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Indiana University Bloomington

Program Resources

Our program is committed to providing students and faculty with access to modern facilities that support vigorous research programs. The biochemistry program has full access to resources including state-of-the-art instrumentation of the departments of biology, chemistry, optometry, psychology, physics, and the Medical Sciences Program.

graduate studentCenter for Genomics and Bioinformatics
The Center for Genomics and Bioinformatics provides state-of-the-art equipment to perform genome wide analysis. The genomics laboratory is equipped with high throughput robotics and DNA chip micro array technology. CGB staff members assist researchers in devising and carrying out DNA chip micro array research projects that have genomics and bioinformatics components.

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Macromolecular Crystallography Facility
IU has state-of-the-art macromolecular X-ray crystallography facilities on campus. Researchers have access to two RAXIS IV + detectors and two X-Stream cryosystems. Furthermore, researchers at IU are members of the Molecular Biology Consortium, which has a synchrotron beamline at the Advanced Light Source in Berkeley. All IU macromolecular crystallographers and their students have access to the new beamline for collection of high-resolution crystallographic data.

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Cryo-Electron Microscopy Facility
A recently purchased state-of-the-art JEOL JEM 3200FS transmission electron microscope (TEM) is shared between the departments of Biochemistry, Chemistry and Biology. This instrument is designed for low dose, low temperature imaging and tomography of biological materials. The electron microscope is also equipped with an energy filter for zero-energy-loss imaging (for biological samples), elemental imaging and electron energy loss spectroscopy (EELS), a high angle annular dark field scanning TEM (HAADF-STEM) detector for Z-contrast imaging and an energy dispersive X-ray (EDX) spectrometer. Though these add-ons are mainly used for materials science applications, recent work has begun to explore the use of such materials science instrumentation with biological materials and the electron microscope here at IU is ideally suited for such explorations. The facility is also equipped with an FEI Vitrobot for robotic vitrification of isolated macromolecular assemblies. The manager of the TEM will assist with initial feasibility studies and project design, data processing and analysis and training users of the instrument.

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IUB Flow Cytometry Core Facility
The IU Bloomington Flow Cytometry Core Facility (FCCF) offers flow cytometry analysis and cell sorting services. It houses the FACS Aria II, a state-of-the-art sorter/analyzer, the COPAS Select, a Drosophila embryo and large particle sorter, the FACSCalibur, a four-color analyzer, as well as Z2 Coulter counter technology used for determining cell concentration and size distribution. Services include technician assisted sorting, as well as training for the four-color analyzer and Coulter instruments. Help with experimental design is also available. The facility maintains a workstation with flow cytometry data analysis software, and also has a copy of this software for use outside of the facility. More information about instrumentation, services, and fees can be found at our website.

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Indiana Molecular Biology Institute
The Indiana Molecular Biology Institute has two state-of-the-art facilities designed for use by multidisciplinary research groups. The DNA facility provides DNA sequencing and genetic fragment analysis on Applied Biosystems 3730 automated sequencing systems, as well as instrumentation and expertise for polymerase chain reaction, electroporation, phosphor imaging and densitometry. The Microscopy facility provides expertise and instrumentation for electron microscopy on a JEOL 5800LV scanning electron microscope with a digital image archive system and a JEOL 1010 transmission electron microscope. The microscopy facility also maintains all necessary equipment for the preparation of samples including stereoscopes, polymerization ovens and ultramicrotomes for transmission electron microscopy, and a critical point dryer and a sputter coater for scanning electron microscopy.

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Light Microscopy Imaging Center
The Light Microscopy Imaging Center, located in Myers Hall 059, 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. Microscopy training, graduate level courses, and day-to-day help are available.

