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Oregon
State University |
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USER INFORMATION AND FACILITY POLICIES |
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PROTOCOLS Powders And Suspensions For "Particle Size"
Microscopy "Those
who wish to succeed must ask the right preliminary questions." The
Electron Microscope Facility receives many requests for work intended to
size and otherwise characterize particles which are presented as dry
powders or liquid suspensions.
Typical specimens are delivered in glass or plastic ware labeled
with a letter or number code or a run or sample identification
designation. When
questioned about the contents, data needed, and how the data needed
relates to an experiment or technical process, clients seldom provide
useful information.
We may be told a vial contains a "drug" or "phosphor",
"clay", or "silica".
We're most frequently told the information needed is "particle
size", with an occasional "porosity" or "contaminant" statement
added. Rarely
are details about the relationships between this data and how it connects
to function provided. The
goals and intent of our services are to be helpful to clients, and
although needs for proprietary or unbiased results are understandable, our
abilities to meet a client's needs as well as our concerns for personal
safety and microscope care are closely tied to the quality of information
provided with specimens.
Taking the last two issues mentioned, specimens need to be prepared
for microscopy and are examined under high vacuum and ionizing radiation
conditions, so questions about health, handling, and material stability
and safety are not inconsequential.
Providing Materials Safety Data Sheets (MSDS) with
specimens, or reasonable written similar information for experimental
substances, is appreciated. Clients
want accurate and useful information.
They also want the results quickly and cheaply.
Both expectations are compromised by the form in which the
specimens are presented.
Because the client has much greater knowledge and insight about
their specimens and how the specimens relate to their application(s), and
usually have access to the equipment needed to collect and manipulate
their unique specimens, it
is critical that the client invest the effort required to fracture, grind,
disrupt, sort, fractionate, centrifuge, filter, suspend in appropriate
solvent, disperse, or otherwise pre-process particle specimens prior to
submitting them for microscopy.
Doing so shortens data return time, permits us to provide more
useful answers to your specific questions, and may appreciably reduce the
charges that are applied if Facility labor is needed to do pre-processing
manipulations necessary to obtain meaningful specimens.
When the fundamental particles remain in aggregates, it is the
client's responsibility to disrupt those aggregates by means compatible
with the specimens and investigative requirements so as to render specimen
submissions that are compatible and appropriate to the analytical goals. Regarding
the data requested and how that information relates to larger issues,
typical submissions contain particles ranging in size from several
millimeters to fractions of a nanometer, and not uncommonly, ultimately
down to the size of the molecules, unit cell crystals, or other atomic
condensations that comprise the material(s).
This is especially common in dry power submissions because
particles clump together or were scraped from filters or surfaces on which
they were concentrated by adhesion.
What are acceptable methods to reduce clumped aggregates to
fundamental particles?
What mechanical disruptive process(es) or solvent(s) are acceptable
to use with what's submitted to break clumps down to fundamental
particles? Are
the aggregates, the fundamental particles, or an intermediate condition
critical to understanding the dynamics of these particles relative to the
application? In routine practice, the results provided when particle size information is requested will be a series of pictures taken at increasingly higher magnification which visually "average" and document an "as received" specimen. Clumped powders may be spread to a thin layer in which particles smaller than the macroscopically visible clumps are possibly revealed. Plant Virus Assay by Transmission Electron Microscopy THE
SERVICE The
Electron Microscopy Facility at O.S.U. offers plant virus assay services
to horticulturalists. The
assay performed is most valuable when used for detection and diagnosis
of plant infecting rod‑like viruses such as lily symptomless
virus, potato viruses X and Y, or tobacco mosaic virus.
The test is not recommended for detection or diagnosis of
spherical viruses like apple mosaic, cucumber mosaic, or tobacco
ringspot viruses, and is NEVER guaranteed to prove a plant free
of an infectious agent. Before
submitting samples, it should be understood that we provide a diagnostic
analysis; we are not in the business of certifying plants as being
specific pathogen free for commercial or research purposes. Clients are cautioned not to misuse, misinterpret, or
otherwise extend our findings beyond the specific plant examined at a
specific point in time. Furthermore,
although we are willing to discuss our client's specific plant disease
problems, we are not a horticultural consulting service and do not make
recommendations about management, marketing, laboratory, greenhouse,
nursery, or field practices. Data
generated for a customer, and customer information of a proprietary
nature is treated as confidential. THE TEST: MATERIALS AND METHODS Fresh,
fully hydrated leaves are preferred samples.
