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This unit describes TEM readying techniques for analyzing particulate samples every bit good as samples showing more complex ultrastructural considerations that require analysis in thin subdivisions. Negative staining is a simple but valuable technique that is utile for everyday scrutiny of particulate samples in suspension runing from bacteriums to viruses to purified supermolecules. .


Aside from the biohazards posed by managing and disposing of infective bugs ( refer to unit 1A.1 ) , many of the chemicals used in the processing of samples for negatron microscopy are either volatile, inflammatory, toxic, carcinogenic, and/or radioactive. It is of import to understand the nature of wellness and environmental jeopardies posed by these chemicals and to manage and dispose of them harmonizing to appropriate safety ordinances ( see units 1A.1, 1A.3 & A ; 1A.4 ) . Expose negatron microscopy grids incorporating negatively stained infective specimens to UV radiation or chemical arrested development before scrutiny and shop in a suited container for safe impermanent storage. Discard grids into a little wide-based container with appropriate decontamination reagents upon completion of the analysis. Rinse forceps used to manage grids with infective samples in intoxicant and fire before and after usage. Specimens processed for implanting and thin sectioning are typically chemically stabilized in a fresh aldehyde-containing fixative, which will inactivate/kill the bulk of viruses and bacteriums. Autoclave other disposable preparatory stuffs that come into contact with pathogens ( e.g. , Parafilm, filter paper ) in appropriate containers prior to disposal.

Fix cells ( Standard protocol )


In a fume goon, add an equal volume of TEM primary fixative 2 to bacterial cells suspended in civilization medium or buffer in a 15-ml conelike extractor tubing.

This will ensue in a concluding fixative concentration of 2 % glutaraldehyde.


Immediately invert mixture and topographic point on a horizontal sociable 60 min at room temperature.


After initial room temperature arrested development, transportation cell suspension to a 4A°C ice bath for an extra 1 hour of arrested development.


Centrifuge cell suspension 10 min at 1000 A- g, 4A°C, and discard supernatant.


Resuspend cells in phosphate/sucrose rinse buffer and incubate at 4A°C for 10 min.


Centrifuge cells 10 min at 1000 A- g, 4A°C, and discard supernatant.

Encase cells in agar and hole once more


Resuspend cells in adequate 2.5 % liquefied agar to cover pellet, mix with a warmed transportation pipet, and reassign to polyethylene microcentrifuge tubings.


Centrifuge the agar and cell suspension 5 min at 5000 A- g, room temperature, to pellet cells.


Chill tubes briefly on ice to solidify agar.


Using a single-edged razor blade, cut through the microcentrifuge tubing merely above the cell pellet in the agar to take the pellet. Slice the removed agar encased pellet into thin pieces, ~0.5 mm broad, and topographic point in arrested development phials incorporating chilled phosphate/sucrose rinse buffer.

Perform post-fixation and en axis staining


Replace buffer with osmium tetroxide post-fixative and incubate 90 min at 4A°C. Rock pellets often during post-fixation or topographic point phials on a platform rocker and stone at low velocity to ease incursion of Os into the tissue.


Rinse pellets twice in chilled phosphate/sucrose rinse buffer.


Rinse pellets six times over the class of 1 hour with chilled distilled H2O to take phosphate buffer residue.


Stain pellets en axis in uranyl ethanoate staining solution for 90 to 120 min at 4A°C with periodic agitation.

Alternatively, discoloration in 0.5 % aqueous uranyl ethanoate overnight at 4A°C.


Wash three times in cold distilled H2O to take uranyl ethanoate.

Dehydrate and embed pellet


Dehydrate through ethanol series by plunging in turn for 10 min each in the undermentioned solutions:

50 % ethyl alcohol, 4A°C

75 % ethyl alcohol, 4A°C

95 % ethyl alcohol, room temperature.

Transportation to 100 % ethyl alcohol.


Rinse tissue three times, each clip for 10 min, in propanone or propene oxide.


Embed in epoxy rosin ( see Basic Protocol 4 ) .

Basic Protocol 4: Embedding of Tissues and Cell Pellets for Thin Sectioning

The undermentioned basic protocol is a continuance of Basic Protocol 3 and Alternate Protocols 4 and 5. All stuff to be thin sectioned for TEM scrutiny must be embedded in a hard-boiled plastic matrix. The unpolymerized plastic matrix must be unstable plenty to wholly infiltrate the specimen. Once polymerized, the plastic must non change the ultrastructure of the specimen ( i.e. , as a consequence of specimen shrinking, swelling, or extraction of cellular constituents ) while being able to defy the emphasis of thin sectioning. The resulting subdivisions should stay stable in the negatron beam and impart adequate contrast to the sample to let for the visual image of ultrastructural item. An extra consideration is the saving of antigenicity in the instance of thin-section immunogold labeling ; a separate process is provided to cover with this issue ( see Alternate Protocol 9 ) .

In general, the end is to present a plastic rosin into the sample over clip by the gradual replacing of desiccating agent and rosin dissolver ( normally ethanol and acetone, or ethyl alcohol and propylene oxide ) with increasing concentrations of rosin and dissolver over clip. Tissue pieces and cell pellets are finally transferred to resin-filled embedding casts for polymerisation. Cells in polymerized rosin can so be prepared for thin sectioning.

Caution: Some rosin constituents are possible carcinogens and others can bring forth allergic reactions in certain single. Their readying may therefore necessitate a fume goon, a appropriately vented oven, and other equal steps for personal protection ( besides see unit 1A.3 ) .


