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28 protocols using ds 5m

1

Quantifying Amyloid Plaque Burden in Alzheimer's Mice

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Aβ42-immunostained dentate gyrus (DG) was observed under a Nikon Eclipse 80i microscope using a 4X objective, and images were acquired with a Nikon DS-5M high-resolution digital camera. The camera settings were adjusted at the start of the experiment and maintained for uniformity. Digital images (five sections/mouse from four different APP/PS1 mice per age group 4-, 6-, and 12-month-old) were analyzed using Visilog 6.3 analysis program (Noesis, France). Immunopositive plaque area within the hilar region of the DG (where the amyloid plaques are mainly concentrated) was identified by bright-level threshold, the level of which was maintained throughout the experiment for uniformity. The grayscale image was converted to a binary image with plaque and DG areas identified. Plaque loading was defined as the percentage of total DG area immunostained for Aβ42. The hilus area in each 4x image was manually outlined. The plaque loading (%) for each mouse was estimated and defined as (sum plaque area measured/sum DG area analyzed) × 100. The sums were taken over all slides sampled, and a single plaque burden was computed for each mouse. The mean and standard deviation (SD) of the plaque loading were determined using all the available data. Quantitative comparisons were carried out on sections processed at the same time.
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2

Quantifying Amyloid Plaques and Microglia in 5xFAD Mice

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Plaque load was defined as the number of Thioflavin-S positive Aβ plaques in the subiculum of 5xFAD mice. The number of labelled gal3/iba1 positive cells were quantified in the subiculum and CA1 pyramidal layer in the brains of 5xFAD. Images were acquired with a Nikon DS-5M high-resolution digital camera connected to a Nikon Eclipse 80i microscope. The camera settings were adjusted at the start of the experiment and maintained for uniformity. Digital 10× images from 2, 6 and 10 weeks old 5xFAD mice were used for plaque and microglial quantification. 6 sections/mouse; n = 4/age/genotype. Analysis of the fluorescent labelled structures was performed with Fiji ImageJ Software (W. Rasband, National Institutes of Health). The colour images for plaques were converted to binary images. Plaques and activated microglial cells were counted manually after setting the brightness threshold. Quantitative comparisons were carried out on sections processed at the same time with same batches of solutions. Pictures were retrieved from the same brain area in the different experimental groups.
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3

Microscopic Analysis of Neurodegeneration

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Sections were examined under optical and fluorescent microscope Nikon Eclipse Ci and Zeiss Axioplan-2 with the aid of two CCD cameras (Basler acA1920 and Nikon DS-5M, respectively). The evaluation was performed on the area of the cortex and the hippocampus. In average 30 optical fields were examined per each group under the magnification of 40X. Results were expressed as positive cells/mm2 (for Gallyas, AT8, AT180 and total Tau), area/mm2 [for GSKβ(S9), GSKβ(Y216) and 3D10]. The microglial activation state was quantified as cells/mm2 and by determining the ramification index (RI), ranging from 0 for ramified “resting” cells to1 for “active” ameboid cells (Wilms et al., 1997 (link)).
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4

Fluorescence Microscopy Imaging Protocol

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All epifluorescent images of fixed specimens were acquired with a fluorescence microscope (Eclipse 80i; Nikon) using a 20×/0.75 NA or 60×/1.4 NA oil immersion objective lens fitted with a digital camera (DS-2; Nikon) and NIS-Elements BR 3.0 software (Nikon). Images were adjusted for brightness and contrast using ImageJ. Images from endothelial repulsion assays were acquired with an inverted florescent microscope (Eclipse TE2000-S; Nikon) using a 4×/0.2 NA objective lens, a digital camera (DS-5M; Nikon), and NIS-Elements BR 3.0 software (Nikon). Images were adjusted for brightness and contrast using ImageJ. Time-lapse videos were recorded at 37°C using an incubator live cell imaging microscope (VivaView FL LCV-110; Olympus) with a UPlan-SApochromat 40×/0.95 NA, WD 0.18 mm objective lens (Olympus) and a camera (Orca R2 CCD; Hamamatsu Photonics). Videos were acquired with MetaMorph for Olympus VivaView FL LCV-110 software, and separated images were adjusted for brightness and contrast using ImageJ.
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5

Plantaris Muscle Fiber Cross-Sectional Area

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Cross-sections (thickness, 10 μm) were cut from frozen samples of 14 days OL plantaris muscle and stained with hematoxylin & eosin (Sakura Finetek) according to standard procedures. Stained cross-sections were observed under a bright field microscope (Eclipse TE300; Nikon, Tokyo, Japan) and captured with a digital camera (DS-5M; Nikon, Tokyo, Japan). From photomicrographs of each muscle, cross-sectional area (CSA) of ≥1000 fibers was measured using ImageJ v. 1.46r (National Institutes of Health, Bethesda, MD, USA). The plantaris muscle has slow fibers in its deep region and fast fibers with different fiber size in its middle to surface region [22 (link)]. To avoid such a region-dependent bias, the measurement of CSA were made evenly for fibers in all captured images. As with muscle weight, fiber CSA is thought to be affected by body weight, so that it was expressed relative to body weight, too (CSA/body weight).
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6