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Mass Spectrometry Laboratory
Since 1965, the Mass Spectrometry Facility (MSF) has provided top-quality mass spectrometry support to the faculty research groups of the Indiana University-Bloomington. The MSF is one of many Technical Support Facilities in the Chemistry Department; its faculty advisor is Dr. David Clemmer. The laboratory is located in rooms A411 between Electronics Instrument Services and the Indiana University Molecular Structure Center. The MSF has two full-time mass spectrometrists to assist students with designing experiments, recording data, and analyzing mass spectra. It is equipped with a Thermo MAT-95 high resolution magnetic sector mass spectrometer (EI, CI, ESI, and FAB sources) and a Waters LCT with LockSpray ESI source for accurate mass analyses. The MSF also has two Waters CapLC/LCT electrospray/time-of-flight mass spectrometers and an Agilent 1200/6310 ESI-quadrupole system for LC-MS analyses, a Bruker Biflex MALDI-TOF, and an Agilent 6890/5973 GC-MS available for walk-up use by IU researchers (after appropriate training). A complete description of its capabilities and fee structure can be found at its website.

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Molecular Structure Center
The Molecular Structure Center (MSC) is a service and research facility in the Department of Chemistry. This center has an international reputation in small molecule crystallography. Staffed by three professional crystallographers, a computer specialist, and other support personnel, the laboratory has developed unique instrumentation and computer systems for use in single-crystal structural analysis.

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Molecular Visualization Facility
The Molecular Visualization Facility consists of more than six Silicon Graphics and other UNIX client workstations, several high-speed Silicon Graphics servers, and a variety of related peripherals. All workstations and servers are interconnected by a high-speed switched network. The MVF also maintains and develops the StereoView Room, a high-technology seminar room equipped to provide molecular visualization in 3D virtual reality and other multimedia presentations for up to 30 researchers.

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Nanoscale Characterization Facility
The Nanoscale Characterization Facility (NCF) is housed on the ground floor in Simon Hall, our multidisciplinary sciences building, and has 2000 square ft of laboratory space and 1300 square ft of clean room space. The NCF will provide faculty, staff, postdoctoral fellows, and graduate and undergraduate students with state-of-the-art instrumentation for generating and characterizing materials having features with nanometer dimensions. We expect the NCF to grow over the next three to five years as a university resource, and the instrumentation within the facility will be available to all research groups at IU.

In the NCF, we presently have a scanning electron microscope (Zeiss SMT 1430) with a nanopattern generation system (Nabity NPGS) for imaging and electron beam lithography. An atomic force microscope (Asylum Research MFP3D) interfaced with a laser scanning confocal microscope (Nikon TE2000-U) provides simultaneous surface probe and optical characterization. Thin metal films can be deposited with a four-source thermal evaporator (Linde Auto 306 Vacuum Coating System). A 300-kV cryogenic transmission electron microscope (cryo-TEM, JEOL JEM-2200FS) is currently being installed in the facility, and a field-emission scanning electron microscope (FEI Quanta 600 FEG) has recently been ordered.

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National Center for Glycomics and Glycoproteomics
Supported by NIH-National Center for Research Resources (NCRR), the National Center for Glycomics and Glycoproteomics (NCGG) at Indiana University is devoted to the development of new methodologies and instrumentation in glycomics, proteomics, and glycoproteomics. In collaboration with researchers in biology and biomedical sciences at the national and international level, NCGG promotes applications of new methodologies in medical research and clinical diagnosis. The Center currently houses a number of sophisticated instruments that are used by staff scientists, postdoctorals, graduate students and undergraduates.

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Nuclear Magnetic Resonance Laboratory
The Indiana MetaCyt Initiative , as part of the MetaCyt Biochemical Analysis Center has underwritten the acquisition of an 800 MHz Varian Inova NMR spectrometer with a cryogenic probe system. This instrument will be placed along side an existing 600 MHz Varian Inova NMR spectrometer with a cryogenic probe. These two instruments will be located on the ground floor of Simon Hall and will comprise the MetaCyt Biomolecular NMR Laboratory, a state-of-the-art facility for biomolecular structure and dynamics determination.

