1. Home //
  2. Research //
  3. Research Cores/Resources

Research Cores/Resources

The Research Cores and Research Resources provide access to state-of-the art, specialized equipment and related expertise to support the research activities of investigators throughout the University of Notre Dame and beyond. Such facilities also enhance the education of undergraduate students, graduate students, and postdoctoral fellows. By expanding the base of sponsored research and providing a strong research infrastructure, these cores and resources promote collaborative research among investigators within the institution and with other scientists throughout the country.

The list below represents the current offerings from several colleges on the Notre Dame campus. We hope to expand the list and provide more University-wide facilities to enhance research collaboration opportunities.

Research Cores (Re-Charge Centers)

The research cores listed here are all available for use by University investigators (and in some cases, external customers). Use of these cores should be coordinated through the contact person listed with each core description.

Genomics and Bioinformatics Core Facility

We provide sequencing and microarray services including consulting for appropriate experimental design, use of technology, and data analysis. The scientific equipment available in this facility include an Applied Biosystems 3730xl automated capillary sequencer, Agilent 2100 Bioanalyzer, Ambion flashPAGE Fractionator System, Affymetrix GeneChip System, Roche NimbleGen MS 200 scanner, and Roche 454 Genome Sequencer FLX pyrosequencer. Our computing facilities are equipped with high performance hardware, a collection of software packages and in-house pipelines, and a team of trained bioinformaticians who are dedicated to analyzing large-scale data sets including data from genomic, metagenomic, gene expression, and proteomic projects.

Service offered include:

  • Sanger-based automated capillary sequencing and fragment length analysis
  • Agilent Bioanalyzer sample quality analysis
  • PicoGreen and RiboGreen fluorescence-based sample quantitation
  • Affymetrix 3’ gene expression and exon tiling microarrays
  • Roche NimbleGen gene expression, comparative genomic hybridization, and resequencing microarrays
  • Microarray data analysisPathway and network analysis
  • Roche 454 GS-FLX sequencing including genome shotgun sequencing, amplicon sequencing, and transcriptome sequencing
  • High and low throughput sequencing and assembly, and genome annotation
  • Phylogenetic analysis
  • Large-scale data storage, accessing, and management
  • Bioinformatics training the form of seminars and workshops
  • Customized consulting and solutions to bioinformatics problems

Please contact the Managing Directors for more information:

The Center for Nuclear Magnetic Resonance Spectroscopy

The Center for Nuclear Magnetic Resonance (NMR) Spectroscopy at the University of Notre Dame supports new and ongoing research in chemistry, chemical engineering, biochemistry, molecular biology and related fields. Our instrumentation enables us to perform state-of-the-art multinuclear, multidimensional high-resolution NMR experiments at various field strengths and temperatures to determine the molecular structures and dynamics of a wide range of compounds.

Determination of molecular structure and dynamics of a wide variety of compounds (e.g. proteins, nucleic acids, carbohydrates, synthetic polymers, natural products, lipids, macrocyclic polyethers) are among the applications of this instrumentation.

For more information on the Center for NMR Spectroscopy, please contact Jaroslav Zajicek, Ph.D. | 574-631-9111.

The Center for Research Computing

CRC has expertise in areas spanning engineering in the aerospace and automotive industries, high performance computing in mining and exploration, information systems for the clinical health sector, and expertise in life and geospatial sciences. This diverse portfolio enables CRC to address the needs of faculty, students and other customers in new or unique areas of research and development.

CRC builds software to world's best practice standards to ensure a long operational life. CRC values open standards, maintainability, extensibility, agile development with continual client feedback and thorough testing. For maximum utility, software is supported by comprehensive documentation, sample data, tutorials and training.

Here are some descriptions of services that CRC provides on a recharge basis:

