Observer d1

Manufactured by Zeiss

Sourced in Germany, United States

The Observer D1 is a high-performance microscope designed for versatile laboratory applications. It features advanced optical components and a robust construction to deliver reliable and consistent performance. The core function of the Observer D1 is to provide users with a precise and detailed view of their samples for various scientific and research purposes.

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Lab products found in correlation

Alexa fluor 488 conjugated secondary antibody, by Thermo Fisher Scientific (6 mentions) 30 mm glass base, by Greiner (4 mentions) Zen 2 acquisition software, by Zeiss (4 mentions) Axiocam mrm camera, by Zeiss (4 mentions) Rm2255 microtome, by Leica (4 mentions) 4 6 diamidino 2 phenylindole (dapi), by Merck Group (4 mentions) Axiocam, by Zeiss (3 mentions) Plan neofluor 0.75 na ph2 dry objective, by Zeiss (3 mentions) Cm1950, by Leica (3 mentions) Fluorescent mounting medium, by Agilent Technologies (3 mentions) Axiovision 4, by Zeiss (2 mentions) Fv1000 confocal microscope, by Olympus (2 mentions) Dihydroethidium, by Thermo Fisher Scientific (2 mentions) Dihydroethidium dhe, by Thermo Fisher Scientific (2 mentions) Nanowizard 4 afm, by Bruker (2 mentions) Lsm 700, by Zeiss (2 mentions) Axiocam mrc, by Zeiss (2 mentions) Slowfade antifade reagent, by Thermo Fisher Scientific (2 mentions) Lysozyme, by Agilent Technologies (1 mentions) Chromogranin a, by Abcam (1 mentions)

75 protocols using observer d1

Histological and Molecular Analysis of Tissue Samples

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HE and PAS/Alcian blue staining was performed by the Histology core of Augusta University, while TEM was conducted by the EM core of Augusta University according to the standard procedures. Immunohistochemistry, immunofluorescent staining, and immunoblotting were performed as described previously^{45 (link)}. Bright field and Epifluorescence images were obtained using Zeiss Observer D1 with AxioVision 4.8 software (Carl Zeiss Microscopy GmbH, Jena, Germany) and Keyence BZ-X700 fluorescent microscope with its corresponding software (Keyence America, Itasca, IL, USA). All histopathological analysis and quantification were performed blindly by lab personnel who had no prior information on the genotypes of animals and tissues.
The antibodies used in this study included: Cdk5rap3 rat polyclonal antibody (Li lab), Uba5 (Li Lab), Ufl1 (Li lab), Ufbp1 (21445-1-AP, Proteintech, Rosemont, IL), phospho-Histone H3 (ser10) (#9706, Cell Signaling), PCNA (#2586, Cell Signaling), Olfm4 (#39141, Cell Signaling), Calnexin (#2679, Cell Signaling), Ufm1 (Ab109305, Abcam), Lysozyme (A0099, Agilent Dako, Santa Clara, CA), Grp78/Bip (#3177, Cell Signaling), Chromogranin A (Ab15160, Abcam, Cambridge, MA), and β-Actin (#3700, Cell Signaling). All affinity-purified and species-specific HRP- and fluorophore-conjugated secondary antibodies were obtained from Jackson ImmunoResearch (West Grove, PA).

Quintero M., Liu S., Xia Y., Huang Y., Zou Y., Li G., Hu L., Singh N., Blumberg R., Cai Y., Xu H, & Li H. (2021). Cdk5rap3 is essential for intestinal Paneth cell development and maintenance. Cell Death & Disease, 12(1), 131.

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Hydrogel-Mediated Diffusion Assay

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Hydrogel was casted at one end of a glass capillary tube (outer diameter, 1 mm; inside diameter, 0.58 mm; World Precision Instruments) using an insulin syringe. Hydrogel-containing capillary tubes were placed in a 50-ml conical tube containing 1× PBS to fully swell overnight at 4°C. Alexa 555–labeled α-bungaroxin (8 kDa; 1:4 dilution in PBS; Thermo Fisher Scientific) was delivered to the other free end of the hydrogel-containing glass capillary tube. Samples were immediately placed in the temperature and humidity-controlled stage of an epifluorescence microscope (Zeiss Observer D1). Time-series images were acquired every 15 min for 3 hours at 37°C. Hydrogel boundary (x = 0) was defined by a region with an average raw intensity of 9.5 at t = 0. Change in the average intensity was quantified from x = 0 to 200 μm over the 3-hour assay period. To determine the diffusion coefficient (D), the data were fitted using the solution of Fick’s second law

φ (x, t) = φ_{0} \cdot erfc (\frac{x}{2 \sqrt{D t}})

Han W.M., Anderson S.E., Mohiuddin M., Barros D., Nakhai S.A., Shin E., Amaral I.F., Pêgo A.P., García A.J, & Jang Y.C. (2018). Synthetic matrix enhances transplanted satellite cell engraftment in dystrophic and aged skeletal muscle with comorbid trauma. Science Advances, 4(8), eaar4008.

