Four microscopic views


The following research facilities are available to the MIT community at large:

BioMicro Center

The BioMicro Center is an integrated facility providing biofabrication, microarray analysis, database storage, bioinformatics, data mining, and data modeling. It is a joint endeavor of the Center for Environmental Health Sciences, MIT Biology, the Koch Institute for Integrative Cancer Research, and Biological Engineering.

This center provides a broad range of genomic, high-throughput, and informatics resources to investigators in the Biology department. The BioMicro Center was initially launched by equipment grants through the CSBi program, the Center for Cancer Research and funds from the Department of Biology and is now supported jointly by the Departments of Biology, Biological Engineering, the Koch Institute, and the Center for Environmental Health Sciences. The core is managed by an outstanding scientist (Stuart Levine) who acts as the Center's Scientific Director, who provides input to the MIT community on experimental design for genomics-based experimentation, and provides high-level advice on the appropriate computational and statistical methods for data interpretation. The Center's staff has expanded to 9 employees over the past two (including 1 UROP and two Co-op students from North Eastern University) in order to handle the significant increase in usage, with the large majority of salary recovery done through chargeback.

The Department of Biology has continued to make significant capital investments in updating the equipment in the BioMicro Center in all areas. High-throughput sequencing has expanded significantly in the last two years with three Illumina GAIIs and an Illumina HiSeq2000 all in operation and running near capacity. In addition, the BioMicro Center has added support for Illumina sample preparation and quality control with the addition of a SPRI-TE robot, a Caliper LabChip GX system and a second Roche 480 light cycler. Significant financial support for this equipment from the department was paired with support from the Moore Foundation to Dr. Penny Chisholm, ARRA funding to Dr. Chris Burge as well as support from Dr. Ernest Fraenkel (BE).

Other technologies have not been neglected with the expansion of sequencing capacity. The BioMicro Center has expanded its capacity to handle microarrays with additional throughput in Affymetrix and plans to upgrade the Agilent scanner to handle higher density arrays. The Koch Institute has also sited a Fluidigm BioMark in the BioMicro Center and is supporting the testing of a Nanostring nCounter. Two Tecan EVO 150 liquid handlers have also been added and are being used both by the BioMicro Center to increase sample throughput as well as by many laboratories for a number of high-throughput projects.

The BioMicro Center has also begun expanding its informatics and Bio-IT capacities. Working closely with the Koch Institute's Bioinformatics and Computing Core, the BioMicro Center now manages significant amounts of data storage (>100TB) for users in the Department of Biology as well as co-operates a computational cluster that is used to process Illumina data. Through funding from a variety of sources, the BioMicro Center has also added a computational scientist to assist users in data analysis with additional hiring planed in this area to meet very high levels of demand.

Location: Building 68-316 [map]; Contact: Stuart Levine biomicro@mit.edu

Biophysical Instrumentation Facility

This facility houses instruments for aiding in the elucidation of macromolecular structure and interactions.  It has a Beckman ProteomeLab XL-I analytical ultracentrifuge which provides data for calculating the molecular mass, stoichiometry, conformation and shape of proteins in solution, an Aviv Biomedical Model 202 circular dichroism spectrometer which reports secondary structure of proteins and can also report transitions at given temperatures, a Wyatt Technology NanoStar dynamic light scatterer which reports the hydrodynamic radii of the different species in a sample and their size distribution, a Malvern VP-ITC isothermal titration calorimeter which reports the heat generated or absorbed when proteins and ligands bind and reports stoichiometry, binding constant, enthalpy and entropy, a Malvern VP-DSC differential scanning calorimeter which reports transitions when a protein sample is slowly taken through a large temperature change and provides information about subunit composition, folding and stability, a ForteBio Octet RED96 bio-layer interferometer which quantifies protein concentrations and monitors protein-protein  and other biomolecular interaction kinetics providing ka, kd and kD,  and a Beckman PA-800 capillary electrophoresis unit which performs analytical separation of proteins or carbohydrates with aqueous solubility.

