Ultrascan 4000

Manufactured by Ametek

Sourced in United States

The UltraScan 4000 is a laboratory instrument designed for high-performance spectrophotometric analysis. It offers precise and reliable measurements across a wide range of wavelengths, enabling users to conduct various analytical and quality control tasks in a laboratory setting.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

Ultrascan 4000 4k × 4k CCD camera (15 citations) Ultrascan 4000 digital camera (7 citations) Ultrascan 4000 CCD Camera Model 895 (5 citations) Ultrascan 4000 4k x 4k CCD camera (3 citations) Ultrascan 4000 4k x 4k CCD Camera System Model 895 (3 citations) Ultrascan 4000 CCD detector (3 citations) SsCCD Ultrascan 4000 (2 citations) Ultrascan 4000 4k × 4k (2 citations) 4kx4k Ultrascan 4000 CCD camera (2 citations) GATAN ultrascan USC 4000 (2 citations)

91 protocols using ultrascan 4000

Negative Staining of Proteoliposomes

Check if the same lab product or an alternative is used in the 5 most similar protocols

For negative staining, 3.5 μL of proteoliposomes were applied to a glow-discharged, carbon-coated, 300-mesh, copper grid (Electron Microscopy Sciences, Hatfield, PA) and stained with 2% uranyl acetate (Adair and Yeager, 2007 (link)). Low-dose EM was performed at the Molecular Electron Microscopy Core facility at UVA using a Tecnai F20 electron microscope (FEI, Hillsboro, OR), operating at 120 kV. Images were recorded at a nominal magnification of 29,000× and a defocus of 3 μm using a 4 × 4 K charge-coupled device camera (UltraScan 4000; Gatan, Pleasanton, CA), corresponding to a pixel size of 3.7 Å on the specimen. Proteoliposome diameters were obtained using ImageJ (NIH, Bethesda, MD) from the average of two measurements per proteoliposome.

Narahari A.K., Kreutzberger A.J., Gaete P.S., Chiu Y.H., Leonhardt S.A., Medina C.B., Jin X., Oleniacz P.W., Kiessling V., Barrett P.Q., Ravichandran K.S., Yeager M., Contreras J.E., Tamm L.K, & Bayliss D.A. (2021). ATP and large signaling metabolites flux through caspase-activated Pannexin 1 channels. eLife, 10, e64787.

+ Open protocol

+ Expand

Automated Particle Size Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

G-SOMEs were negatively stained with 1% sodium silicotungstate on continuous carbon-film grids, and electron micrographs of single particles were recorded using an Ultrascan4000 charge coupled device camera (Gatan, Pleasanton, CA) at 93,000x nominal magnification. Particles were then automatically selected by a computational screening function provided by the proprietary data processing software package PARTICLE (Angstrom BioImaging, Cambridge, MA, http://www.image-analysis.net/EM/), from which statistics on the particle size and other morphological descriptors were generated.

Agrawal A., Bisharyan Y., Papoyan A., Bednenko J., Cardarelli J., Yao M., Clark T., Berkmen M., Ke N, & Colussi P. (2019). Fusion to Tetrahymena thermophila granule lattice protein 1 confers solubility to sexual stage malaria antigens in Escherichia coli. Protein Expression and Purification, 153, 7-17.

+ Open protocol

+ Expand

TEM Imaging of Extracellular Vesicles

Check if the same lab product or an alternative is used in the 5 most similar protocols

For TEM analysis, 5 μL of the 5 mg/mL purified EMV sample was loaded onto a freshly glow-discharged holey carbon EM grid (Quantifoil R 2/2, Quantifoil Micro Tools GmbH, Germany). Semiautomated sample verification was performed by using a Vitrobot Mark IV (FEI Company, Eindhoven, Netherlands) at 4°C and 90–100% relative humidity. The vitrified sample was imaged under low dose conditions by using a Tecnai G² Spirit TEM (FEI Company, Eindhoven, Netherlands) that was operated at 120 kV acceleration voltage. Images were recorded by using an UltraScan 4000 charge-coupled device camera (Gatan Inc., Pleasanton, CA, USA) at a nominal magnification of ×26,000 and −1–2 μm underfocus.

Choi C.W., Park E.C., Yun S.H., Lee S.Y., Kim S.I, & Kim G.H. (2017). Potential Usefulness of Streptococcus pneumoniae Extracellular Membrane Vesicles as Antibacterial Vaccines. Journal of Immunology Research, 2017, 7931982.

