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125 protocols using d7000

1

Scorpionfly Specimen Collection and Imaging

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All the material examined in this study is deposited in the Biological Science Museum, Dali University, Dali (DALU), or Sun Yat-sen University, Guangzhou (SYSU). Adult scorpionflies were caught with a collecting net, and preserved in 95% ethanol or pinned. Photographs were taken with a Nikon D7000 digital camera in conjunction with a Nikkor AF-S Micro 105 mm f/2.8 lens (Figs 1F, 2A-B, 3A-B, 4, 5A-B), a Sony Alpha 77 II digital camera in conjunction with a Sony 50 mm f/2.8 macro lens (Fig. 1A-E, G-I), or a Nikon D7000 digital camera in conjunction with a Canon MP-E 65 mm f/2.8 1-5X macro lens with a handmade mount adapter (other images). Measurements follow Wang & Hua (2021) (link). The female habitus images were modified to omit the left antennae, wings and legs. The map was obtained from SimpleMappr (http://www.simplemappr.net) and modified in Adobe Illustrator ver. CC to add distributional information. All pictures were adjusted and grouped with Adobe Photoshop ver. CC.
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2

Lipid Extraction and TLC Analysis of Transformed Yeast

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After the transformed yeast strains were grown on SGal-URA medium for 3 days, the cells were placed in 80 °C water for 10 min, collected and washed twice with sterile water, freeze-dried, and weighed. Then, 0.3 g of dried sample was placed in liquid nitrogen and ground into powder. Subsequently, 5 mL of chloroform:methanol (v:v = 2:1) was added, and the sample was kept at room temperature for 3 h. After centrifuging at 3000 rpm for 3 min to collect the supernatant, 1 mL of chloroform:methanol (v:v = 2:1) was added and mixed. After centrifuging at 3000 rpm for 3 min to collect the supernatant, 2 mL 0.9% NaCl was added and mixed. Then, the sample was centrifuged at 3000 rpm for 3 min to collect the lower organic phase. The organic phase was dried by importing nitrogen. Thereafter, 40 mg of extracted lipid dissolved in 1 mL of chloroform was obtained, and 5 μL was measured on a silica gel plate for TLC analysis [30 (link)]. The developing agent used was hexane:ether:glacial acetic acid (v:v:v = 70:30:1). Color was developed via iodine vaporization. Pictures were captured with a Nikon camera D7000.
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3

Sperm Whale Photo-Identification Methodology

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Sperm whales, as well as many other cetacean species, can be identified individually based the shape, coloration and marks on their flukes or dorsal fins [23 ]. In previous sperm whale studies, 90% of encountered individual could be reliably identified this way [24 ]. Photographs of the flukes of diving sperm whales were taken with an APS-C digital single-lens reflex camera (Canon EOS 40D, 70D, 7D, and Nikon D7000) equipped with a 70–300 mm zoom lens. Photographs were matched to an identification catalog following the methods of Arnbom [25 ]. A quality rating (Q) between 1 and 5 was assigned to each photograph and only high-quality photographs with a Q ≧ 4 were used for the analyses. Photo-identification data were not collected blindly (i.e., we often knew the identities of the animals that we were photographing) because our study involved observations of focal animals in the field.
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4

Mycological Collection Analysis Protocol

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Specimens from the “Dr. Gastón Guzmán Huerta” fungal collection at the Herbarium of the Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico (ENCB), and the “Jose Castillo Tovar” collection at the Instituto Tecnológico de Ciudad Victoria (ITCV) were revised. The color codes follow Kornerup and Wanscher [10 ] and Bessette et al. [11 ]. Microscopic observations were made of tissues rehydrated in 5% aqueous KOH and Melzer’s reagent; ascospore dimensions included the ornamentation. The macroscopic features were photographed with a Nikon D7000 camera and the micrographs with a Sony DSCWX350. Additionally, scanning electron microscopy (SEM; Hitachi SU1510, Hitachi, Tokyo, Japan) was used to observe the details of spore walls. The meanings of the taxonomic terms are based on Ulloa and Hanlin [12 ].
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5

Visual Identification and Characterization of Microplastics

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Plastics were manually extracted from neuston samples under dissecting microscopes and identified visually by their color, shape, and texture. We followed Norén (39 ) and Hidalgo-Ruz et al. (40 (link)) for visual identification of synthetic particles and used the following criteria: 1) texture should be hard, durable and not easily broken or crushed; 2) no cellular or organic structures should be visible; 3) colors should be homogenous; and 4) fibers should have uniform diameter throughout their length. Extracted plastics were dried, weighed, and photographed (Nikon D7000) under standardized lighting conditions. Images were analyzed using ImageJ (40 (link)) providing the total count, area (square millimeters) and feret diameter (i.e., maximum caliper distance) for each individual plastic particle. To reduce the possibility of counting artifacts in images (false positives), we excluded all detected particles with feret diameter <0.3 mm, which was the size of the mesh cod end for all neuston plankton tows.
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6