A small piece of leaf tissue is macerated in a water‑based
electron dense stain on a TEM specimen grid, excess fluid is blotted
away, and the dried sap/stain residue examined by transmission electron
microscopy. In
preparing the sample, fresh stain made from powdered reagents and
sterile, distilled water is used. The
stain is filter sterilized into a sterile glass serum bottle and
thereafter handled in a sterile syringe.
The work counter is surface sterilized with 70% ethanol before
each group of samples is prepared.
New TEM support grids, coated with polyvinyl formal, are fastened
to clean glass microscope slides with adhesive tape.
Forceps used to obtain and macerate the leaf tissue are alcohol
flame sterilized both before and after preparing each individual sample
to prevent contamination of samples by our tools.
Blotting of liquids is done with fresh, clean chromatography
paper pieces; one or more pieces are used to blot each grid. Only
one leaf sample is removed from its shipping container and prepared at a
time to prevent possibilities of either sample cross‑contamination
or mislabeling. The unused
leaf material is returned to its shipping container after the grid has
been prepared. A stain blank is prepared for every group of specimens made
as a control to prove the stain free of contaminating material.
Each grid is examined by microscopy.
If virus is detected, examination may be for under a minute.
However, if virus is not detected, examination is continued for
at least ten minutes, after which a second sample is prepared, again in
accordance with the above methodology, and that grid also examined for
at least ten minutes. Occasionally even a third sample will be tried if there is
reason to suspect the presence of a low level infection. If virus is not
detected by repeated examinations, the result is reported as "virus
not detected." RESULTS Virus Detection:
A simple "detected/not detected" answer is often the
only concern of a client. Results
of our assay will be reported by letter, or in some cases, by telephone
followed by confirming correspondence. Verbal reports may be supplemented with micrographs to
further document the nature of detected virus.
Micrographs will be provided to show any virus detected in a
sample. Obviously, if virus
is not detected, micrographic evidence cannot be obtained. When
virus is detected, the verbal report will read "virus
detected," or, when virus cannot be found, will read "virus
not detected." Even if
we find but one virus in a sample, we report the plant as
"virus detected." Occasionally
incomplete virus‑associated structures may be detected.
These have been reported in scientific literature as
"associated proteins," "fibers," and "coated
lines." We detect this condition both with and without the presence
of actual virus, and report this condition as "incomplete particles
detected." Sizing: We can provide data about the size of detected virus.
This information is useful in ascertaining the specific virus(es)
involved in the infection and determining possible corrective or
preventative management practices. Precise sizing is possible, but must be done on photographic
images to be accurate, and, to be statistically meaningful, many
particles should be available for measurement.
It is necessary that the customer advise us that size information
is needed at the time samples are submitted.
Both the size information and the documenting photograph will be
included in our report. Multiple Infection:
It is possible to detect multiple infection by more than one type
of virus or by virus and bacteria or mycoplasma.
Our report will indicate this condition and the nature of the
infectious agents whenever it is applicable. Relative Concentration:
An estimate of relative levels of virus(es) detected can
be made from the microscopic examination.
This is a subjective visual impression based on what the
microscopist sees. There
are statistical limitations to both visual estimates and photographic
techniques, but either one can give the client a feeling for the
relative concentration of virus in a particular sample.
The report will express relative virus concentrations as
"low," "moderate," or "high"
concentration. When
knowledge about relative virus concentration is required, the client
should relay that information to us when submitting samples. RELIABILITY Through
the stained sap technique and our quality assurance procedures herein
described, we endeavor to give clients accurate, reliable information
that if properly understood and used can be valuable for their
production, management, and marketing decisions.
However, because these procedures assay only one very small piece
of tissue from one plant at one point in time, we cannot unequivocally
guarantee a particular plant is specific pathogen free.