  1. Programming (Research programmers)
    CRC is the perfect partner for any scientific or technically-focused software project. CRC has broad software development experience across a wide range of research areas, and technologies. CRC's unique structure means that technically minded software developers and subject matter experts are brought together with software best practices and the latest domain knowledge to deliver successful customized solutions to real-world problems. CRC's accomplished and talented software developers and domain experts and computational scientists, including proficient mathematicians, scientists, engineers and designers, can design software and project management processes tailored to research and development needs, no matter how demanding.
  2. Computational scientist
    Computational scientist can be hired by faculty to help constructing mathematical models and quantitative analysis techniques and using computers to analyze and solve scientific problems. In practical use, they  typically apply  computer simulation and other forms of computation to problems in various scientific disciplines. computational scientists are assisted by research programmers, and usually their services require some research programming effort.
  3. GIS and Visualization
    CRC is a core facility that provides GIS (Geographical Information Systems) and Visualization service for ND researchers. GIS is a  term that describes any information system that integrates, stores, edits, analyzes, shares, and displays geographic information. In a more generic sense, GIS applications are tools that allow users to create interactive queries (user-created searches), analyze spatial information, edit data, maps, and present the results of all these operations. Geographic information science is the science underlying the geographic concepts, applications and systems, and is taught in degree and certificate programs at Notre Dame as a common effort between CRC, Climate Change SRI and the Department of Civil Engineering at College of Science.
    CRC provides also scientific visualization support services.  Scientific visualization is an interdisciplinary branch of science primarily concerned with the visualization of three-dimensional phenomena (architectural, meteorological, medical, engineering, biological, etc.), where the emphasis is on realistic renderings of volumes, surfaces, illumination sources, and so forth, very often with a dynamic (time) component.
  4. HPC Services
    High-performance computing (HPC) uses supercomputers and computer clusters to solve advanced computation problems. Today, computer systems approaching the teraflops-region are counted as HPC-computers. CRC has a group of HPC engineers and parallel application developers who can assist in developing, scaling and tuning parallel applications as well as maintaining faculty owned clusters. These services will be charged for all the faculty owned clusters that are procured after July 1, 2010. Maintenance services for all the clusters that are open for sharing with other users are free of charge. For more information please refer to the CRC Cluster Partnership Program and other policy documents.

Center for Zebrafish Research

The Center for Zebrafish Research (CZR) at the University of Notre Dame is housed in approximately 3,000 square feet in the Galvin Life Science building. The CZR consists of eight double-sided racks and 38 single-sided racks that allow for a flexible arrangement of tanks from 1.5 to 8 liters in size. Racks are maintained on multiple, independent life-support systems to minimize a catastrophic event to the entire system. A separate room houses the zebrafish nursery. The approximate total capacity of the CZR is 120,000 adult zebrafish (one of the largest systems in the Midwest).

The CZR provides several services including the generation of ENU-induced mutants and screening of mutant phenotypes, the introduction of morpholinos into embryos and some adult tissues to assay for loss-of-function phenotypes of specific target proteins, and microinjection of DNA constructs and subsequent analysis of transgenic lines.

For more information, contact David Hyde, Ph.D. | 574-631-8054.

The Fluorescence Activated Cell Sorting (FACS) Facility

The BD Biosciences FACSAria III cell sorter is BD’s most advanced cell sorter. The sorter is equipped with 405nm, 488nm, and 633nm lasers and is capable of up to 9 color simultaneous detection.

Multiple sorting options are available: populations can be sorted in up to 4 tubes which can also be temperature controlled by use of an available waterbath heated sorting block. Populations or single cells may also be sorted directly onto slides, or into standard or customized plates.

Operation of the cell sorter is performed only by the core manager and must be arranged in advance by appointment. Please contact Dr. Rashna Balsara or Dr. Charles Tessier

Sample Preparation Guidelines:

Discuss in advance the following:

  1. What type of cells are to be sorted
  2. What fluorochromes will be used (test or know your flurochrome & antibody combination well)
  3. What is the percentage of the desired cells from the original population
  4. Whether the sorting needs to be done into tubes or into a plate or slides

Your cell density should be 10-20 x 106 cells/ml and filtered through a 35-40µm filter. Limit the amount of serum in your final suspension buffer to < 2% as high serum concentrations can cause distortion of light scatter signals. The healthier the cells the better they will hold up after the sorting process. You should also provide a collection medium that is appropriate for your applications to be added to the collection tubes so that cells remain as healthy as possible after the sort.

Please note: Sorting is a complex process and efficiency and quality of the sort is determined by a number of different factors. Therefore, it is strongly recommended that all sorting projects be discussed with the core manager well in advance to ensure that the desired results are attainable. Even still, it is important for users to understand that different cell types sort differently, so users should expect that multiple sorts may be necessary to optimize conditions to their individual experiment.

