Last updated: Feb. 23, 2009
Boilerplate text for some IUB facilities of relevance to Biology proposals
Order of facilities listed:
Biology Computing Facilities
Center for Genomics and Bioinformatics
CISAB Lab
Cultivation and Bioprocessing Facility
Drosophila media kitchen
Flow Cytometry Core Facility (FCCF)
Herbarium
Indiana Molecular Biology Institute (IMBI) Microscopy Facility
Light Microscopy Imaging Center
Physical Biochemistry Instrumentation Facility (PBIF)
Computing facilities and equipment in the Department of Biology
For more information: Jeremy Niemann (jniemann@indiana.edu)
The Department of Biology supports 10 web, database, file and backup servers, over 700
desktop and laptop computers, and site licenses for nucleic acid and protein sequence
analysis software as well as two ABI 3730 DNA analyzers, gel imaging equipment and
software, and SEM, TEM, confocal and deconvolution microsocopes. Color laser and
poster printing is made available, as are 35 mm, flatbed, and high-capacity scanners and
high-speed bulk printing and reprographics. The university makes several multiprocessor
clusters and a 1.6 petabyte storage system available to all researchers, and maintains 24x7
phone support, as well as separate offices for bioinformatics, and support for statistics
and mathematical software.
Center for Genomics and Bioinformatics (http://cgb.indiana.edu)
For more information: Jennifer Steinbachs (stein@cgb.indiana.edu)
The Genomics Laboratory contains 12 bench stations and standard equipment for a
fully operational molecular lab, including gel- electrophoresis systems and power
supplies, refrigerators, -20°C freezers, 10 Revco -80°C freezers, three micro-centrifuges,
balances, pH meter, autoclave, 3 fume hoods, 1 sterile flow bench and hood, mechanical
and electronic pipettes, repeater pipettes, water baths, incubators, 2 environmental
chambers, etc.
In addition, the Genomics Laboratory houses a vast amount of equipment specific to
genomics research:
 Roche Genome Sequencer FLX
 GeneMachines Hydroshear DNA Shearing Device
 Beckman Coulter Z series particle counter
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Misonix Sonicator* S4000 Homogenizer
Veritas Microdissection Instrument model 704 with IR capture laser and UV
cutting laser with epifluorescence
Beckman Coulter Biomek FX
2 MJ Research Tetrad thermal cyclers and 10 Eppendorf Mastercyclers
ThermoSavant speedvac vacuum concentrator for microtitre plates
Beckman Coulter Allegra 6R tabletop centrifuge
Beckman Coulter Allegra 25R tabletop centrifuge
Eppendorf Microcentrifuges Model 5424 and Model 5804 tabletop centrifuge
Molecular Devices Spectra Max 190 microplate spectrophotometer
Kodak 440CF Image station
GeneMachines Omnigrid microarray printer
Axon Instruments GenePix 4000A microarray scanner and GenePix 4200A
microarray scanner
2 BioMicro Systems MAUI 4-bay hybridization stations
Stratagene Mx3000P Quantitative PCR Thermal Cycle
Agilent Bioanalyzer 2100
NanoDrop ND-1000 Spectrophotometer
Turner BioSystems TBS-380 Mini Fluorometer
CGB Computing Infrastructure: The CGB Core Computing Facility provides access to
a wide variety of software for bioinformatics analysis, primarily through our BioPortal
project. Currently the environment is home to 50 enterprise class systems ranging from 216 cores and 8-32GB memory each. Approximately 232 terabytes of raw storage capacity
is available.
CISAB Lab (http://www.indiana.edu/~animal/research/ABLAB/CISABLab.html)
For more information: Rose Stewart (stewarra@indiana.edu)
CISAB’s Animal Behavior Lab provides bench space, supplies and specialized
equipment to IU faculty, post-docs, graduate students and affiliates interested in
incorporating molecular and endocrine techniques into their animal behavior research. It
also has grown to play an integral role in student training for CISAB’s NSF-supported
summer “Research Experiences for Undergraduates (REU)” program, our NIH-funded
training grant, Common Themes in Reproductive Diversity (CTRD) and graduate-level
animal behavior techniques courses. Specific techniques performed in the lab (or in
collaboration with partner labs at IU) include: hormone extraction, EIA, RIA, DNA/RNA
extraction, PCR, RT-PCR, gel electrophoresis, DNA sequencing, microsatellite
genotyping and RFLP/SNP genotyping. The lab is staffed by one full-time research
associate who oversees the lab and assists users with their research goals. CISAB’s
Animal Behavior Lab is non-profit, and researchers are charged only for the supplies and
reagents they use, as well as a 15% equipment maintenance fee.