Fixed and processed tissue ( Basic Protocol 3 ) , cell pellet ( Alternate Protocol 4 ) , or bacterial sample ( Alternate Protocol 5 )

Luft ‘s epoxy mixture ( see formula )

Acetone or propene oxide

Orbital shaker

Transfer forceps or applier stick

Implanting casts or capsules ( available from Ted Pella ; BEEM level implanting casts, cat. no. 111-2, PTFE level implanting casts, cat. no. 10509, or BEEM implanting capsules, size 00, cat. no. 13 )

60A°C oven


Pipet out the last rinse of propanone or propene oxide from the arrested development phial and replace with a mixture of 50 % ( v/v ) Luft ‘s epoxy mixture and 50 % propanone or propene oxide. Put the phial on an orbital shaker and revolve sufficiently to suspend the tissue pieces or pellet in the rosin.

Upon initial debut of the rosin, the tissue pieces or pellets will drift to the top. With clip, they will drop as they become infiltrated.


Incubate at room temperature for 30 min with rotary motion on the orbital shaker to help infiltration.


Remove all of the 50-50 rosin mixture and replace with a mixture of 75 % ( v/v ) Luft ‘s epoxy mixture and 25 % propanone or propene oxide. Incubate at room temperature for 30 min with rotary motion to help infiltration.

The pellets will once more drift to the top of the suspension and will easy drop as the rosin infiltrates the pellets.


Remove the rosin from measure 3 and replace it with 100 % Luft ‘s epoxy mixture. Rotate on an orbital shaker for 1 hour at room temperature, so take the epoxy mixture and replace with newly prepared 100 % Luft ‘s epoxy mixture.


Remove the rosin and, utilizing transportation forceps or an applier stick, carefully reassign pellets to suitable implanting casts incorporating newly prepared 100 % Luft ‘s epoxy mixture. Transfer casts to a vented 60A°C oven and incubate overnight.

A assortment of implanting casts and capsules are commercially available that allow tissue to be optimally positioned for segmenting one time released from the cast. For pelleted stuff, polythene caps for snap-cap sample phials ( Electron Microscopy Sciences # 64257-30 ) work good for this intent. They come in a assortment of sizes, let for easy arrangement of the sample, have plentifulness of surface country for outgassing of residuary dissolver if necessary, and are reclaimable ; in add-on, the polymerized rosin is easy removed. Pellets or tissue can be excised from the rosin utilizing a jewelry maker ‘s proverb or a single-edged razor blade if the rosin is somewhat heated and mounted on a clean BEEM capsule or Plexiglas nog ( Ladd Research # 21830 ) utilizing superglue. Small pieces of tissue can be straight placed in resin-filled BEEM capsules for polymerisation. However, when BEEM capsules are used for direct embedding of tissue, it is frequently advantageous to use level implanting casts for implanting excess pieces of tissue if the demand arises.

Arrested development and Initial Processing of Samples for Immunogold Labeling of Thin Sections

The arrested development and processing of samples that will allow labeling of antigens in thin-sectioned stuffs pose significant challenges. Methods normally used for optimum ultrastructural morphology must normally be modified to guarantee that antigens are non merely retained but available for labeling. This frequently involves optimisation, with via medias between the arrested development, processing, and implanting stairss ; nevertheless, careful choice of readying methods can give high-quality combinations of structural item and immunochemical labeling.

Extra Materials ( besides see Basic Protocol 3 )

Tissue or cell sample

TEM primary fixative 3 ( see formula )

Aldehyde slaking solution ( see formula )


For tissue specimens: In a fume goon, fix tissue specimens by incubating with TEM primary fixative 3 for 12 to 24 hour at 4A°C.


For free cells or cell suspension: In a fume goon, fix cells or pellet by incubating with TEM primary fixative 3 for 2 to 4 hour at 4A°C.


Rinse in phosphate/sucrose rinse buffer three times for at least 10 min each at 4A°C.


Incubate in aldehyde slaking solution for 30 min at 4A°C to take residuary free aldehydes.


Wash in phosphate/sucrose rinse buffer two times for 15 min each at 4A°C.


Dehydrate through ethanol series by plunging in turn in the undermentioned solutions for the indicated sums of clip:

50 % ethyl alcohol, 4A°C

10 min

75 % ethyl alcohol, 4A°C

10 min

95 % ethyl alcohol, room temperature

10 min

100 % ethyl alcohol, room temperature

30 min

100 % ethyl alcohol, room temperature

30 min.


Directly embed in rosin ( see Alternate Protocol 9 ) .

Note that this process omits the propanone or propene oxide infiltration measure included in the old tissue arrested development and processing protocols.

. Resin Embedding for Thin Section Immunogold Labeling

Preservation of sample antigenicity is of paramount importance when taking an embedding rosin for thin subdivision immunogold labeling. Dehydration and implanting protocols must minimise loss of possible antigenic sites. This by and large requires the usage of ethyl alcohol entirely as the dehydrating agent, an altered infiltration agenda, and the usage of a more hydrophilic implanting rosin coupled with room-temperature or cold polymerisation. Several specific rosins are available, all acrylic based, that offer good antigen protection, although some require luxuriant chilling Chamberss in order to optimise their superior antigenic saving qualities during polymerisation. The rosin protocol described below utilizes a one-part rosin, which merely needs an gas pedal for room temperature polymerisation and outputs consistent consequences.


