University of Michigan Center for Gastrointestinal Research

UMHS Home

Search
Home   |
| | | |


Protein Localization, Identification and Folding Core

In Vivo Animal and Human Studies Core

Molecular Biology Core

Microbiome and Metabolomics Core
Services
Facilities and Resources
Discounts

Microbiome and Metabolomics Core

Facilities and Resources

Overview:

The Microbial Systems Core Laboratories of the Host Microbiome Initiative (HMI) utilizes approximately 2800 sq. ft. of laboratory space in MSRB I, fully equipped for molecular biology experiments, next generation sequencing (NGS) and advanced microorganism cultivation practices. The space has areas set up for the following applications: DNA purification, PCR, qPCR and RT-PCR, sequencing, bacterial cultivation, tissue culture and animal necropsy. Additional laboratory space provides benches for molecular and microbial research; and desk space for postdoctoral research fellows, graduate students and technical support personnel. High throughput liquid handling via BioMek FXp as well as Eppendorf EP Motion robotic systems and a MultiFlo device are maintained in the laboratory. The lab is equipped for high throughput sequencing with three Illumina MiSeq sequencers.


   The germ-free mouse colony, directed by Dr. Kathryn Eaton, is housed in the basement of the Life Sciences Institute building (which is within the medical school complex; 5 minute walk from Dr. Young's office). It contains four 50-cage isolators for housing breeding mice, 12 additional isolators for housing experimental mice, 10 laminar flow hoods to house mice for short-term experiments, and two Tecniplast Isocage® racks capable of housing 100 self-contained sterile units. The facility is fully equipped with transfer equipment, autoclave cylinders, and other equipment necessary to maintain germ-free conditions. The colony is staffed by three trained and experienced full-time technicians and several part-time technicians. In addition, a surgical laminar flow hood is equipped with a Nikon SMZ1500 stereo zoom microscope with ring lighting and slide warmer, surgical supplies, slide warmers, cages, and all necessary equipment for aseptic embryo transfer and manipulations of germ-free mice.


   The Metabolomics Core laboratories are housed at the Brehm Tower on the UM campus. The labs are fully outfitted, flexible, and were custom built for the metabolomics facility-intensive use. Two main laboratories occupy approximately 2000 sq. ft. of space with walk-in cold rooms and freezers, four chemical hoods, a room dedicated for sample processing, and a service corridor for nitrogen generators and pumps. There is shared space for equipment storage (freezers/refrigerators) and supply storage. The facility provides access to modern mass spectrometric techniques and state-of-the-art instrumentation to address a wide range of research problems.


   Center Microbiome/Bioinformatics Support Core is located in 6504 MSRBI (same building as the Microbial System Core lab of the HMI). The Bioinformatics support lab space is about 200 ft with 15 ft of bench space. It is equipped with 120 C and -80 C freezer, RT-PCR machine, Eppendorf microcentrifuge, Mother E-Base electrophoreisis device and Epel 96 and Nanodrop spectrophotometer. The lab is equipped with 2 Apple Ma Pro with 2-6 Core xenon processors running at 2.66 GHz and 32 GB RAM, and 1 Dell Desktop PC. Center Core lab has full access to the HMI for computational medicine and Bioinformatics computer cluster.

Microbiome Core Laboratory
The Host Microbiome Initiative (HMI) utilizes approximately 3500 sq. ft. of laboratory space in MSRB-1, fully equipped for molecular biology experiments, next generation sequencing (NGS) and advanced microorganism cultivation practices. The space has areas set up for the following applications: DNA purification  PCR, qPCR and rtPCR, sequencing, bacterial cultivation, tissue culture and animal necropsy. Additional laboratory space provides benches for molecular and microbial research as well as provide desk space for postdoctoral research fellows, graduate students and technical support personnel. Clinical study coordinators also have desk space within the laboratory.