OUR ASSAY IS TO BE CONSIDERED AS A DIAGNOSTIC TOOL - IT IS
A MUCH BETTER ASSAY TO PROVE THE PRESENCE OF A PATHOGEN THAN TO
PROVE ITS ABSENCE. After
selecting the sample, any subsequent handling of a plant by
anyone can potentially cause introduction of a pathogen to a clean
plant. Consequently,
although we diagnose plants to the best of our abilities and the limits
of specimen preparation technique, we cannot guarantee nor in any other
way certify a plant is disease free.
Any material cloned or cultured from a checked, apparently clean
plant should not be assumed to be virus free by our client.
Our role is diagnostic, and is most useful in the early stages of
producing virus free plants or when a disease outbreak is noted.
Quality assurance of healthy plants is the responsibility of the
grower and is not assumed by the Electron Microscope Facility. Many
clients have confidence in statistical methods for screening their
plants for disease agents. We
do not recommend reliance on statistics.
We examine the specific plant(s) of interest for a client and
report our findings about that specific plant at one specific point in
time. To have continuing
confidence in a pathogen‑free plant or a disease treatment
program, parent material and offspring and/or clones, or additional
samples of treated plants, should be checked at intervals not exceeding
180 days. Minimum
detectable infection and reliability of EM on stained sap as a
diagnostic tool for detection of rod-like plant viruses is
comparable to the detection and reliability obtained by the ELISA
method. By immuno-electron
microscopy, the minimum detectable infection level is lower due to the
greater sensitivity of that procedure. ALTERNATIVE METHODS ELISA: Enzyme-linked immunosorbent assay (ELISA) is an
immunological test with minimum detectable infection accuracy and
reliability comparable to examination of stained sap by electron
microscopy. It is not a microscopical technique and is not available
through our Facility. ELISA
is a relatively rapid assay recommended for large batch checking. It is favored as a quality assurance assay by growers in
extensive production or marketing situations.
Virus concentration and multiple infection (especially with
bacteria) information can be missed by ELISA unless specially designed
into the test. Immuno-Electron Microscopy:
Immuno-EM, also called immunosorbent electron microscopy,
combines an ELISA-like immunological test with the electron
microscopic examination of stained sap. This procedure is at least 4 orders of magnitude more
sensitive in detecting a low level virus infection than either ELISA or
the conventional stained sap EM assay used alone.
Although immuno-EM testing can be performed by the Electron
Microscope Facility, it costs 5 times as much as a conventional stained
sap assay, and the customer must supply at least 10 square centimeters
of leaf for each plant to be tested and the antiserum(a) against
the virus(es) of interest. There
are few commercial sources of antisera to common viruses of interest.
Clients must either produce their own antisera or obtain it
through special arrangements with a university or biochemical supply
house. Specific activity
and quality assurance of antisera from diverse and unreliable sources is
a problem and may influence accuracy of results. Immuno-EM is recommended when information about very low levels of infection is needed. Additional to its greater sensitivity, it retains the variety of data available by electron microscopy. It is slow, costly, and not suited for routine or batch checking. Please
avoid submitting specimens which are in a condition which compromises
our abilities to provide quality specimen preparation. Biological
specimens which have been through one or more freeze-thaw cycles,
transported under conditions where high or sub-zero temperatures or
desiccation might be expected (e.g.; long car trips unprotected in the
trunk or back seat), have been improperly fixed or washed prior to
receipt, have been over or under centrifuged, or suspensions pelleted in
deep glass or plastic (ETFE, styrene, polypropylene, polysulfone,
polycarbonate) tubes will have been compromised before reaching us. Specimens
may be submitted in a vigorous living condition, in fixative, or fixed
and moved into a wash buffer. Fixed specimens should never be washed nor stored in either water or saline! Samples
should be fixed a minimum of 2 hours and generally not more than 24
hours. Fixed specimens may be kept in buffer up to a week. Tissues with
trapped air spaces (stems, leaves, muscle, etc) need to be fixed in a
modest (20-30 inch) vacuum. If
you do the fixation, use of an appropriate EM fixative is imperative to
quality EM results. The organic fixation chemicals glutaraldehyde,
formaldehyde, or acrolein must be highest purity EM grade materials from
freshly opened ampoules, not from pint, quart, or gallon
