamorph. cto+ cell numbers were averaged and significance was determined by two-tailed t-tests. In Figure 5B, and S5C using a Leica TCS SPE confocal microscope, we took a 10uM projection of mob4 and smedwi-1 expression to ensure that mob4 expression was in the same plane as neoblasts, which are 5-10 μm in size. Double positive cells were counted manually from 5 separate worms Leica LAS software.
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