Cultivation:
The HMI provides support for advanced bacterial cultivation in a shared 588 sq. ft. cultivation facility within MSRB-I. The HMI maintains two Coy anoxic and hypoxic chambers for the targeted cultivation of anaerobes and micro aerobes. In addition to the cultivation chambers two sparging stations are also available for Hungate technique cultivation.

Germ-free & Gnotobiotic Mouse Facilities

Animal:
The HMI utilizes a federally approved Unit for Laboratory Animal Medicine (ULAM), with facilities that maintain specific pathogen-free (SPF) conditions and clean rooms for performing small animal surgery. The germ-free mouse colony, directed by Dr. Kathryn Eaton, is housed in the basement of the Life Sciences building. It contains 4 50-cage isolators for housing breeding mice, 12 additional isolators for housing experimental mice, 10 laminar flow hoods to house mice for short-term experiments, and two Tecniplast Isocage® racks capable of housing 100 self-contained sterile units.  The facility is fully equipped with transfer equipment, autoclave cylinders, and other equipment necessary to maintain germ-free conditions.  The colony is staffed by three trained and experienced full-time technicians and several part-time technicians. In addition, a surgical laminar flow hood is equipped with a Nikon SMZ1500 stereo zoom microscope with ring lighting and slide warmer, surgical supplies, slide warmers, cages, and all necessary equipment for aseptic embryo transfer and manipulations of germ-free mice.  The colony provides germ free mice, germ free housing, and animal handling and services on a fee-for-service basis.

In addition to the germ free mouse colony, approximately 75,000 square feet of modern animal facilities are available in the Medical Science Building Complex. The facilities are managed by ULAM, and include all types of housing for immunocompromised and transgenic animals, and access to animal surgery and veterinary clinical services. 

Computer:
HMI personnel have multiple personal computers with software for data analysis and DNA/protein sequence analysis. These personal systems are connected to the University of Michigan Ethernet backbone and have high-speed access to other systems on campus and on the internet. Statisical packages (including SAS and R) are housed on the personal computers.

Connections are available to high-performance computing clusters on campus including those at the Center for Computational Medicine and Bioinformatics (CCMB), which supports a computing infrastructure that consists of a number of computing clusters and independent computing and application servers all connected to a high-speed campus network. These servers have access to storage systems that collectively total greater than 200 TB of storage. Battery backup, fault monitoring, data snapshots, site-distinct mirroring and off-site backups are part of our comprehensive backup/recovery strategy. CCMB has a large and diverse research computing base, including the National Center for Integrative Biomedical Informatics (NCIBI), one of seven NIH-funded National Centers for Biomedical Computing; the Molecular and Behavioral neuroscience Institute (MBNI); and the Medical School Information Systems (MSIS). MSIS provides servers, virtual servers, and storage and networking connectivity for the UMHS backbone. CCMB and MSIS together have developed research IT support for the UM Sequencing Core especially for next-generation sequencing technologies and data anaylsis needs; with access to an 80 core computer cluster with over 100 TB of dedicated storage. NCIBI/CCMB computational infrastructure consists of database servers, computer servers, virtual servers, storage backup and recovery, and staff.

The computing sites are connected by a campus network backbone consisting of a mixture of Gigabyte and increasingly 10-Gigabyte Ethernet. The campus network is connected to the Internet and Internet2. University of Michigan researchers and CCMB are also affiliated with several computing consortia, such as computational infrastructure initiatives.

Bioinformatics and Bioinformatics Support Core

In addition to the computational support provided through the HMI, bioinformatic support will be provided through Dr. Patrick Schloss. The bioinformatics component of the Schloss lab consists of Unix and Macintosh computers, which are attached to the university network.  The network is maintained by a staff of technicians that are experienced in Windows XP, UNIX, and MacOSX.  A MacPro computer runs the laboratory server, which has a quad core 3.0GHz processor and 16GB of RAM.  In addition computational work will be run on 5 dedicated HP ProLiant DL1000 Multi Node Servers each containing 4 DL170 G6 servers.  Each server consists of 2x E5520 Intel Nehalem quad core CPUs, 96GB RAM, and a 500GB 7.2k SATA harddrive.