Fixed and processed tissue or cell sample ( Alternate Protocol 7 )

LR White rosin ( Polysciences )

LR White gas pedal ( Polysciences )

Implanting casts ( available from Ted Pella ; BEEM level implanting casts, cat. no. 111-2, PTFE level implanting casts, cat. no. 10509, or BEEM implanting capsules, size 00, cat. no. 13 )

Cooled H2O bath or chilling block ( optional )

Jeweler ‘s proverb

Plexiglas nog ( Ladd Research, cat. no. 21830 ; hypertext transfer protocol: // )

Cyanoacrylate gum ( e.g. , Superglue, Krazy Glue )


Following the last two washes of tissue in 100 % ethyl alcohol described Alternate Protocol 7, infiltrate the sample with LR White rosin as follows. Remove the ethyl alcohol and replace with 100 % LR White rosin, incubate 1 hour at room temperature, so replace with fresh 100 % LR White rosin and incubate an extra 1 hour at room temperature. Finally, replace once more with fresh 100 % LR White rosin and incubate an extra 1 hour to overnight at room temperature.

See proficient informations sheet for LR White resins at hypertext transfer protocol: //


To 10 milliliters LR White rosin, add 20 Aµl LR White gas pedal and mix good. Partially fill implanting cast ( s ) with the resin/accelerator mixture. Remove LR White resin-infiltrated tissue pieces or pellets from their phials utilizing fine-tipped forceps or a wooden stick with a all right tip. Lodge the tissue pieces into the resin-containing embedding cast ( s ) . Let casts to polymerise for 48 hour at room temperature.

If level embedding casts are used, it may be necessary to except air from the surface of the rosin and cover the cast with a piece of ACLAR movie ( Ted Pella, cat. no. 10501-10 ) to except as much air as possible from the surface of the cast. Implanting in BEEM or gelatin capsules is preferred over the usage of level implanting casts, as the surface country exposed to air is minimized and the capsules do non necessitate the movie sheathing.


Remove polymerized block ( s ) from implanting cast ( s ) or capsule ( s ) . If the tissue has been flat-embedded, cut out the coveted country with a jewelry maker ‘s proverb and saddle horse on Plexiglas specimen-mounting nog ( that tantrum into the specimen chows of the ultramicrotome ) utilizing cyanoacrylate gum.

Basic Protocol 5: Overview of Ultramicrotomy

As noted antecedently, the end of ultramicrotomy is to fix thin subdivisions between 50 and 90 nm midst. The coevals of subdivisions that adhere to one another as consecutive threads utilizing an ultramicrotome is an highly ambitious manual accomplishment that requires a high degree of sleight. Ultramicrotomy is non a technique that can be efficaciously learned utilizing a protocols manual and is hence given as an overview instead than a method in this unit.

While it is assumed that the reader has entree to ultramicrotomy support service or hands-on preparation in this cardinal component of specimen readying for analysis of thin subdivisions, a brief description of ultramicrotomy follows. In order to thin-section embedded tissue that has been placed in an embedding cast, it must be mounted in a holder for paring. Some ultramicrotomes have different types of holders that can grip level embedded tissue or keep a cylinder of plastic with a tapering terminal ( pyramid form ) incorporating the tissue. The tapering terminal must be trimmed farther to organize a little trapezoid of ~200 Aµm2. This is normally done by manus with a single-edged razor blade under a stereo microscope and requires considerable sleight and pattern. Some microtomes have specimen holders, which permit rapid trimming of the block to organize the trapezoid with a extremely polished face.

Thin subdivisions are cut with either a glass or diamond knife. Glass knives are usually made newly with a knife-maker instrument, which breaks ~1-in. ( ~2.5-cm ) squares of glass from high-quality glass strips. The squares of glass are scored diagonally and carefully broken to organize triangular pieces, one border of which contains the knife border. A commercially made plastic trough is sealed with dental wax. Alternatively, a trough or “ boat ” is fashioned around the knife border with Mylar or other tape that will supply a distilled water-filled reservoir that reaches the border of the knife and that will let subdivisions to drift off from the border of the knife from the block during the cutting shot of the microtome arm. The broad side of the trapezoid-shaped block face makes first contact with the knife border during the cutting shot of the microtome. Prior to roll uping subdivisions, the block face must be “ polished ” in readying for thin sectioning by cutting initial subdivisions until the block face appears to hold a mirrored surface. Thin subdivisions are so cut, and single trapezoid-shaped subdivisions adhere to the knife border until the subsequent subdivision displaces the old subdivision during the cutting shot of the microtome arm. With each back-to-back subdivision, a thread resembling the form of a cestode floats into the boat ( Fig. 2B.1.2 ) . These threads are typically manipulated into parallel rows with a all right cilium attached to the terminal of a little applier stick merely prior to picking up the subdivisions on a 3-mm-diameter negatron microscope grid. Sections are adhered to the grid by take downing it with a brace of forceps above the subdivisions, gently touching the grid to the surface of the H2O, and so raising the grid off the H2O surface in a smooth gesture. Residual H2O is removed from the border of the grid with a cuneus of filter paper as is done for negative staining.


Figure 2B.1.2 Thin subdivisions ( ~70 to 80 nanometers ) prepared on a diamond knife as seen through a stereo microscope. Trapezoid-shaped subdivisions are cut consecutive, adhering to the knife border and forming threads during segmenting ( black pointer ) . They are seeable as the consequence of reflected visible radiation from above, which generates an intervention form that can be used to gauge subdivision thickness. As subdivisions accumulate, they can be separated into smaller threads, which float on the H2O surface and can be aligned for aggregation onto a grid. The breadth of the trough of the diamond knife shown is ~10 millimeter.

