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Upright microscope

Manufactured by Zeiss
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The Upright Microscope is a versatile lab equipment designed for high-quality optical microscopy. It features a sturdy, upright configuration that provides stable observation of samples. The instrument offers high-resolution imaging capabilities, enabling detailed examination of various specimens.

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Lab products found in correlation

Matlab, by MathWorks (3 mentions) Biostation im q, by Nikon (2 mentions) Sylgard 184, by Dow (2 mentions) Patchmaster software, by HEKA Elektronik (2 mentions) Epc 10 patch clamp amplifier, by HEKA Elektronik (2 mentions) Originpro, by OriginLab (2 mentions) Inverted microscope, by Zeiss (2 mentions) Monoclonal anti vinculin antibody, by Merck Group (2 mentions) Goat anti mouse alexa 488 secondary antibody, by Thermo Fisher Scientific (2 mentions) X63 oil immersion objective, by Zeiss (1 mentions) Lsm 510 confocal laser scanning microscope, by Zeiss (1 mentions) Senescence associated β galactosidase kit, by Beyotime (1 mentions) Paraplast plus, by Merck Group (1 mentions) Rm2255, by Leica (1 mentions) Toluidine blue o, by Merck Group (1 mentions) Tert butyl alcohol, by Merck Group (1 mentions) Cryotome, by Leica (1 mentions) Tissue tek, by Sakura Finetek (1 mentions) Prolong gold reagent, by Thermo Fisher Scientific (1 mentions) Axiocam icc3 camera, by Zeiss (1 mentions)

42 protocols using upright microscope

1

Ultrastructural analysis of HIFU-exposed bacteria

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For light microscopy and for initial TEM fixation, HIFU-exposed or unexposed bacterial samples were fixed with half-strength Karnovsky’s fixative. A drop of the fixed suspension was applied onto a polylysine-coated histologic slide, air-dried and then stained using the standard Romanovsky-Giemsa procedure. Image acquisitions were carried out under oil immersion, using a Zeiss upright microscope with 100 × objective (total magnification 1500 ×) and with an AxioCam MRc 5 megapixel camera.
For transmission electron microscopy (TEM), treated or unexposed bacteria were concentrated by centrifugation at 8,000 g × 20 min, and the supernatant was discarded. Pelleted fixed cells were treated with 1% osmium tetroxide solution for 30 min and dehydrated in a progressive series of ethanolic solutions (30%, 50%, 70% and 100%). After routine procedures, the pellets were stained with 1% uranyl acetate in 70% ethanol during dehydration and then embedded into epon-araldite. Ultrathin sections (70 100 nm) were then obtained on an LKB-III ultra-microtome (Mariehäll, Sweden). The sections were further contrasted with Reynolds lead cit-rate solution. Images were captured using a transmission electron microscope JEOL 1011 (Tokyo, Japan), equipped with a Gatan camera.
Brayman A.A., MacConaghy B.E., Wang Y.N., Chan K.T., Monsky W.L., Chernikov V.P., Buravkov S.V., Khokhlova V.A, & Matula T.J. (2018). INACTIVATION OF PLANKTONIC ESCHERICHIA COLI BY FOCUSED 1-MHZ ULTRASOUND PULSES WITH SHOCKS: EFFICACY AND KINETICS UPON VOLUME SCALE-UP. Ultrasound in medicine & biology, 44(9), 1996-2008.
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2

Real-Time Visualization of AGR2 Infiltration

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The infiltration
of a fluorescent-labeled AGR2 protein (Atto-647N
dye) into the aptasensor was monitored in real time by confocal laser
scanning microscopy (CLSM). Scans were conducted with a LSM 510 confocal
laser-scanning microscope (Carl Zeiss, Inc.) linked to a Zeiss upright
microscope that was equipped with a Zeiss X63 oil immersion objective.
PSi PL and Atto-647N-labeled AGR2 were excited with laser lines of
458 and 633 nm, respectively. For three-dimensional image projection
of the porous structure, z-scans in 0.73 μm
increments over a depth of ∼15 μm were taken every 30
s and projected with a standard Carl Zeiss software (ZEN 2010). Initially,
the PL and AGR2 fluorescence signals were scanned within the aptasensor
with 10 μL of SB buffer for 10 min. Then, a 1 μM solution
of Atto-647N-labeled AGR2 in SB (40 μL) was introduced, and
the PL and AGR2 fluorescence were measured continuously for additional
50 min. We used a relatively low AGR2 concentration for the measurements
to obtain a time-resolved visualization of the protein infiltration
before signal saturation was reached. Image analysis was performed
by Imaris Bitplane scientific software.
Arshavsky-Graham S., Ward S.J., Massad-Ivanir N., Scheper T., Weiss S.M, & Segal E. (2021). Porous Silicon-Based Aptasensors: Toward Cancer Protein Biomarker Detection. ACS Measurement Science Au, 1(2), 82-94.
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3