+ Open protocol

+ Expand

Imaging COQ7-COQ9 Complex by Negative-Staining EM

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

4.0 μl aliquots of purified COQ7-COQ9 complex (0.05 mg ml⁻¹) was applied onto glow-discharged continuous carbon-coated grids, blotted with filter paper, and stained with freshly prepared 0.75% (w/v) uranyl formate. Negatively-stained electron microscopy grids were imaged on Tecnai T12 microscope (FEI Company) equipped with a 4k × 4k CCD camera (UltraScan 4000, Gatan) and operated at a voltage of 120 kV. Images were recorded at room temperature with a nominal magnification of 52,000x, corresponding to a calibrated pixel size of 2.21 Å on the specimen. A total of 121 micrographs were collected and CTF parameters were estimated by CTFFIND4 (Rohou and Grigorieff, 2015 (link)). Particles were manually picked, extracted with a box size of 200 × 200 pixels, and reference-free 2D classification was used to generate the templated for the automatic particle picking by using Relion 3.0 software package (Zivanov et al., 2018 (link)). Then, 262,589 particle projections were semi-automatically picked from the micrographs and sorted through multiple rounds of 2D classification to discard poorly defined particle classes using Relion 3.0. A subset of 231,879 particles with well-defined shapes was selected following multiple rounds of 2D classification to demonstrate 2D class averages of COQ7-COQ9 complex.

Manicki M., Aydin H., Abriata L.A., Overmyer K.A., Guerra R.M., Coon J.J., Peraro M.D., Frost A, & Pagliarini D.J. (2022). Structure and functionality of a multimeric human COQ7:COQ9 complex. Molecular cell, 82(22), 4307-4323.e10.

+ Open protocol

+ Expand

Virus Enumeration Using Latex Beads

Check if the same lab product or an alternative is used in the 5 most similar protocols

Equal volumes of virus suspension and polystyrene latex spheres (Agar Scientific, AGS130-02) at a known concentration per ml were mixed in 2 volumes of TNE buffer (20 mM Tris [pH 7.5], 0.5 M NaCl, and 1 mM EDTA). 5 μl of suspension was then added to a glow discharged EM grid (Agar Scientific, S162-4), allowed to rest for 1 min, washed three times in deionised water, and stained with Ammonium Molybdate (2% (w/v) pH 7.2). Dry grids were examined using a JEM2200 FS electron microscope (JEOL) and images captured using an Ultrascan 4000 charge-coupled-device (CCD) camera (Gatan). Multiple images (n ≥ 6) per sample were used for virus particle and latex bead enumeration and used to calculate the number of particles per ml of virus stock inoculum.

Alandijany T., Roberts A.P., Conn K.L., Loney C., McFarlane S., Orr A, & Boutell C. (2018). Distinct temporal roles for the promyelocytic leukaemia (PML) protein in the sequential regulation of intracellular host immunity to HSV-1 infection. PLoS Pathogens, 14(1), e1006769.

+ Open protocol

+ Expand

Cryo-ET of U2OS and HeLa Cell EBs

Check if the same lab product or an alternative is used in the 5 most similar protocols

For cryo-electron tomography, 27 single-axis tilt series (12 from U2OS cells, 15 from HeLa cells) were collected with SerialEM at a 2° increment over a range of ± 66° and cumulative dose of ∼ 150 e/Å². A total of 46 EBs were captured by cryo-electron tomography. Images were recorded at 12 µm defocus on a 200 kV F20 or 300 kV Tecnai Polara electron microscope equipped with a 4k × 4k CCD camera (Ultrascan 4000, Gatan). For F20 datasets, the nominal magnification was 25 000, which corresponds to a 0.93 nm pixel size after applying a binning factor of 2. For Polara datasets, the nominal magnification was 29 000, which corresponds to a 0.71 nm pixel size after binning by 2. Energy filtration was not used in this study. Tilt images were aligned (using 10 nm gold fiducials) and volumes were reconstructed in IMOD. Non-linear, anisotropic filtering was applied to the tomograms to enhance contrast (Frangakis and Hegerl, 2001 (link)). Representative tomograms have been deposited in the EMDB (accession code EMD-2641).

Nans A., Saibil H.R, & Hayward R.D. (2014). Pathogen–host reorganization during Chlamydia invasion revealed by cryo-electron tomography. Cellular Microbiology, 16(10), 1457-1472.

+ Open protocol

+ Expand

Transmission Electron Microscopy of Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols

Cells were collected and washed in 100 mM sodium cacodylate at pH 7.2. Afterwards, cells were fixed in 100 mM sodium cacodylate containing 2.5% glutaraldehyde and 4% formaldehyde at pH 7.2 at room temperature. The buffer was exchanged after 20, 60, and 120 min. All other steps were done as described previously (Nordhues et al., 2012 (link)). Samples were analysed with a JEM-2100 (JEOL) transmission electron microscope (operated at 80 kV). Micrographs were taken using a 4080×4080-pixel CCD camera (UltraScan 4000; Gatan) and Gatan DigitalMicrograph software (version 1.70.16).