Copper grids are routinely used for most biological samples ; nickel grids are normally used with samples prepared for immunogold negatron microscopy. The 50- to 90-nm thickness of each subdivision can be estimated by seting the microtome stereomicroscope screening and light system to observe intervention colourss reflecting from the subdivisions. By and large, grey subdivisions indicate a thickness of less than 60 nanometers, while silver subdivisions range from 60 to 90 nanometers ( the typical subdivision thickness for most biological samples ) , and gold subdivisions range from about 90 to 150 nanometers. The diamond knife, which contains a high-quality diamond with a cleaved knife border mounted in an aluminium holder fashioned into a trough for drifting subdivisions, is a well more expensive and longer-lasting option to disposable, newly made glass knives.

Alternate Protocol 10: Immunogold Post-Embedding Staining of Thin Sections

Localization of antigens in thin sectioned stuff normally requires particular arrested development processs to restrict the extent of macromolecular cross-linking, every bit good as embedment in a plastic rosin which preserves antigenic sites. The followers is one of many alternate processs that can be used to place antigens with immunogold reagents.


Thin subdivisions on 300-mesh Formvar-coated Ni grids ( Basic Protocol 5 )

Immunogold barricading buffer ( see formula )

Primary antibody against antigen of involvement and control ( irrelevant ) primary antibody of same Ig category

TBS-Tween ( see formula )

Reagents for colloidal gold labeling-one of the followers:

Colloidal gold-labeled secondary antibody against species from which primary antibody was obtained

Biotinylated secondary antibody against species from which primary antibody was raised, and streptavidin-conjugated colloidal gold

Colloidal gold-labeled protein A and/or protein G

TEM primary fixative 2 ( optional ; see formula )

Whatman no. 4 filter paper

Spray bottle

Grid box

Extra reagents and equipment for etching of epoxy implanting rosin ( optional ; see Support Protocol 2 ) and uranyl acetate/lead citrate staining of thin subdivisions ( see Basic Protocol 6 )


If the sample is non embedded in LR White rosin, execute Support Protocol 2.

Block sample


Topographic point an ~50-Aµl bead of immunogold barricading buffer onto Parafilm and drift sample-containing grid on top of it for 30 min as a blocking measure.

Dainty with primary antibody


Prepare appropriate dilution of primary antibody in TBS-Tween, topographic point 50-Aµl droplets of the diluted antibody onto Parafilm, so topographic point grids on droplets and incubate at room temperature for 2 hour.

Controls can be processed at the same clip and should include both an irrelevant primary antibody of the same category and another readying without primary antibody.


Remove grid and pull off extra solution with a filter paper cuneus ( see Basic Protocol 1 ) and gently rinse with a watercourse of TBS-Tween from a spray bottle.

Label with colloidal gold


To utilize colloidal gold-conjugated secondary antibody: Topographic point appropriate dilution of colloidal gold-conjugated secondary antibody onto Parafilm in 50-Aµl droplets, so reassign grids onto droplets and incubate at room temperature for 60 min.


To utilize biotinylated secondary antibody: Topographic point appropriate dilution of biotinylated secondary antibody onto Parafilm in 50-Aµl droplets, so reassign grids onto droplets and incubate at room temperature for 1 hour. Wash grids briefly in 50-Aµl droplets of distilled H2O, so reassign to 50-Aµl droplets of streptavidin-conjugated colloidal gold and incubate at room temperature 60 min.


To utilize protein A and/or protein G: Topographic point appropriate dilution of colloidal gold-conjugated protein A, protein G, or protein A/G onto Parafilm in 50-Aµl droplets, so reassign grids onto droplets and incubate at room temperature for 60 min.


Rinse grids 1 min in a sequence of four or five 50-Aµl droplets of TBS-Tween on Parafilm.

Post-fix ( optional ) and discoloration with heavy metals


Optional: Post-fix by reassigning grid to a 50-Aµl droplet of TEM primary fixative 2 for 10 min, so rinse in a 50-Aµl droplet of TBS-Tween for 1 min.


Wash grid with a watercourse of Milli-Q or deionized distilled H2O from a spray bottle.


Stain grids with uranyl ethanoate and lead citrate as described in Basic Protocol 6.


Rinse grids in a soft watercourse of distilled H2O and take extra H2O with a filter paper cuneus.


Ensure that grids are wholly dry and put them into a grid box. Shop in a desiccator until ready to image in the negatron microscope.

Basic Protocol 6: Heavy Metal ( and Immunogold ) Staining of Thin Sections

Heavy metal staining of thin subdivisions is usually required to leave contrast in thin-sectioned biological stuffs. Two of the most widely used heavy metal post-staining solutions ( i.e. , uranyl ethanoate and lead citrate ) are described. It is besides possible to immunolocalize antigens in thin subdivisions utilizing colloidal gold atoms of assorted sizes ( 5 to 20 nanometers ) that efficaciously scatter negatrons, which can be easy seen even when subdivisions are post-stained with uranyl ethanoate and lead citrate.


Thin subdivisions collected on Cu grids ( Basic Protocol 5 )

Uranyl ethanoate staining solution ( see formula )

Lead citrate staining solution ( see formula )

Whatman no. 4 filter paper

Spray bottle with distilled H2O

Grid box


Topographic point 50-Aµl beads of uranyl ethanoate staining solution onto a clean Parafilm surface utilizing the technique described in Basic Protocol 1.