The Freimann Life Science Center

The Freimann Life Science Center (FLSC) at the University of Notre Dame is a state-of-the-art animal research facility with 30,000 square feet of flexible use space.  The FLSC is fully accredited and registered, and has a highly trained, professional staff.
The staff is certified and available to assist with surgical and other technical procedures.  The FLSC has individually ventilated caging for rodents, the capability for housing non-human primates, and is home to the Lobund-Wistar rat model of metastasizing prostate cancer.

For more information on the FLSC, contact Dr. Mark Suckow | 574-631-6085.

Mass Spectrometry and Proteomics Facility

The University of Notre Dame Mass Spectrometry (MS) Facility provides instrumentation and expertise for the analyses of compounds ranging from small organic molecules to large biomolecules with applications in the areas of metabolomics, proteomics, and lipidomics. In early 2009, an expanded and upgraded facility will relocate to newly renovated space in Stepan Hall of Chemistry and Biochemistry.

Available instruments include a Bruker Autoflex III MALDI-TOF-TOF, Bruker MicrO-TOF II time-of-flight (TOF), Bruker MicrO-TOF QII quadrupole time-of-flight (Q-TOF), Micromass QuattroLC triple quadrupole, and JEOL AX505HA and GCMate magnetic sector mass spectrometers. A Bruker HCT Ultra ion trap equipped with electron transfer dissociation and interfaced with a Dionex Ultimate 3000 2DLC system will be available in mid-2009. These instruments include ionization methods such as EI, CI, FAB, ESI, nanoESI, and MALDI. Analyses include low resolution MS and MS/MS, high resolution MS and MS/MS, and accurate mass measurements. Hyphenated techniques include GC/MS, LC/MS, and LC/MS/MS via capillary GC, HPLC, capillary HPLC, and ultrahigh pressure LC systems. Proteomics applications (post-translational modifications, peptide mass fingerprinting, in-gel, and in-solution protein digests), metabolomics studies (LC/MS and LC/MS/MS), and imaging MS (TLC separations and tissue sections) experiments via MALDI-TOF and MALDI-TOF-TOF are also possible.

For more information on the MS Facility, please contact William Boggess, Ph.D. | 574-631-4027 | website.

Molecular Structure Facility

The Molecular Structure Facility at the University of Notre Dame provides for X-Ray structural studies of small (ca. 2kDa) molecules.  The Facility has the capability to examine a wide range of molecules from “light atom” biologically relevant to metal-complexed compounds which can be readily analyzed using non-destructive techniques.

Applications of these techniques include molecular and atomic identification (can differentiate atom types), molecular interactions (solid state), electrostatic interactions, and Van der Waals interactions. The Molecular Structure Facility provides an accurate starting point for molecular simulation (computational) studies and stereochemical analysis is essential for understanding bioactive molecules.

The Facility houses three instruments: two of which produce molybdenum wavelength radiation and one of which produces copper radiation.  Copper radiation is ideal for stereochemical analysis of light atom structures.  All of the instruments utilize area detector format readout and allow for a high-throughput of samples.

For more information on the Molecular Structure Facility, please contact Allen Oliver, Ph.D | (574) 631-5935.

The Notre Dame Integrated Imaging Facility

The Notre Dame Integrated Imaging Facility (NDIIF) is a new state-of-the-art research core that houses and integrates three areas of Notre Dame imaging expertise: electron microscopy, optical microscopy, and small animal imaging.

In addition, the NDIIF supports an interactive network of research groups, who are connected by their interest in imaging technology, and allow them to cross-fertilize ideas and form interdisciplinary collaborations. The NDIIF makes available an integrated suite of sophisticated microscopes and imaging stations that enable the expert users to attack the most complex modern research problems and, equally important, the resident professional staff (technicians and research specialists) to guide non-expert users and allow them to conduct experiments that were previously beyond their limits. Below is a list of capabilities and contacts for early 2009. To see updates, please visit nd.edu/~ndiif.

Electron Microscopy:

  • Field Emission Scanning Electron Microscope
  • Dual Source Focused Ion Beam
  • Transmission Electron Microscope (end of 2009)

Contact Alexander Mukasyan, Ph.D., Research Professor – Electron Microscopy | 574-631-9825.

