Iowa State University Service Facilities for Biotechnology Research

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9/26/2012


1

Iowa State University

Service Facilities for Biotechnology Research


A major initiative of Iowa State University has been the establishment and support of state
-
of
-
the
-
art
instrumentation for biotechnology resea
rch. The Iowa State University
Instrumentation Facilities for
Biotechnology Research are located on the university’s campus in Ames, Iowa. The facilities are open
to faculty and students from the university, other educational institutions and industry scientists.


In addition to instru
mentation facilities, the university has in place an organization whose primary
function is the support of researchers’ equipment needs. The Research Equipment Assistance
Program (REAP) maximizes use of res
earch and teaching equipment by
maintaining an eq
uipment
location database and loan program through which interdepartmental loaning and sharing of
equipment is conducted. The REAP office has in inventory various pieces of research equipment that
are available for loan.


F
ollowing are brief descriptions

of the services offered by each of the instrumentation facilities. For
additional information, see
www.biotech.iastate.edu/service_facilities
.

_________________________



Animal Gene Trans
fer Facility


T
he facility provides a variety of services to individuals who wish to utilize transgenic animals as
part of their research program. The facility maintains equipment necessary for the creation of
transgenic animals via microinjection or somat
ic cell nuclear transfer. The facility is available to life
science researchers for technical service and for training of a limited number of individuals. All work
intended
to be performed in this facility must be scheduled with the professor
-
in
-
charge, as

the
facility is not staffed full
-
time.


Equipment housed in the facility includes two microinjection workstations, micropipette pullers, a
micr
oforge, stereo
-
zoom microscope and CO
2

incubator. Additional supporting equipment located in
nearby laboratories

to which access may be granted includes a heated microcentrifuge, tri
-
gas
incubators, stereo
-
zoom microscopes, inverted microscope, biosafety cabinet, osmometer, pH meter,
embryo freezing machine, cell fusion machine, gel electrophoresis equipment and UV
transilluminator.

_________________________


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Atmospheric Air Quality Laboratory


T
he Atmospheric Air Quality Laboratory is situated at the National Swine Research and Information
Center and serves as a focal point for collaborative research and
training in the area of air quality
engineering and livestock odor. The laboratory specializes in continuous air quality monitoring,
environmental analysis, quantification of organic compounds with gas chromatography and mass
spectrometry, and simultaneous

chemical and olfactometry analyses.


Odor, flavor and aroma

The lab specializes in state
-
of
-
the art chemical and sensory analysis of odor, flavors and aromas.
Chemical method detection limits are between part
-
per
-
billion and part
-
per
-
quadrillion levels.


Gases, particulate matter and greenhouse gases

The laboratory is equipped with a variety of real
-
time analyzers for gaseous ammonia, hydrogen
sulfide, carbon dioxide, methane, nitrous oxide, volatile organic compounds, particulate matter and
ozone. It is a
lso equipped to conduct field air sampling and analysis of organic gases with sorbent
tubes and SPME.


Multidimensional GC
-
MS
-
olfactometry

The unique MDGC
-
MS
-
O system includes a custom
-
made GC
-
MS system with heat
-
cutting
capability based on a Dean switch c
apable of simultaneous chemical and olfactometry

analyses.


Solid phase microextraction (SPME)

SPME is used for extractions of gases emitted from a variety of samples, including livestock and
poultry manure, air, food, beverage, packaging, bio
-
based produ
cts, live insects, plants, breath and
general applications related to quality control and quality assurance.


Biological fluid analyses

Breath and urine analyses for biomarkers are available.


Biofuels analyses

Separation, identification and quantification

of major, minor and trace fractions service are available.


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Forensic analyses of street drugs are available.

_________________________








Atomic Force Microscopy Facility


T
hree atomic force microscopes are available for use in the Roy J. Carver Laboratory for Ultrahigh
Resolution Biological Microscopy of the Institute for Combinatorial Discovery.


Digital Instruments Dimension
TM

3000 Scanning Probe Microscope

The Dimensi
on 3000 scanning probe microscope (SPM) brings together all SPM techniques in a single
platform and handles a wide range of sample sizes and types. A rigid, low vibration construction of
the Dimension 3000 SPM ensures high quality images and measurements.


Samples up to eight inches in diameter can be scanned in ambient air or fluids using the Dimension
3000 SPM. The Dimension 3000 SPM requires little or no sample preparation, and the simple vacuum
mounting system allows easy and convenient setup. Superi
or linearity and resolution in all three
dimensions are obtained, even for large samples. Integrated top
-
view video optics with motorized
zoom and 1.5 µm optical resolution help identify areas of interest for detailed scanning quickly and
easily. Changin
g scanning techniques, for example from AFM to STM, requires no tools.


The NanoScope IIIa system controller is a main part of the SPM system, providing the

software and
electronics that drive the microscope. Digital tracking and feedback control ensure
accuracy and
speed at all scan sizes and positions on the sample.


Digital Instruments MultiMode with a Tapping Mode
TM

The MultiMode system features multiple scanners that permit the user to tailor the system for
individual research. Scanners with large
scan ranges up to 120 microns on the X

Y axes, and a Z
range up to 6 microns, as well as high
-
resolution scanners with 0.5 micron X

Y axes and submicron Z
range are available. The vertical
-
engage “JV” and “EV” scanners allow the tip to be positioned at an
y
point on the surface, without adjusting for lateral movement during approach. The MultiMode is
9/26/2012


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controlled with a NanoScope IIIa controller. This controller provides 16
-
bit resolution on all three
axes, with three independent 16
-
bit digital
-
to
-
analog co
nverters (DACs) in X and Y for control of the
scan pattern, scaling and offset. This configuration provides 16
-
bit resolution of the lateral scanning
motion at any scan size.


Digital Instruments Dimension
TM

3100 Scanning Probe Microscope

The Dimension 310
0 is controlled with a Nanoscope IV controller. The NanoScope IV features up to
ten
-
times
-
faster scanning, as well as increased functionality, bandwidth, flexibility and expandability.

_________________________







Biomolecular Nuclear Magnetic
Resonance Facility


T
he Biomolecular Nuclear Magnetic Resonance (BNMR) Facility is supported by the Office of
Biotechnology and the Roy J. Carver department of biochemistry, biophysics and molecular biology.
The facility currently operates Bruker Avance 700 and 500 spectrome
ters, both capable of performing
a broad range of modern multi
-
nuclear, multi
-
dimensional NMR experiments on biomolecules. The
700 is equipped with an H/C/N cryoprobe, an H/C/BB conventional probe and an H/BBX/BBY
-
MAS solids probe. The 500 is equipped wi
th an H/C/N cryoprobe as well as H/C/N and BB/H
conventional probes.


The facility has computational resources for processing and analyzing NMR data and obtaining
molecular structures. The facility provides consultation on the application of NMR to solv
e research
problems. NMR data can be acquired and interpreted as an analytical service. Projects larger in
scope can be pursued on a collaborative basis. In the latter case, the facility will provide training and
guidance for researchers to operate inst
ruments and interpret data.

_________________________



Center for Crops Utilization Research


T
he Center for Crops Utilization Research (CCUR) is a resource to assist ISU researchers and external
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5

businesses in developing new value
-
added processes, product
s and markets for Midwest crops,
especially corn and soybeans. CCUR strives to add value to grain and other crop
-
derived materials
by conducting grant and contract research; offering short courses, workshops, seminars and training
experiences; providing a
nalytical, pilot plant processing and consumer evaluation services; providing
technical consulting services and information retrieval; and operating small
-
business incubator
services. The center has grain, food and material processing equipment in state
-
o
f
-
the
-
art laboratory
and pilot plant facilities.


The pilot plant facilities include a 5,000
-
square
-
foot wet
-
processing pilot plant (soy protein isolation,
corn wet milling, brewing, etc.); a 2,600
-
square
-
foot dry
-
processing pilot plant (dry corn milling
,
drying, grinding, sieving, etc.); a 900
-
square
-
foot hazardous solvents extraction facility (vegetable oil
extraction, grain, plant material extractions); a 3,000
-
square
-
foot product development laboratory
(plastic extrusion, molding and film blowing; bui
lding material processing, etc.); and various process
development and analysis laboratories (chromatography, grain analysis, vegetable oil refining,
baking, laboratory
-
scale process development, etc.). A small theater and conference facilities are
availab
le for technology transfer activities.


CCUR partly administers and works closely with the ISU Fermentation Facility, the Iowa Grain
Quality Initiative and the Grain Quality Laboratory.


CCUR also manages the BioCentury Research Farm (BCRF), the first
integrated biomass
-
to
-
biofuel
production and processing facility in the world, located seven miles west of the ISU campus on U.S.
Highway 30. It offers opportunities for pre
-
commercial
-
scale research in biomass feedstock
production, harvest, transport, st
orage, preparation, biorefinery processing and laboratory testing.
Field plots for crop production trials, field equipment modification facilities, biomass storage facilities
and a prototype biorefinery conversion facility are available for on
-

and off
-
ca
mpus users. The
biomass processing facility houses three, 2,700
-
square
-
foot pilot plant processing trains which include
biomass chemical fractionation and other technologies, four laboratories totaling 2,100 square feet,
and 1,000 square feet of office sp
ace. The BCRF also has 4,200 square feet of dry biomass feedstock
storage and 420 square feet of cold storage. Services include biomass feedstock preparation (sizing
and drying) and fermentation production of fuels and industrial chemicals (75, 250, 500
and 1,000
liter capacities).