Using forceps, topographic point grids incorporating subdivisions face-down onto uranyl acetate beads utilizing the technique described in Basic Protocol 1, and incubate for 3 to 10 min at room temperature.


Remove grids from uranyl ethanoate beads and carefully direct a soft watercourse of Milli-Q or deionized distilled H2O from a spray bottle onto the subdivision side of the grid for 10 to 15 sec, easy wetting the back side of the grid ( i.e. , the side without the subdivision ) .


Remove extra H2O with a cuneus of Whatman no. 4 filter paper ( see Basic Protocol 1 ) ; do non allow subdivision prohibitionist.


Topographic point 50-Aµl beads of lead citrate staining solution onto a clean sheet of Parafilm and lodge the grid, section-side-up, into the bead. Incubate 2 to 5 min at room temperature. Use a new bead of discoloration for each grid.


Remove grids and gently run a watercourse of Milli-Q or deionized distilled H2O from a spray bottle down the tips of the forceps onto the grid to take residuary discoloration.


Remove extra H2O with a filter paper cuneus and guarantee that no H2O remains between the tips of the forceps by skiding a piece of filter paper down between them while let go ofing the grid from the forceps onto a clean piece of filter paper.


Ensure that grids are wholly dry and put them into a grid box. Shop in a desiccator until ready to image in the negatron microscope.


Place lead and uranyl waste in appropriate containers for disposal.

Reagents and Solutions

Use Milli-Q-purified or deionized, distilled H2O in all formulas and protocol stairss. For common stock solutions, see appendix 2A ; for providers, see providers appendix.

Aldehyde slaking solution

Prepare 100 millimeter glycine by fade outing 0.75 g in 100 milliliters phosphate/sucrose rinse buffer ( see formula ) . Alternatively, fix 100 mM ammonium chloride by fade outing 0.53 g ammonium chloride in 100 milliliters phosphate/sucrose rinse buffer. Store up to 1 month at 4A°C.

Immunogold antibody dilution buffer

To 180 milliliters Milli-Q-purified H2O or distilled H2O attention deficit disorder:

1.04 g Na phosphate, monobasic ( Na2PO4A-H2O )

8.70 g Na phosphate, dibasic, heptahydrate ( Na2HPO4A-7H2O )

4 g bovine serum albumen ( BSA ) , fraction V

0.6 milliliter Tween 20

Milli-Q-purified or deionized distilled H2O to 200 milliliters

Shop up to 2 months at 4A°C

Final concentrations 1 millimeters PBS incorporating 2 % BSA and 0.3 % Tween 20.

Immunogold blocking buffer

To 100 milliliters TBS-Tween ( see formula ) attention deficit disorder:

1 g bovine serum albumen ( BSA ) , fraction V

3 milliliter normal serum from species in which secondary antibody was generated

Stir to fade out

Shop up to 6 months at 4A°C

Concluding concentrations: 1 % ( w/v ) BSA, 3 % ( v/v ) serum in TBS-Tween.


To 1 litre of distilled H2O attention deficit disorder:

6.1 g Trizma base

9 g NaCl

Mix to fade out

Adjust pH to 7.6 utilizing 1 N HCl

Add 0.5 milliliter Tween 20

Shop up to 6 months at 4A°C

Concluding concentrations: 0.5 M Tris-buffered saline, 0.05 % Tween 20.

TEM fixative stock solutions

The most convenient beginning for EM-grade fixative stocks is from commercial negatron microcopy providers ( e.g. , Electron Microscopy Sciences, Energy Beam Sciences, Structure Probe/SPI Supplies, or Ted Pella ) . For illustration, stock solutions of 16 % paraformaldehyde, 8 % or 25 % glutaraldehyde, and 4 % aqueous Os tetroxide can be purchased in 10-ml measures in certain phials separately or in boxes of 10 or more units. These stocks typically have a shelf life of 12 months if unopened, but one time opened must be used in fixative solutions on the same twenty-four hours, sooner within hours of readying.

Uranyl ethanoate staining solution

Immunoelectron microscopy

In general, immunoelectron microscopy applications involve the direct negatron microscopy imagination of antigen-antibody composites. A broad scope of applications have been developed to better the sensitiveness of bug sensing and to uncover the ultrastructure of elusive beings. When used to increase sensing sensitiveness, antibodies serve to aggregate viruses or bacteriums in solution or onto a grid for negative staining. Immunogold staining can be combined with negative staining to supply a sensitive technique that enables the designation and visual image of single antigens by TEM, and which can be utile in the designation of the biologic agent itself.

Arrested development techniques for TEM

Ultrathin subdivisions of samples provide penetrations sing the internal construction of chemically stabilized samples. Individual subdivisions that are used to supply images in the TEM represent planar positions of 3-dimensional objects ; hence, considerable attempts must be made to understand the 3-dimensional ultrastructure of a sample. It is besides of import to appreciate that the visual aspect of the thin-sectioned sample is the consequence of the multiple stairss in the protocol, including isolation of the sample, one or more chemical arrested development stairss, desiccation and embedding, sectioning, and staining.

Immunoelectron microscopy

Adequate controls must be incorporated into the process for the proper analysis of experimental consequences. Controls should include a grid in which the primary antibody incubation is omitted and a grid incubated with a nonspecific IgG of the same species as the primary antibody to place nonspecific binding. Adjustments to increase labeling and lessening nonspecific binding may include, for illustration, usage of different or extra blocking agents and/or concentrations and barricading times, altering concentration or incubation clip of primary antibody, or add-on of more rinses ( see Table 2B.1.2 ) .

