The largest database of trusted experimental protocols

12 protocols using ultrascan 1000 ccd

1

Structural Characterization of Antibody-Antigen Complexes

Check if the same lab product or an alternative is used in the 5 most similar protocols
The antibody-antigen complexes at approximately 8 μg/mL were applied to glow-discharged, carbon-coated copper grids. The grids were washed and stained with 0.75% (wt/vol) uranyl formate for 30 sec. The specimens were imaged with a FEI Tecnai F20 electron microscope operated at 120 kV. Micrographs were recorded with a Gatan UltraScan 1000 CCD at 1.21 Å/pixel and at an average defocus of 1.3 μm. The images were corrected for contrast transfer function, and determined the defocus value using CTFfind343 (link). The projections of the particles were boxed using DoG picker44 (link) in Appion45 (link), and classified to 2D classes at 3.63 Å/pixel using the software package ISAC46 (link) and Relion47 (link). The 3D initial models were generated by EMAN2 ab initial common line method48 (link). The initial models were refined with approximately 60,000 particles using Relion47 (link) to 23 Å resolution with gold standard FSC = 0.5 cutoff. Crystal structures of Fab and HER2 ECD (PDB 3wsq) were fit to the 3D model to map the binding region using UCSF chimera49 (link).
+ Open protocol
+ Expand
2

Transmission Electron Microscopy of Sample Grids

Check if the same lab product or an alternative is used in the 5 most similar protocols
The sample grids were prepared as previously described17 (link). TEM images were obtained using a CARL ZEISS Libra 120 (Carl Zeiss AG, Oberkochen, Germany) or a HITACHI-7100 (Hitachi, Ltd, Tokyo, Japan) transmission electron microscope, in both cases running at 100 kV, coupled with a Gatan Ultrascan 1000 CCD (2000 × 2000 pixels) camera (GATAN, Pleasanton, California, USA) to record the images.
+ Open protocol
+ Expand
3

Ultrastructural Analysis of Cell-Derived MPs

Check if the same lab product or an alternative is used in the 5 most similar protocols
Transmission Electron Microscopy was performed on Zeiss Libra 120 Transmission Electron Microscope and images were acquired using a Gatan Ultrascan 1000 CCD. The d3 HSPCs were incubated with MPs (30 MPs/cell) in 100 µL medium for 5 hours and then fixed in 2% EM grade glutaraldehyde and 2% paraformaldehyde (Electron Microscopy Sciences, EM grade) in 0.2 M cacodylate buffer. Samples were then rinsed 3 times, 15 min each, in 0.1 M sodium cacodylate buffer containing 2 mM CaCl2 and fixed for 1 hour in 1.5% potassium ferrocyanide, 2 mM CaCl2, 2% OsO4 in 0.1 M sodium cacodylate buffer on ice. After 3 washes with H2O, the samples were post-fixed in 2% OsO4 for 1 hour at room temperature, followed by 4 washes in H2O. Then samples were stained en bloc overnight at 4°C with filtered 1% uranyl acetate. After 3 washes in H2O, the samples were dehydrated in a series of ascending acetone solutions. The samples were then infiltrated within n-BGE and then Quetol-NSA resin on a rotator. Samples were embeded in labeled BEEM capsules and polymerized at 60°C for 24–48 hours. The ultrathin sections were prepared using a Reichert Jung Ultracut E ultramicrotome, and were collected onto 200 mesh formvar/carbon coated copper grids. Grids were stained with 2% methanolic uranyl acetate and Reynolds’ lead citrate.
+ Open protocol
+ Expand
4

Ultrastructural Analysis of Mouse Brain

Check if the same lab product or an alternative is used in the 5 most similar protocols
Animals used for the TEM study were sacrificed at 7 and 30 DPI. Samples were collected and processed as previously described [24 (link), 25 (link)]. Briefly, anesthetized mice were perfused transcardially with saline containing heparin at room temperature, and then with cold 4% paraformaldehyde. One-mm thick brain sections were cut with the brain matrix (Ted Pella, Inc., Altadena, CA, USA) and fixed with primary fixative solution (100 mM sodium cacodylate, 2% glutaraldehyde, and 2% paraformaldehyde, Electron Microscopy Sciences, Hartfield, PA, USA). Brain sections were further stereologically cut into 1 mm3 tissue from cerebral cortices under the light microscope. Tissues were stored in 0.1 M NaCacodylate buffer (pH = 7.4) containing 0.13 M sucrose and then embedded with 1% osmium tetroxide (Ted Pella, Inc. Redding, California) in Cacodylate buffer. Each tissue block was trimmed approximately 150 μm deep and the surrounding tissues to avoid potential artifacts. Approximately 250 μm × 200 μm tissue blocks were selected for sectioning at 85 nm thickness using an ultramicrotome (Ultracut UCT, Leica Microsystems, Germany) and a diamond knife (Diatome, Hatfield PA). Images were acquired with a JEOL JEM 1400 transmission electron microscope (JEOL, Peabody, MA) at 80 kV on a Gatan Ultrascan 1000 CCD (Gatan, Inc, Pleasanton, CA).
+ Open protocol
+ Expand
5

