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Preparation of biological specimens

for Electron Microscopy

Serving Advanced Technology

for

TEM

CONTENTS

Introduction

I Procedure of sample preparation


of a biological specimen

I 1 Preparing a biological sample
for ultramicrotomy

4 1 Various staining solutions

4 2 Procedure of staining

I 2 Fixation of biological tissue

I 4 Conventional staining of ultra-thin sections

12

uranyl acetate, lead citrate

II Observation of single particles

and viruses by negative staining

2 1 Extraction of tissue

II 1 Contrast in negatively staining

13

2 2 Fixation

II 2 Staining procedures

13

2 3 Dehydration

2 4 Substitution

2 5 Embedding

2 6 Polymerization

III Preparation of supporting film

Appendix: Preparing solutions used in microtomy

I 3 Steps in sectioning with an ultramicrotome

3 1 Trimming

3 2 Sectioning

Setting a specimen

Making of ultrathin sections

Thickness of ultrathin section

Picking up sections

Grid types

f How to make glass knifes

g Diamond knife


III 1 Preparation of collodion supporting film
(wet method)

14


III 2 Preparation of formvar supporting film
(dry method)

14

Introduction
There are several methods to prepare biological specimens depending on the nature of the
specimen and the purpose of the study.
This presentation introduces some commonly used methods.
Please, be careful in handling chemicals used in these methods as some are toxic.

I Procedure of sample preparation of a biological specimen


I 1 Preparing a biological sample for ultramicrotomy
Tools and chemicals listed here are necessary for preparation.
(Procedure)
1.

Extraction of
tissue

(Instruments/Chemicals)
Tweezers

6.

Glass bottles

Sectioning

Razor

Ultramicrotome (Top photo)


Grid
Diamond knife (Middle photo)
( Glass knife)

2.

Fixation

Glutaraldehyde

7.

Osmium tetroxide

Staining

Phosphate buffer

( Knife maker) (Bottom photo)

Uranyl acetate

Fixation

Lead citrate

3. Dehydration

Ethanol

8. Observation

Propylene oxide

Ultramicrotome

Embedding plate

4.

Embedding

( Disposable syringes)
( Disposable beakers)
Epoxy resin
Diamond knife

5. Polymerization

Embedding plate
(Top photo),
Embedding capsule
(Middle photo)

Embedding capsule

Oven for polymerization


(Bottom photo)

Knife maker

Oven for polymerization

I Procedure of sample preparation of a biological specimen

I 2 Fixation of biological tissue


b Washing in phosphate buffer. 10 min 2-3 times

I - 2 -1 Extraction of tissue

(Liquid is exchanged 2 or 3 times every 10minutes.)

I - 2 - 2 Fixation

c Post-fixation (Fixes lipids) 1~2 hr. (4C)

Pre-fixation (fixes proteins) 1~2 hr.

1~2% OsO4 in Phosphate buffer

2.5% glutaraldehyde in Phosphate buffer

d Washing in phosphate buffer. 10 min


Glutaraldehyde solution

A)

I - 2 - 3 Dehydration

A) The extracted tissue is dipped in the


chemical fixation solution.

50% ethanol
b 70% ethanol
c 80% ethanol
d 90% ethanol

Specimen

B)

Razor

e 95% ethanol

B)Cutting the tissue with two razor blades


as indicated will prevent unnecessary
deformation of the tissue.

f 100% ethanol *
g 100% ethanol *

10 min.
10 min.
10 min.
10 min.
10 min.
20 min.
20 min.

*Water is removed through a molecular sieve

Methods of washing & dehydration


aspiration
Next
solution

C)

C) The sample is transferred to a second


glutaraldehyde solution by keeping
the droplet with tissue held between
the two razors blades by the buffers
Tweezers
surface tension.
Glass bottle
specimen
Glutaraldehyde solution

Liquid is quickly replaced before the sample can dry.

I - 2 - 4 Substitution

Preparation of Epoxy resin

Only propylene oxide (PO) 10 min 2-3 times

[In the case of TAAB EPON 812 resin]

(Change Liquid 2 or 3 times every 20minutes.)

Put EPON 812 DDSA MNA in beaker.

b Mixed-solution of PO and resin


PO : Epoxy resin = 2:1

30 min.

PO : Epoxy resin = 1:1

1 hr.

PO : Epoxy resin = 1:2

1 hr.