Confirming HSP60 Recombinant Protein Expression

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Human embryonic kidney 293 cells (HEK293) were used to confirm that whether the HSP60 recombinant protein was expressed in eukaryotic cell as previous description [14 (link)]. In brief, HEK293 cells grown in 6-well plate were transfected with 10.0 μg pVAX-HSP60 endotoxin-free plasmid using lipofectamine 2000 (Invitrogen, Carlsbad, California, USA) as instructed by the manufacturer. Three days post-transfection, the samples were fixed, permeabilized, blocked and incubated with goat anti-Toxoplasma serum at 37.0°C and subsequently secondary antibody at room temperature (RT) with darkness for 60 min. The dilutions of primary and secondary antibodies were as follows: the serum stored in our laboratory, 1:50; Alexa Fluor® 488-AffiniPure Donkey Anti-Goat IgG (H+L) (Jackson ImmunoResearch Laboratories Inc, West Grove, Pennsylvania, USA), 1:1,000. Group transfected with pVAX I vector was used as the control. The fluorescent images were recorded by fluorescence microscope (Olymplus IX 51, Olympus, Tokyo, Japan) with camera D7000 (Nikon, Tokyo, Japan).
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7

Visualizing Root Surface Bacteria

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To view bacteria on the root surfaces, seedlings were examined with a Nikon Eclipse TE2000-U microscope equipped with a 60× Plan Apo oil objective lens, and pictures were taken with a Nikon D7000 digital camera (real-time movie) or with a Hamamatsu digital camera (model ORCA-ER; for fluorescence detection). Figure 1 presents frames from Movie S1 in the supplemental material that were selected with the iMovie software. The fluorescence signal was detected using a CFP/yellow fluorescent protein (YFP) dual-band filter set (catalog no. 52019; Chroma). All images were taken at the same exposure time, processed identically for compared image sets, and prepared for presentation using MetaMorph and Photoshop software. Each image is representative of at least 12 root colonization assays performed in three independent experiments.
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8

Photographic Documentation of Skin Lesions

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Digital photographs were taken of designated active lesions and the surrounding, unaffected skin using a Nikon D7000 digital SLR camera.
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9

Microscopic Examination of Aquatic Crustaceans

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Individuals were examined using a stereo-microscope. Specimens of thermosbaenaceans, stygiomysids, mysids, and amphipods were studied as follows: cleared and stained exoskeletons were dissected under a Leica M125 stereo microscope. The dissections were then mounted on slides and examined using a Leica DM 1000 compound light microscope (Fišer et al. 2009 ; Angyal et al. 2015 (link)). For the identification of the collected material the following publications were used: Álvarez et al. 2005 (link); Álvarez and Iliffe 2008 ; Angyal et al. 2018 (link); Botosaneanu and Iliffe 1999 , 2000 , 2002 , 2006 ; Bowman 1966 (link), 1977 ; Bruce 1986 ; Creaser 1936 ; Hobbs and Hobbs 1976 (link); Hobbs et al. 1977 (link); Hobbs 1979 ; Holsinger 1977 , 1990 ; Horwitz et al. 1995 ; Kallmeyer and Carpenter 1996 (link); Lowry and Myers 2013 (link); Meland et al. 2015 (link); Pérez-Aranda 1983a , 1983b , 1984a , 1984b ; Tinnizi and Quddusi 1993 ; Wagner 1994 . Photographs were made using an OMAX 14 OMP digital USB microscope camera, a Nikon D5300, and a Nikon D7000 with 60 mm macro lens.
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10

High-resolution corneal scar imaging

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The corneal scars were imaged as previously described. (Sriram et al., 2014 (link)) Briefly, a Nikon D7000 digital camera was outfitted with a macro lens capable of a native 1:1 reproduction (60 mm Nikkor). The D7000 was set to the “Standard” program, ISO 100, manual exposure with a shutter speed of 1/250 s and f/57. Shutter speed is the amount of time the shutter in the camera remains open. The f-stop value (f/57), or the aperture of the camera, controls how much light can enter the camera (i.e. the smaller the aperture, the smaller the amount of light allowed to enter). To visualize and measure haze, the flash power was set manually (1/6th), and neither the flash nor the lens had a filter. For all images, the lens was set to manual focus and pre-focused to a 1:1 reproduction ratio, and the camera was mounted on a tripod and focused by moving the camera closer or further from the subject. Guide lights on the flash heads were used to facilitate haze visualization and focusing. Due to the high shutter speed and low aperture, the images were highly reproducible since the influence of background light conditions were significantly reduced.
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