Cell Microscopy:

  • Deconvolution Fluorescence Microscope
  • Spinning Disk Confocal Microscope with TIRF
  • Laser Scanning Confocal Microscope
  • Two-photon Laser Scanning Confocal Microscope

In Vivo Imaging:

  • Optical Animal Imaging, Fluorescence, Bioluminescence
  • Planar X-ray Imaging
  • Micro-CT X-ray Animal Imaging Station

Contact: W. Matthew Leevy, Ph.D., Research Assistant Professor – Biological Microscopy | (574) 631-1683.

Histology Core:

Services include tissue processing and staining, including a variety of immunohistochemical stains. Histopathological interpretation is available.

Contact Sara Chapman | 574-631-3813 | website.

The Notre Dame Nanofabrication Facility

Housed in recently completed certified cleanroom space within Stinson-Remick Hall at Notre Dame, the NDNF includes approximately 9,000 net square feet (white space) of cleanroom. The facility is approximately 50% ISO class 5 (class 100), 40% ISO class 6 (class 1000) and 10% ISO class 7 (class 10,000). The facility includes a comprehensive toolset supporting CMOS, III-V, and MEMS fabrication. Key capabilities include contact and projection optical lithography, electron-beam direct write lithography with demonstrated resolution to ≤4 nm, in-house mask making for rapid turn-around of designs, reactive-ion etching (RIE), inductively-coupled RIE (ICP-RIE, DRIE), plasma etching, thermal and electron-beam evaporation, dc and magnetron sputtering for metal deposition, plasma-enhanced chemical vapor deposition (PECVD), atomic-layer deposition (ALD), atmospheric-pressure CVD, low-pressure CVD, and magnetron sputtering for dielectric deposition, automated chemical-mechanical polishing (CMP), rapid thermal annealing and constant-temperature furnace thermal processing, and general wet chemistry.; Several significant upgrades are planned in 2010/2011, including the addition of a high-throughput, high-resolution electron beam lithography system (Vistec EBPG-5200), two additional sputter deposition systems and an additional metal evaporation system, a plasma ALD deposition system, an additional ICP-RIE, an Olypmus LEXT 3D laser confocal microscope, an enhanced conventional optical microscopy suite (Olympus), and a P7 profilometer.

For more information contact the director, Patrick Fay, Professor
Department of Electrical Engineering
University of Notre Dame
261 Fitzpatrick Hall
Notre Dame, IN 46556
phone: (574) 631-5693

Research Resources

The research resources listed here are available to the University community. Use of these resources should be coordinated through the contact person listed for the resource.

The Center for Environmental Science and Technology (resource)

The Center for Environmental Science and Technology (CEST) is a common use analytical laboratory facility housing a wide array of instruments for chemical analysis and materials testing of environmental samples. CEST, housed in the Fitzpatrick Hall of Engineering, is a cooperative effort between Notre Dame's Colleges of Science and Engineering, fostering interdisciplinary environmental research and education by providing cutting-edge analytical technologies needed to address complex environmental problems. The center is directed by Professor Jeremy Fein, and has a seven-member advisory board. A full-time technical support staff maintains the instruments and provides training and supervision for all users. CEST users come from a wide range of university departments, including Biological Sciences, Civil Engineering and Geological Sciences, Chemistry and Biochemistry, Chemical and Biomolecular Engineering, Anthropology, and Physics, and users include graduate students, faculty, staff, postdoctoral researchers, and local high school students. In addition, each year dozens of undergraduate students use CEST as part of course work, independent study, and/or through formalized REU (Research Experience for Undergraduates) programs. CEST analytical capabilities for characterization of both inorganics and organics are extensive, and include inductively-coupled plasma - optical emission spectrometry, uv-vis spectrophotometry, gas chromatography - mass spectrometry, liquid chromatography, organic carbon analyses, elemental analysis for C,H,N,S, and O, ion chromatography, and stable isotope ratio mass spectrometry. CEST also maintains a number of instruments for materials characterization, including surface area and pore characterization with a BET analyzer, and suspended particle charge with a zeta potential analyzer. Additionally, CEST annually awards a number of Bayer graduate fellowships to support interdisciplinary research in environmental science and/or engineering.

For more information contact
Jeremy Fein, Professor, Director
152A Fitzpatrick Hall
Notre Dame, IN 46556
(574) 631-8376

Keck Center for Transgene Research (resource)

All use of Keck Center resources should be coordinated through Dr. Rashna Balsara | (574) 631-2958

Mouse Strains with altered hemostatic genes

The Keck Center has the largest repository of mice with alterations of hemostatic genes in the world (see attached list). Keck Center personnel are well versed in the varying phenotypes of these mice and are willing to work with other investigators that may find these gene-altered mice valuable for their research. Some mice in the inventory may be freely shared; others may require permissions from other investigators.