TableA 2B.1.2 Troubleshooting Guide for Negative Stain Immunoelectron Microscopy


Possible cause


No gold labeling

The antigen may be present in really low sums

Use longer incubation times and more concentrated primary antibody

The primary antibody may be bad, e.g. , due to hapless titre, age, improper storage, improper dilution, or inordinate freeze and melt

If available, run a positive control to look into

The pH of solutions may be overly acidic or alkaline

Adjust the pH

Heavy negative staining may dissemble gold atoms

Reduce the concentration of negative discoloration and/or usage larger gold atoms. Use higher magnification to visualise gold atoms ( e.g. , 200,000A- for 5 nanometers ; 100,000A- for 10 nanometers ; 80,000 for 15 nanometers ; 50,000 for 20 nanometer ) .

The subdivision may non hold been exposed to solutions ( as a consequence of being wrong-side-up ) if on a plastic movie

Be careful when reassigning and rinsing grids that the side of the grid incorporating the sample is kept confronting up

The antigen may be destroyed by preparatory processs

Use a different process. See brief arrested development in 1 % paraformaldehyde.

Excessive background gold atoms

Ionic concentration of solutions may be excessively low

Use increased salt concentration ( up to 2.5 % ) . Add egg white, BSA, or normal caprine animal serum ( non for protein A ) to ~1 % in incubation solutions.

Sections may hold been inadequately washed between incubations

Increase rinsing stairss

Nonspecific charge attractive force of antibody can do background

Use 1 % detergent ( e.g. , Tween 20 ) in all solutions. Include normal caprine animal serum ( non for protein A ) in all solutions. Increase concentration of normal caprine animal serum before primary antibody incubation.

Free aldehyde groups in fixed tissue may be a beginning of background

Reduce by exposing subdivisions to 0.5 M ammonium chloride for 1 hour before incubations.

The primary antibody concentration may be excessively high

Dilute by orders of magnitude

The gold conjugate concentration may be excessively high

Dilute farther

Bunch of gold atoms

Clumped primary antibody.

Use fresh antiserum

Clustering can be caused by the natural elaboration factor of the gold conjugate. For IgG-gold conjugates, up to 10 conjugated gold atoms may attach to the Fc constituent of the primary antibody, bring forthing the visual aspect of bunchs on the subdivision. This does non happen with protein A conjugates.

Use higher dilution of gold conjugates if desired

Gold atoms over surface of support movie

Nonspecific binding

Incorporate extra blocking stairss prior to bringing of primary antibody

When sing the usage of the protein A- , protein G- , or protein A/G-gold process, it is of import to understand that, while these conjugates interact with mammalian Igs, their single affinity for Igs is non tantamount for all species or for all antibody subclasses. For illustration, in the instance of polyclonal antibodies, protein A or protein G can be used for human, hog, coney, or mouse. Horse and cow Igs have comparatively high affinity for protein G, while sheep, caprine animal, poulet, hamster and rat antibodies will adhere protein G weakly. Guinea hog Igs will adhere protein A. For usage with monoclonal antibodies, human isotypes IgG1, IgG2, and IgG4 have good affinity for protein A or protein G, while human IgG3 has good affinity for protein G merely. Protein G is used with rat isotypes, whereas mouse isotypes IgG1, IgG2a, IgG2b, and IgG3 all bind protein G, and mouse IgG2a and IgG2b besides bind protein A. The usage of protein A/G can hence be utile if the antibody isotype is unknown.

Another of import consideration is size and affinity of the conjugated gold atoms for the primary antibody. In general, the smaller the gold atom, the lower the steric hinderance to antigen sensing ; nevertheless, a confusing consideration is that the smaller the gold atom, the fewer the molecules of protein A edge per gold atom. For illustration, it has been estimated that a 5-nm gold atom can adhere about four protein A molecules, whereas a 20-nm atom can adhere ~48 protein A molecules. Similarly, a 5-nm gold atom can adhere about three secondary antibody molecules, while 10-nm gold atoms can adhere ~12 antibody molecules and 20-nm gold atoms can adhere ~ 48 antibody molecules. Therefore, the affinity of the gilded atom can increase with increasing size. An extra consideration when immunogold staining is combined with negative staining is that the smallest gold atoms ( e.g. , 5 nanometer ) are much more hard to observe in negatively stained readyings ; hence, the recommended scope of gold atom sizes is from 10 to 30 nanometers.

The usage of colloidal gold-tagged secondary antibodies described supra is an alternate to protein A/G and involves a secondary antibody generated in a different species against the Fc fragment of the primary antibody. A 3rd alternate involves the usage of biotinylated secondary antibodies that are later rendered seeable in the TEM by adhering of colloidal gold-conjugated streptavidin. Immunolocalization of two antigens in the same readying is besides possible if compatible primary antibodies are available ( e.g. , primary antibodies generated in different species ) . This process involves the consecutive indirect labeling of two primary antibodies with secondary antibodies conjugated to gold atoms of different size.