sized stocks or previously opened supplies. Sorensens monobasic/dibasic
sodium phosphate or sodium cacodylate are the recommended buffer
options. Use of ion or tonicity adjusters (NaCl, MgCl, KCl, sucrose,
etc.) in the fixative is acceptable. Suspension
specimens should be submitted as centrifuged pellets in polyethylene microfuge tubes. Excessively centrifuged
materials may be damaged or the resulting pellets too firm for
processing chemicals to penetrate. Too lightly pelleted specimens
resuspend, disperse, and result in sections with few cells. Recovering
pellets from deep tubes or tubes of plastics other than polyethylene
drastically compromises the integrity of the pellet. The EM Facility
does not have a high speed centrifuge and may not be able to pellet (or
re-pellet) specimen suspensions. Finally,
if a sample is submitted, it's important we know the sample arrived,
what the sample is, and at what processing step we have obtained the
sample. Things left on our bench or in our fridge with little or no
information might become compromised through communications oversights
or presumptions. Immunological
methods used in conjunction with microscopy are used to visualize
location and distribution of antigens, antibodies, or site-specific
proteins on cells or subcellular structures. The following comparison
summarizes the common methods. LIGHT MICROSCOPY
TRANSMISSION ELECTRON MICROSCOPY
SCANNING ELECTRON MICROSCOPY
Requirements
for high immunological sensitive, high spatial resolution, and high
magnification frequently necessitate EM immuno methods, especially those
using TEM. These technically complex procedures involve many steps where
materials, direct action, and critical decisions are responsibilities of
the research scientist. The EM Facility staff can assist in immuno-EM
experiments with specimen processing steps involving sample fixation,
dehydration, embedding, sectioning, and examination. All specimen
immunochemistry details remain the responsibility of the research
scientist. The following points may be helpful to planning immuno-EM
studies. Critical
considerations in immuno-EM experiments include the tissue type(s) to be
immuno-assayed; when and how to fix, dehydrate, embed, and immuno-label
samples; and reaction time, temperature, and reagent concentration
factors. As an aid to experiment design, review of literature reporting
immuno-EM experiments similar to those proposed is recommended. The
goals in immuno-EM are to preserve biological structure while
simultaneously retaining immunochemical reactivity. EM preparation
procedures can significantly alter cellular chemistry, so compromises
among goals and technique limitations which retain adequate
immunological activity within adequately preserved structures must be
obtained. Central to this compromise is the necessary crosslinking of
proteins needed to stabilize structure in ways that keep the
crosslinking minimal so the critical proteins remain immunologically
recognizable. Tissues
may be fixed before or after the immuno-labeling reaction(s). Most
procedures endorse fixation, embedding and sectioning prior to labeling.
Tissue "fixation" may be accomplished by chemical or cryogenic
methods. CHEMICAL METHODS Chemically
fixed specimens are dehydrated with organic solvents, embedded in
plastic resin, and then sectioned. The embedded tissue and the sections
are permanently stable, giving the advantages of repeatable immuno-testing
and examination. However, the extensive chemical processing required may
reduce or block immunological activity. The
acrylic embedding resin LR WHITE has advantageous characteristics for
post-embedding immuno-labeling. This resin sections easily, has low
bonding affinities with cell proteins, readily accepts immuno-labeling
reaction methods, and has stability in an electron beam. CRYOGENIC METHODS Cryogenically
fixed specimens may be cryo sectioned, with the sections examined by
cryo microscopy or after freeze drying. Cryogenic methods maximize
retention of immunological competency but frozen tissues and cryo
sectioned materials examined by cryo microscopy must be forever
maintained at cryogenic temperatures to preserve structure. Freeze
drying gives permanency to the cryo sections but may significantly
disrupt structure. FREEZE SUBSTITUTION METHODS Cryogenically
fixed specimens may be embedded in plastic resin (freeze substituted),
then sectioned, thus combining the advantages of minimized chemical
modification and specimen permanency with the disadvantages of more
extensive chemical modification of immunological activity. LOWICRYL
resins are the embedding media of choice in freeze substitution methods. LABELING Macro-molecular
markers for immuno-ultrastructural studies must be visible (ie, contrast
against) biological structures and be suitable for specimen labeling,
preservation, and examination methods. A variety of markers are
available, including latex, ferritin, hemocyanin, and colloidal gold.
