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Molecular Biology Core Facilities (MBCF)
Encyclopedia
The Molecular Biology Core Facilities (MBCF) was created to allow investigators at the Dana-Farber Cancer Institute
(DFCI) access to cutting edge molecular biology
tools which would be tested and developed in a shared setting. Collaborations can be set up with anyone in the world. Although these services are primarily focused on Cancer
and AIDS
research, there is a broad spectrum of research that uses these resources.
s to researchers. Marvin Caruthers at the University of Colorado determined how to synthesize small oligonucleotides by solid-phase synthesis
using the phosphoramidite method. Carruthers and Leroy Hood
at the California Institute of Technology constructed the first automated DNA Synthesizer
which the MBCF successfully tested after discussions with Don Taylor.
Because of the growing demand for oligonucleotide primers to initiate DNA replication and for probes, a plan was put into place to develop a core facility to produce reagents for molecular biologists as well as instrumentation for the analysis of DNA and protein samples. This plan stated that a charge-back method would be put in place to fairly spread the resources as a shared facility.
A Peptide Synthesizer
using Bruce Merrifield's solid phase peptide synthesis was brought online in 1988 when Fmoc chemistry became commercially available. A Protein Sequencer
using Edman degradation
was installed in 1989 quickly followed by several DNA Sequencers
which were the first to use fluorescent dye terminator chemistry. Mass Spectrometers were acquired to provide analysis of synthesized peptides but soon grew into a stand-alone service in high demand. Biacore
instrumentation added for ligand kinetics in 1996 (and updated by Shared Instrumentation Grant to a Biacore
3000 in 2004). In 2007 a large expansion of high throughput proteomics
using mass spectrometry has been funded by private donation. Blais Proteomics Center. (BPC)
The Molecular Biology Core Facilities has had a continuous web presence since 1992 and began receiving primer sequence for high throughput DNA synthesis by web forms in 1995 when new high volume DNA synthesizers were brought on-line. Since 2004 all interactions between researchers and the core services have been moved to a web based LIMS system.
The MBCF is constantly evaluating new instrumentation which could eventually become a shared resource. The future massively parallel DNA sequencers which can resequence entire genomes in just a few days, (454
, Solexa+Illumina
, Helicos, SOLiD, Visigen, PacBio, ION Torrent), are being made available to researchers by various methods. In 2009 the Heliscope from Helicos BioSciences
began being evaluated in the genomics facility. An Illumina
MiSeq has been purchased and will be installed in the fall of 2011. The Mass Spectrometry proteomics facility has also undergone a large expansion to undertake more complex high-throughput projects as part of the Blais Proteomics Center.
All MBCF staff are Association of Biomolecular Resource Facilities
ABRF members in good standing.
Dana-Farber Cancer Institute
Dana–Farber Cancer Institute is part of a Comprehensive Cancer Center designated by the National Cancer Institute. It is a major affiliate of Harvard Medical School and is located in the Longwood Medical Area in Boston, Massachusetts.-Overview:...
(DFCI) access to cutting edge molecular biology
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
tools which would be tested and developed in a shared setting. Collaborations can be set up with anyone in the world. Although these services are primarily focused on Cancer
Cancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
and AIDS
AIDS
Acquired immune deficiency syndrome or acquired immunodeficiency syndrome is a disease of the human immune system caused by the human immunodeficiency virus...
research, there is a broad spectrum of research that uses these resources.
History
The MBCF at DFCI was first started in 1984 to supply small oligonucleotideOligonucleotide
An oligonucleotide is a short nucleic acid polymer, typically with fifty or fewer bases. Although they can be formed by bond cleavage of longer segments, they are now more commonly synthesized, in a sequence-specific manner, from individual nucleoside phosphoramidites...
s to researchers. Marvin Caruthers at the University of Colorado determined how to synthesize small oligonucleotides by solid-phase synthesis
Solid-phase synthesis
In chemistry, solid-phase synthesis is a method in which molecules are bound on a bead and synthesized step-by-step in a reactant solution; compared with normal synthesis in a liquid state, it is easier to remove excess reactant or byproduct from the product. In this method, building blocks are...
using the phosphoramidite method. Carruthers and Leroy Hood
Leroy Hood
Leroy Hood is an American biologist. He won the 2011 Fritz J. and Dolores H. Russ Prize “for automating DNA sequencing that revolutionized biomedicine and forensic science” and the 2003 Lemelson-MIT Prize for inventing "four instruments that have unlocked much of the mystery of human biology" by...
at the California Institute of Technology constructed the first automated DNA Synthesizer
Solid-phase synthesis
In chemistry, solid-phase synthesis is a method in which molecules are bound on a bead and synthesized step-by-step in a reactant solution; compared with normal synthesis in a liquid state, it is easier to remove excess reactant or byproduct from the product. In this method, building blocks are...
which the MBCF successfully tested after discussions with Don Taylor.