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Microinjection of Antisense Oligonucleotides in Sea Urchin

Cited 1 time

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Microinjection was performed as previously described (5 (link)). Two gene-specific MO-substituted antisense oligonucleotides (5′-AAAATATATGCATTCATGTTGATCA-3′) complementary to the start codon region of the sea urchin Cara7 gene and a second MO (5′-CGACCTTCAGATATATTCTCACAAA-3′) complementary to the 5′-untranslated region were obtained from Gene Tools. In addition, a scramble MO 5′-CCTCTTACCTCAGTTACAATTTATA-3′ that has no biological target in the sea urchin was used to obtain the control groups. The MOs were dissolved in injection Buffer (20 mM Hepes, 120 mM KCl, 24% glycerol, pH 8.0) and were injected into the freshly fertilized egg (one-cell stage) using a microinjection system (Picospritzer III, Parker) mounted on an inverse microscope (Zeiss Observer D1) equipped with a cooling stage.

Matt A.S., Chang W.W, & Hu M.Y. (2022). Extracellular carbonic anhydrase activity promotes a carbon concentration mechanism in metazoan calcifying cells. Proceedings of the National Academy of Sciences of the United States of America, 119(40), e2203904119.

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Bacterial Colonization on Bone Cement

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Bacterial tests were carried out in a broth solution (Patent No. P 409082 [65 ]) consisting of a nutrient medium (Table 2) and five strains of bacteria (the relative volumes shown in Table 3) mainly responsible for hospital infections. The bone cement samples were placed in the solution and examined after the 1st day and after 6-month exposure, to reflect the influence of an environment of a living organism. After this period, the samples were taken out of the broth solution to identify the bacteria with a biological microscope (Zeiss Observer D-1, Zeiss, Oberkochen, Germany), and to examine the colonization of bacteria on the surface using a scanning electron microscope (JSM-7800F, JEOL, Tokyo, Japan).

Świeczko-Żurek B., Zieliński A., Bociąga D., Rosińska K, & Gajowiec G. (2022). Influence of Different Nanometals Implemented in PMMA Bone Cement on Biological and Mechanical Properties. Nanomaterials, 12(5), 732.

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Immunostaining and Microscopy Protocol

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Immunofluorescent staining and Immunoblottings were performed as described previously⁶. Confocal images were acquired using Zeiss 510 META confocal microscope with Zen software (Carl Zeiss Microscopy GmbH, Jena, Germany), while epifluorescence images were obtained using Zeiss Observer D1 with AxioVision 4.8 software (Carl Zeiss Microscopy GmbH, Jena, Germany).
The antibodies used in this study include: UFBP1 and Uba5 rat antibody (Li lab and [6 (link), 26 (link)]), eIF2α, phospho-S51-eIF2α (Cell Signaling, Danvers, MA, USA), ASC1 (A300-843A, Bethyl Laboratories, Montgomery, TX, USA), JNK and phospho-JNK (Santa Cruz Biotechnology Inc., Dallas, TX, USA), GATA-1 and KLF1 (Abcam, Cambridge, MA, USA), α-tubulin and β-actin (Sigma). All affinity-purified and species-specific HRP- and fluorophore-conjugated secondary antibodies were obtained from Jackson ImmunoResearch (West Grove, PA, USA).

Cai Y., Pi W., Sivaprakasam S., Zhu X., Zhang M., Chen J., Makala L., Lu C., Wu J., Teng Y., Pace B., Tuan D., Singh N, & Li H. (2015). UFBP1, a Key Component of the Ufm1 Conjugation System, Is Essential for Ufmylation-Mediated Regulation of Erythroid Development. PLoS Genetics, 11(11), e1005643.

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Fluorescence Microscopy Imaging Protocol

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Imaging experiments were performed at 37°C in 0.5 mM or 1 mM Ca²⁺ Ringer's buffer (as indicated in the figure legends) using either a Zeiss Cell Observer Z1 microscope equipped with a 40× oil “Fluar” (N.A.: 1.3) objective, multi‐filter system, fast acquisition EMCCD camera (Evolve® 512 Delta) and LED system (Colibri, Zeiss) or a Zeiss Observer D1 equipped with a 40X oil Neofluar (N.A.: 1.3) objective, Axiocam 702 mono and LED system (Colibri, Zeiss) or a Zeiss Axio Observer 7 equipped with 40× oil “Neofluar” (N.A.: 1.3), Axiocam 702 mono and LED system (Colibri 7, Zeiss). Subsequent obtained data were processed with the AxioVision, Zen 2.6, or Zen 3.2 softwares (Zeiss, Oberkochen, Germany). All plasmids and constructs used are listed in Table EV2.