The common marker in immuno-EM methods is colloidal gold, which is
nontoxic, available in a variety of particle sizes (3-40 nm), offers
high contrast, has recognizable, well defined shape, and is available
commercially prepared for immuno- applications. Direct labeling conjugates the labeling
marker to the antigen. The conjugate, incubated with tissue, reacts with
antibody. Sites where immunological binding reactions occur complex the
conjugate and antibody. The marker reveals these reaction sites. Indirect labeling requires antibody and
antigen be reacted together. Independently, the labeling marker is
conjugated with a second protein complex. When the marker conjugate is
then reacted with the bonded antibody/antigen, the complex formed, which
incorporates the labeling marker, reveals the reaction sites. Please
request additional information if you are interested in using these
techniques. The
EM Facility can assist with chemical or freeze subsitution preparation
of biological specimens for immuno-cytochemical studies but does not
have equipment for cryo-ultramicrotomy. Special pricing, timing, or
procedural situations may be needed, so PLEASE discuss your research
need(s) with the Facility Manager well in advance of an experiment.
X-ray
spectroscopy is accomplished through collection of x-rays produced from
a sample bombarded with an electron beam.
X-ray energies emitted from the sample are dependent on the
element(s) from which the x-rays originate.
Differences in x-ray energies are distinguished and graphed as an
x-ray spectrum for the specimen under examination.
X-ray spectra contain both qualitative and quantitative
information. QUALITATIVE
ANALYSES Information
contained in the x-ray spectrum is used to determine detectable
elements present in a specimen. A
detectable element must have an atomic number greater than 5
(boron), and must be present in the specimen at a concentration greater
than one to five atoms per thousand atoms of sample, i.e., 1000 to 5000
ppm, or 0.1 to 0.5 atomic percent.
Elements with atomic numbers less than 6, (carbon) or elements
present at concentrations under one to three atoms per thousand atoms of
specimen cannot be detected. Computerized
aids simplify the identification of detected elements. In
some instances x-ray energies of two elements overlap and may appear as
a single spectral peak. Specialized
routines may help in discovering what elemental components may be
contributing information into these peaks.
Other artifacts, called ESCAPE PEAKS, occur frequently in x-ray
spectra. These peaks must
be correctly identified and removed from the analysis. ELEMENT
DISTRIBUTION Once
the detectable elements in a sample are identified, it may be possible
to determine spatial distribution of constituent elements, provided a
specimen matrix is NOT chemically homogenous.
Element distribution information may be formatted as LINE
PROFILES or as ELEMENT MAPS. Line Profiles report relative x-ray
intensity detected from a designated element as the electron beam traces
a single line (i.e. transects) over the specimen detail of interest.
The result is a visual, semi quantitative comparison of element
concentration at all points along the scanned line.
Line profiles are used to show changes in element concentration
associated with diffusion or with boundaries such as structural layers,
inclusions, or zones, layers, pockets or particles of contaminant. Element Maps document the pattern of a
designated element's distribution over an area of specimen.
The "map" consists of an image formed by dots which
correspond to x-rays collected from that element.
The dots are positioned spatially on the image so as to represent
or "image" those locations in the specimen which contain
detectable concentrations of the selected element.
Element map information is primarily yes/no data about the
presence of an element in a given area of a specimen. QUANTITATIVE
ANALYSES Quantitative
x-ray spectroscopy suggests amounts or percentages of elements detected
within a specimen. Depending
on characteristics of the specimen, an analysis can have anywhere from
only "ball park" to very high accuracy. Specimen
characteristics have profound effects on the validity of any
quantitative result. The following questions are an aid in determining
what kind of accuracy might be expected from a particular sample. 1. What elements do you expect to find
2. What are the supposed concentrations of the elements in
the sample?
3. On an elemental level, how homogeneous is the sample?
4. What is the sample's physical topography?
5. Do you have standards, or are standards available, for
your sample?