Dr. Schloss also has access to the resources at the Center for Computational Medicine and Bioinformatics (CCMB), which supports a computing infrastructure that consists of a number of computing clusters and independent computing and application servers all connected to a high-speed campus network.  These servers have access to storage systems that collectively total 200+ TB of disk.  The computing infrastructure is divided between three sites: the Palmer Commons building (PC), the Michigan Academic Computing Center (MACC), and the Center for Advanced Computing (CAC) in the College of Engineering.  These sites are geographically separated on the University of Michigan campus in Ann Arbor, Michigan.  Battery backup, fault monitoring, data snapshots, site-distinct mirroring and off-site backups, are part of our comprehensive backup/recovery strategy.  CCMB has a large and diverse research computing base, including the National Center for Integrative Biomedical Informatics (NCIBI), one of seven NIH-funded National Centers for Biomedical Computing; the Molecular and Behavioral Neuroscience Institute (MBNI); and the Medical School Information Systems (MSIS). MSIS provides servers, virtual servers, and storage and networking connectivity for the UMHS backbone.  CCMB and MSIS together have developed research IT support for the UM Sequencing Core especially for next-generation sequencing technogies and data analysis needs;  with access to an 80 core compute cluster with over 100 TB of dedicated storage.  NCIBI/CCMB computational infrastructure consists of database servers, compute servers, virtual servers, storage, backup and recovery, and staff.

The computing sites are connected by a campus network backbone consisting of a mixture of Gigabit and, increasingly, 10-Gigabit Ethernet. The campus network is connected to the Internet and Internet2.  University of Michigan researchers and CCMB are also affiliated with several computing consortia, such as Blue Water petascale computing initiative, CaBIG, TeraGrid, BIRN, and other grid computing and computational infrastructure initiatives.

Major Equipment:
The HMI laboratory space occupies a central shared area with PCR prep rooms, media preparation hoods, microscopes and centrifuges. The HMI laboratory is outfitted to perform molecular biological and microbiological research with centrifuges, refrigerators, freezers, tissue culture hood, CO2 incubators, thermocyclers, electorphoresis equipment, computers and basic bench equipment. There is a Nikon Eclipse 50i microscope set up for fluorescence microscopy coupled to a SPOT cooled CCD digital camera. The laboratory has several PAGE horizontal and vertical electorphoresis units with power supplies, four thermocyclers (with programmable gradients), a Roche LC96, an Agilent 2100 bioanalyzer, a Nanodrop for DNA quantification and quality control, as well as various other conventional items (pH meters, balances, water purification systems, water baths, incubators, microcentrifuges, etc) that are fully adequate for support of all laboratory core services. Glassware dishwashers and autoclaves are housed in the central equipment room on the same floor as the research lab. High throughput liquid handling via four Eppendorf EP Motion robotic systems and a MultiFlo device are maintained in the laboratory. The lab is equipped for high throughput sequencing with three Illumina MiSeq sequencers.

Other:
Other investigators at the University of Michigan have equipment that is readily available including biorobots, capillary DNA sequence equipment and image-analysis workstations. The Uof M campus has extensive core facilities for confocal microscopy, flow cytometry, a DNA array manufacturing/analysis, peiptide/oligonucleotide sysnthesis, DNA sequencing and quantitiative PCR analysis. The DNA Sequencing Core on campus has multiple Illumina HiSeq platforms for additional sequencing capacity. The Sequencing Core also has facillities for genetic analysis and DNA array analysis (both GeneChip and spotted arrays). The Michigan Regional Comprehensive Metabolomics Resource Core led by Dr. Charles Burant is a key resource on campus that provides state of the art metabolomics analysis.