_________________________



Chemical Instrumentation Facility


T
he Chemical Instrumentation Facility has more than five million dollars worth of analytical
9/26/2012


6

instrumentation available to faculty, graduate students, industry and other educational

institutions. The staff of five highly qualified professionals supports uni
versity research by keeping
the analytical equipment available and operable and by providing application support and user
training. Services available to the research community include the following:


Magnetic Resonance

Six NMR spectrometers of varying fre
quencies from 300 to 600 MHz are available. Magnetic
resonance spectroscopy allows the use of atomic nuclei as magnetic probes within a molecule.
Chemical analysis and spatial orientation are determined by using this technique. A fully equipped
EPR system
also is available. Equipment located in the facility includes a Bruker Avance II 600
(solids) NMR, a Bruker Avance III 600 (solution) NMR, a Bruker DRX
-
400 NMR, an Agilent MR
-
400
NMR, a Varian VXR
-
300 NMR, a Varian VXR
-
400 NMR, and a Bruker ER
-
200 EPR.


Ma
ss Spectrometry

The mass spectrometry lab is equipped to provide both low
-

and high
-
resolution GC
-
MS on mixtures
and high
-
resolution measurements for determining the elemental composition of pure samples and
multi
-
component mixtures. Electrospray and APCI
are used routinely for the ionization of medium
and higher molecular weight compounds, including synthetic organics and compounds of biological
origin. Three dedicated LC
-
MS instruments are available for routine work and special projects. MS
-
MS (parent
-
dau
ghter relationship) experiments are routine. Equipment located in the facility includes
a Finnigan Magnum ITD GC
-
MS, a Waters Micromass GCT
-
MS, a Shimadzu LCMS2010, a Finnegan
LCQ LCMS, and an Agilent 6540 Q
-
TOF LC MSMS.


Xray Diffraction

A
completely
-
equipped X
-
ray diffraction laboratory provides instrumentation for the study of the
molecular structures of small molecules and powders. The equipment includes Bruker APEX II CCD
and SMART 1000 single
-
crystal diffractometers equipped with low
-
te
mperature devices and Scintag
XDS
-
2000 and Rigaku Ultima 4 powder diffractometers available for general use. The facility’s
crystallographer provides complete reports that are suitable for publication.


Spectrophotometry

A variety of spectrophotometers is
available for routine use in the facility. These instruments provide
fingerprint spectra for characterizing and identifying compounds. These instruments currently
include a Bruker IFS 66V FT
-
IR, a Hewlett
-
Packard HP
-
8453 Diode Array UV
-
Vis, a Cary 100 Bio
double beam UV
-
Vis, and a Jasco J
-
710 circular dichroism spectrophotometer.


Isothermal Titration Calorimetry (ITC)

A Microcal ITC is available to study the thermodynamics of chemical reactions initiated by the
addi
tion of a binding component. ITC

is often used to characterize biomolecular interactions.


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7

Elemental Analysis

A Perkin
-
Elmer Model 2400 Series II CHN/S elemental analyzer is available for sample submission
or for investigator use. Normally, the instrument is configured for carbon, hydro
gen and nitrogen,
but sulfur al
so can be analyzed upon
request.


Computation

In addition to computer systems associated with the instrumentation, numerous PCs and
workstations are available for network
-
based data processing and modeling.

__________________
_______



Comparative Pathology Core Services


T
he Comparative Pathology Core Service (CPC) provides pathology services and consultation for
investigators working with animal models of human and animal diseases. The veterinary
pathologists in the CPC provide services for all phases of research involving

animal models. This
includes animal model selection, experimental design, gross and microscopic tissue examination,
clinical pathology evaluation/interpretation, histomorphometric analysis, and support for grant
applications. Consultations with a CPC path
ologist prior to project initiation will often provide the
most effective pathology support. In addition, the core can develop and implement ancillary
techniques which include immunohistochemical methods, special imaging (fluorescence microscopy,
morphomet
ric analysis), flow cytometry, laser capture microdissection, and photomicroscopy. CPC
costs are based on histopathology lab services and pathologists’ effort. Pathologist effort will vary
based on the needs of the project.

_________________________



Confocal Microscopy

and Multiphoton

Facilities


T
he Confocal Microscopy and Multiphoton Facilities of the Office of Biotechnology and the Plant
Sciences Institute have confocal and multiphoton microscopes available for use by internal and
external research
ers.


The confocal microscopes are located in 0117 Molecular Biology Building and 0071 Roy J. Carver Co
-
Laboratory. Researchers can choose which microscope best fits their research needs.


Confocal microscopes remove out
-
of
-
focus fluorescent light from the

image allowing clearer imaging
of the sample, including the ability to view structures and components that were obscured by excess
9/26/2012


8

fluorescence that would be generated by standard fluorescence microscopes. Some applications of
confocal microscopy include
fluorescence microscopy when spatial distribution of cellular or other
structures is important to the research being conducted, acquisition of a stack of images that can be
used for 3D
-
reconstruction, viewing structures in thick tissue and removing backgro
und and cross
-
talk fluorescence or fluorescence from other structures that obscure viewing of the desired structure.


Molecular Biology Building

The confocal microscope in the Molecular Biology Building allows for real
-
time optical sectioning of
fixed and
living specimens, providing significant improvements in optical contrast and resolution
over traditional light and fluorescence microscopy. The facility is equipped with a Leica SP5 X MP
confocal/multiphoton microscope system with an inverted microscope fr
ont end. New technology
available on this system includes a white light laser, IR laser and optical parametric oscillator (OPO).
Researchers are no longer limited to three or four lasers at three or four fixed wavelengths but can
tune the white light laser

to any wavelength between 470 and 670 nm, which has a similar effect to
having 200 lasers and 200 wavelengths. This allows researchers to select the excitation wavelength
that is best suited to their samples and will result in maximum fluorescence emissio
n. On the
emission side, the system has an Acousto
-
Optical Beam Splitter (AOBS) which allows researchers to
precisely set the emission wavelengths they would like to capture rather than be limited to preset
emission ranges determined by fixed filter sets.
Both of these technologies help to separate
fluorescence signals with close excitation and/or emission spectra.


Other features include faster scanning, higher resolution and increased sensitivity. Researchers will
now be able to work with live cells over
an extended period using live cell equipment, including a
heated stage with microcontainment or macrocontainment system, active gas regulation, cell
cultivation chamber and microinjection system. For capturing images of fast moving samples or
events that
occur in a fraction of a second, the resonant scanner enables video rate scanning with
speeds up to 16,000 lines per second. In addition, the system has FRET, FRAP, timelapse,
hyperspectral signal separation software, 3D imaging, colocalization, deconvolut
ion, region of
interest (ROI) scanning, brightfield and DIC capabilities. A 405 laser provides UV excitation and an
Argon laser provides CFP excitation and extra power for bleaching. The system also has an X
-
Y
scanning stage and automatic composition softw
are to capture high resolution images of samples that
are too large to fit within one field of view and a color digital camera.


The system allows users to easily switch between confocal and multiphoton mode. In multiphoton
mode, users can image deeper int
o their samples than is possible with confocal systems. The higher
excitation wavelengths are less damaging to live samples as well. The OPO expands the excitation
range of the multiphoton laser to include the red and high red ranges, enabling use of essen
tial
fluorophores such as mCherry, DsRed2, mRFP, Texas Red, Alexa Fluor 660 and others. Researchers
are able to precisely set the emission wavelengths they would like to capture.

9/26/2012


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Roy J. Carver Co
-
Laboratory

The facility at the Plant Sciences Institute is

equipped with a Nikon C1si confocal microscope with
both standard fluorescence confocal detection and spectral imaging capabilities. The 440, Argon, 561,
and 638 lasers offer excitation wavelengths of 440, 457, 476, 488, 561, and 638 nm. Capture of
transm
itted light images is also available. The system offers 40x and 60x water dipping objectives in
addition to 10x dry, 20x dry, 60x water, and 100x oil objectives. While in standard confocal detection
mode, the system can capture up to three fluorescence cha
nnels and one transmitted light channel
simultaneously. Additional capabilities include time lapse, FRET and FRAP. The system’s spectral
imaging mode is useful for separating closely overlapping emission wavelengths from multiple
fluorescent probes and/or
autofluorescence. In spectral imaging mode, the system can
simultaneously acquire up to 32 channels (2.5nm, 5nm, or 10nm individual channel widths) of
fluorescence spectra in a single pass. Additional capabilities in spectral imaging mode include FRET
and
time lapse. A digital camera also is available on the system for standard (non
-
confocal)
microscopy images.

_________________________



DNA Facility


T
he DNA Facility of the Office of Biotechnology performs DNA synthesis, DNA sequencing, high
-
throughput
DNA sequencing, massively parallel (Next Gen) sequencing, plant genomic and plasmid
DNA extraction, automated fluorescent genotyping, real
-
time PCR and automated microarray slide
hybridization.


DNA Sequencing

(www.dna.iastate.edu/mainpage_seq.html)

Sequen
cing samples are run on the DNA Facility’s Applied Biosystems 3730xl DNA Analyzer. The
AB 3730xl uses a four
-
color dye system and provides up to 900 bases of usable sequence data per
reaction. DNA can be sequenced as plasmid, lambda, cosmid or BAC DNA, or
as PCR products
(direct sequencing). Custom primers can be used with all types of templates. Clients submit
sequencing orders using the OnCore software. Use of this software allows clients to track the
progress of their orders and will automatically notify

them when their data are ready to download. A
four
-
color printout of the data is provided. When no problems are encountered with a template, the
results are generally returned within 24
-
48 hours after receipt of the samples. The facility also
provides a p
rimer walking service (www.dna.iastate.edu/framepwalk.html).