*The use of disposable syringes and beakers facilitates the post washing.

b Mix it well.
c Add DMP-30 and stir well.

c Only Epoxy resin 2hr. or overnight

*Since an added volume is small, the use of syringes for tuberculin is recommended.

I - 2 - 5 Embedding (The freshly mixed resin should be used.)

The specimen is placed in a well of a silicone embedding plate.


Resin is poured over the tissue. Ensure no air bubbles are
trapped within the resin.

Epoxy resin
[In the case of TAAB EPON 812 resin]
EPON 812
b DDSA
c MNA
d DMP-30

48g
19g
33g
2g

*For a specimen with various orientations, use a silicone embedding plate.


Specimen

Resin

Silicone embedding plate

Gelatinous capsule embedding capsule Beam capsule

Resin
Specimen

I Procedure of sample preparation of a biological specimen

I - 2 - 6 Polymerization
(35C 1 day)
45C 1 day
60C 1 day

Appendix Preparing solutions used in microtomy


How to prepare 2.5% glutaraldehyde solution
1. Add 40mL of distilled water to 10mL of 25% glutaraldehyde
solution (commercially available: GA). (=>5% GA solution is
prepared.)
2. Add 50mL of 0.2M phosphate buffer.
=> 100mL of 2.5% GA-0.1M phosphate buffer (pH7.4) is prepared.

How to prepare 0.2M phosphate buffer (Sorensens phosphate buffer)


Solution A: Phosphate sodium (NaH2PO4) 27.6g/L
Oven for polymerization (1 stage type)

Solution B: Phosphate sodium (Na2HPO4) 53.6g/L

Oven for polymerization (3 stage type)

A : B = 28mL : 72mL => pH7.2


A : B = 19mL : 81mL => pH7.4

How to prepare 1% osmium solution


1. Dissolve 1g of osmium crystal in 25mL of distilled water.
=> 4% osmium solution (kept in a dark place and in a refrigerator)
2. Add 5mL of distilled water and 10mL of 0.2M phosphate buffer
to 4% osmium solution (kept in a dark place and in a refrigerator)
prepared in Step 1.
=> 20mL of 1% osmium-0.1M phosphate buffer (pH7.4) is prepared.
*Preparation must be performed in a fumehood.

I 3 Steps in sectioning with an ultramicrotome

I 3 2 Sectioning
Setting a specimen

I - 3 -1 Trimming

A sample block and a knife are set on a microtome.

Expose the tissue.


Trim the tip using a razor to form a pyramidal shape.
A cutting surface is made into a square,
rectangle or trapezoid.

1mm
0.5mm

1mm

0.5mm

Examples of trimming

Square

Square

Rectangle

Ultramicrotome
(Leica EM UC6)

Trapezoid

: Ideal for when ultra-low magnification images are

Sample block

needed.

Diamond
knife

b Rectangle : Suitable when sequential sections are cut and when the

block contains both hard and soft tissue.


c Trapezoid : Ideal for keeping track of the order of sections in a ribbon.

I Procedure of sample preparation of a biological specimen

b Making of ultrathin sections

d Picking up sections

Sectioned thin specimens float and are flattened on water in the knife boat.
A) The sections floated in the surface.

Pick up thin specimens on water using a TEM grid.


A) Press Method
Place a grid on a thin specimen with a support film
side down.

Daimond knife

Viewed from top

Place a grid on a thin specimen

B) A actual section

Sections

Knife boat
(with distilled water)

Sections

Advantage : Simple and easy


Disadvantage : Thin specimen may be wrinkled
Thin specimens may be overlaid

B) Pull up Method
Place a TEM grid under thin specimens with a support film on the top.
Bring thin specimens on the grid by using an eyelash probe.

c Thickness of ultrathin section


The thickness of thin specimens may vary depending on the hardness of
resin and room temperature.

Immerse a grid in water.

It is necessary to judge the thickness by color of interference.


The interference color and thickness of an ultrathin section
The optimal thickness

Thickness

Gray

< 60 nm

Silver

60 ~ 90 nm

Gold

90 ~ 150 nm

Purple

150 ~ 190 nm

Blue

190 ~ 240 nm

Green

240 ~ 280 nm

Yellow

280 ~ 320 nm

Eyelash probe
(eyelash attached to probe head)

The optimal
thickness for
observation in a
120 kV TEM.