The BIF is staffed 40 hours a week by Debby Pheasant who is available to train new users and provide advice to anyone considering potential of the equipment in the facility. 

Location: Building 68-470 [map]; Contact: Debby Pheasant pheasant@mit.edu

Structural Biology Core Facility

The Biology Department maintains a central core facility providing access to state-of-the-art equipment for X-ray crystallography. This facility is open to the entire MIT community. Dr. Robert Grant staffs the facility full-time. Dr. Grant is an experienced crystallographer and oversees the day-to-day operation of the facility. A cornerstone of the facility is an automated pipeline for high-throughput crystallization screening. MIT was one of the first major universities that recognized the benefit of such capacities for academic research. At the beginning of the pipeline, an Art Robbins Phoenix, and a Formulatrix NT8 liquid handling robot are employed for drop set ups. With these two tools crystallization screens can be performed employing a broad range of vapor and batch diffusion methods, in a variety of 24, 48, or 96 well plates. Crystallization plates are stored and imaged using two Formulatrix Rock Imager 1000 hotels, set up at 4°C and 18°C. Optimization of crystallization screens is supported by a Formulatrix Formulator screen maker. In addition the crystallization pipeline, the facility still maintains an X-ray generator for in-house data collection (The vast majority of data collection is performed at various national synchrotron facilities, particularly at the Advanced Photon Source in Argonne, IL) . The X-ray setup consists of a Rigaku MicroMax007-HF rotating anode X-ray generator, a cryosystem for sample cooling, and a Saturn 944 CCD detector for data collection. For data processing, several Linux-based workstations including hardware-stereo equipment and TB storage capacity are available in a shared computer room adjacent to the crystallization pipeline and the X-ray setup.

Location: Building 68- [map]; Contact: Robert Grant ragrant@mit.edu

The Swanson Biotechnology Center

In addition to core facilities located in building 68, the Swanson Biotechnology Center (SBC) is a brand new life science based high technology core facility center located in Building 76, directly adjacent to Building 68. Launched in March 2011, the SBC comprises ~ 27K square feet and currently hosts 10 core facilities, with another 3 in development. These operating units provide the MIT research community with cost-advantaged high-technology instrumentation and services. The following SBC research facilities are available to the MIT community, at-large:

Applied Therapeutics Core Facility

This resource enables longitudinal testing of potential vaccines, therapeutic agents, and drug delivery and detection systems in whole animal tumor models. The core goal of the facility is to provide coordinated services that enable researchers to perform clinical trials in mice regardless of lab expertise including providing consultation on experimental design, animal breeding and housing, drug dosing, image acquisition and analysis. Researchers may also avail themselves of training opportunities throughout the process. The facility interfaces with the MIT Department of Comparative Medicine on matters of animal care and coordinates access to whole animal imaging instrumentation in partnership with the KI Imaging Core Facility. New capabilities can be added as dictated by, and appropriate to, specific cancer research projects.

Bioinformatics & Computing Core Facility

The primary mission of the Bioinformatics and Computing Core Facility is to ensure research projects are provided expanded bioinformatics and computing support. By maintaining a current awareness of newly developing bioinformatics methods and technologies relevant to cancer research, facility staff provides the intellectual expertise that cancer researchers may access on a fee-for-service basis as well as through numerous training opportunities that will set them on a path towards essential bioinformatics self-sufficiency. Support is also provided to both research labs and other shared resource Core Facilities for hardware systems, desktop computing and software tools required for the collection, analysis, dissemination and storage of data.

Biopolymers & Proteomics Core Facility

The overall mission of the Biopolymers and Proteomics Core Facility is to provide researchers access to cutting-edge methods and state-of-the art instrumentation critical to many aspects of their research involving DNA, RNA or proteins. The facility offers a diverse set of capabilities, ranging from standard, commonly-used services, to high-end techniques that include next generation sequencing technology, custom synthesis of membrane-based peptide arrays and mass spectrometry services for proteomic analysis. The facility provides key infrastructure, including technical expertise and operational oversight, required to maintain an extensive group of high-end, technologically sophisticated equipment.