High
-
Throughput DNA Sequencing

9/26/2012


10

(www.dna.iastate.edu/mainpage_htp.html)

For clients who have high
-
throughput sequencing projects, samples can be submitted in 96
-
well
format. The Applied Biosystem
s 3730xl is capable of processing 12 sets of 96 samples in a 24
-
hour
period. The facility should be contacted prior to submission of samples.


Massively Parallel (Next Gen) Sequencing

(www.dna.iastate.edu/nextgen.html)

Access to both short
-

and long
-
read
massively parallel sequencing instruments is made possible
through an instrument
-
sharing agreement between Iowa State University and the University of Iowa.
The Illumina HiSeq2000 operated by the ISU DNA Facility generates an average of 150 million short
-
r
eads (50
-
100 bases per read) per lane. Applications include ChIP
-
seq, mRNAseq, whole genome and
candidate gene re
-
sequencing, and small RNA identification and profiling. The University of Iowa
DNA Facility operates a Roche 454 Genome Sequencer FLX that is
capable of long
-
read sequencing
(400 bases) and is especially well
-
suited for
de novo

sequencing of new genomes for which no
reference sequence exists.


The facility provides library construction services for all Illumina applications and also accepts
client
-
prepared libraries.


The following individuals at Iowa State University and the University of Iowa may be

contacted to obtain information regarding sample submission requirements, data handling and
pricing.


Iowa State University DNA Facility

Micha
el Baker

515
-
294
-
4705

mdbaker@iastate.edu


University of Iowa DNA Facility

Kevin Knudtson, Director

319
-
335
-
7251

kevin
-
knudtson@uiowa.edu


DNA Template Preparation

and Miscellaneous Services

(www.dna.iastate.edu/mainpagetemp.html)

The facility performs
plant genomic DNA preparation using the AutoGen 740 instrument. Plasmid
template preparation in 96
-
well format also is available. In addition, the facility offers a seed grinding
service using its Spex Certiprep GenoGrinder.


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11

Agilent Bioanalyzer 2100

(www.
dna.iastate.edu/mainpage_bioanalyzer.html)

This instrument is used for analysis and quantification of DNA, RNA and protein. Each chip can be
used to assay from 1 to 12 samples. Users will receive training in the instrument’s operation and be
responsible fo
r running their own samples. Users running protein samples must supply their own
chips.


Automated Genotyping

(www.dna.iastate.edu/mainpage_genotype.html)

The facility processes primarily microsatellite and AFLP markers using an Applied Biosystems 3730
DN
A analyzer to electrophorese samples and collect the gel image. Each sample can have as many
markers as the client can identify. The data are analyzed, and automated allele calling of
microsatellites can be performed by the AB GeneMapper software. Electron
ic files are provided via
the facility server.


DNA Synthesis

(www.dna.iastate.edu/mainpage_syn.html)

The DNA synthesis service synthesizes DNA oligomers in two scales, 50
-
nmol and 200
-
nmol, and can
make modified oligomers such as the fluorescent primers used
in genotyping applications. In
addition, primer design for primer walking s
equencing projects is
available
(www.dna.iastate.edu/framepwalk.html). Oligos are synthesized using a BioAutomation MerMade
-
192 DNA synthesizer.


Quantitative Real
-
Time PCR

(www.dna.iastate.edu/mainpageqpcr.html)

The DNA Facility has available two quantitative, real
-
time PCR in
struments


the Stratagene
Mx4000 and the Stratagene Mx3005


and will accept jobs on a ready
-
to
-
run basis. Applications
include gene expression studies, validation of microarray data, allelic discrimination, SNP analysis,
and screening for GMOs. DNA staff

are also available to advise or assist clients at any point in the
experimental process from initial project design through chemistry and material selection and data
analysis.


Microarray Slide Services

(www.dna.iastate.edu/mainpagemicroserve.html)

Slide
Hybridization



An Amersham Lucidea SlidePro hybridization unit is available for use by on
-
campus users. This instrument can perform hybridization and washing of up to six microarray slides
in a uniform and highly
-
reproducible manner.


Slide Scanning

The f
acility houses two scanners. The Pro Scan Array HT microarray scanner integrates image
9/26/2012


12

acquisition and analysis for both genomic and proteomic applications and features a patented 20
-
slide autoloader and e
-
mail notification function. The Applied Precision’
s array WoRxe® Biochip
Reader is a high
-
resolution, white light, CCD
-
based system that provides high quality images with
accurate and reproducible results.

_________________________



Doubled Haploid Facility


Th
e Doubled Haploid Facility (DHF) provides
haploid doubling for maize to ISU scientists, as well as
off
-
campus academic researchers and breeders. The start
-
up phase is supported by the Department of
Agronomy which provides use of its laboratories, greenhouses and nursery.


The development of
homozygous lines is an important, but time
-
consuming, process in plant
breeding and research. The induction and subsequent doubling of haploids is an efficient alternative
to generate homozygous offspring in two generations.





The mission of DHF is to:



p
rovide expertise and service in the production of doubled haploid lines in maize



improve the technology in order to get higher success rates and lower costs



teach and train scientists and students


The production of doubled haploid lines consists of three
main steps:



haploid induction by pollination with inducer lines,



selection for haploid kernels,



doubling of haploid plants and subsequent seed production.


Haploid Induction

For haploid induction, maternal inducer genotypes, such as RWS described by Roeber

et al. 2005 are
used. In the experiments, an average induction rate (IR) of about 8% in diverse plant materials is
found.


Haploid Kernel Selection

Kernels with a haploid or F1 embryo can be distinguished by means of the expression of the
dominant anthocy
anin marker gene R1
-
nj. The expression of this gene provides an anthocyan
pigmentation of the embryo and the endosperm. Kernels with a pigmented endosperm and a
nonpigmented embryo are selected as haploids.

9/26/2012


13


Doubling

Spontanous chromosome doubling occurs b
ut is dependent on the genotype. To obtain more
consistent doubling rates, plants are treated with colchicine following the procedure (method II)
described by Eder et al. 2002. Doubling rates (DR) of up to 20% are realized. On average, 8.4% of the
initiall
y grown haploid seeds resulted in a doubled haploid line (DHL) in 25 diverse donor
populations from 10 different breeding companies.


The production of the double haploid lines requires two generations. For one generation, a winter
nursery in Chile is used
.

_________________________



Environmental E
ngineering
Research Laboratory


T
he laboratory; a service of the civil, construction and environmental engineering department;
provides chemical analysis and related training and consultation services in support

of university
-
sponsored research. Documented quality control receives top priority and is made available to
researchers wishing to verify the quality of results.


Facility staff can function as consultants to assist the ISU research community by preparin
g quality
assurance plans for research proposals, configuring computer systems for data acquisition and
manipulation, training departmental personnel in analytical instrumentation and methodology,
implementing chemical hygiene plans and preparing specifica
tions for instrument purchases. Most
of the laboratory’s major instrument systems are available for use by researchers who wish to do their
own analytical work. The laboratory provides training and supervision for those researchers.


Atomic Absorption Sp
ectrophotometry

Flame atomic absorption and emission are available. A 150
-
position autosampler and a GBC 932 Plus
Atomic Absorption Spectrophotometer can be used to determine metals in large numbers of samples.


Automated Analysis

A Seal Analytical AQ2
+

a
utomated discrete analyzer is available for unattended automated analysis
of nitrogen, phosphorus, silica, sulfate, chloride and cyanide.


A BD
-
40 block digester is available for simultaneous, semi
-
automated Kjeldahl nitrogen and total
phosphorus digestion
s. Data collection, computation and reporting are carried out with a
microcomputer data station.


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14

Mercury Analysis

A Leeman Labs Hydra AF Gold Plus automated mercury analyzer is available to analyze for trace
levels of mercury. The analyzer uses cold vap
or atomic fluorescence with dual stage gold
amalgamation and dual detectors.


GC/MS

A Varian Saturn 2100 ion trap GC/MS system that includes MS/MS, SIS and CI capabilities is
available. The system includes an autosampler and GC/MS data station.


Gas
Chromatography

Four gas chromatographs served by EZ Chrom Elite Chromatography Data Systems provide a wide
range of options for organic analysis. FID, ECD, TCD, ELCD, PID and NPD detectors are available.
Autosamplers are available for liquid injection as

well as purge
-
and
-
trap sampling. Chromatographs
are equipped for operation with packed, capillary or Megabore columns. Sample preparation
techniques include continuous or discrete liquid
-
liquid extraction for water samples and sonication
or Soxhlet extr
action for soil, tissue and other solid samples.


Carbon Analysis

A Shimadzu TOC
-
Vws TOC Analyzer is available to analyze carbon in liquid samples by the UV
-
promoted persulfate oxidation method.


Other

The laboratory is equipped for most types of wet chemi
cal analysis, including related
spectrophotometric and potentiometric methods. Membrane filter techniques are used for bacterial
testing.