Because of the growing demand for oligonucleotide primers to initiate DNA replication and for probes, a plan was put into place to develop a core facility to produce reagents for molecular biologists as well as instrumentation for the analysis of DNA and protein samples. This plan stated that a charge-back method would be put in place to fairly spread the resources as a shared facility.
A Peptide Synthesizer
Solid-phase synthesis
In chemistry, solid-phase synthesis is a method in which molecules are bound on a bead and synthesized step-by-step in a reactant solution; compared with normal synthesis in a liquid state, it is easier to remove excess reactant or byproduct from the product. In this method, building blocks are...
using Bruce Merrifield's solid phase peptide synthesis was brought online in 1988 when Fmoc chemistry became commercially available. A Protein Sequencer
Edman degradation
Edman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues....
using Edman degradation
Edman degradation
Edman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues....
was installed in 1989 quickly followed by several DNA Sequencers
DNA sequencer
A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. It can be also considered an optical instrument as it generally analyses light signals originating from fluorochromes attached to nucleotides....
which were the first to use fluorescent dye terminator chemistry. Mass Spectrometers were acquired to provide analysis of synthesized peptides but soon grew into a stand-alone service in high demand. Biacore
Surface plasmon resonance
The excitation of surface plasmons by light is denoted as a surface plasmon resonance for planar surfaces or localized surface plasmon resonance for nanometer-sized metallic structures....
instrumentation added for ligand kinetics in 1996 (and updated by Shared Instrumentation Grant to a Biacore
Surface plasmon resonance
The excitation of surface plasmons by light is denoted as a surface plasmon resonance for planar surfaces or localized surface plasmon resonance for nanometer-sized metallic structures....
3000 in 2004). In 2007 a large expansion of high throughput proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
using mass spectrometry has been funded by private donation. Blais Proteomics Center. (BPC)
The Molecular Biology Core Facilities has had a continuous web presence since 1992 and began receiving primer sequence for high throughput DNA synthesis by web forms in 1995 when new high volume DNA synthesizers were brought on-line. Since 2004 all interactions between researchers and the core services have been moved to a web based LIMS system.
The MBCF is constantly evaluating new instrumentation which could eventually become a shared resource. The future massively parallel DNA sequencers which can resequence entire genomes in just a few days, (454
454 Life Sciences
454 Life Sciences, is a biotechnology company based in Branford, Connecticut. It is a subsidiary of Roche, and specializes in high-throughput DNA sequencing.-History and Major Achievements:...
, Solexa+Illumina
Illumina (company)
Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and...
, Helicos, SOLiD, Visigen, PacBio, ION Torrent), are being made available to researchers by various methods. In 2009 the Heliscope from Helicos BioSciences
Helicos Biosciences
Helicos BioSciences Corporation, is a publicly-traded life science company headquartered in Cambridge, Massachusetts focused on genetic analysis technologies for the research, drug discovery and diagnostic markets. The firm's Helicos Genetic Analysis Platform was the first DNA-sequencing...
began being evaluated in the genomics facility. An Illumina
Illumina
Illumina is the second album by Alisha's Attic to be released worldwide in 1998. Three tracks were released from it, these being "The Incidentals", "Wish I Were You" and "Barbarella". It peaked at #15 on the UK album chart...
MiSeq has been purchased and will be installed in the fall of 2011. The Mass Spectrometry proteomics facility has also undergone a large expansion to undertake more complex high-throughput projects as part of the Blais Proteomics Center.
All MBCF staff are Association of Biomolecular Resource Facilities
Association of Biomolecular Resource Facilities
The Association of Biomolecular Resource Facilities is dedicated to advancing core and research biotechnology laboratories through research, communication, and education...
ABRF members in good standing.
Research tools available
- DNA sequencingDNA sequencingDNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
- Massively Parallel Sequencing "next-gen sequencing"
- Full genome sequencingFull genome sequencingFull genome sequencing , also known as whole genome sequencing , complete genome sequencing, or entire genome sequencing, is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time...
- Gene mappingGene mappingGene mapping, also called genome mapping, is the creation of a genetic map assigning DNA fragments to chromosomes.When a genome is first investigated, this map is nonexistent. The map improves with the scientific progress and is perfect when the genomic DNA sequencing of the species has been...