Scientific Environment:
The outstanding scientific environment at the University of Michigan will help ensure progress on this project. The HMI encourages interactions and collaborations among clinicians, basic scientists and clinical laboratory personnel on a variety of translational projects. These collaborations provide excellent perspective and insights on the bacterial and host aspects of proposed research projects . The HMI research laboratories are housed within multidisciplinary buildings with close ties to researchers in multiple departments/programs including Pharmacolgy, Genetics, Pediatrics, and other divisions within Internal Medicine.

Bioinformatics Support Core

Owyang Laboratory

Both Dr. Merritt Gillilland and the Bioinformatics Support Core are located in 6504 MSRB I on the Medical Campus of the University of Michigan in the laboratory of Dr. Owyang.  The Bioinformatics Support lab space is approximately 75 ft2 with 15 feet of bench space. 

Equipment

The Bioinformatics Support Core has the following equipment:  -20C freezer; PCR machine; Eppendorf microcentrifuge; Mother E-BASE electrophoresis device and E-gel 96; and 1 dual water bath.  The Bioinformatics Support Core has access to other shared equipment which includes: 4C refrigerator; -80C freezer; super speed refrigerated centrifuge; Mini-Beadbeater-16; two Bio-safety cabinets; BIO-RAD CFX Connect Real-Time PCR System; and a Nanodrop spectrophotometer.

Computers

The Bioinformatics Support Core has Apple and Windows computer systems.  The Core also has access to the Center for Computational Medicine and Bioinformatics (CCMB) computer cluster.  The CCMB cluster is a dedicated 32-node computing cluster managed by the College of Engineering's Center for Advanced Computing. The cluster is composed of dual processor Opteron nodes with 2-64 GB RAM/each (each having at least 2 CPUs or 2 cores).  Readily available software for Bioinformatics analysis includes the latest version of the bioinformatics pipeline mothur, the statistical packages R and Systat 13; Graph Pad Prism, and the Microsoft Office Suite. 

Office Space

Dr. Gillilland has a desk and Dell Desktop PC within the laboratory space of Dr. Owyang and access to office supplies and equipment.

Metabolomics Core

Laboratory

The Metabolomics Core laboratories are housed at the Brehm Tower on the UM campus. The labs are fully outfitted, flexible, and were custom built for the metabolomics facility-intensive use.  Two main laboratories occupy approximately 2000 sq. ft. of laboratory space with walk in cold rooms and freezers, 4 chemical hoods, a room dedicated for sample processing, and a service corridor for nitrogen generators and pumps. There is shared space for equipment storage (freezers/refrigerators) and supply storage. The facility provides access to modern mass spectrometric techniques and state-of-the-art instrumentation to address a wide range of research problems. The focus of the laboratory is on the characterization and quantification of small molecules with special emphasis on biomarkers, drugs, and drug metabolites. The facility offers training for independent operation of instruments as well as sample analysis by facility personnel.

The Biochemical Nuclear Magnetic Resonance Core, located in the C.C. Little Building, provides support and consultation in the planning, implementation and analysis of experiments performed on a state-of-the-art   high field 500 MHz NMR spectrometer.

The metabolomics laboratories are part of the University of Michigan Biomedical Research Core Facilities which supports the MRC2 administratively, supporting sample submission, billing and other interaction with researchers.

Computer

Laboratory computers are linked to a local area network for access to a wide variety of scientific, data analysis and word processing programs.  An automated data backup and recovery system is in place both on-site and at an off-site University server.

In addition to instrument specific and personal computers the untargeted metabolomics laboratory has a server-based Metabolomics Laboratory Information Management System (MetLIMS) that supports and integrates all analytical laboratory processes.  MetLIMS is the Laboratory Information Management System around which all of our lab activities revolve.  The objective of MetLIMS is to manage Compound and Sample inventory and to automate sample run and data processing while integrating samples, instrumentation and results.  MetLIMS has various user level authentications and in general allows users to manipulate and reuse the client, project, experiment and sample data. It has been built to cater to the needs of the lab personnel and has user friendly interfaces which allow the users to add, modify and search sample and compound related data.  A MetLIMS user can also create and run a sample worklist and document sample preparation details.  MetLIMS controls the injection sequence of samples; it has an injection queue for each instrument on the server and knows which sample is currently being injected. The 'MetworksMessaging' module of MetLIMS specifically allows the integration of the Masspecs and the data processing servers with MetLIMS and makes it possible for data to be available in close to real time.