_________________________





Fermentation Facility


T
he Fermentation Facility is designed to help researchers develop new fermentation

technologies and products and provide benchtop
-

and pilot
-
scale fermentation equipment. The
facility has equipment for scaling up the production of industrially important ch
emicals, chemical
feedstocks, genetically modified organisms and enzymes. The facility also manages large
-
scale
fermentation activities conducted at the BioCentury Research Farm (BCRF) that are focused on
biofuels, industrial chemicals, and biobased produc
ts. The Fermentation Facility is a partnership of
9/26/2012


15

the Center for Crops Utilization Research, Office of Biotechnology, College of Agriculture and Life
Sciences, Department of Food Science and Human Nutrition, Department of Chemical and Biological
Engineerin
g, and Bioeconomy Institute.


Equipment housed in the Food Sciences Building includes four NBS Bioflo 310 benchtop fermentors
with 1
-

and 5
-
liter working volume capacities and pilot
-
scale fermenters with 15
-

to 115
-
liter working
volume capacities. Benchtop

fermentors located in Sweeney Hall include two NBS Bioflo 110 units
with 1
-

and 5
-
liter working volume capacities. Downstream processing equipment includes a hollow
fiber ultrafiltration system, semi
-
continuous centrifuge, French pressure cell press, bio
-
hood, and an
eight
-
shelf freeze dryer with stoppering capability.


Pilot
-
scale equipment housed in the Biomass Processing Facility at the BCRF, located seven miles
west of Ames on U.S. Highway 30, includes two ABEC fermentors with working volumes of 50 and

200 liters, two Applikon fermentors with working volumes of 500 and 1,000 liters, a Sharples P660
continuous horizontal decanting centrifuge, stirred tanks, pumps, and a platform scale. A distillation
skid system, falling film evaporator, and rotary dryin
g system have recently been installed and are
currently operational.

_________________________



Flow Cytometry Facility


The Flow Cytometry Facility of the Office of Biotechnology offers flow cytometric analysis and cell sorting for
a wide range of resear
ch applications. Facility personnel are trained to assist researchers in flow cytometry

experimental design, sample preparation techniques, and data analysis. Training sessions to provide
general instruction in these areas are also offered in the facility.

All facility services are open to
internal Iowa State University clients, as well as to external institutions and individuals.


Flow cytometry is used to analyze bacteria, mammalian cells, fungi, yeast, insect cells, microscopic
parasites, plant cells, nu
clei, organelles and chromosomes. Immunofluorescence measurements are
used to provide information on intracellular and cell surface receptor densities. DNA/RNA
-
specific
stains supply information on genome size, chromatin structure, and cell cycle kinetics.

Fluorochromes are available for quantitating a number of cellular metabolic functions, such as
calcium mobilization and oxidative burst. Phagocytosis of fluorescently labeled particles (beads, yeast
or bacteria) can be quantified. Cell viability and conce
ntration can be measured for mammalian cells,
as well as bacteria. Fluorescent lipophilic dyes are available that have been utilized as a means of
tracking cell life and tissue localization
in vivo
. Levels of enzyme marker gene expression, such as
b
-
galactosidase, can be correlated with the fluorescence intensity of cleaved substrate by flow
9/26/2012


16

cytometry. Intracellular protein products can be measured by immunofluorescent labeling of fixed
cells. Fluorescence
in situ

hybridization (FISH) techniques prov
ide information on the mRNA
expression level of a specific gene and can be used in conjunction with flow cytometry to provide
quantitative gene expression information on a cell
-
by
-
cell basis. Necrotic versus apoptotic
-
mediated
cell death can be distinguish
ed using flow cytometry. It is also possible to sort individual cell
populations via flow cytometry, enabling researchers to separate and further characterize
subpopulations of cells.


Flow Cytometry Data Acquisition and Cell Sorting

The Flow Cytometry Fac
ility maintains three flow cytometers for data acquisition and cell sorting: a
BD Biosciences FACSAria III, BD Biosciences FACSCanto and Miltenyi Biotec MACSQuant. The
facility also maintains several computer workstations with software packages for perform
ing off
-
line
analysis of flow cytometry data.


BD Biosciences FACSAria III

The BD FACSAria III is a sorting flow cytometer. The power of multi
-
color flow cytometry and the
highly sensitive analysis platform of this instrument allow investigators to
categorize an almost
endless variety of unique cell subpopulations. Once cells of interest are identified, the high
-
speed
sorting platform of the FACSAria III can simultaneously isolate and collect these target events for
further study.


The FACSAria III h
as three excitation lasers (405, 488 and 633 nm) and is configured to detect nine
fluorescent parametes (Pacific Blue, AmCyan, FITC, PE, PE
-
TexasRed, PerCP
-
Cy5.5, PE
-
Cy7, APC
and APC
-
Cy7), as well as forward and side scatter. This gives investigators exten
sive flexibility in
reagent selection and experimental design. The FACSAria III has the capacity for 11
-
parameter
detection on particle sizes ranging from 0.5 to 50 µm in diameter. Thus, viable cell, aseptic sorts can
be performed on a wide range of cell t
ypes (i.e. bacteria, mammalian leukocytes, plant protoplasts,
etc.). Up to four unique populations can be sorted simultaneously into 1.5 mL microtubes, 12 x 75
mm, or 15 mL tubes. Cells can also be sorted into several different types of tissue culture plat
es and
slides, and both sample and collection chambers can be maintained at pre
-
determined temperatures.


Digital electronics allow the FACSAria III to achieve data acquisition rates as high as 70,000 events
per second. For many common sorting experiments,

an event rate of 25,000 per second will
consistently attain ≥98% sort purity and ≥80% of expected yield. Higher event rate sorts (i.e. 50,000


70,000 per sec.) can be achieved in many instances with minimal loss of sort purity and only
moderate loss of e
xpected yield.


The FACSAria III is located in the Molecular Biology Building (MBB) main facility and is operated by
9/26/2012


17

facility personnel only. Data acquired on the FACSAria III is loaded onto a network server which
allows customers to retrieve data files fo
r analysis from their office/lab via an Ethernet connection.
The Flow Cytometry Facility also maintains a backup of user data. An appointment to schedule an
experiment on the FACSAria III can be made by contacting Flow Cytometry Facility personnel.


BD Bi
osciences FACSCanto

The FACSCanto is a data acquisition flow cytometer that combines a patented optical design, digital
electronics and a novel sample injection system supporting carryover of less than 0.1%. High
-
speed
data processing, industry
-
leading sen
sitivity and minimal sample
-
to
-
sample carryover make this
instrument uniquely suited for rare event analysis. The FACSCanto has the capacity for 10
-
parameter
detection on particle sizes ranging from 0.5 to 50 µm in diameter, which includes leukocytes, cell

lines, platelets, bacteria, multiplexed bead technologies and more.


The FACSCanto has two excitation lasers (488 and 633 nm) and is configured to detect eight
fluorescent parameters (FITC, PE, PE
-
TexasRed, PerCP
-
Cy5.5, PE
-
Cy7, APC, Alexa Fluor 700, and
A
PC
-
Cy7), as well as forward and side scatter. Data are acquired with digital electronics. The system
can handle high sample flow rates (up to 120 mL/min.) and fast acquisition rates (up 10,000 events
per sec.). Digital electronics also facilitate compensat
ion, with no limits to inter
-

and intra
-
beam
compensation, allowing post
-
acquisition compensation. Data files are stored raw and compensated as
part of the FCS files, allowing flexibility for off
-
line compensation when viewing data.


The FACSCanto instrume
nt is located in the MBB main facility and is operated by facility personnel
only. FACSCanto
-
generated data are loaded onto a network server which allows customers to
retrieve data files from their office or lab via an Ethernet connection. The Flow Cytomet
ry Facility
also maintains a backup of user data. An appointment to schedule an experiment on the FACSCanto
can be made by contacting facility personnel.


Miltenyi Biotec MACSQuant

The MACSQuant is a data acquisition flow cytometer that is located in the V
eterinary Medicine
Complex satellite facility. It is equipped with three excitation lasers (405, 488, and 633 nm) and is
configured to detect seven fluorescent parameters (Pacific Blue, FITC, PE, PerCP
-
Cy5.5, PE
-
Cy7, APC
and APC
-
Cy7). The MACSQuant is user

operated. Required training is available through facility
personnel. Once trained, an online calendar allows users to reserve instrument time through any web
browser (www.biotech.iastate.edu/cgi
-
bin/calweb/calweb.cgi). Archiving MACSQuant
-
generated
data f
iles is the responsibility of individual users.


Large
-
Scale Cell Separation

The facility maintains an Miltenyi Biotec AutoMACS Pro magnetic cell separation instrument within
9/26/2012


18

the Veterinary Medicine Complex satellite office. The AutoMACS Pro is a fully aut
omated bench
-
top
sorter that can be used to perform sterile bulk sorts.


Designed for ultra high
-
speed positive selection as well as depletion, the AutoMACS Pro can isolate
virtually any cell type and is compatible with almost any direct or indirect MACS
reagent. Users need
only label cells to be sorted and choose an AutoMACS Pro separation program. The separation is
done automatically. Several separation programs can be selected from a touch screen menu. By using
the positive selection program, the AutoMA
CS Pro is capable of isolating up to 2x10
8

pure target cells
within minutes. Cells as rare as 1 in 10
6

can be enriched to high purity through the use of double
positive selection programs. “Untouched” cells may be obtained just as easily by depleting unwan
ted
cells with the AutoMACS Pro depletion programs. The AutoMACS Pro and associated reagents are
completely compatible with flow cytometry. Fluorescent and magnetic labeling of cells can be
performed simultaneously. After AutoMACS Pro sorting, cells are im
mediately ready for flow
cytometric analysis. The AutoMACS Pro is user
-
operated. Potential users must complete a
mandatory training session, which is provided upon request by facility personnel.