• Purification by liquid chromatography to purify protein, peptides, conjugates, small molecules, nucleic acids, etc
• Peptide synthesis in either SPOT format (600 synthetic peptides per membrane) or in micromole scale, including modifications
• MALD-TOF mass spectometry for molecular weight determination
• Analytical scale HPLC to quantify or quality control biomaterial
Location: 76-181; Contact: Dick Cook cook@mit.edu

• Proteomics: identification of proteins from gel band or complex mixture, binding partners, expression changes
• Quantitative proteomics: isobaric mass tags (TMT or iTRAQ) or SILAC to quantitatively compare up to 10 different variables
• Identification of post-translational modifications on a single protein or in an unbiased manner
• Intact mass measurement: measure protein molecular weights accurately for single proteins up to 60kDa.
Location: 76-185; Contact: Amanda Del Rosario aweaver@mit.edu

Stem Cells and Transgenics

The use of novel mutant mouse strains is a cornerstone of the research performed at Koch Institute, with over 200 strains of mice containing targeted mutations generated in Koch Institute laboratories. The objective of the Transgenic Animal Core Facility is to make transgenic, gene-targeting and lentivirus-mediated transgenesis technologies accessible to cancer research laboratories regardless of their previous experience with the generation and analysis of mouse models. The facility provides expert consultation in the design of mouse models and conducts numerous procedures associated with the generation of genetically modified mice including ES cell targeting, de novo ES cell isolation, pronuclear and blastocyst injections and tetraploid fusions. The facility places considerable emphasis on investigator education and will provide interested researchers with state of the art training in any of these procedures. The facility also serves as a repository for commonly used Cre, FLP and reporter strains so that they are available for immediate access.

Location: 76-195; Contact: Aurora Burds Connor, Noranne Enzer escore@mit.edu

Flow Cytometry Core Facility

The Flow Cytometry Core Facility is a heavily used resource that provides cancer research investigators with state-of-the-art cell sorting instrumentation, data analysis, and technical expertise and training. High-speed cell sorting is available with technical assistance (four instruments) and six bench-top analyzer instruments, with a diverse set of light source, fluorescent detection and sampling capabilities are available to researchers round the clock. In addition to highly individualized training, facility staff provides the expertise and up to date technical knowledge for critical support of experimental design, reagent selection and data interpretation. The ability to modify instruments and/or methods allows the facility to provide highly customized service, meeting the needs of individual investigators. By centralizing expensive flow cytometry instrumentation and expertise, the facility is able to provide a more comprehensive range of services.

Flow Cytometry
• Cytometer Analyzer for simultaneous multiparametric analysis of up to 20,000 cells/sec; detection of up to 15 fluorophores; samples can be loaded from tubes or automatically from a 96-well or 384-well plate
• Cell Sorting for physical separation of mixed cell populations into up to 4 different tubes or into 96-well or 384-well plates
• Applications include fluorescent protein detection, cell death, immunophenotyping, cell cycle, cell proliferation and functional tests.
Location: 76-259; Contact: Glenn Paradis flowcore@mit.edu

Nanowell Cytometry
• Access to “Microengraving technology”; a platform that enables measurement of multiple traits from individual cells derived from various cell or tissue types
• Fluorescence multispectral imaging of cells to measure functional and phenotypic characteristics on a single cell level
• Ability to retrieve single cells for further genetic analysis or developing clonal colonies
• Applications of platform include tumor profiling of various cancer types, studying immune cell functions of cells or antibody discovery.
Location: 76-273; Contact: Shanu Mehta shanu@mit.edu

Histology Core Facility

The use of vertebrate model organisms to study the role of cancer genes in both normal development and tumorigenicity is a key component of cancer research programs at the Koch Institute. State-of-the-art histological services provided by the Histology Core Facility are a critical underpinning of these studies. The facility produces high quality slides from fixed and frozen samples, permitting diagnosis of developmental and tumor phenotypes as well as recovery of tissue samples required to further investigate underlying molecular changes. Cancer researchers may also benefit from training in all aspects of sample preparation. The facility also provides access to an expert pathology consultant to enable appropriate diagnoses of tumor and developmental phenotypes and to provide intellectual expertise and training to both researchers and facility staff.