- SNP analysis
- GenotypingGenotypingGenotyping is the process of determining differences in the genetic make-up of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence. It reveals the alleles an individual has inherited from their...
- Linkage analysisGenetic linkageGenetic linkage is the tendency of certain loci or alleles to be inherited together. Genetic loci that are physically close to one another on the same chromosome tend to stay together during meiosis, and are thus genetically linked.-Background:...
- Genomic sequencing
- ChIP-Seq
- RNA-Seq
- GRO-Seq
- Digital gene expression
- Genome resequencing
- Protein SequencingEdman degradationEdman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues....
- N-terminal sequencingEdman degradationEdman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues....
- Radioactive tracer detectionRadioactive tracerA radioactive tracer, also called a radioactive label, is a substance containing a radioisotope that is used to measure the speed of chemical processes and to track the movement of a substance through a natural system such as a cell or tissue...
- N-terminal sequencing
- Mass spectrometryMass spectrometryMass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
- MALDI-TOF
- Ion trapIon trapAn ion trap is a combination of electric or magnetic fields that captures ions in a region of a vacuum system or tube. Ion traps have a number of scientific uses such as mass spectrometery and trapping ions while the ion's quantum state is manipulated...
- NanosprayElectrospray ionizationElectrospray ionization is a technique used in mass spectrometry to produce ions. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized...
- DNA synthesisSolid-phase synthesisIn chemistry, solid-phase synthesis is a method in which molecules are bound on a bead and synthesized step-by-step in a reactant solution; compared with normal synthesis in a liquid state, it is easier to remove excess reactant or byproduct from the product. In this method, building blocks are...
- Peptide synthesisSolid-phase synthesisIn chemistry, solid-phase synthesis is a method in which molecules are bound on a bead and synthesized step-by-step in a reactant solution; compared with normal synthesis in a liquid state, it is easier to remove excess reactant or byproduct from the product. In this method, building blocks are...
- Amino acid analysis
- BiacoreSurface plasmon resonanceThe excitation of surface plasmons by light is denoted as a surface plasmon resonance for planar surfaces or localized surface plasmon resonance for nanometer-sized metallic structures....
- HPLCHigh-performance liquid chromatographyHigh-performance liquid chromatography , HPLC, is a chromatographic technique that can separate a mixture of compounds and is used in biochemistry and analytical chemistry to identify, quantify and purify the individual components of the mixture.HPLC typically utilizes different types of stationary...
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- Sequence analysisSequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
- Genome annotation
- Gene expressionGene expressionGene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
- Protein expressionProtein expressionProtein expression is a subcomponent of gene expression. It consists of the stages after DNA has been translated into polypeptide chains, which are ultimately folded into proteins...
- Mutational analysis
- Structure predictionSecondary structureIn biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
- Sequence analysis
Funding
The MBCF is for the most part funded as a straight fee for service chargeback core facility. At times other sources of funding for research and development or expansion are incorporated into the overall budget.- From 1986 to 1999 the MBCF was part of the Dana-Farber Cancer InstituteDana-Farber Cancer InstituteDana–Farber Cancer Institute is part of a Comprehensive Cancer Center designated by the National Cancer Institute. It is a major affiliate of Harvard Medical School and is located in the Longwood Medical Area in Boston, Massachusetts.-Overview:...
Comprehensive Cancer Center grant funded by the National Cancer InstituteNational Cancer InstituteThe National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S...
of NIH. - From 1989 to 2004 the MBCF was part of the Harvard Medical SchoolHarvard Medical SchoolHarvard Medical School is the graduate medical school of Harvard University. It is located in the Longwood Medical Area of the Mission Hill neighborhood of Boston, Massachusetts....
Center for AIDS Research (HMS CFAR). - From 2004 to the present the MBCF has been part of the Harvard UniversityHarvard UniversityHarvard University is a private Ivy League university located in Cambridge, Massachusetts, United States, established in 1636 by the Massachusetts legislature. Harvard is the oldest institution of higher learning in the United States and the first corporation chartered in the country...
Center for AIDS Research (HU CFAR). - The National Center for Research Resources (NCRR) has funded several instruments through Shared Instrumentation Grants.
External links
- MBCF Molecular Biology Core Facilities
- DFCI Dana-Farber Cancer Institute
- HMS Harvard Medical School
- ABRF Association of Biomolecular Resource Facilities
- NCBI National Center for Biotechnology Information
- ASMS American Society for Mass Spectrometry
- TPS The Protein Society
- NCI National Cancer Institute