Additional Laboratory Equipment

Refrigerated table
-
top
centrifuge, carbon dioxide incubators, biohazard hood, temperature
-
controlled
water baths, analytical balances, pH meter, refrigerators, freezers and a cryostorage system are
available.

_________________________



GeneChip
®

Facility


T
he GeneChip
®

Facility of the Office of Biotechnology and the Plant Sciences Institute provides
services for analysis of Affymetrix GeneChip
®

microarrays that can be used for the study of global
patterns of gene expression.


Affymetrix GeneChip
®

Instrumentation System

Two levels of service are available to users:


1) Full GeneChip
®

analysis is available for analysis of gene expression in eukaryotic samples.
RNA samples are submitted to the facility for labeling, hybridization and scanning.
GeneChip
®

microarrays can b
e purchased through the facility or provided by the users.


2) Hybridization and scanning are available for analysis of gene expression in both eukaryotic
and prokaryotic samples. Labeled samples are submitted to the facility for hybridization and
9/26/2012


19

scannin
g. GeneChip
®

microarrays can be purchased through the facility or provided by the
users. Because the facility does not label prokaryotic RNA samples, users wishing to assay
gene expression in prokaryotes must provide labeled samples for hybridization and

scanning.


After scanning, the facility will perform initial data analysis to ensure data quality and then provide
users with raw and/or normalized data.

_________________________



Genome Informatics Facility


The Genome Informatics Facility of the Iowa
State University Office of Biotechnology provides
bioinformatics services for investigators within academia, industry and government. Quality analysis
starts with understanding the nuances of the biological question and the assumptions made by
informatics
tools. Facility staff members are available to work closely with researchers to provide the
best solution for biological enquiry.


Available Services



Genome assembly and annotation



Transcriptome assembly and annotation



SNP/InDel calling



RNA
-
seq analysis



ChIP
-
seq



Introgression mapping



Novel gene discovery



Personalized GBrowse for data visualization



Access to high performance computing


To request bioinformatics support or service, please email the facility at GIF@iastate.edu. Include in
the email the type
of organism and the types of analyses envisioned. An appointment can then be
made to further discuss the project.

_________________________



Genomic Technologies Facility


T
he Genomic

Technologies Facility (GTF), a service facility in the Plant Sciences Institute, provides
expertise and equipment for biological research at the genomic level. Services include Sequenom
9/26/2012


20

MassARRAY
®

iPLEX
®

for high
-
throughput genotyping and Ion Torrent squi
nnying technology for
transcript expression analyses. The GTF also offers a Sequenom
-
based maize mutant mapping
service, Bulk Segregation Analysis (BSA). BSA capitalizes on Sequenom’s multiplex assay technology
to pinpoint the mutant gene location by utili
zing over 1,000 validated SNP markers. Two real
-
time
thermocyclers, a Stratagene Mx4000 and a Roche LightCycler 480, are available for high
-
throughput
gene expression analysis and single SNP genotyping with Taqman or KASPar. The GTF offers
NimbleGen sequen
ce capture and comparative genomic hybridization services. In addition, high
quality DNA and RNA extraction for next generation sequencing is also available in GTF on a fee
-
for
-
service basis.


Ion Torrent™ Services

Ion Torrent™ sequencing offers an array of applications from
de novo

sequencing, genotyping by
sequencing to RNA
-
Seq. A 100bp sequencing run on the Ion Torrent™ takes just 75 minutes. A 200bp
run takes only 2 hours.


Custom NGS library Preparation Service
s

The GTF offers custom library preparation service for Illumina and Ion Torrent™ sequencing. The
available library preparation types include amplicon sequencing using fusion primers, Ion shear
DNA library, RNA
-
Seq library and small RNA library.


Sequenom
Services

The MassARRAY
®

system offers a suite of applications for quantitative and qualitative genomic
analysis via MALDI
-
TOF mass spectrometry. iPLEX
®

is a SNP genotyping technology that can
analyze a multiplex of up to 40 SNPs in each reaction, providing

up to 150,000 genotypes per day.
QGE
®

measures gene expression levels using real competitive PCR and can multiplex up to 24
targets in one reaction. Users provide the sequences of their targets of interest for assay design.
Facility staff will confirm the

design with users.

Researchers who wish to use an existing set of maize
SNP primers developed and validated by the Schnable Laboratory may contact the facility manager.


NimbleGen Array Hybridization Services

Genomic variation can be assessed using
comparative genomic hybridization (CGH) and sequence
capture technologies. Users will work with NimbleGen to custom design and order NimbleGen
arrays based on their organisms/genes of interest. Users will then submit DNA samples to the GTF
for sequence cap
ture hybridization and subsequent sample preparation for Next
-
Generation
sequencing.


Before accessing facility equipment and services, users are required to provide a signed and
approved user agreement to the facility manager. After training, users can op
erate some equipment
and conduct analyses themselves. In such cases, fees for labor will be applied for the initial training
9/26/2012


21

and for experiment preparation. Reservations to use instrumentation may be made using the facility’s
on
-
line scheduler.

__________
_______________



Grain Quality Laboratory


T
he laboratory provides instrumental analyses of the chemical and physical properties of grain and
other agricultural products. The services are intended to support high
-
throughput genetic
evaluations, surveys of

grain quality and other large
-
scale monitoring operations. The facility also
calibrates various types of instruments for manufacturers and users.


Chemical composition is measured with a non
-
destructive, near infrared (NIRS) analyzer. For best
accuracy, t
his test requires 400 grams or more of product. Sample sizes down to 150 grams will work
with corresponding reductions in accuracy.


Crop
-
specific tests



Corn: moisture, protein, oil, starch and density.
Ethanol yield and feed value can be
calculated from the NIR results



Soybeans: moisture, protein, oil, fiber, total saturates and linolenic acid.
Meal and oil
processed value (EPV) can be calculated from the NIR results.



Soybean meal: moisture, protein, o
il and fiber



Distillers grain: moisture, protein, oil and fiber


General Tests



Seed weight and size



Breakage susceptibility (corn)



Test weight



Thins (corn)



Spec
ific gravity (measure o
f hardness) by nitrogen displacement



Other contracted services


Adaptatio
n of NIRS instrumentation for individual situations and specialty measurements is
provided upon request.


The facility’s calibration service program creates calibrations for electronic measurement equipment
of various types and trains users in quality cont
rol validation. These can be done for instrument
manufacturers or for individual users on a wide range of products and instrument types.

9/26/2012


22


The lab has an in
-
house quality management system to verify accuracy and reproducibility of data.
Advice and set
-
up of

quality control programs for analytical data can be provided.

_________________________



Hybridoma Facility


The Hybridoma Facility of the Office of Biotechnology provides valuable resources for scientists who
need monoclonal or polyclonal antibodies but

do not have the appropriate equipment or are not
experienced in antibody production techniques. A wide array of procedures can be customized to
meet the researcher’s individual requirements. These techniques are provided on an individual
charge basis and
include animal immunization, cell fusion and hybridoma culture maintenance, cell
culture and maintenance of other cell lines used in biotechnology and virology labs, large
-
scale
mammalian cell culture (bioreactor), blood sera collection, antibody purificat
ion and isotyping,
cryopreservation and cryostorage of cell lines (
-
140 degrees centigrade), and ELISA tests. The
hybridoma projects are usually screened and selected by the client; however, the facility can do the
screening and/or training of lab personne
l when needed. A hybridoma project usually requires three
to five months for completion. The following timetable is used for general planning of a hybridoma
project:




Mouse immunization, 4
-
6 weeks



Selection of primary hybridomas after cell fusion, 2 weeks



Expansion and freezing of primary hybridomas, 2 weeks



Cloning and screening of clones, 2 weeks



Expansion and freezing of clones, 2 weeks



Bioreactor/ascites fluid production, 4 weeks


Polyclonal antibody production in rabbits is available for on
-
campus clie
nts only. Polyclonal services
include the purchase and care of rabbits through the Laboratory Animal Resource group on campus,
blood collection and processing of sera, adjuvant addition and injection of antigen and administration
of procedures according to

an approved protocol and timetable.



Additional equipment:

9 cubic foot,
-
80 C freezer

2, 18
-
foot ultra low (cryogenic) freezers for long term storage of biological materials

8 tissue culture incubators


All hybridoma services are open to Iowa State Univ
ersity clients and off
-
campus individuals or
9/26/2012


23

companies. The Hybridoma Facility and users will work together to develop an estimate for an
individual project based on current pricing. Current price information for each procedure offered
may be obtained by c
alling 515
-
294
-
9837 during regular business hours or by sending an e
-
mail
message to hybrid@iastate edu.

_________________________



Image Analysis Facility


T
he Image Analysis Facility of the Office of Biotechnology provides 2D and 3D imaging resources for
researchers interested in sample measurement or visualization. Services include: 2D image analysis
(morphometry, particle analysis, densitometry, etc.), 3D
image analysis (volumetric sample
measurement) and reconstruction, image editing instruction and photomicroscopy. Analysis is
performed with IPLab or Imaris software.


Equipment in the facility includes:



Imaris for 3D reconstruction and image analysis



IP
Lab for 2D image analysis



Upright microscope with fluorescence



Automated scanning stage with recomposition software for capturing images of large
samples at high resolution



Stereo microscope



Digital cameras for all microscopes and copy stand



Laser capture
microdissection system to identify and r
etrieve individual cells from
tissue
sections. The retrieved cells can be used for assessment/analysis of RNA,

DNA,
protein and other biochemical properties.