The Chemistry Department Nuclear Magnetic Resonance facility consists of seven Varian spectrometers in three laboratories with an experienced staff of professional Ph.D. scientists. The undergraduate teaching laboratory contains a full featured 200 MHz instrument. The Chemistry Department NMR lab features four Varian spectrometers from 300MHz to 500MHz for work on liquid samples. The 400 MHz spectrometers feature 4-nucleus probes and gradients for multidimensional and multinuclear NMR experiments. The 500 MHz instrument is a full featured 3 channel instrument with a variety of probes and 3 axis gradients. It is used to perform almost any modern NMR experiment from demanding BioNMR experiments to diffusion studies and microimaging.

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Physical Biochemistry Instrumentation Facility (PBIF)
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 a round the clock 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; a Packard 1600TR Scintillation Counter for quantitation of assays and substrates; and a BIA CORE 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.

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Simon Hall - MSBSimon Hall Multidisciplinary Science Building
Simon Hall is Indiana University's newest flagship research building. The completion of construction and occupancy occurred in the fall of 2007. This building has an interdisciplinary science theme - housing faculty from many different scientific disciplines that have overlapping interests. Designed to encourage interdisciplinary study in structural biology, biochemistry, bioanalytical chemistry, bioorganic chemistry, biophysics, nanobiology/nanofabrication, biocomplexity, microbial biochemistry, and molecular virology, the facility redefines boundaries and broadens scientific advancement.

In addition to over 220 researchers, the building houses several instrumentation facilities such as the DNA sequencing facility, NMR facility, Nanofabrication facility, Cryo-electron microscopy facility, and Physical Biochemistry Instrumentation Facility.

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Yeast-Two-Hybrid Facility
Genetic analysis has been a very successful tool in modern biology. We have now identified the genes responsible for important cellular and developmental processes in many organisms and, in many fields, attention is being focused on determining the molecular function of the proteins these genes encode. Y2H is a mature technology to determine molecular interactions between proteins. Two major advantages of this system are its accessibility to laboratories with expertise in molecular genetics (the only starting materials required are cDNA clones of the genes of interest) and, because the protocols are largely the same for all proteins regardless of the species of origin, the ability to perform experiments in a high throughput environment. A major disadvantage of the Y2H technology is it requires a great deal of work to set up (it requires a many types of media, suitable libraries, and expertise in large-scale yeast transformation). Once established, however, it is relatively little work to perform additional assays. Therefore, the Indiana METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc., has provided funding for the establishment of a yeast-two-hybrid interaction facility at Indiana University.

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Instructional Computing Facilities
Information Technology Group (ITG) is just one of our eight technical services in Chemistry, but it is unique in that it serves and assists the whole of Chemistry - faculty, staff, and students - in their academic, administrative, and research-based computing activities

Many devices exist within the Chemistry network, including printers, Apple systems, Windows workstations/servers, UNIX servers, HPC clusters, climate control/monitoring systems, STC labs, acquisition systems, and instrumentation systems. ITG is responsible for monitoring, securing, and maintaining all 2014 of these devices on and off the network.

ITG maintains sixteen departmental servers that provide web servers, SQL database management, point of sales, application/database serving, file serving, backups, domain/email administration, and print serving to the department. The group also utilizes a system that monitors network security for Chemistry workstations. ITG supports appliances in the Chemistry Building, Simon Hall SB1, and at Wrubel Computing Center Machine Room for chemists.

ITG also supports specialized clusters of Intel/Windows and Macintosh systems. These systems include not only the extensive software available to students in the public clusters, but specialized Chemistry software as well. ITG also maintains a two Shared Resources Centers with peripherals such as scanners, printers, wide bed plotters, laminators, film recorders, and projectors. These resources are used by other departments such as Biology, Math, Life Science, IN Geological Survey, and Physics.