Arrested development techniques for TEM

Preparation of the sample and the pick of fixative, discolorations, and plastic rosin can impact the quality of the readying. Unfortunately, there is no optimum fixative for all biological samples, although newly prepared fixatives incorporating glutaraldehyde are considered among the best primary fixatives presently available. The utile belongings of glutaraldehyde, a five-carbon dialdehyde, is its ability to cross-link proteins. Newly prepared glutaraldehyde at impersonal pH will besides polymerise into longer concatenation dialdehydes, which provide cross-links of variable size that expeditiously stabilize protein construction. Paraformaldehyde is normally combined with glutaraldehyde to better stabilise biological samples. In general, when fixatives are identified as incorporating paraformaldehyde, it normally means that they contain formaldehyde generated from the paraformaldehyde polymer of methanal. The advantages of this freshly prepared one-carbon monoaldehyde, methanal, which reacts in an aqueous solution as methylene ethanediol, are its rapid incursion belongingss and ability to polymerise and cross-link proteins and nucleic acids, and besides modify the chemical belongingss of lipoids. While non included here, propenal is another extremely reactive fixative that is frequently used in combination with other aldehydes such as glutaraldehyde and/or paraformaldehyde for repairing really heavy specimens.

The primary aldehyde-fixation measure is often combined with a post-fixation measure affecting Os tetroxide, which acts as a fixative and electron discoloration and besides as a mordant to heighten staining of the subdivisions with lead. The primary fixatives and post-fixatives described in these protocols are by and large considered to be good get downing points for the saving of solid tissues and cells in either suspension or pellets. More specific protocols are available in the literature that reference specific arrested development demands of specific beings and cells ( Fassel et al. , 1997 ; Karlyshev et al. , 2001 ) . Variations on fixative concentrations, arrested development times, buffer types and osmolarity are all of import considerations for optimum saving of any peculiar sample.

The readying of single cells or sums of cells airss particular challenges. Generating a sample of equal size for treating normally requires concentration of cells by centrifugation into pellets. Care of pellet unity is besides an of import consideration during primary arrested development, post-fixation, post-staining, desiccation, and implanting. If cells are non sufficiently concentrated during centrifugation before add-on of fixative, as described in Alternate Protocol 5, there can be a inclination for the pellet to disintegrate during subsequent processing. If the pellet is of sufficient size to give multiple pieces for processing, some cell loss can be tolerated. If non, so it is of import to incase the pieces of pellet in a thin bed of agar to continue the unity of the pellet. Proper temperature direction of the agar used to incase suspension fixed cells is besides of import during the preparatory process. The agar must be warm plenty to stay liquefied when the cells are introduced while at the same clip non being hot plenty to damage tissue and/or to let the cells to efficaciously whirl out of the agar during centrifugation. It is advisable, if the sample size licenses, to subdivide the sample and execute multiple tallies to guarantee saving of the pellet.

Preparation of tissues and cells for immunogold labeling requires a balance between saving of tissue/cell ultrastructure and the saving of antigens. The end is to optimise these via medias in order to unite equal structural item and equal immunochemical labeling. Concentrations of glutaraldehyde that are usually used for ultrastructure most frequently destroy or cross-link antigens. Therefore paraformaldehyde entirely or in combination with dilute glutaraldehyde ( 0.1 % to 1 % ) is a utile starting point for arrested development. Tissues processed for immunolabeling in thin subdivisions require particular embedding processs, as discussed below.

The protocols presented in this subdivision can be classified as stand foring classical attacks to the saving of tissue for scrutiny by thin-section negatron microscopy. Other techniques are available that offer the advantages of potentially better saving of specimen ultrastructure and perchance shorter processing times at the disbursal of holding specialized processing equipment, extra safety concerns, and particular alterations of the negatron microscope itself. Freeze permutation, accomplished by the formation of vitreous ice within the sample by either immersing the sample into cooled liquid propane or C2H6 or exposing samples to a jet of liquid propane or to high-pressure freeze, offers the advantage of better saving of ultrastructure, and normally better antigen saving as good. Microwave treating techniques offer the advantage of rapid specimen arrested development and implanting times. All of these techniques require specialised readying protocols adapted to accommodate the specific equipment on manus, and are beyond the range of this chapter.

Implanting techniques for TEM

By their nature, epoxy rosins and their constituents are syrupy, and this viscousness tends to increase with clip after the single constituents of the rosin are mixed. Because of this, it is advisable to fix rosins in little batches merely prior to utilize. Dilutions of complete rosin mixtures in desiccation agents are prepared by distributing the rosin constituents into new disposable beakers. Preparations of rosin and desiccation agent are kept capped to forestall vaporization of the agent over clip, an particularly of import consideration when working in a fume goon. In the instance of epoxy rosin, accurate deliberation of all constituents and dilution of rosins is of critical importance in their readying to guarantee a rosin mixture that will give the proper features. It is besides of import that the single constituents of the rosin be wholly assorted. Inadequate commixture of rosin constituents can ensue in ill infiltrated samples that subdivision ill, that have hapless specimen contrast, and that do non keep up in the negatron beam. Shaking or vigorous stirring consequences in good assorted rosin. Any ensuing entrapped air is liberated upon standing or can be removed by usage of a vacuum chamber for 5 to 10 min or until the coevals of gas bubbles Michigans ( the vacuity provided by a one-stage rotary pump is sufficient ) . Caution must be used when degassing the rosin mixture, as it can boil out of the disposable beaker ; careful monitoring of the mixture in the vacuity chamber is necessary. Furthermore, the ability to present air into the chamber to minimise initial boiling of the rosin during degassing is besides necessary.