_________________________



Isothermal Titration

Calorimetry Facility


I
sothermal Titration Calorimetry (ITC) is a thermodynamic technique for monitoring chemical
reactions initiated by the addition of a binding component. It is often used to characterize
biomolecular interactions. The ITC Facility is a
fee
-
for
-
service facility and it provides access to a
MicroCal VP
-
ITC to support research efforts. Users may operate the instrument 24/7 after
completion of appropriate training.


Reservations are encouraged. Each day is divided into three time periods (b
locks). Block one is from
9/26/2012


24

midnight until 9:00 a.m. Block two is from 9:00 a.m. until 4:00p.m. Block three is from 4:00 p.m. until
midnight.

_________________________



Macromolecular X
-
ray

Crystallography Facility


he Macromolecular X
-
Ray
Crystallography Facility of the Office of Biotechnology provides a
Rigaku/MSC rotating anode generator for single crystal x
-
ray diffraction studies, Nikon SMX
-
800
stereomicroscopes and temperature and vibration controlled chambers for crystallization, trai
ning in
crystallography techniques and computers with crystallography software. Facility services are
provided on a fee basis and include consultation on protein purification, crystallization, and crystal
optimization, as well as assistance with crystal s
creening, data collection, data processing and
structure determination and analysis. The following outline is used for general planning of a
crystallography project:





Protein purification:


co
ncentrated protein > 95% pure



Crystallization:


3D, mountable
crystals



Crystal screening:


search for high qual
ity, high resolution crystals



Data collection:


using faci
lity or synchrotron equipment



Structure determination:


processing, phasing, refinement, modeling, analysis, deposition

_________________________



Materials Analysis and Research Laboratory


T
he Materials Analysis and Research Laboratory (MARL) is a core facility of the Office of
Biotechnology at Iowa State University. MARL’s function is three
-
fold, namely research and
development, teaching, and
service. Its facilities are used for chemical and physical characterization
of a wide variety of materials to support research and teaching programs within the university.
MARL also conducts research on unusual material evaluation problems for outside agen
cies.


Scanning Electron Microscopy (SEM)

The laboratory has two SEMs


an FEI Quanta 250 field emission SEM with environmental
capabilities (E
-
SEM) and a Hitachi S
-
2460N variable
-
pressure SEM (VP
-
SEM). Both microscopes are
equipped with secondary electron

and backscattered electron detectors, motorized stages, x
-
ray
analyzers and image analyzers.


T

9/26/2012


25

X
-
ray Analysis for Microcharacterization (EDS)

Both SEMs are equipped with energy
-
dispersive spectrometers (EDS) for elemental analysis on a
microscopic scale. T
he FEI Quanta 250 is equipped with an Oxford Aztec system, and the Hitachi S
-
2460N is equipped with an Oxford Instruments ISIS system. Both systems have light
-
element
detectors for analysis of elements as light as boron. They are equipped for quantitative
analysis,
digital imaging, line
-
scan x
-
ray profiles, multiple element x
-
ray maps, image analysis and stereo
imaging. The system on the FEI is equipped with an 80
-
mm2 detector to permit good x
-
ray
acquisition even at low beam currents.


Image Acquisition,
Processing, and Analysis

Both of the SEM x
-
ray analyzers are equipped for recording digital images from the SEMs. The FEI
SEM has the capability of recording movies.


A CCD camera is available for capturing images through the light microscopes or from a c
amera
stand. Noesis Vision’s Visilog software is available for image processing and analysis. A variety of
public domain tools for processing and analysis, including Image J, are also available.


Light Microscopy

Light microscopes are available for reflect
ed light (Olympus BH), transmitted light (Olympus BH
-
2)
and for stereo (Olympus SZH) imaging. Lenses are available to interface the Pixera camera to the
microscopes, for recording still images or movies.


Network and Computer Support

MARL operates its own

local area network for exchange of data within the laboratory. It operates its
own WWW and FTP servers so that results are available for immediate retrieval.

_________________________



Materials Preparation Center


T
he Materials Preparation Center (MPC)
is a U.S. Department of Energy, Office of Science, Office of
Basic Energy Sciences, Division of Materials Sciences and Engineering specialized research center
located at the Ames Laboratory. MPC is recognized throughout the world
-
wide research community
fo
r its unique capabilities in preparation, purification, single crystal growth and characterization of
rare earth metals, alkaline
-
earth metals, and refractory metal materials. MPC operations are primarily
funded by the Materials Discovery, Design and Synth
esis team’s Synthesis and Processing Science
core research activity.


9/26/2012


26

Established in 1981, the MPC is a one
-
of
-
a
-
kind facility, which is acutely sensitive to the needs of
researchers. Providing research and developmental quantities of high
-
purity materials

and unique
characterization services to scientists at university, industry and government facilities on a cost
-
recovery basis, the MPC allows access to novel materials and new technologies as they are
developed.


The MPC is renowned for its outstanding te
chnical expertise in alloy preparation, creating

materials that exhibit ultra
-
fine microstructures, high strength and high conductivity



properties of great potential value to American technology. The MPC has established a

reputation for close interact
ion with its clients, providing the kind of personal service required to
meet each client’s individual needs. The MPC yearly satisfies hundreds of requests for

customized materials and services that are unavailable from commercial suppliers and

unmatched

in quality anywhere else in the world. The range of utilization is demonstrated by the
scientific publications in which the facility is cited.


Equipment and services information is available on the MPC website,
www.ameslab.gov/mpc
.

_________________________



W. M. Keck Metabolomics Research Facility


T
he W. M. Keck Metabolomics Research Laboratory houses seven different analytical platforms,
including Agilent gas chromatography instruments with EI and CI
ionization methods; an Applied
Biosystems Q
-
Star LC/MS instrument with both ESI ad MALDI capabilities; an Agilent ion
-
trap
LC/MS instrument with ESI, APCI and APPI ionization capabilities; a Beckman capillary
electrophoresis instrument with UV and laser in
duced fluorescence; an Agilent 1100 HPLC with UV
-
DAD and ELSD detectors; and a Synergy Two multi
-
mode microplate reader with the ability to assay
optically active molecules via luminescence, fluorescence, fluorescence polarization, and UV
-
Vis
absorbance (m
onochromator
-
based).


The laboratory has expanded to include a Bruker Solarix FT
-
ICR instrument, located in 101 Molecular
Biology Building. FT
-
ICR is a high
-
end mass spectrometer that provides ultra high
-
accuracy mass
measurements to sub
-
ppm level.


Analys
is of samples for external researchers is offered for a fee. After training, internal researchers
may choose to analyze their own samples.

_________________________



9/26/2012


27

Microfabrication Facility


T
he W. M. Keck Laboratory for the Fabrication o
f Microminiatur
ized Analytical
Instrumentation
(Keck Lab) of the Institute for Combinatorial Discovery provides the ISU and industrial communities
with access to state
-
of
-
the
-
art microfabrication technologies. With its approximately 1,000 square feet
of class 10/100 cle
an rooms, the Keck Laboratory supports all phases of microfabrication and its use
in fields ranging from analytical chemistry to cell biology. Drawing from affiliates across campus
and its resident support staff, expertise in micromechanics, microfluidics
, microchip arrays, biology,
chemistry, physics and microelectronics can be integrated in translating research ideas into
experimental reality.


Research capabilities in the laboratory include developing microanalysis systems, chip
-
scale
chromatography, mi
croelectrode assemblies, biochips and cell culture platforms. The laboratory also
houses equipment for optical lithography, wet and dry chemical etching and thin film deposition.
Analysis and testing equipment, computer workstations and drying and vacuum

annealing ovens
also are available.

_________________________



Microscopy and
NanoImaging
Facility


T
he Microscopy and NanoImaging Facility (MNIF) of the Office of Biotechnology provides a variety
of instrumentation, technical assistance, consultation
and training to individuals and groups of life
sciences and biotechnology researchers who want to use photomacrography, light microscopy,
scanning and transmission electron microscopy, cryopreservation, cytochemistry, autoradiography,
tomography, X
-
ray mic
roanalysis and image analysis. In addition to the round
-
the
-
clock open hours,
the MNIF carries out service work for both on
-

and off
-
campus researchers. The director and
assistant scientist of the MNIF are available for consultation and individual help.


Electron Microscopy

Electron microscopy instrumentation includes a 200kV JEOL 2100 scanning/transmission electron
microscope (STEM) with elemental analysis, cryo
-
imaging, tomography, and image analysis systems,
and a variable pressure JEOL 5800LV scanning

electron microscope (SEM) with elemental and image
analysis systems.


The JEOL 2100 STEM, with <1.4Å resolution, consists of the basic STEM, a Noran System 6 light
-
element energy dispersive x
-
ray spectrometer (EDS) and integrated software package for
comp
uterized control. The digital microscope and analytical system allow elemental analysis of the
9/26/2012


28

composition and structure of specimens with a nanometer resolution. Special features include a
darkfield/brightfield detector (STEM), hi
-
angle tilt holders for

tomography, cryo
-
preparation system
and holder for cryo
-
TEM imaging, and two Gatan digital cameras (1K side mount and 2K bottom
mount) for image recording, as well as image analysis software.


Ancillary equipment available for preparation of specimens for

electron microscopy include an
Edward’s 502A vacuum evaporator, Denton critical point apparatus, Denton Desk II sputter coater, a
Pelco Biowave microwave processing unit, propane jet freezer, two new Reichert UC6
ultramicrotomes, two Reichert ultracut S u
ltramicrotomes (one with FCS cryo
-
sectioning system) and
a new Leica glass knife maker.