To summarize: If
concentration accuracy approaching 100% +/-2% is required from an x-ray
spectroscopic analysis, the sample must
Within
the levels of existing technology, these specifications hold true no
matter what x-ray spectroscopy equipment is used or what operator does
the analysis. Many
samples may not conform to the strict limitations necessary for a
"fully" quantitative analysis, so it is important to ask if a
"fully" quantitative analysis is essential to answer
the question one has about a sample.
If absolute numbers are required, then the sample must
meet stated requirements or another method of assessing the chemistry
must be employed. If exact
accuracy is not essential, specimen specifications can be relaxed and a
number of analysis routines employed that can give good quantitative approximations
from non-ideal specimens. Since
many SEM specimens will not be ideal candidates for x-ray
spectrochemical accuracy, these analytical procedures are often most
beneficial. They include: RATIOS Ratios
may be computed between peaks within a spectrum or between spectral
peaks and background. Ratio
data may suggest compounds formed between elements.
Furthermore, ratio data permits comparative statements to be
made, such as: Sample B has
twice as much barium as is contained in sample A, even if we do not know
the exact amount of barium in either specimen.
Whether B contains 20% barium to A's 10%, or 80% to A's 40%, the
proportion is the same. SPECTRAL MATCHING A
spectrum acquired from a sample may be matched to other spectra stored
in memory. A qualitative
match can be made either between only designated peaks or across the
complete spectrum using a Chi Square analysis.
The result obtained is a list of "best fit" spectral
matches with their associated Chi Square "goodness of fit"
values. When
standards with precisely known chemistry are available, their spectra
and chemical composition data can be stored in memory. The known concentrations of elements in the standard spectra
may then be used to estimate element concentrations in the analyzed
specimen using an algorithm which constructs curves from which the
quantitative results can be derived.
This algorithm does not use matrix effect corrections employed in
more "quantitative" algorithms, assuming instead that matrix
effects are similar if the specimens are similar. STANDARDLESS ANALYSES Semi-quantitative
algorithms may be used when standards are not available or do not exist.
Computer generated model spectra of ideal specimens having identical
chemistry as the sample, and examined under identical operating
conditions, are constructed, ratioed to data acquired from the analyzed
specimen, and element concentration values estimated. Matrix effect
corrections are then applied to derive the result. ANALYSIS FROM STANDARDS Analysis
against standards of exactly known chemistry is also possible and
provides the best qualitative and quantitative accuracy. However,
working against standards takes the greatest amount of analysis time.
Spectra from the standards and the unknowns must be collected, stored,
and analyzed under identical conditions of excitation, geometry, and
data reduction. IT IS THE CLIENT'S RESPONSIBILITY TO PROVIDE BOTH THE
"UNKNOWN" AND THE STANDARD SPECIMENS. The following criteria
relate to the selection of standards. A.
Every standard must have exact and completely known chemistry. B.
Each standard specimen matrix must be a completely homogeneous
mix of all elements in that standard. C.
You should have a minimum of three (3) standards for each element
you may want to analyze for:
1. At least one
should be a pure element or compound standard.
2. At least one
should probably be in the form of a powder.
3. At least one
should approximate the matrix of the unknowns you plan to analyze (ie,
metal, geological, powder, semiconductor, etc). D.
Concentration of the elements in the standard should be no less
than 5 to 10%. We normally do not use standards with concentrations
below 5%. E.
At least one standard should have a low concentration of the
element of interest (ie, 5 to 10%). The other standards should have
concentrations of the element equal to or greater than the concentration
you expect in the unknowns. F.
All standards and unknowns should be analyzed at the same
geometry and excitation to the extent the specimens will permit. G.
Avoid standards with peak overlaps unless you expect to analyze
unknowns with similar peak overlaps. If your unknowns will have peak
overlaps, at least one standard with similar peak overlaps will be very
helpful. H.
You should have two spectra saved on disc for every standard. One
should be the "raw" spectrum acquired from the standard. The
other should be the "analyzed" version of the "raw"
spectrum. I.
Clients are responsible for obtaining appropriate standards and
controls and for obtaining and providing the fully and correct chemical
analysis for each standard or control submitted. Analysis must be by a
method(s) other than XES. EMF will reject inappropriate standards or
controls. |
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| Revision: 2003-2004 |