Other

The untargeted metabolomics laboratory includes a library of over 1,000 authentic chemical compounds for reference.

Equipment

These include Sorvall centrifuge; Beckman Ultracentrifuge; 2 SpeedVac concentrators; -80C and -20C freezers and one refrigerator; chromatography cabinet; Thermo-Finnigan Spectrophotometer and multiple electrophoretic equipment.

1)         Two Agilent 6890 gas chromatograph (GC) equipped with HP5973 mass detector GC/MS system with electron impact ionization (EI) and GC/ECNI/MS and positive/negative ion capabilities. The instruments are equipped with an autosampler and an on-column injector. The GC/MS systems will be used to measure derivatized amino acids, low molecular polar and non-polar metabolites, nucleic acids and lipid metabolites.  In addition, this versatile instrument is capable of analysis of complex lipoproteins, glycolipids, sphingolipids and other small molecule analytes quantitatively.

2)         Two Agilent Triple Quadrupole mass spectrometers (6410 and 6490) coupled with Agilent 1290 UHPLC.  These instruments offer exceptional sensitivity for directed metabolomics in the MRM mode for lipids, amino acids and products of intermediary metabolism. They have the ability to perform both ESI and atmospheric pressure chemical Ionization (APCI) and can be utilized both for directed and undirected metabolomic analysis.

3)         An Agilent LC/MSD Time of flight mass spectrometer. This instrument has high mass accuracy and is ideal for directed and undirected metabolomic profiling of small molecules for accurate mass determination. It can also be utilized to perform both ESI and APCI.

4)         Three Quadrupole TOF instrument (Q-TOF) instruments coupled Agilent Rapid Resolution HPLC or UPLC which provide high sensitivity, high mass accuracy, high mass range, and rapid throughput
ideal for metabolomic profiling. This instrument has high mass accuracy and capability to perform tandem MS analysis making it ideal for both directed and undirected metabolomic studies. This can provide extremely valuable structural information and may simplify, for example, in determining complex metabolite structures.  Additionally, these instruments can be utilized for untargeted metabolomics.

5)         The Core also has an Agilent 6890 GC and a Jasco HPLC system equipped with variable UV detector, fluorescence detector, electrochemical detector and diode array detector.  Both instruments
have an autosampler. These instruments are capable of analyzing a wide variety of small molecules, preparing internal standards for GC/MS and LC/MS analysis and purifying the samples prior to injection into the mass spectrometer.

6)         The Core personnel have access to other MS facilities in campus which include Biomedical Mass Spectrometry Facility (http://sitemaker.umich.edu/mass-spectrometry/home) which has a Linear Ion
Trap mass spectrometer which offers the ability to perform multi-stage MS analyses. For example, fragments of a first generation fragment ion can be analyzed (MS2), and this process can be iterated (MSn). This can provide extremely valuable structural information and may simplify, for example, in determining complex metabolite structures. This facility also has a Thermo TSQ Quantum Triple Quadrupole Mass Spectrometer and a Waters Matrix-assisted laser desorption/ionization (MALDI) TOF ideally suited for MRM analysis of directed and undirected quantitative metabolomics.

7)         One ABSciex 5600 Triple TOF which will be used primarily for 'shotgun' lipomic analysis of samples. A state-of-the-art Varian 400 NMR spectrometer has pulsed field gradients, auto tune, auto shim and a 5mm ONE probe. Multinuclear capabilities allow the observation of most NMR active nuclei (e.g. 1H, 11B, 13C, 15N, 19F, 29Si, 31P, etc.). It is a "research grade" instrument capable of performing all of the solution NMR techniques commonly reported in the literature. Commonly performed experiments include simple spectra, T1 and T2 relaxation experiments, solvent suppression, selective decoupling and nOe experiments, as well as two-dimensional (2D) COSY, NOESY, HSQC and HMBC. Other experiments required by the user can be implemented with the aid and supervision of the spectroscopist.