Live cell imaging and quantitative analysis

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Live cell imaging was performed using BioStation IM-Q (Nikon). Filopodial dynamics were tracked using an ImageJ plugin MTrackJ, only for cells that did not divide during the time35 (link). Fluorescence images were obtained using an inverted confocal laser scanning microscope (Nikon A1R) or TissueGnostics cell imaging and analysis system mounted to an upright microscope (Zeiss). Quantification of the cell morphology and proliferation was done on phalloidin and EdU stained fluorescent images which are analysed using routines incorporating a build-in ‘particle analysis’ function in ImageJ software28 . Quantification was performed on images obtained from two independent experiments with at least 200 randomly selected cells per substrate.
Tantakitti F., Boekhoven J., Wang X., Kazantsev R., Yu T., Li J., Zhuang E., Zandi R., Ortony J.H., Newcomb C.J., Palmer L.C., Shekhawat G.S., de la Cruz M.O., Schatz G.C, & Stupp S.I. (2016). Energy landscapes and function of supramolecular systems. Nature materials, 15(4), 469-476.
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4

MyHC Immunostaining of Myotubes

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Differentiated myotubes were processed for pan-MyHC immunostaining. Cells were imaged using Zeiss upright microscope and analysis was performed from aleatory fields of the well. Myotubes were identified as elongated MyHC (+) cells containing at least two nuclei. Fusion index was calculated as the percentage of nuclei within myotubes relative to the total number of nuclei. Approximately 500 nuclei and 100 myotubes were counted for fusion index and number of nuclei per myotube, respectively, for each replicate.
Selvaraj S., Mondragon-Gonzalez R., Xu B., Magli A., Kim H., Lainé J., Kiley J., Mckee H., Rinaldi F., Aho J., Tabti N., Shen W, & Perlingeiro R.C. (2019). Screening identifies small molecules that enhance the maturation of human pluripotent stem cell-derived myotubes. eLife, 8, e47970.
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5

Senescence Induction and SA-β-Gal Assay

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Senescence was induced by spontaneous immortalization, etoposide treatment, or irradiation. Senescent cells were identified by a senescence-associated β-galactosidase kit (Beyotime, Shanghai, China) according to the manufacturer’s protocol. For senescence induced by spontaneous immortalization, MEFs during serial passages were harvested and fixed for SA-β-Gal staining. For etoposide-induced senescence, immortalized MEFs were treated with 10 μM etoposide for 24 h and cultured in normal medium for another 5 days. For IR experiments, MEFs were irradiated with 3 Gy and 6 Gy using an X-ray irradiator. The cells were harvested on day 6 for SA-β-Gal assays. Fresh tissues from 5-month-old WT, Trex1−/− and littermate controls were fixed in 4% Paraformaldehyde for 12 h and then transferred to 30% sucrose overnight. Tissues were then embedded in cryo-embedding medium (OCT) and cryosectioned at 8 μm for staining of SA-β-gal (pH 6.0) at 37°C for 16–24 h in SA-β-gal staining solution. Slides were imaged at 10× with upright microscope (ZEISS).
Du H., Xiao N., Zhang S., Zhou X., Zhang Y., Lu Z., Fu Y., Huang M., Xu S, & Chen Q. (2023). Suppression of TREX1 deficiency-induced cellular senescence and interferonopathies by inhibition of DNA damage response. iScience, 26(7), 107090.
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6

Histological Preparation of Heat-Stressed Detenicka atrakce

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SAM of heat-stressed ‘Detenicka atrakce’ was fixed with 4% paraformaldehyde, followed by vacuum for 20 min. An ethanol series of 30, 50, 70, 95, and 100% was used to dehydrate the fixed samples. The dehydrated samples were cleaned with tert-butyl alcohol (Sigma-Aldrich, USA) series (35, 50, 70, and 100%). The cleaned samples were infiltrated and embedded in Paraplast Plus (Sigma-Aldrich) at 58 °C. Embedded samples were cut into 8-μm thick sections using a microtome (Leica RM2255). For observation, sectioned samples were stained with 0.05% toluidine blue O (Sigma-Aldrich) in citrate buffer (pH 4) and coverslips were applied using Canada balsam (Duksan Science, Korea). Finally, slides were observed under an upright microscope (Carl Zeiss, Jena, Germany).
Lee S.H., Yoon J.S., Jung W.J., Kim D.Y, & Seo Y.W. (2023). Genome-wide identification and characterization of the lettuce GASA family in response to abiotic stresses. BMC Plant Biology, 23, 106.
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7