Advantage : No wrinkles on specimens



You can place specimens

as you desire
Disadvantage : Skill needed

e Grid types

f How to make glass knifes

Grids of various shapes are available; circular holes, square holes, hexagonal

1) Place a glass bar (6 to 10 mm (T), 25 mm (W), 400 mm (L)) on the knife

holes, slit holes, single hole and marked holes. Grids with large square or

maker and equally divide this rod into two portions.

hexagoinal holes, or with a single slot are often used to pick up ultrathin sections.
The grid sizes range from 50 to 2000 mesh, which indicates the number of holes

2) Repeat equal division to make glass squares 25 mm on edge.

per inch. Thus, the larger the value, the smaller the grid square is.
400mm
Grating
Hole
200mm

Circle holes

Square holes

Marked holes

25mm

Slit holes

Single hole

Examples of grids

C
Knife maker

It is advantageous to select an appropriately shaped grid depending


on the research.
Example) Slit holes: For sequential sections

Single hole: For ultra-low magnification observation

Material: Cu, SS, Ti, Mo, Pt, Al, etc.

Cu is used in many cases, but for chemical analysis by EDS, the grid
should not contain any elements targeted for analysis.
Be careful when using Ni grids, as this material is paramagnetic.

A) Lock the glass bar.


B) Score the glass surface.
C) Fracture along the score line.

10

I Procedure of sample preparation of a biological specimen

3) Place a 25 mm square glass block in the knifemaker with the fresh cut to

Typical diamond knives

the right.
4) Score the block along a diagonal line and by applying pressure fracture
the glass along the score line.

Ultra

Used in room temperature.


For thin sectioning.

45 rotation

Cryo dry

Used in low temperature.


For thin sectioning

Two knifes from one 25 mm square block

Ultratrim

For preparation of resin block

g Diamond knife

11

I 4 Conventional staining of ultra-thin sections

b Washing
Run water (very gently!) parallel to the surface of a grid or place the grids on

I - 4 -1 Various staining solutions

droplets of distilled water.

Uranyl acetate (stains nucleic acids)

Washing bottle dispensing


distilled water

Usually, 2~5% (w/v) uranyl acetate in water is used.

Grid held in
tweezers

*Since it easily decomposes in light and high temperatures, it should preferably be kept in
a refrigderator.

Beaker
glass

b Lead citrate (stains protein and glycogen granules)

Method of Reynolds (There are several other methods.)


1.33 g of lead nitrate, 1.76 g of sodium citrate, and 30 mL of distilled

water are mixed.

c Lead staining 10minutes

b 8 mL of 1N NaOH is added. (Transparent liquid)


c Then, distilled water is added so that the whole quantity is 50 mL.

Drop Lead citrate liquid on Parafilm. Float a TEM grid on it.

*Lead forms crystal by reacting with CO2. Put the mixed liquid in a syringe. Place silicon

*Place NaOH grains around liquid.

plug on the tip of needle and store it in a refrigerator.

Grid held in tweezers

I - 4 - 2 Procedure of staining
Grid

Uranyl acetate staining 10minutes

Drop of lead citrate

Place a droplet of uranyl acetate solution on Parafilm. Float the grid on the
droplet with the tissue down.

Parafilm

Tweezers which
sandwiched the grid
Drop of uranyl acetate

Grid

Laboratory

Grids are covered with a laboratory dish. dish

Parafilm
Parafilm
Laboratory dish

NaOH grains

d Washing
Run water (very gently!) parallel to the surface of a grid.

e Drying

Grids are covered with a laboratory dish.

Wick excess water by blotting with a piece of filter paper.

12

I Procedure of sample preparation of a biological specimen

II Observation of single particles and viruses by negative staining


II 1 Contrast in negatively staining

II 2 Staining procedures

Negative staining solutions (uranyl acetate, phosphotungstic


acid, ammonium molybdate, etc.) envelope the specimen
and upon drying form a glass-like, electron dense film that
increases the contrast of the specimens, i.e. the specimen
is viewed against a dark background.

a Apply the specimen to a TEM grid

b Mount specimen on a TEM grid


Clamp a grid with support film in a tweezer. With a pipette, apply the
specimen. Remove excess liquid with a filter paper.