Cultivation and Bioprocessing Facility (http://www.indiana.edu/~bcbf/index.htm)
For more information: Pengyun Li (lip@indiana.edu)
1. Purchase equipments and hiring.
Spend about ~$100,000 on equipments and reagents. Now E.coli, yeast, insect
cell and mammalian cell culture can be routinely carried out in CBF.
2. Collect or make molecular or cell biological reagents
CBF has 16 different cell lines, 17 different vectors, which can meet most of
molecular and protein biochemistry experiment purposes.
3. Routinely provide gene cloning and protein purification services to other labs.
CBF has set up close relationship with more than ten groups and finished or
carrying on more than 20 projects for those groups.
4. More than 5 students or research associate are trained in CBF for gene cloning,
protein purification or cell culture.
5. CBF has been providing consultant or protocols to other groups on gene cloning
or protein production.
6. CBF has been exploring new methods in gene cloning and protein production. A
set of ligation independent cloning(LIC) vectors which have His, GST, MBP,
therodoxin or SUMO-tag have been made in facility, which will facilitate cloning
and fusion-tag screening greatly. Another sequence ligation independent cloning
(SLIC) methods and vectors are being exploring in CBF, which can put traditional
a few weeks cloning work into just one reaction. A new mutagenesis strategy has
been developed in CBF, more than 7 mutants has been made for other groups by
that methods.
7. CBF is collecting gene resources for many popular reagents. CBF is currently
providing competent cell and TEV protease to other labs at extremely low price.
Taq DNA polymerase, MMLV-RT, T7 DNA polymerase, pFu DNA polymerease,
phusion DNA polymerase et al is under developing in CBF.
8. Administration of some highly used equipments such as Cell cracker, sonicators.
Drosophila media kitchen
For more information: Kathy Matthews (matthewk@indiana.edu)
Media is prepared in a 61.3 sq. m. (660 sq. ft.) kitchen located in the basement of Jordan
Hall. It is equipped with a 379 liter (100 gal.) electric water-jacketed kettle with a
dedicated water heater and metered water dispenser. Food is pumped from the kettle
outlet to the chamber of a manually operated vial filler that dispenses it into 100 vials at a
time. Media is stored in an adjacent 10.2 sq. m. (110 sq. ft.) constant temperature room
until use. Used vials are cleaned in a separate departmental glassware washing facility."
Flow Cytometry Core Facility (FCCF) (http://facs.bio.indiana.edu/)
For more information: Christiane Hassel (chassel@indiana.edu)
The Indiana University-Bloomington FCCF houses four flow cytometry
instruments: the FACSAria II, FACSCalibur, COPAS Select, and Z2 Coulter counter.
The FACSAria II is a cell sorter and analyzer that can sort up to 70,000 events per second
and can analyze up to 15 parameters. It has four lasers (488nm, 633nm, 407nm, and
355nm), four nozzle sizes (70, 85, 100 and 130µm), aerosol containment and temperature
control systems, and an Automated Cell Deposition Unit (ACDU) for slide and multiwell plate sorting. The FACSCalibur analyzer is a two laser system (488nm and 633nm)
with a sample injection diameter of 150µm, and can analyze up to four colors. It has an
automated loader function and can perform limited low speed sorting. The COPAS
Select is a Drosophila embryo and large particle sorter with a single 488nm laser tunable
to 488 and 514nm excitation wavelengths. It is capable of sorting cells and organisms
from approximately 50-350µm in diameter. The Z2 Coulter Counter measures cell
concentration and size. The IU-Bloomington FCCF also has personnel and faculty to
assist in experimental design and a full-time experienced technician who operates and
trains users on the analyzer instruments.
Fees for the instruments are as follows; the FACSAria II may only be run by the
dedicated FCCF technician at a fee of $80/hour. The FACSCalibur is available for
training and users may choose to either self-run after training or have the dedicated FCCF
technician run their samples. The fee for training and tech run samples is $80/hour, while
self-running the instrument is $50/hour. Fees for the COPAS are $30 for set up and
$40/hr for sorting. Rates for the Z2 counter are $15/hour. Discounted rates are given for
new method set up and new lab training. Fees are subject to change.
Herbarium (http://www.bio.indiana.edu/resources/herbarium/index.html)
For more information: Eric Knox (eknox@indiana.edu)
The Indiana University Herbarium is a research museum located in the Smith Research
Center on East Tenth Street, and contains over 140,000 specimens. It is the official
herbarium for the State of Indiana, and holds the collections of Charles Deam, which
served as the basis of his work, The Flora of Indiana. The herbarium is the specimen
repository for faculty and student researchers at Indiana University, and is an essential
campus facility enabling specimen-based research at Indiana University, because by
convention most organizations loaned specimens only to established herbaria, not to
individual researchers.