Serial Sectioning and Electron Tomography

Check if the same lab product or an alternative is used in the 5 most similar protocols
Serial sections with thickness of 200 nm or 250 nm were prepared and collected on copper slot grids (2 × 0.5 mm oval slots) with carbon supports, on which overlaid with 10 nm fiducial gold pretreated with BSA. The grids were stained with Reynold’s lead citrate before the second layer of fiducial gold was applied. The specimens were imaged with FEI Tecnai TEM operating at 200 kV and the micrographs were recorded with a Gatan UltraScan 1000 CCD at 0.87 nm/pixel (9,600x). Tilt series from −60° to +60° with 2° increments were acquired using Xplore3DTM (FEI). Double tilt series were collected using a double tilt holder (Model 2040 Dual-Axis Tomography Holder, Fischione). Serial tomograms were reconstructed, joined using IMOD, and segmented using Avizo 3D software (FEI).
+ Open protocol
+ Expand
6

Transmission Electron Microscopy of Bathycoccus Virus

Check if the same lab product or an alternative is used in the 5 most similar protocols
Fresh Bathycoccus Clade II virus lysates (~109 viral particles ml−1) passed through a sterile Nalgene Rapid‐Flow 0.45 μm PES membrane filter were used for imaging. Virus lysates (10 µl) were deposited onto formvar-coated 200 mesh copper TEM grids (Ted Pella, Redding, CA, USA) and incubated for 15 min at room temperature. The remaining volume was removed and an additional 10 µl of lysate deposited and incubated for 15 min. Grids were washed with distilled water twice, and negatively stained with 10 µl of 2% uranyl acetate for 15 sec. Samples were imaged on a FEI Tecnai G2 Spirit TEM at an acceleration voltage of 80 kV. Viral capsid diameters were measured using ImageJ 1.50i software [42 ]. For host micrography, 90 nm sections were collected on formvar-coated grids using a Reichert UltracutE ultramicrotome (Leica Microsystems, Germany). Sections were post-stained using 2% uranyl acetate in water and Reynold’s lead citrate prior to being imaged in an FEI Tecnai 12 TEM (FEI, Hillsboro, OR) operated at 120 kV. Images were recorded using a Gatan Ultrascan 1000 CCD with Digital Micrograph software (Gatan Inc., Pleasanton, CA).
+ Open protocol
+ Expand
7

TEM Imaging and Collagen Fibril Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Samples were prepared at the Electron Microscopy Core Facility, University of Missouri following a modified version of National Center for Microscopy and Imaging Research (NCMIR) methods for 3D EM61 (link). Images were acquired with JEM 1400 transmission electron microscope (JEOL) at 80 kV on Ultrascan 1000 CCD (Gatan, Inc). Difference in length of d-period for collagen fibrils was measured as described previously62 (link).
+ Open protocol
+ Expand
8

Transmission Electron Microscopy of Hearts

Check if the same lab product or an alternative is used in the 5 most similar protocols
Transmission electron microscopy was performed by the University of Missouri Electron Microscopy Core. Briefly, hearts were perfusion fixed with 2% paraformaldehyde and 2% glutaraldehyde in 100 mmol/L sodium cacodylate buffer (pH 7.35). The hearts were excised, minced, and secondarily fixed with 1% osmium tetroxide in cacodylate buffer. En bloc staining was performed with 1% aqueous uranyl acetate, followed by a graded dehydration series (ethanol to acetone). Dehydrated tissues were then infiltrated with Epon resin and polymerized at 60 °C overnight. Sections (85 nm) were cut with an ultramicrotome (Ultracut UCT; Leica Microsystems) and a diamond knife (Diatome, Hatfield, PA). Images were acquired with a JEOL JEM 1400 transmission electron microscope (JEOL, Peabody, MA) at 80 kV on a Gatan Ultrascan 1000 CCD (Gatan, Pleasanton, CA).
+ Open protocol
+ Expand
9

Transmission Electron Microscopy Imaging

Check if the same lab product or an alternative is used in the 5 most similar protocols
Grids carrying ultrathin sections of both embedded samples, cryo-fixed and chemically fixed, were post strained using 2 % (w/v) aqueous solution of uranyl acetate and lead citrate. Images were obtained using a transmission electron microscope JEM 2011 FasTEM Jeol UK operating at 200kV, equipped with a Gatan Ultrascan 1000 CCD camera and a Gatan Dual Vision 300 CCD camera.
+ Open protocol
+ Expand
10

Cryo-electron Tomography of Cellular Ultrastructure

Check if the same lab product or an alternative is used in the 5 most similar protocols
The procedure was performed as previously described (Jiang et al., 2017a , b (link)). Serial sections with a thickness of 200 nm were prepared and collected on copper slot grids (2 × 0.5 mm oval slots) with carbon supports, which were overlaid with 10 nm fiducial gold that was pretreated with BSA. The grids were stained with Reynold’s lead citrate before the second layer of fiducial gold was applied. The specimens were imaged with an FEI Tecnai TEM operating at 200 kV. The micrographs were recorded with a Gatan UltraScan 1000 CCD at 0.87 nm/pixel (9600×). Tilt series from –60° to +60° with 2° increments were acquired at 10 μm defocus using Leginon automatic data collection software (Suloway et al., 2009 ). Double tilt series were collected using a double tilt holder (Model 2040 Dual-Axis Tomography Holder; Fischione). Serial tomograms were reconstructed, joined using IMOD, and segmented using Avizo 3D software (FEI).
+ 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?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!