Condensation Patterns on Silicon Surfaces

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A freshly prepared silicon sample was bonded to a Peltier stage (Deben MK3 Coolstage) with thermal paste and placed under a top-down optical microscope (Nikon Eclipse LV150). The ambient temperature was T = 21.3 ± 0.3 °C and the relative humidity was H = 40 ± 3%, corresponding to a dew point of TDP = 7.2 ± 1.3 °C. The substrate was initially kept dry at 10 °C and was then cooled beneath the dew point to 5 °C to allow condensation to form in order to make the patterns visible. The desired pattern type (circles, triangles, or stripes) was centered and focused under a 5× objective lens, such that the 2P, 4P and 8P arrays were all visible within the microscope’s field-of-view.
Once the field-of-view was set, the sample was immediately heated to 40 °C to dry the surface. The wafer was then cooled back down to 10 °C, followed by further cooling to either 5 °C or −10 °C to observe the resulting condensation with a digital camera (Nikon DS-5M) attached to the microscope. The transient of the Peltier stage was 5 ± 1 s to cool from 10 °C to 5 °C and 30 ± 1 s to cool from 10 °C to −10 °C. The forming condensation was imaged for 10 min, and the surface was then heated back to 40 °C to dry out the surface for the next trial. Three trials were obtained for both condensation temperatures and a new chip was used for each pattern type to minimize surface contamination.
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7

Quantifying Duckweed Vein Patterns

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To determine frond vein numbers, 10 duckweed colonies, with two/three fronds each, were washed with deionized water and cleared with 70% ethanol for 3 weeks prior to observations using a Nikon stereomicroscope (Nikon SMZ1000) equipped with a Nikon digital camera (DS-5M). Duckweed colonies were observed under bright and dark field conditions at ×20 and ×10 magnification.
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8

Histological and Immunohistochemical Analysis of Rabbit Knee Joints

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After the rabbits were sacrificed, the knee joint samples were removed and fixed in 10% neutral buffered formalin for 3 days and were then dehydrated through an alcohol gradient (30%–100%) and embedded in paraffin wax. The specimens were cut to a thickness of 5 μm along the longitudinal axis of the tendon. These sections were treated with haematoxylin and eosin (H&E) and Masson’s trichrome stain (Masson’s) for histological evaluation. The sections stained with H&E and Masson’s were observed using a light microscope (Eclipse 80i, Nikon), and the images were captured using a camera (DS-5M, Nikon). For immunohistochemistry staining, endogenous peroxidase was blocked by incubation with 3% (v/v) hydrogen peroxide in methanol for 10 mins. Then, the sections were blocked for 20 mins with a blocking reagent containing goat serum in PBS after washing three times with PBS. After overnight incubation at 4°C with a primary antibody, the sections were washed and then incubated with a secondary antibody (MaxVision kit; Maixin Biotechnology) for 15 mins at room temperature. Dimethyl aminoazobenzene (DAB) (Simple Stain DAB Solution, Maixin Biotechnology) was used for colour development. Hematoxylin staining was used to reveal the nuclei. The results were evaluated by three individuals who were blinded to the treatments.
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9

Analyzing Aluminum Stress Responses

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To analyze root length, five-day-old seedlings grown on agar (for details see Plant Material) were transferred on agar plates containing 1/8 MS, pH 4 supplemented with 200 μM AlCl3. After 9 day incubation, plates were scanned (Canon CanoScan 8800F) and the root growth was measured using the JMicroVision 1.2.7 software.
To measure pollen tubes length, tobacco pollen was transiently transformed with AtNPC4:YFP by particle bombardment. After 6 h of germination in dark, pollen tubes were incubated in liquid simple sucrose medium (pH 5) with or without 50 μM AlCl3 for additional 2 h. Mean growth rate of pollen tubes expressing AtNPC4:YFP and vector-only control was evaluated using the fluorescence microscope Olympus BX-51.
To determine survival rate, 7-day-old seedlings grown on agar (for details see Plant Material) were transferred to 6-well plates with liquid 1/8 Hoagland’s (Kocourková et al., 2011 (link)) solution (pH 4) with 100 μM AlCl3 for 22 days. Plates pictures were taken by Nikon SMZ 1500 zoom stereoscopic microscope coupled to a Nikon DS-5M digital camera. The survival rate was calculated as a number of viable true leaves.
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10

Morphological Assessment of Tinnea Genus

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Morphological assessments were based on herbarium specimens and our field collections. Further, protologues of all published names in the genus Tinnea from Africa and all relevant taxonomic literature [1 (link)–3 , 15 , 16 , 20 ] were consulted and reviewed. To delimit the potential new taxa from closely similar species, morphological variations were compared with herbarium (FHI, GSUH, K, S; acronyms follow [21 ]) specimens including type materials on JSTOR [22 ] and POWO [2 ]. A dissecting microscope (Leica GZ4) or stereomicroscope (Leica S9i) fitted with digital camera (Nikon DS-5M) and eyepiece micrometer were used to measure and photograph stems, leaves, inflorescences, flowers and fruits.
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