TEM of thin subdivisions

Staining with uranyl ethanoate and lead are comparatively straightforward processs. Occasionally, electron-dense precipitates occur that are the consequence of a staining job. Care is taken with lead citrate to minimise the exposure to CO2, which can come from one ‘s breath and consequence in the precipitation of indissoluble lead carbonate. Precipitates can be formed from contaminations in glutaraldehyde and Os tetroxide, and, as noted antecedently, uranyl phosphate signifiers an indissoluble precipitate. For valuable samples, post-staining precipitates can sometimes be removed by utilizing the plastic etching solution for 10 min, rinsing in a watercourse of distilled H2O, and so restaining ( see Aldrich and Mollenhauer, 1986 ) .

Trouble-shooting suggestions for immunogold staining of negatively stained readyings are summarized in Table 2B.1.2 and are by and large relevant to immunogold staining of thin subdivisions. It is of import that a suited nonspecific binding control be included for all samples. This should at least consist of a subdivision blocked harmonizing to the standard process described above and so incubated on the colloidal gold suspension, extinguishing the primary antibody incubation measure. The add-on of a grid incubated with a purified Immunoglobulin g from the same species as that in which the particular primary antibody was raised and used at the same concentration as the primary antibody is besides appropriate. Before any meaningful appraisal of labeling is performed, these controls must be evaluated for labeling. In add-on, the grade of labeling in the parts of the grid incorporating merely support movie and, if present, plastic without sample, provides an index of background labeling. While it is non perfectly necessary to utilize Formvar-coated grids in this process, they greatly aid the keeping of subdivisions on the grid, as the legion wash stairss in this process increase the opportunities of losing subdivisions from uncoated grid surfaces.

LR White implanting rosin was chosen for the above-referenced protocol due to its good antigen-preservation features. Tissues embedded in epoxy rosins may necessitate to be etched to expose antigenic sites. Etching involves basic onslaught on the end-linked epoxide rings. Some proteins and peptides and many amino acids have been successfully deplasticized by etching methods to reconstruct immunoreactivity lost in the embedding procedure.

Anticipated Consequences

Immunoelectron microscopy

Arrested development techniques for TEM

At the decision of the arrested development and initial processing of samples for thin-sectioning processs, samples sufficiently stabilized to continue ultrastructural organisation are now ready for the measure of implanting in plastic. This measure is necessary to stabilise tissues in a matrix that is uniformly hardened to let ultrathin segmenting with glass or diamond knives.

Implanting techniques for TEM

At the decision of the implanting procedure, tissues are infiltrated with a hardened matrix which is able to defy the emphasis of ultrathin sectioning ( i.e. , ultramicrotomy ) with glass or diamond knives.

Time Considerations

TEM of thin subdivisions

Successful heavy metal staining of thin subdivisions consequences in subdivisions that are comparatively easy to visualise on the phosphor screen of the negatron microscope. The deposition of sufficient discoloration is required to enter images, as designation of optimum focal point in a TEM is another process that requires considerable attention and pattern. Figure 2B.1.3 and Figure 2B.1.4 show illustrations of samples appropriately stained with uranyl ethanoate and lead. Figure 2B.1.8 provides an illustration of the usage of immunogold localisation of antigens followed by heavy metal staining. In this figure, differences between the negatron sprinkling of 10-nm gold atoms and heavy metal discolorations that generate contrast in the TEM can be appreciated.


Figure 2B.1.8 Propionibacterium fixed and ab initio processed for immunogold labeling and embedded in LR White rosin. In panels ( A ) and ( B ) shown at the same magnification, the LR White-embedded subdivisions were labeled foremost with a primary monoclonal antibody specific for this peculiar isolate of Propionibacterium ; this was followed by secondary labeling with 10-nm protein G-gold ( white pointers ) . Panel A shows built-in specimen contrast without staining uranyl ethanoate and lead staining of the subdivision, whereas panel B shows the added contrast obtained by using those discolorations. Note that while the ultrastructural item of cells is improved with heavy metal staining, the visual image of gold atoms can be more hard and may necessitate scrutiny of subdivisions at higher magnification.

Immunoelectron microscopy

These processs require extended use of grids and several incubations, which will necessitate several hours to finish. It is hence desirable to treat several girds at the same time, non merely to rush up the procedure of measuring samples, but to guarantee that a sufficient figure of samples are observed along with appropriate controls. It is besides possible to run several dilutions of antibody and gold conjugate at the same time to hasten the process.

Arrested development techniques for TEM

Preservation of cells for scrutiny by thin subdivisions is an extended protocol that requires multiple stairss to carry through. If a sample is presented early in the work twenty-four hours, it is possible to hold the infiltrated sample polymerizing in the oven by the terminal of the twenty-four hours. However, it is more likely that these processs will be performed over several yearss. Fortunately, there are several points at which the processing can be arrested until such clip that it can be resumed without making harm to the sample, all of which involve storage at 4A°C. Some possible points at which it is possible to hold the process include the primary fixative phase ( if the tissue is being fixed overnight at 4A°C ) , after the first buffer rinse following primary arrested development, after the buffer rinse following post-fixation, or when the sample is in the 100 % rosin mixture.

Implanting techniques for TEM

In the embedding procedure, it typically takes several hours to replace the resin/solvent mixture with unpolymerized rosin, which is so normally hardened in an oven overnight. On the undermentioned twenty-four hours, blocks are removed from the oven and either trimmed in readying for ultramicrotomy or stored in appropriate containers until samples are needed for readying of thin subdivisions. Embedded tissue will last many old ages when kept at normal room temperature and humidness.

TEM of thin subdivisions

Staining with uranyl ethanoate and lead normally takes about 30 min. Immunogold staining of antigens on thin subdivisions typically takes 4 to 6 hours to finish.

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