Stejerean‐Todoran I., Zimmermann K., Gibhardt C.S., Vultur A., Ickes C., Shannan B., Bonilla del Rio Z., Wölling A., Cappello S., Sung H., Shumanska M., Zhang X., Nanadikar M., Latif M.U., Wittek A., Lange F., Waters A., Brafford P., Wilting J., Urlaub H., Katschinski D.M., Rehling P., Lenz C., Jakobs S., Ellenrieder V., Roesch A., Schön M.P., Herlyn M., Stanisz H, & Bogeski I. (2022). MCU controls melanoma progression through a redox‐controlled phenotype switch. EMBO Reports, 23(11), e54746.

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Quantifying Intracellular Autophagosome Dynamics

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All images were captured with a custom-built Zeiss Observer D1 using a Zeiss 100x objective lens and a 1.4 NA. Images were captured using a Photometrics CoolSNAP HQ2 and analyzed using Metamorph software for punctae number, size, and intensity. Images were deconvoluted and thresholded using Autoquant X2 software. Deconvolution was done blind at 40 iterations. LC3 punctate structures were defined as at least 10 pixels in size with fluorescence intensities of at least twice that of average background intensities. Flurochromes used included Pacific Blue, cy5, cy3, and FITC.

McLeod I.X., Saxena R., Carico Z, & He Y.W. (2021). Class I PI3K Provide Lipid Substrate in T Cell Autophagy Through Linked Activity of Inositol Phosphatases. Frontiers in Cell and Developmental Biology, 9, 709398.

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Live and Fixed Cell Imaging

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Live imaging was performed using Zeiss Observer D1 with AxioCam. Fixed cells were analyzed by Olympus FV1000 confocal microscope. Five to ten random fields per coverslip, 1–2 coverslips per condition, at 200× magnification were counted for every condition, of at least 5 independent experiments. Values are expressed as mean ± S.E.M. Statistical analysis were performed by Student’s t-test for independent samples combined with Levene’s test for equality of variances. Holm-Bonferroni method was used to correct for multiple comparisons.

Wohl S.G, & Reh T.A. (2016). miR-124-9-9* potentiates Ascl1-induced reprogramming of cultured Müller glia. Glia, 64(5), 743-762.

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Fluorescence Microscopy of Live Cells

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HeLa LAP2b:RFP or tubulin:GFP cells were seeded onto Petri dishes with a 30-mm glass base (Greiner), and an inverted fluorescence microscope (Observer D1; Zeiss) was used. Fluorescence or phase-contrast images were taken by using a 63× Plan Neofluor 0.75 NA Ph2 dry objective (Zeiss). Imaging was performed at 37°C in 5% CO₂ by using a Zeiss AxioCam MRm camera and Zeiss ZEN 2 acquisition software. Drugs were added to the medium immediately before filming as appropriate.

Petsalaki E, & Zachos G. (2020). An ATM–Chk2–INCENP pathway activates the abscission checkpoint. The Journal of Cell Biology, 220(2), e202008029.

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Immunocytochemical Evaluation of scFvs Binding Tau Aggregates

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To test reactivity of the scFvs with tau aggregates generated by human neuronal cells, we cultured the human neuroblastoma cell line SH-SY5Y and its derivative SH-SY5Y-TMHT441 which overexpresses a human mutant tau 2N4R species (Loffler et al., 2012 (link)). Cells were cultivated as previously described (Tian et al., 2013 (link)) on aseptic glass slides. Growth media for the SH-SY5Y-TMHT441 cells also contains 300μg/ml Geneticin G-418. For immunocytochemistry analysis, cells were grown and fixed in 4% formaldehyde in PBS at room temperature for 15 minutes, then treated with 0.2% Triton 100 at room temperature for 15 minutes, washed three times with PBS and blocked for 1 hour with PBS containing 5% goat serum. The cells were incubated overnight with a 0.3 mg/ml aliquot of one of the anti-tau scFvs, F9T or D11C. The rabbit anti-c-Myc antibody (Abcam, 1:1500) was applied for 30 min. The cells were washed 3 times with PBS and incubated with 1/1000 dilution of the secondary antibodies, goat anti-mouse IgG Alexa Fluor 488 (Life Technologies, New York, NY) and DAPI (Sigma), for 1 hour at room temperature. Images were taken using a fluorescent microscope (Observer D1, Zeiss). Polyclonal rabbit antibody against human tau (Catalog: PA1-18272, Thermo-scientific, 1:400) was used as a positive control to detect tau species in SH-SY5Y-TMHT441 neurons.

Tian H., Davidowitz E., Lopez P., He P., Schulz P., Moe J, & Sierks M.R. (2014). Isolation and characterization of antibody fragments selective for toxic oligomeric tau. Neurobiology of aging, 36(3), 1342-1355.

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