Spaniol B., Lang J., Venn B., Schake L., Sommer F., Mustas M., Geimer S., Wollman F.A., Choquet Y., Mühlhaus T, & Schroda M. (2021). Complexome profiling on the Chlamydomonas lpa2 mutant reveals insights into PSII biogenesis and new PSII associated proteins. Journal of Experimental Botany, 73(1), 245-262.

+ Open protocol

+ Expand

Negative Staining and Single-Particle Analysis of PANX1

Check if the same lab product or an alternative is used in the 5 most similar protocols

For negative staining, 3.5 μl of purified, monomeric PANX1 proteins (full-length or caspase-cleaved, 10–20 μg ml⁻¹) or 6(0CT)-GFP (before and after TEVp cleavage; 10–20 μg ml⁻¹) were applied to a glow-discharged, carbon-coated, 300-mesh, copper grid (Electron Microscopy Sciences) and stained with 2% uranyl acetate35 (link). Low-dose EM was performed using a Tecnai F20 electron microscope (FEI), operating at 120 kV. Images were recorded at a nominal magnification of × 62,000 and a defocus of -0.9 μm using a 4 × 4 K charge-coupled device camera (UltraScan 4000, Gatan), corresponding to a pixel size of 1.82 Å on the specimen. EMAN2 software36 (link) was used for single-particle analysis. A total of ∼6,000 full-length and caspase-cleaved PANX1 particles from ∼150 micrographs were semi-automatically selected and extracted within boxes of 196 × 196 pixels using the Swarm tool in the e2boxer.py program of EMAN2. The contrast transfer function was estimated and corrected by e2ctf.py with standard EMAN2 parameters. Particle images were normalized and then high-pass (100 Å) and low-pass (10 Å) filtered and centred. The program e2refine2d.py was used to perform 2D classification by iterative, multivariate statistical analysis. Six-fold symmetry was applied to the 2D class averages using the program e2proc2d.py.

Chiu Y.H., Jin X., Medina C.B., Leonhardt S.A., Kiessling V., Bennett B.C., Shu S., Tamm L.K., Yeager M., Ravichandran K.S, & Bayliss D.A. (2017). A quantized mechanism for activation of pannexin channels. Nature Communications, 8, 14324.

+ Open protocol

+ Expand

Cryo-EM Data Collection Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

The cryo-EM data were collected, as previously described²³, in low-dose mode on an FEI (Hillsboro, Oregon) Tecnai F20 TEM at 200kV extraction voltage and about 80,000× magnification using the automatic image collection program Leginon^{53 (link)}. Micrographs were recorded on a Gatan UltraScan 4000 CCD camera binned by 2× with effective CCD magnification of 110,637× and pixel size of 2.71 Å on the object scale.

Chen B., Boël G., Hashem Y., Ning W., Fei J., Wang C., Gonzalez RL J.r., Hunt J.F, & Frank J. (2014). EttA regulates translation by binding to the ribosomal E site and restricting ribosome-tRNA dynamics. Nature structural & molecular biology, 21(2), 152-159.

+ Open protocol

+ Expand

Electron Tomography Imaging Workflow

Check if the same lab product or an alternative is used in the 5 most similar protocols

Electron tomography (ET) was performed as previously described^{48 (link)} Tomographic fiducial markers (15 nm protein A-coupled gold beads) were adsorbed to both sides of the EM grids. Transmission electron microscopy (TEM) images for correlation, and Scanning transmission electron microscopy (STEM) tilt series were acquired using a Tecnai F20 (Thermo Fischer Scientific) at 200 kV, using SerialEM^{49 (link)}. The TEM images for correlation were acquired at 4.47 nm pixel size using an UltraScan 4000 camera (Gatan). Tilt series were acquired over a 60° to −60° tilt range (1° increment) at 1.67 nm pixel size in nanoprobe mode using the bright-field detector, with a 10-µm C2 aperture and 320 mm camera length. The tomograms were reconstructed using IMOD software package (versions 4.9.4)^{50 (link)}. Correlations of fluorescence and TEM images were performed using the ec-CLEM plugin with the Icy software^{51 (link)}.

Elbaz-Alon Y., Guo Y., Segev N., Harel M., Quinnell D.E., Geiger T., Avinoam O., Li D, & Nunnari J. (2020). PDZD8 interacts with Protrudin and Rab7 at ER-late endosome membrane contact sites associated with mitochondria. Nature Communications, 11, 3645.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!