Cryosectioning and H&E Staining of NHDF Organoids

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To monitor the overall tissue morphology of the NHDF organoids, such were harvested at d1 and d14 (n = 3 donors) and fixed with 4% PFA/PBS and cryoprotected via sucrose gradient. Samples were embedded in Tissue-Tek (Sakura Finetek, Alphen aan den Rijn, The Netherlands), cut longitudinally using a cryotome (Leica, Nussloch, Germany) and 10 µm-thick sections were collected onto glass slides and stored at −20 °C until use. For H&E staining (chemicals from Carl Roth, Karlsruhe), sections (n = 3) were rehydrated in PBS for 5 min, placed in hematoxylin solution for 5 min, quickly rinsed with 0.1% HCl, washed in tap water for 5 min and counterstained in eosin for 2 min, rinsed with distilled water, and dehydrated by an ascending alcohol series. After being immersed in xylene, slides were mounted and images were taken on an upright microscope (Carl Zeiss Microscopy, Jena, Germany).
Kroner-Weigl N., Chu J., Rudert M., Alt V., Shukunami C, & Docheva D. (2023). Dexamethasone Is Not Sufficient to Facilitate Tenogenic Differentiation of Dermal Fibroblasts in a 3D Organoid Model. Biomedicines, 11(3), 772.
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8

Immunofluorescence Staining and Microscopy

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After fixation with 4% PFA, cells were incubated with PBS containing 10 mM NH4Cl for 10 min at 22 °C to quench autofluorescence. Cells were incubated with a solution of 5% BSA/ 0.1% Triton X-100 in PBS for 30 min at 22 °C and then with primary antibodies in 5% BSA/0.1% Triton X-100 in PBS overnight at 4 °C. After washing, the cells were incubated with the secondary antibodies for 45 min at room temperature and mounted in Prolong Gold reagent (Thermo Scientific). Images were acquired with a Zeiss upright microscope equipped with a Plan-APOCHROMAT objective (×63; NA: 1.4), allowing acquisition of optical section images (Apotome 2 microscope).
Boutry M., Pierga A., Matusiak R., Branchu J., Houllegatte M., Ibrahim Y., Balse E., El Hachimi K.H., Brice A., Stevanin G, & Darios F. (2019). Loss of spatacsin impairs cholesterol trafficking and calcium homeostasis. Communications Biology, 2, 380.
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9

Live cell imaging and quantitative analysis

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Live cell imaging was performed using BioStation IM-Q (Nikon). Filopodial dynamics were tracked using an ImageJ plugin MTrackJ, only for cells that did not divide during the time35 (link). Fluorescence images were obtained using an inverted confocal laser scanning microscope (Nikon A1R) or TissueGnostics cell imaging and analysis system mounted to an upright microscope (Zeiss). Quantification of the cell morphology and proliferation was done on phalloidin and EdU stained fluorescent images which are analysed using routines incorporating a build-in ‘particle analysis’ function in ImageJ software28 . Quantification was performed on images obtained from two independent experiments with at least 200 randomly selected cells per substrate.
Tantakitti F., Boekhoven J., Wang X., Kazantsev R., Yu T., Li J., Zhuang E., Zandi R., Ortony J.H., Newcomb C.J., Palmer L.C., Shekhawat G.S., de la Cruz M.O., Schatz G.C, & Stupp S.I. (2016). Energy landscapes and function of supramolecular systems. Nature materials, 15(4), 469-476.
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10

Electrophysiological Characterization of hNSC-Derived Neurons

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For electrophysiological recordings coverslips with hNSC derived neurons were transferred to a recording chamber mounted on an upright microscope (Zeiss, Oberkochen, Germany) and kept in a bath solution containing (in mM): NaCl 130, KCl 3, NaHCO3 10, CaCl2 1.5, MgCl2 1, Glucose 11, HEPES 10, pH 7.3 with NaOH. Patch pipettes with 2−4 M were filled with (in mM) K-gluconate 125, KCl 20, EGTA 0.5, MgATP 4, MgCl2 4, Na2GTP 0.3, HEPES 10, pH 7.4 with KOH. Measurements were done with an EPC10 amplifier and Patchmaster software (HEKA, Lambrecht, Germany). For puff-application of KCl or glutamate, a pipette with 15 μm tip diameter was placed 60–100 μm away from the recorded cell. Pressure ejection was controlled by a pico pump (PV830, WPI, Sarasota, FL).
Palm T., Bolognin S., Meiser J., Nickels S., Träger C., Meilenbrock R.L., Brockhaus J., Schreitmüller M., Missler M, & Schwamborn J.C. (2015). Rapid and robust generation of long-term self-renewing human neural stem cells with the ability to generate mature astroglia. Scientific Reports, 5, 16321.
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