Analytical Ultracentrifuge (Beckman XL-I)

The reversible self-association of proteins, lipids, carbohydrates, and nucleic acids is a frequently encountered phenomenon in the biological realm, but the characterization of such events can be difficult. Using analytical ultracentrifugation (AUC), the sedimentation equilibrium behavior of such biomolecules can be examined to address the existence of dimeric and/or higher order multimers in a variety of solution conditions. This methodology draws on the fact that the equilibrium distribution of an analyte in a centrifugal field is related to its buoyant molecular weight. In our instrument, the gradient of analyte can be assessed by either absorbance optics (200–800 nm) or interferometry. Any biomolecule of mass greater than 200 Da can be examined by this method. AUC can also be performed in sedimentation velocity mode. In this case, the speed at which an analyte sediments in a centrifugal field can provide an estimate of the, size, shape, and homogeneity of the species. Sedimentation is particularly useful for determining if a change in the conformation of the macromolecule (as reflected by a change in its hydrodynamic volume) attends ligand binding.

Circular Dichroism (CD) Spectrometer (Aviv 202 SF)

CD spectroscopy exploits the chiral nature of biological macromolecules and is grounded in the precept that chiral species interact differently with left- and right-circularly polarized light. The method is most frequently applied for assessing the secondary structure of proteins and peptides. A simple wavelength scan of a solution of the protein or peptide in the far ultraviolet range (195-240 nm), followed by software-assisted deconvolution of the resultant spectrum, can provide an estimate of the fractional conformer content, including alpha-helix, beta-sheet, beta-turn, and random coil contributions. The sample compartment can access temperatures ranging from 5 °C to 95 °C, a feature that can be used to generate melting curves at select wavelengths. The instrument is also equipped with a stopped-flow mixing module that can permit investigation of protein folding events that occur on timescales of 5 ms or longer.

Laser Capture Microdissection (LCM)

LCM allows for the isolation and purification of single cell tissue populations. A laser is focused through a microscope to capture specific areas of tissue, specific organs, or specific cells. The tissue samples can then be used for RNA preparations for gene analysis or other analyses. An Arcturus PixCell II system and Veritas system are in place.

The Keck Center has used this technique to capture normal, adenoma, and carcinoma samples from the same murine subject.  This method has provided very pure populations of cells for analysis.

Veterinary Ultrasound

Mice are anesthetized using isoflurane, and imaged using ultrasound technology by VisualSonics (Vevo 770).  Contrast agents can also be utilized for increased visualization of specific organs and other structures.
The Keck Center has successfully used ultrasound to visualize tumor growth, neovascularization, monitor pregnancy, assess atherosclerotic plaque build-up, etc. in murine models.

Veterinary Endoscope

Mice are anesthetized using isoflurane and the Storz endoscope is inserted for visualization of the intestinal track.  Various tips are available for use on the endoscope which allow for injecting various reagents, measuring tissue mass, tissue collection, and polyp removal.

The Keck Center has used this instrument for counting the number of masses, polyp removal and subsequent tissue analyses, and overall intestinal health observations.

Whole Animal Lung Resistance

Lung hyper-responsiveness can be measured using the plethysmograph (Buxco).  Whole body chambers allow the mice to move about freely.  An aerosol delivery system introduces irritants for challenge conditions.

The Keck Center has used this equipment to study asthma/lung inflammation in wild type and gene-altered mice.

Cell Culture Core

Gene-altered mice are a valuable resource. Cell cultures obtained from these altered mice may be invaluable in many studies. The Cell Culture Core of the Keck Center has mastered techniques to isolate pure populations of a variety of primary cell cultures. Among the cell types that can be isolated are mouse aortic and colonic endothelial cells, and splenic and bone marrow dendritic cells. These cells can be obtained from wild-type and/or gene-altered mice.

Fermentation

The Keck Center has two BioFlo 3000 benchtop bioreactors for conducting yeast fermentation. Yeast expression systems offer unique capabilities for protein production. Large quantities of protein can be produced in a very simple media.

The simplicity of the media, having one carbon and one nitrogen source, allows for total labeling of the protein with stable isotopes. This is especially useful for NMR and other protein characterization studies.