Indiana Molecular Biology Institute (IMBI) (http://imbi.bio.indiana.edu/
Microscopy Facility
For more information: Barry Stein (bstein@indiana.edu)
The Microscopy Facility at the Indiana Molecular Biology Institute is located in room
040 of Myers Hall. It contains a JEOL 5800LV scanning electron microscope and a
JEOL 1010 transmission electron microscope. There is equipment for the preparation of
samples including polymerization ovens and ultramicrotomes for transmission electron
microscopy, a critical point dryer and a sputter coater for scanning electron microscopy.
The facility is open to use by all researchers. Instruction is provided for the use of any of
the equipment.
Transmission Electron Microscope (JEOL JEM-1010)
The JEOL JEM-1010 transmission electron microscope has a magnification range of 50X
- 500KX and an accelerating voltage range of 40KV - 100KV. Images can be taken with
both a Gatan MegaScan 4K CCD camera and with a plate camera that uses 8.3 x 10.2 cm
negatives. This electron microscope provides an excellent means for the ultrastructural
analysis of biological samples, but it is also capable of selected area electron diffraction.
Other features include a tilting goniometer sample stage for electron diffraction and 3-D
imaging, a minimum exposure operation mode to prevent electron beam damage to
fragile samples, and a measurement function for the quantification of lengths and areas of
structures within samples. The computer aided - menu driven operation makes it
extremely user friendly. A FEI Vitrobot is used to fast freeze samples for cryo-TEM.
These samples are transferred to the TEM by a Gatan Model 626 system.
Scanning Electron Microscope (JEOL JSM-5800LV)
This microscope is outstanding for studying surface features of biological and nonbiological specimens. It can operate at high vacuum using either secondary or
backscatter electrons to view dry specimens or at low vacuum allowing for the
observation using backscatter electrons to view specimens with high water content or low
conductivity. The magnification range is from 18x to 300,000x. Resolution is 3.5nm at
high vacuum. Samples up to 8 inches in diameter can be viewed. Images can be
recorded by 4x5 inch film or digitized. Accelerating voltages are from 0.3 to 30 KV.
Sample Preparation: Leica Ultracut T and Sorvall Porter-Blum MT 2 Ultramicrotomes,
Denton DV502 Vacuum Evaporator, Balzers Critical Point Dryer, Polaron Sputter
Coater, and all other standard prep. equipment.
Light Microscopy Imaging Center (http://www.indiana.edu/~lmic/index.html)
For more information: Jim Powers (japowers@indiana.edu)
The Indiana University Light Microscopy Imaging Center, located on the Bloominton
campus, exists to provide user-friendly access to state of the art light microscopy for the
entire IU research community. The facility includes widefield, scanning and spinning
disk confocal, deconvolution, high throughput screening and micro-dissection
microscopes, all with digital imaging capabilities. The facility is available 24 hours a
day, seven days a week on a very reasonable fee for use basis. User fees include training
on the microscopes, help with experimental design, help with image processing and
quantification, and day to day help with imaging problems. For more information,
including information on access policy and fees, see the Imaging Center website,
(www.indiana.edu/~lmic).
Physical Biochemistry Instrumentation Facility (http://www.indiana.edu/~physbio/)
For more information: Todd Stone (tstone@indiana.edu)
The Physical Biochemistry Instrumentation Facility supports research in structures,
stabilities, and interactions of biomolecules. Thorough hands-on training, state-of-the-art
instrumentation, and analysis software are available 24 hours a day, and equipment time
may be booked at any time via a web-based reservation system. The PBIF is directed by a
Ph.D. scientist who assists researchers in the design, implementation, and analysis of
experiments and results.
The PBIF features optical instruments for the study of structure, folding, binding
thermodynamics and kinetics, and quantitation experiments: a Perkin Elmer LS50B
Luminescence Spectrometer; a Jasco J-715 Circular Dichroism Spectrometer with Peltier
sample temperature control; an Amersham Biosciences Typhoon 9210 Variable Mode
Imager equipped with the versatile ImageQuant TL analysis package; and a Varian Cary
100 Bio UV / Visible Spectrometer for oligonucleotide melting studies. Other available
instrumentation includes: a Microcal Isothermal Titration Calorimeter (VP- ITC); a
Beckman Coulter Optima XL-I Analytical Ultracentrifuge with both absorbance and
interference capabilities for probing size and associative properties in solution; a Packard
1600TR Scintillation Counter for quantitation of assays and substrates; and a BIACORE
3000 Surface Plasmon Resonance instrument that is capable of detailed, direct binding
measurements and kinetic analysis of nucleotides and proteins. A recently purchased
Malvern Zetasizer Nano-S dynamic light scattering instrument for quick molecular size
characterizations has also been added to the PBIF capabilities.