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Spotlight
The BioMicro Center now provides the GeneTraffic Database for use with both spotted and Affymetrix arrays. The BioMicro Center offers a wide range of equipment for your microarraying needs, from custom fabrication of cDNA and oligo arrays, to Affymetrix and Agilent microarrays. The BioMicro Center provides software to enable the analysis of complex datasets, including Affymetrix LIMS and Data Mining Tools and Spotfire. The BioMicro Center offers specialized training and services to aid researchers in data analysis and handling.

Introduction
Introduction to the MIT BioMicro Center

The BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing factility at Massachusetts Institute of Technology. The Center is a joint endeavor of the Center for Environmental Health Sciences, the Department of Biology, the Center for Cancer Research, and Biological Engineering Division.

The Center aims to provide an integrated facility for biofabrication, DNA microarray processing, protein microarraying, real time PCR, and RNA validation.

The operations of the BioMicro Center are directed by Dr. Rebecca Fry. The BioMicro team is comprised of three members.The team focuses on microarrays, microarray fabrication and technology advancement. The BioMicro Center maintains a strong commitment to new technology development anddeployment. A focus on new technology also helps to ensure that the BioMicro Center remains at the cutting edge of high throughput analytical methods.

Introduction to Biofabrication
The BioFabrication Laboratory at MIT's BioMicro Center offers a range of services and materials to facilitate highly parallel molecular biological experiments. The BioFabrication Laboratory is located in the Koch Building on the East end of the main MIT campus, Building 68 suite 316.

The lab maintains the scanning and analytical capacity required for commercial microarray users (Affymetrix, Agilent). The Biofabrication Laboratory also provides infrastructure necessary for custom array production and analysis.

The Biofabrication facility services the needs of the MIT community for microarray infrastructure, as well as providing a platform for the development of new technologies.

The facility offers services including Real Time PCR, RNA analysis, and complete labeling for Affyemtrix and Agilent Arrays.

Downloads
These forms and protocols are available for download in PDF format.





* including: o Affymetrix Array Processing, o Custom Array Biofabrication, o Agilent Bioanalyzer, and o equipment available to MIT users

Affymetrix Fluidics Station and Scanner

* Information about fluidics and scanner * Sign up to use fluidics and scanner

arrayWorX_e Scanner

* Information about arrayWorX_e Scanner * Sign up to use arrayWorX_e Scanner

arrayWorX Auto Loader

* Information about ArrayWorx Auto Loader * Sign up to use ArrayWorx Auto Loader

Beckman BioMek FX

* Information about Beckman BioMek FX           * Sign up to use Beckman BioMek FX

MJ Research Real-time PCR machine

* Information about Real-time PCR machine * Sign up to use Real-time PCR machine

MolecularWare Computer (left)

* Information about MolecularWare Computer (left) * Sign up to use MolecularWare Computer (left)

MolecularWare Computer (right)

* Information about MolecularWare Computer (right) * Sign up to use MolecularWare Computer (right)

Research
The BioMicro Center provides state-of-the-art microarray and data mining technology. The following summaries illustrate some of the research projects utilizing the BioMicro Center.

John Essigmann (Biological Engineering) is studying the expression of genes that are up regulated, down regulated and not affected by treatment of human cells with aflatoxin B1 are determined. In parallel, DNA containing enriched DNA adduct pools (e.g., DNA enriched with the aflatoxin-FAPY adduct) is introduced into cells by transfection to determine the elements of the transcriptional response that may be specific to individual adducts. The hypothesis tested is that there will be certain gene expression patterns that reflect the level and type of challenge to the cell from this toxin. (expanded research description)

James Fox (Biological Engineering) is examining the mechanisms by which chronic infection with environmentally acquired pathogens causes cancer in humans. One of these organisms, H. hepaticus, causes chronic, active hepatitis and liver cancer in A/JCr mice, as well as dysplasia and colon cancer in other mouse models. Using H. hepaticus oligo arrays printed using Core facilities, they confirmed the identity of the strains (DNA hybridization) and quantified H. hepaticus expression levels (mRNA hybridization) in liver samples from the A/J mice; cultured cells as well as colon tissue will be analyzed shortly. (expanded research description)

Linda Griffith (Biological Engineering) is looking at the responses of the liver bioreactor to those of native liver under treatment by toxicants. Transcriptional profiling is used to compare responses of cells maintained standard cell culture methods, perfused bioreactor, to those in vivo. The first phase of the project focused on methods development for conducting transcriptional profiling of the rat tissue obtained from the bioreactor. (expanded research description)

ChoKyun Rha (Biomaterial Science and Engineering) is investigating the gene expression profiles of human cells in response to compounds isolated from Centella asiatica and Eurycoma longifolia, two Malaysian plants of pharmaceutical interest. In addition, the laboratory focuses on the Eukaryotic response to cellular stress and aging by studying Saccharomyces cerevisiae. (expanded research description)

Leona Samson (Center of Environmental Health Science) is investigating the gene expression and phenotypic analysis of E. coli, yeast and mice. One of these projects is entitled, Transcriptional Responses of Mice to Alkylating Agents, has a major goal of painting an integrated picture of how mammalian cells, in culture and in the intact organism, respond upon exposure to alkylating agents. The specific agents are chosen to represent environmental toxicants as well as those commonly used for chemotherapy. (expanded research description)

David Schauer (Biological Engineering) is examining the expression profiles of hepatocytes following infection with the cancer-causing bacterium Helicobacter hepaticus. Male A/J mice, which are susceptible to Helicobacter hepatitis and hepatocellular carcinoma, are experimentally infected with H. hepaticus, and are euthanized 6 to 12 months later. Preliminary results indicate that H. hepaticus infection induces expression of a number of genes involved in apoptosis, protein synthesis, and DNA replication in isolated hepatocytes. (expanded research description)

James Sherley (Biological Engineering) is studying the genes that are specifically up-regulated during asymmetric cell kinetics. Asymmetric cell kinetics are a characteristic of adult stem cells. Therefore, their hypothesis is that some genes that are specifically up-regulated during asymmetric cell kinetics may also identify adult stem cells. Currently, genes that uniquely identify adult stem cells have not been discovered. The identification of such genes is highly desired in efforts to identify, isolate, and manipulate adult stem cells for new therapies. (expanded research description)

Phillip Sharp (CCR) is examining the Oct-1transcription factor that interacts with a DNA binding motif termed the octamer. The octamer motif present in the gene regulatory regions (promoters) is both ubiquitous (H2B, snRNA) and cell type-specific (immunoglobulin, Il-2) genes. In a number of these cases, the octamer has been shown to be functionally important for the expression of those genes. We have investigated the physiological role of Oct-1 through the use of gene knockout technology. (expanded research description)

Anthony Sinskey (Biology) is looking at metabolic engineering in Corynebacterium glutamicum: C. glutamicum is a nonpathogenic, gram-positive, food-grade microorganism with a long fermentation history, and thus is potentially useful as a host strain for producing a number of recombinant DNA products. We have developed fundamental genetic tools enabling one to directly address questions of gene organization, structure and regulation at the molecular level. The primary objectives of recent research include using DNA microarrays and functional genomics to dissect the genetic elements responsible for amino acid production in Corynebacterium. (expanded research description)

Getting Started
Please contact Manlin Luo at 452-2563 for microarray experiment-related information.