ITG serves as the technical leader in the development of the Chemistry Department's Computer Assisted Learning Method (CALM) .  CALM is a distant outreach learning tool designed to provide students with enhanced problem-solving skills through directed inquiry. Based upon a Socratic pedagogy, it presents students with individualized, algorithmically-generated questions on a given topic that provide immediate feedback. Currently CALM supports several active Indiana University COAS Courses assisting more than 3200 students in a school year.  Outreach to high school chemistry programs has been emphasized within Indiana, reaching over 200 schools, but CALM can also be found in schools as far away as New Jersey.  With a focus of harnessing the power of the educational community as a whole, CALM is an evolving tool that empowers teachers with the means of accessing the rapidly growing impact of technology to enhance the learning environment, at no cost to the teachers or students that use it.

The Biology Department Biocomputing Office is headed by Don Gilbert, who is internationally known for molecular biology software that he develops, and for the IUBio Archive server of biology software and data.

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Genetic Resources and Special Facilities
The Department of Biology also houses the National Drosophila and FlyBase, an Internet data base for Drosophila genetics. Additional biological equipment and facilities include confocal and Electron Microscope Facility, Fermentation Facility, Greenhouses and cultivation fields, a Herbarium, and a Microbiology Stock Culture Collection.

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Instrument Centers
The departments of Biology, Physics and Chemistry house an impressive number of instrumentation centers such as:

Computer Support Groups:
The Research Systems Engineering Group (RSEG) in the Department of Chemistry and the Biocomputing office in the Department of Biology provide support for the nearly 600 computer systems located in the departments as well as assisting with specialized networks necessary to interconnect the varied systems. In addition, these groups specialize in the design and construction of unique computer interfaces for data acquisition and instrument control. A specialized laboratory at the RCEG facility allows the design and construction of multilayer printed circuit boards as well as the use of modern surface-mount components.

Electronic Instrument Services:
The Departments of Chemistry and Biology each house Electronic Instrument shops that provide services for the design, modification, construction, and repair of chemical and electronic instrumentation. The shops are equipped with modern CAD, assembly, and test equipment. The Chemistry Department provides space and support for students and researchers to work independently or in conjunction with the engineering staff.

Glass Shop:
Both routine and unique glassware are fabricated in the Glass Shop, staffed by a professional glassblower. Specialized equipment—including two lathes, drills, saws, and glass grinding and polishing equipment—are available.

Mechanical Instrumentation Shop:
The Chemistry Department also contans a Mechanical Instrument Services Facility (MIS), a well-equipped machine shop staffed by seven instrument makers. In addition to mechanical lathes and milling machines, three computer-driven (CNC) milling machines are used in the construction of original, unique, or commercially unavailable apparatus for the department. Apparatus design, sheet metal shops, and heliarch welding, as well as high vacuum construction and leak testing facilities, are also available. A fully equipped student shop is available, and instruction is given to students who wish to construct their own equipment.

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Library Resources

The Indiana University Bloomington Libraries have been recognized by peers as the top university library in the country, a national library association announced in spring 2010.

Indiana University has six science libraries on campus. You will have access to subscriptions to hundreds of electronic journals of interest to scientists, many with direct links to the abstracting and indexing databases. A variety of other databases are provided on public computers through the IU libraries, including the Beilstein CrossFire plus Reactions and the Gmelin databases.

The print collection of the Chemistry Library covers the major chemistry and biochemistry journals, reference sources, and books which are housed in a modern facility staffed by professional librarians and several assistants. Reference service is also provided by graduate students enrolled in the Chemical Information Specialist program.

The Life Sciences Library in Jordan Hall is an exceptionally rich resource for students and faculty who need access to the biological and biomedical sciences literature. Approximately 750 current journal subscriptions are maintained, and the entire collection numbers over 100,000 volumes. In addition, patrons can conduct on-line literature searches on any of a large number of computer generated databases on the biological sciences literature.

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