Bacteriophage (Negative staining)

Electrons

c Negatively staining

Staining liquid

Apply a droplet of uranyl acetate liquid on the grid before the specimen
dries. Remove excess liquid with a filter paper.

Specimen

d Dry the specimen


13

III Preparation of supporting film


III 1 Preparation of collodion supporting film (wet method)

III 2 Preparation of formvar supporting film (dry method)


Clean a glass slide with lens paper.

Prepare distilled water.


Put distilled water (temperature 30 to 40C)
in a Bchner funnel (diameter: 10 to 15 cm).

b Immerse the glass slide in 2% (w/v) formvar solution.


b Arrange grids.
Place a wire mesh in the funnel and arrange grids
on the mesh.

c In a smooth motion, gently pull the glass slide up.


Wire stage
Arrange grids on the wire mesh.

The quicker you pull the glassslide up, the thicker the film will be.

c Using a gtlass pipet, apply a drop 0.5-2% (w/v) of collodion

It is possible to pull up
the slide glass with a
constant speed.

solution (in iso-amyl acetate) on the water solution.


After applying, the droplet quickly expands on the water and forms a thin
collodoin film after the iso-amylacetate evaporates.

d Pull out distilled water.


Slowly drain the distilled water at the bottom of the
Bchner funnel, and allow the thin film to settle
on the grids.

Drain water here.

Sandwich the slide glass.

e Dry the thin film.


Place the wire mesh with grids and the collodoin support film on a filter

Supporting film preparation device

paper and allow to air dry.

14

I Procedure of sample preparation


III Preparation
of a biological
of supporting
specimen
film

d Score the edge of the collodoin film.

g Lift the supporting film.

To help floating off the collodoin film on water, score the edges of the glass

Place a piece of Parafilm on the collodoin with the grids, and then slowly lift

slide with a razor.

it up.

Grids arranged on the floated


collodoin support film.

e Float the collodoin film.


Slowly immerse the glass slide in water with the slide at a 20 to the water
surface.

Floated collodoin support film


Place the Parafilm.

f Arrange the grids.


Arrange the grids on the film floating on the water.

Floated collodoin support film

Lift the Parafilm with the


collodoin film and grids

h Allow the grids with the collodoin support film to air dry.

15

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Preparation of biological specimens


for Electron Microscopy

for

TEM

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UAE
BUSINESS COMMUNICATIONS LLC. (Abu Dhabi)
P.O. Box 2534, Abu Dhabi UAE
Telephone: 971-2-6348495
Facsimile: 971-2-6316465
BUSINESS COMMUNICATIONS LLC. (Dubai)
P.O. Box 233, Dubai, UAE
Telephone: 971-4-2220186
Facsimile: 971-4-2236193

USA
JEOL USA, INC.
11 Dearborn Road, Peabody, MA 01960, U.S.A.
Telephone: 1-978-535-5900
Facsimile: 1-978-536-2205/2206
JEOL USA, INC. WEST OFFICE
5653 Stoneridge Drive Suite #110
Pleasanton, CA 94588, U.S.A.
Telephone: 1-925-737-1740
Facsimile: 1-925-737-1749

VENEZUELA
GOMSA Service and Supply C.A.
Urbanizacion Montalban III
- Residencias Don Andres - Piso 7 - Apartomento 74
Avenida 3, entre calles 7 y 6
Montalban, Caracas, Venezuela
Telephone: 58-212-443-4342
Facsimile: 58-212-443-4342
VIETNAM
TECHNICAL MATERIALS AND RESOURCES IMPORTEXPORT JOINT STOCK COMPANY(REXCO)
Hanoi Branch,
No. 13-Lot 12 Trung Yen, Trung Hoa Street, Cau Giay Dist,
Hanoi, Vietnam
Telephone: 84-4-562-0516,17/562-0535
Facsimile: 84-4-853-2511

MGMT. SYS. MGMT. SYS.


R v A C 024 R vA C 42 5
ISO 9001 & 14001 REGISTERED FIRM
DNV Certification B.V., THE NETHERLANDS

ISO 9001 & ISO 14001 Certificated

Certain products in this brochure are controlled under the


Exchange and Foreign Trade Law of Japan in compliance
international security export control. JEOL Ltd. must pr
Japanese Government with End-users Statement of Assura
and End-use Certificate in order to obtain the export
needed for export from Japan. If the product to be exported
category, the end user will be asked to fill in these cert

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