The digital JEOL 5800LV SEM with 35Å resolution, operates at either high (30
-
15) or low (10
-
0.3) kVs
and at either high or low pressures to allow for the observation

of both fixed and fresh specimens.
Cryopreservation, X
-
ray microanalysis and image analysis are available for special specimens.
Images are captured using the analySIS ADDA II digital system with OSIS Pro software.


Light Microscopy

Light microscopy ins
trumentation includes: a Zeiss Axioplan II compound microscope with
AxioCam color and B/W digital cameras and the following optical modes


bright
-
field, phase
-
contrast, polarizing, dark
-
field, fluorescence and Nomarski (DIC). In addition, this microscope

has
an Apotome for creating thin optical slices; an Olympus stereomicroscope with reflected and
transmitted light sources and a high
-
resolution digital color camera; dissecting microscopes; a Leitz
microspectro
-
photometer / fluorometer; and Olympus compou
nd microscopes, one with a digital
camera. Microscopes with digital cameras have image analysis capabilities.


Preparative equipment and space for light microscopy include: fixing and processing hoods; paraffin
and resin embedding areas; rotary
-
, cryo
-

an
d ultra
-
microtomes, knife maker, knife sharpener,
Vibratome, microwave, vacuum oven and centrifuges.



Specialized Rooms

The 24
-
room MNIF, in addition to the microscope and microtomy suites, has two specimen
preparation labs; a copy room housing a Bencher

photo duplication system and macro photography
equipment; a computer suite; a cryoprep lab next to STEM room; an autoradiography/
in situ

hybridization and developing lab containing an isotope incorporation hood, balance, rotary
microtome, tissue culture s
haker, refrigerator, oven and processing sink and area; a propane
-
jet
cryopreparation lab with ultralow freezer for substitution; a small prep room with dishwashing sink,
deionized water system and autoclave; a conference room with a library; and a four
-
ro
om complex
for teaching.

9/26/2012


29


Instruction

An Individual Module Training Program (IMTP) was started in Spring 2010 to replace the three
graduate
-
level courses in microscopy that were taught for many years. IMTP trains individuals to
specifically process and
visualize their research materials using only the methods and
instrumentation to accomplish their objectives. This program allows an individual to begin the IMPT
within a short time after an initial consultation and signed acceptance of the training condi
tions.
Costs for IMTP include technical training assistance and instrument, lab and materials fees. The
length of an IMPT depends on the individual’s abilities and aptitudes and the complexity of the
training. Individuals may contact the MNIF director o
r supervisor for further details and/or to
schedule a consultation.

_________________________



Molecular Printing Facility


A new tool for scientific research called the Nano eNabler
TM

from BioForce Nanosciences, Inc., is
available for use in the Roy J. Carver Laboratory for Ultrahigh Resolution Biological Microscopy of
the Institute for Combinatorial Discovery.


The Nano eNabler
TM

system is a multifunctional surface patterning platform

for dispensing attoliter
to femtoliter volumes of biomolecules, nanoparticles and other liquids onto a wide variety of
surfaces. The system prints spots and lines from 1 to 60 microns with a 100msec printing cycle, 20 nm
stage resolution, 50 mm XY travel

and multiplexing ability. This new technology is being applied to
a variety of research fields, and the whole spectrum of application of this technology is still being
explored.



Printable Materials



Proteins




Quantum dots



Nucleic acids




UV
-
curable adhesives



Lipids



Etchants



Colloids



Catalysts


Compatible Surfaces



Glass



Silicon



GaN



AlGaN




PDMS



Silanes



Hydrogels



Metals



Nitrocellulose



Alkanethiol
monolayers




Polystyrene


9/26/2012


30

Cell Patterning

By patterning substrates with sub cellular domains of proteins, it is possible to influence individual
cells in a variety of ways.
Signaling proteins can be precisely placed and cells grown on the surface
contacting deposited materials. Patterning cellular adhesion molecules and blocking the surrounding
area make it possible to create arrays of individual or small groups of cells. T
he highly flexible nature
of the instruments allows immediate changes to the patterning of a surface.


Biosensor Functionalization

The Nano eNabler
TM

system can be used to functionalize transducing domains in a large variety of
biosensors. Small spot size
s mean more testing domains on smaller tests.



Small Volume Biomolecular Assays

Biomarker detection and quantification are a good example of small
-
volume assays with applications
including cancer detection, staging, and monitoring, as well as toxicity de
tection.

_________________________



Nutrition and Wellness
Research Center


T
he Nutrition and Wellness Research Center (NWRC) is designed to facilitate research projects
involving human subjects, featuring a variety of research, laboratory space and
equipment for
controlled studies that involve diet, exercise and behavior change. Equipment may be used by
researchers to collect data on metabolic risk factors, body composition and/or physical fitness. An
exercise area with private locker room and shower

facilities provides convenient space for controlled
exercise studies. Exercise equipment includes a treadmill, three cycle ergometers and metabolic carts.


The NWRC is available for grant processing, pilot and research studies. Individual testing rooms ar
e
available to conduct a variety of clinical measurements. Two rooms are set up with metabolic carts
and can be used for assessing resting and exercise
-
related energy expenditure. Another room is
designated for body composition via BODPOD and PeaPod, and b
one densitometry via dual
-
energy
x
-
ray absorptiometry (DXA). An adjacent room is available for body composition assessment using
bioelectrical impedance analysis (BIA) and anthropometry. Two phlebotomy rooms are available for
collecting blood and other cli
nical data. The NWRC has a fully
-
equipped metabolic kitchen with a
professional oven, microwave ovens, two dishwashers, refrigerator/freezer, walk
-
in pantry, walk
-
in
cold room, walk
-
in freezer and an ice machine. Adjacent dining rooms provide capacity to s
erve
meals for up to 40 people simultaneously. Additionally, the on
-
campus facility has a fully equipped
kitchen, as well as a dining room with the capacity to serve meals for 24
-
40 participants
simultaneously, phlebotomy room and a private room for clinic
al counseling/interviewing.

9/26/2012


31

_________________________



Plant Transformation Facility


T
he ISU Plant Transformation Facility is supported by the department of agronomy, the Office of
Biotechnology and the Plant Sciences Institute. It offers research partne
rships for the genetic
transformation of crops. The target crops are corn, soybeans, rice and
Brachypodium distachyon
.

The
facility uses the Bio
-
Rad Biolistic Apparatus and
Agrobacterium tumefaciens

as the gene delivery
systems for transformation of corn immature zygotic embryos. The
Agrobacterium
-
mediated
transformation method is used in the soybean, rice and
Brachypodium

systems.


The facility provides expertise in corn, soybean, rice and
Brachypodium

transformation for on
-

and off
-
campus researchers. Products provided include transgenic callus, transgenic plantlets and transgenic
seeds. The facility also provides a variety of instrumentation, technical assistance, consultation and
training

to individuals and groups of plant sciences and biotechnology researchers who want to
conduct plant transformation. A graduate workshop entitled “Plant Transformation and Transgenic
Plant Analysis” (GDCB 542D) is given by the facility every spring semeste
r.


Equipment in the facility includes a Bio
-
Rad Biolistic PDS
-
1000/He Apparatus, dissecting
microscopes, Percival biological incubators, laminar flow hoods, a refrigerated shaker incubator and
an SZH10 Olympus fluorescent microscope with digital camera fo
r GFP detection.


Fees for services can be found at
http://www.agron.iastate.edu/ptf/

_________________________



Protein Facility


T
he Protein Facility provides equipment and expertise for the analysis,
characterization and synthesis
of proteins and peptides and is open to both internal and external investigators. The Protein Facility
is supported by the Office of Biotechnology, the Roy J. Carver biochemistry, biophysics and
molecular biology department a
nd the Plant Science Institute’s Center for Plant Genomics.

The following instrumentation is available in the facility:




Amersham
-
Pharmacia IPGPhor IEF unit



Amersham Pharmacia DALT 2D electrophoresis system



Amersham Pharmacia Image Scanner with transparenc
y module

9/26/2012


32



Applied Biosystems Model 494 Procise protein/peptide sequencer



Applied Biosystems DE
-
Pro MALDI mass analyzer



Applied Biosystems Q
-
Star XL quadrapole
-
TOF tandem mass spectrometer



(located in the W. M. Keck Metabolomics Research Laboratory)



Three

Beckman System Gold high
-
performance liquid chromatographs



Model 125A Analytical Solvent Module with Model 166 programmable UV detector



Model 110A Semi
-
prep/prep Solvent Module with Model 166 programmable



UV detector



Model 125S Microanalytical Solvent
Module with Model 166 programmable



UV detector and SC100 fraction collector



Beckman Coulter P/ACE MDQ Capillary Electrophoresis System



Biacore T100 Surface Plasmon Resonance Instrument



Biorad minigel and blotting apparatus



C.B.S. Scientific spot
-
picking

workstation with UV lightbox



Genomics Solutions ProGest



Jasco J
-
710 Spectropolarimeter



Molecular Dynamics Typhoon 9410



NanoDrop ND1000 Spectrophotometer



Savant SpeedVac Plus



Virtis Model 3.5L DBTZL Benchtop FreezeDryer (lyophilizer)


Software for the anal
ysis of 1D and 2D gels is also available.


The following services are offered.


Circular Dichroism

The facility provides circular dichroism (CD) spectroscopy as an optical technique to allow the
detection and quantitation of the chirality of molecular stru
ctures. The CD equipment also is
available as a user
-
operated instrument after a required training session.