Location: 76-182; Kathy Cormier cormier@mit.edu

Microscopy Core Facility

Nearly all research programs in the Koch Institute rely on one or more types of microscopy. Koch Institute researchers use imaging technology to examine whole animals, tissues, cells and subcellular components as well as to visualize living cells with transmitted light or fluorescent probes. The rapid development of new imaging technologies and their expense make it impractical for most individual investigators to establish and maintain state-of-the-art imaging systems in their own laboratories. The Imaging Core Facility therefore addresses a key research need by enabling access to a broad range of high-end instrumentation combined with sophisticated and up-to-date expertise. The facility provides the infrastructure for instrument operation, as well as experimental guidance and highly individualized training enabling access by the cancer research community. The facility interacts and coordinates efforts with other entities at MIT involved in bioimaging applications and services, including the Whitehead Institute/MIT BioImaging Center.

W. M. Keck Microscopy Facility

This W.M. Keck Microscopy Facility provides scientists with the equipment and training necessary to generate and interpret light and electron microscope images. With state-of-the-art imaging platforms and image processing and analysis software, the facility provides a full-service menu including consulting on imaging projects. A particular expertise of the facility is immunoelectron microscopy imaging services. In addition to serving the Whitehead and MIT communities, the facility is open to the local research community.

Location: Whitehead Institute, fourth floor [map]; Contact: Nicki Watson watson@wi.mit.edu

Two-photon Microscopy Core Facility

The McGovern Institute two-photon microscopy core facility offers MIT researchers a sophisticated and unique combination of two-photon imaging and uncaging technology. The system was designed for neuroscience research, but it is potentially useful for a wide variety of biological applications.  It includes two workstations, one designed for slice experiments and one for in vivo work with small animals.  It has two tunable Ti:Sapphire lasers plus two additional lasers (at 471nm and 563nm), which can be used simultaneously in many configurations. Training is available, and core users also have access to Neurolucida software for morphological analysis of neural images.

Viral Core Facility

The viral gene transfer core was established in 2008 by the Picower Institute for Learning & Memory and the McGovern Institute for Brain Research, to make viral vectors accessible to the MIT neuroscience community. Directed by Rachael Neve, its overall goals are to provide the most advanced viral vector technologies, and to drive the development of new applications that will benefit neuroscience research. The core currently offers HSV and BacMam vectors, including packaging, vector construction and advisory consultations. The core also offers AAV packaging through an external provider, Virovek, with whom the core has negotiated a discount. In addition to custom vectors, a variety of useful HSV-based constructs (eg with cell-type-specific promoters and a variety of reporter genes) are available in small aliquots, and new ones are added frequently.

Martinos Imaging Center

The Athinoula A. Martinos Imaging Center, directed by John Gabrieli, is a state-of-the-art brain imaging facility that serves the biomedical research community at MIT and throughout the Boston area. Its resources include human and small-animal MRI, electroencephalography (EEG) and magnetoencephalography (MEG). The center is housed within the McGovern Institute for Brain Research in building 46. 

Cutting-edge research is increasingly reliant on the services and specialized equipment that are too costly for departmental procurement, let alone individual researchers. Subsequently, the Department of Biology has collaborative agreements with other units (BE, KI, CEHS, CSB, and WI) to provide these services through core facilities that are available to all biology department members, most notably our junior faculty. Maintaining support for these facilities is critical. We are grateful that the President and Provost recognize the value of these services and that they have demonstrated their support with and expressed desire to provide services to all life science researchers at MIT.