8)         A state-of-the-art Varian 500 NMR spectrometer has pulsed field gradients, auto tune, auto shim, a 3mm ONE probe and a twelve slot sample changer robot. It is a "research grade" instrument capable of performing all of the solution NMR techniques commonly reported in the literature. Commonly performed experiments include simple spectra, T1 and T2 relaxation experiments, solvent suppression, selective decoupling and nOe experiments, as well as two-dimensional (2D) COSY, NOESY, HSQC and HMBC. Other experiments required by the user can be implemented with the aid and supervision of the spectroscopist.

Informatics Infrastructure

Database Servers:  Relational databases are at the core of many of the NCIBI applications. We currently operate MS-SQLServer, Oracle and MySQL RDBMS.  The production SQL Server currently hosts 15 databases, available 24x7 for public access. On average, 52 transactions occur on the server at any given period of time. 30+ databases are in development for SQL Server and Oracle.  The database sizes continue to grow, with the largest being 500 GB (Pubmed). In addition we also maintain private databases where data is only accessible to specific research personnel.  To efficiently support software development, we have separated the production database from the development and test servers. We routinely back up the production and development database to ensure the recoverability of individual databases. Database auditing and authorization procedures are used on a continuous basis to monitor the security health of the NCIBI database servers. The computer hardware is a mixture of 4-core and 8-core HP servers with 16-32 GB RAM each.

Computer Servers:  Many of the tasks performed on the NCIBI Data require significant compute capacity. NCIBI-Comp1, Comp2 and Comp3 are all 8-core HP servers with 32 or 64GB of RAM each. These servers are currently not available for the public, but are used to generate data; examples are parsing and tagging of PubMed sentences, and R-server for large statistical calculations for ConceptGen.

Virtual Servers:  NCIBI-VIRT01 is an 8-core machine with 32 GB RAM which is divided up into virtual servers which run many of the NCIBI tools such as Metscape, Metab2MeSH, ConceptGen and ConceptMetab.

Storage: The main storage capacity for NCIBI, including the relational databases, is the HP MSA storage. Two different sets of Disks with 10K RPM and 15K RPM are combined into a mixed storage array of 72 TB (raw). The fast disks are used for predicted high I/O applications and data access. In addition, we have LSI OnStor Bobcat storage arrays mirrored at 2 sites with 24 TB each, storage for NCIBI and CCMB projects as well as data mirroring.

Backup/Recovery: Tivoli Backup system with LTO4 Tape drive and maximum capacity of 96 TB compressed storage is used for archive and backup of critical files and projects as well as database archives.

The computing sites are connected by a campus network backbone consisting of a mixture of Gigabit and, increasingly, 10-Gigabit Ethernet. The campus network is connected to the Internet and Internet2. University of Michigan researchers and CCMB are also affiliated with several computing consortia, such as Blue Water petascale computing initiative, CaBIG, TeraGrid, BIRN, and other grid computing and computational infrastructure initiatives.

 

 

 

U-M Medical School
| Hospitals & Health Centers | U-M | TEXT-ONLY

University of Michigan Health System
1500 E. Medical Center Drive  Ann Arbor, MI 48109   734-936-4000
(c) copyright Regents of the University of Michigan
Template developed & maintained by: Public Relations & Marketing Communications
Contact UMHS

 
The University of Michigan Health System web site does not provide specific medical advice and does not endorse any medical or professional service obtained through information provided on this site or any links to this site.
Complete disclaimer and Privacy Statement

UMHS HOME

Health Topics A-Z

For Patients & Families

For Health Professionals

Search Tools & Index