High Performance Liquid Chromatography (HPLC)

The facility offers microanalytical, analytical and preparative HPLC purification of proteins and
peptides. The HPLCs also are available as user
-
operated instruments after a required

training session conducted by facility personnel.


MALDI
-
TOF Mass Spectr
ometry

The facility provides mass spectrometry services for pro
teins, peptides, glycoproteins,
oligosaccharides, oligonucleotides and other polymer
s using a matrix
-
assisted laser
9/26/2012


33

desorption/ionization time
-
of
-
flight (MALDI
-
TOF) mass spectrometer. The mass
spectrometer also is
available as a user
-
operated instrument after a required training session.


Molecular Interactions

A Biacore T100 Surface Plasmon Resonance instrument is available for measuring affinity and
kinetics of molecular interactions. The Biac
ore T100 is also available as a user
-
operated instrument
after a required training session.


Peptide Synthesis

The facility can do both large
-

and small
-
scale peptide synthesis, including the synthesis of
phosphopeptides, peptides containing unusual amino
acids and multiple antigen peptide systems
(MAPS) for vaccine production or monoclonal antibody production. The facility also has the
capability to synthesize combinatorial peptide libraries.


Protein/Peptide Sequencing

The facility provides N
-
terminal pro
tein/peptide sequence analysis of samples in solution or of
samples electroblotted onto polyvinylidene difluoride (PVDF) membrane. The facility personnel also
perform chemical and enzymatic digestion of proteins in solution or proteins blotted onto PVDF to

provide internal sequence information.


Q
-
Star Tandem Mass Spectrometry

The ABI Q
-
Star XL quadrapole
-
TOF tandem mass spectrometer is equipped with an oMALDI source,
providing a wide range of sensitivity. For both gel
-
based and chromatographic separations,

proteins
will be identified, when possible, by searching databases with both MS and MS/MS data using
Mascot software. For organisms which do not have complete protein databases,
de novo
sequences
from trypsin fragments can be obtained from MS/MS data. Dig
estion with other proteases is also
available to increase coverage when required. MS
-
based methods are also available for the
identification and mapping of post
-
translational modification of proteins. A data analysis
workstation containing the programs req
uired for the interpretation of mass spectra and database
searching is available in the facility. Data analysis can be conducted by individual investigators, with
assistance and training from facility staff.


In
-
gel Digestion/Peptide Mass Fingerprinting

Th
e facility provides in
-
gel digestion of protein samples from
1D or 2D gels. Gel spots can be
digested with a variety of enzymes including trypsin, Arg
-
C and Glu
-
C. The resulting peptides from
the digestion can then be analyzed by MS or MS/MS methods. The p
eptides from the digested
proteins can also be separated by HPLC for further analysis by N
-
terminal sequencing or MALDI
-
TOF. A UV lightbox and spot picking tools are available for manual gel processing.


9/26/2012


34

SDS
-
PAGE/Electroblotting

The facility provides
SDS
-
PAGE analysis of proteins for purity and molecular weight estimation and
western blotting to nitrocellulose or to PVDF for immuno
-
detection and protein/peptide sequencing,
respectively. Stained gels (Sypro Ruby
®
, Coomassie Brilliant Blue, silver, etc.)

can be scanned and
analyzed in the facility. The SDS
-
PAGE equipment also is available as a user
-
operated service after a
required training session.


2
-
D Gel Electrophoresis

The facility provides two
-
dimensional electrophoresis by separating proteins in th
e first dimension
according to charge [isoelectric focusing (IEF), followed by separating the focused proteins in the
second dimension according to molecular weight by SDS
-
PAGE]. The proteins may be visualized by
staining with Coomassie Brilliant Blue R250
, silver stain or fluorescent dyes. These spots can be
excised for further analysis or the 2D array can be analyzed for differences in protein quantity or in
proteins present in the gel. 2D gels also can be electroblotted to PVDF or nitrocellulose membrane
s
for further analysis. The 2D electrophoresis equipment also is available as a user
-
operated service
after a required training session.


Isoelectric Focusing (IEF)

The facility provides IEF as a method for separating proteins based on isoelectric point
prior to SDS
-
PAGE. The IEF equipment also is available as a user
-
operated instrument after a required training
session, allowing researchers to perform the second dimension in their own labs.


2
-
D Gel Analysis

SameSpots from Nonlinear Dynamics allows for t
he alignment and analysis of 2
-
D gels in a short
amount of time and returns data that shows the expression of proteins under different biological
conditions. The software presents a list of the most significantly changing spots within a set of gels,
allowi
ng for the rapid screening of the protein spots that may be of the most interest in a set of gels.
These spots can then be further analyzed by other equipment in the Protein Facility (trypsin digestion
followed by peptide mass fingerprinting or internal se
quencing, direct N
-
terminal sequencing of the
blotted gels or MS/MS using the Q
-
Star tandem mass spectrometer). This package has the ability to
align the gels for complete spot matching. SameSpots is also available for individual use.


Image Scanning and A
nalysis

A Typhoon 9410 Variable Mode Imager is available for scanning of 1D and 2D gels and for phosphor
imaging. A screen eraser is available for erasing phosphor imaging screens. The scanner is equipped
with three lasers and can scan gels stained with Cy

dyes (2D
-
DIGE gels), Sypro, ProQ and Deep
Purple fluorescent gel stains, as well as the common visible stains like silver and Coomassie Blue. The
facility also has a flatbed scanner with transparency module for scanning gels and blots. Gel analysis
9/26/2012


35

softwa
re is available for analyzing 1D and 2D gels, and Amersham’s Decyder Program is available
for analysis of DIGE gels. The Typhoon is available for user
-
based operation as well.

_________________________



qPCR Consultation Services


T
he qPCR Consultation
Service provides in
-
person and on
-
line consultation for comprehensive qPCR
theory and assay design assistance. All steps are discussed and/or printed out as easy
-
to
-
follow
processes for immediat
e in
-
lab use.


Services offered:



Basic information/qPCR
theory and math



Primer
-
probe design assistance



Identification of appropriate reagents, master mixes and machine platforms for



One
-

and Two
-
Step qPCR, including LCM
-
qPCR



MIQE
-
based RNA isolation and other MIQE guideline concerns, DNAse treatment


and re
verse transcription reaction formulation suggestions and guidance



Nucleic acid quality assessment and quantity measurement suggestions and guidance



Processing of global assay parameters using ISURF software #03407



Consultation regarding detection and avoid
ance of RT and PCR inhibition for all



sample types and isolation methods



File system creation and initial qPCR test plate set
-
up printouts and consultation



Processing of test plate results into final set
-
up parameters and procedural printouts for


fina
l sample qPCR


Excel spreadsheets custom
-
created for E
AMP
-
corrected data analysis and graphing.


All plant and animal species considered.


For more information on fees and services, contact the manager.


_________________________



Sensory Evaluation Unit


T
he Sensory Evaluation Unit of the Nutrition and Wellness Research Center provides facilities and
9/26/2012


36

expertise for the sensory evaluation of food research products and/or ingredients.


The unit’s facilities include a computerized ten
-
booth testing area, a pa
nelist training room, a sample
preparation area, and an adjoining food science and human nutrition laboratory equipped for
measuring food color, texture and viscosity.


Services include sensory project design; panelist recruiting, screening, and training;
data collection;
graphic presentation of data; and analysis and interpretation of data.


Analytical tests available include discrimination tests, descriptive analysis and time intensity.
Consumer tests include product preference and acceptance.

__________
_______________



Roy J. Carver Laboratory for Ultrahigh Resolution Biological Microscopy



T
he Roy J. Carver Laboratory for Ultrahigh Resolution Biolo
gical Microscopy located in the
Molecular Biology Building provides an atmosphere for the development of
interdisciplinary
research between the life and physical sciences. Researchers can use the instrumentation housed in
the laboratory to perform optical and scanning force imaging of their samples. Housing is available
for students working on projects in t
he laboratory. In addition, the Carver Lab has a fully equipped
cell culture facility and a data processing center where experiments can be analyzed and the results
copied onto CDs for use in researchers’ home laboratories.


Optical Workstation

The
workstation consists of an inverted Nikon Eclipse 200 microscope with bright
-
field and
differential interference contrast optics, fluorescence and wavelength separation to two digital
cameras. Software controlling the optical workstation is designed to aut
omate image acquisition. The
fluorescent system on the workstation has filter sets for DAPI, FITC, CY3/TRITC, CY5, GFP, CFY and
YFP. Images are stored on a hard drive and are available for export via the Internet and CD. The
Nikon Eclipse is equipped with
high numerical aperture objectives from 2X to 100X.


Hyperspectral Workstation

The latest addition to the laboratory is an Optical Insights hyperspectral microscope. Designed
specifically to eliminate problems inherent in fluorescence microscopy, this sys
tem allows spectral
separation of defined objects in the data set of imaged specimens. This workstation consists of the
Optical Insights instrument attached to an inverted Nikon Eclipse 2000 equipped with a Photometrics
Cascade 512B digital camera. The s
ystem has a wide range of customized fluorescent filter cubes and
9/26/2012


37

microscope objectives. This system has software specific for hyperspectral data acquisition and
analysis, in addition to the latest MetaMorph (7.0) imaging software which allows 4D viewing
and 3D
measurements.


Additional hyperspectral and MetaMorph analysis software is installed on computers in the
laboratory’s data processing room.