ATCC applies a wide variety of molecular authentication services to support the ATCC collection. The major molecular authentication tests are supported by the ATCC Molecular Authentication Resource Center, also known as the genomic core, while other identification and characterization analyses are performed by our immunology and proteomic cores.
Genomics
The ATCC genomics core (MARC) provides a wide variety of molecular authentication services to support the ATCC collections. Some of these applications include:
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Cloning and gene synthesis
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Real-time PCR analyses
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Site-directed mutagenesis
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Sequencing
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STR, SNP and fingerprint analyses.
The genomics core utilizes scientific knowledge and technical expertise to design and perform numerous authentication and confirmatory assays (such as DNA barcoding and species identification, quantitative gene expression and transcriptome analyses) for ATCC collections.
Genomics Staff
Name: Pranvera Ikonomi, PhD, University of Paris XI in regulation of eukaryotic organisms (1986); B.S., University of Tirana, Albania in physics (1984).
Responsibility: Research Scientist – MARC
Special Interest: Dr. Ikonomi focuses on assay development with an emphasis on gene regulation. The Molecular Authentication Resource Center at ATCC, which is directed by Dr. Ikonomi, carries out the current authentication and validation of ATCC collections, while focusing on development of new detection assays for authentication and validation of biological materials at ATCC. Dr. Ikonomi’s group is also involved in the translational research studies being conducted at ATCC with specific focus on the discovery of novel biomarkers for early detection of type 2 Diabetes. Prior to joining ATCC, Dr. Ikonomi was a staff scientist at Invitrogen, where she was part of the research team involved in the development of a new fluorescence-based method for PCR amplification LUX (light upon induction). Dr. Ikonomi has published research findings in journals such as International Journal of Systematic and Evolutionary Microbiology, Applied Microbiology and Biotechnology, Nucleic Acid Research, Biotechniques and Blood. While working at ATCC, Dr. Ikonomi has submitted three US Patents.
High-throughput proteomic technology has provided an effective complementary means for evaluating the total protein content of a given biological sample. Equipped with techniques such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS), electrospray ionization mass spectrometry (ESI-MS), and 2-D technologies, ATCC has complemented traditional authentication and identification methods with these state-of-the-art proteomics technologies. An example of one such initiative is the application of MALDI-TOF-MS to evaluate over 50 prokaryotic genera from ATCC’s collection to date, with the goal of producing a complete reference database of all protein spectral fingerprints from every type of culture specimen retained at ATCC.
Protein fingerprints are valuable for authentication purposes because they reveal deviations in the protein content for a given sample when compared to a reference standard which may be indicative of contamination or antigen drift. Protein fingerprinting is imperative for identification purposes. A protein fingerprint produced for an unknown sample can be compared to the reference fingerprints contained within the database for candidate identification matches using a decision-tree approach.
Advantages offered by mass spectrometry based proteomics for protein fingerprinting include:
· Reproducibility
· Minimal sample usage
· Low reagent cost
· Speed
Proteomics Technologies
The following technologies have been established at ATCC for evaluating and authenticating biological samples:
- 2D SDS PAGE — Two-dimensional sodium dodecylsulphate polyacrylamide gel electrophoresis
- MALDI-TOF-MS — Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
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SELDI-TOF-MS — Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry
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ESI-MS — Electrospray ionization mass spectrometry
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PF-2D — Two-dimensional liquid chromatography
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Bio-Plex — A multiplex suspension array system
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BioLogic DuoFlow — Liquid chromatography for protein purification
Proteomics Research Staff
Name: Liping Liu, PhD, Nankai University in biochemistry (1994); B.S., Nankai University in chemistry (1990).
Responsibility: Product Development Scientist – Translational Research
Special Interest: Dr. Liu’s group focuses on the discovery and development of diseases and associated biomarkers using state-of-the-art proteomics technologies. Prior to joining ATCC, Dr. Liu was a senior R&D Manager at MannKind Corporation, a biopharmaceutical company developing inhaled insulin and cancer immunotherapy. Dr. Liu was director of antigen discovery at CTL Immunotherapy Corp. prior to its merging with MannKind. Dr. Liu is a scientific advisory board member of MBVax Bioscience, a biotech company which develops cancer therapy, a member of the American Association for Cancer Research (AACR), the American Diabetes Association (ADA), the European Association for the study of Diabetes (EASD) and the American Peptide Society (APS). Dr. Liu has published 21 peer-reviewed journal articles and is a co-inventor on 10 patent applications.
Immunology
The ATCC Hybridoma and ImmunologyCenter (HAIC) was established at ATCC to develop and characterize immunological reagents and immunoassays. The HAIC broadens and enhances the scope of essential services provided to the global scientific community by the ATCC. Since the advent of hybridoma technology, monoclonal antibodies (mAbs) have served as essential elements in the areas of genetic research, immunology and therapeutic applications. Currently, ATCC is developing a range of immunological reagents, including:
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Polyclonal sera
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Hybridoma cell lines
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purified mAbs
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Ascites
The HAIC’s goal is to provide a cost-effective and efficient service with a focus on product quality and customer satisfaction. The center currently provides services using a variety of antigens including cell extracts, purified proteins and synthetic peptides to generate immunological reagents using both established and proprietary immunization strategies.
ATCC specializes in development of mAbs for challenging immunogens. Fusion of lymphoid tissues is conducted to generate a panel of hybridoma cell lines for each antigen of interest, which are subsequently cloned and screened by various methods, including ELISA, Western blot or flow cytometry, depending on the specific scientific requirements of the investigator.
Following selection of the appropriate clone(s), batches of purified monoclonal antibodies are produced in-house using scalable in vitro bioproduction methods. The product is then subjected to rigorous QC testing, including sterility, isotyping, concentration and purity. Hybridoma cell lines are routinely archived using the same cryopreservation techniques utilized by the ATCC Cell Biology Collection to ensure the long-term availability of both the cell line and the secreted product.
Immunology Staff
Name: John R. Simms, PhD, University of Sheffield (U.K.) in Virology and Immunology; B.S., University of Leeds (U.K.) in microbiology.
Responsibility: Product Development Scientist – Translational Research
Special Interest: Dr. Simms is a founding member of the ATCC Translational Research group, which seeks to develop monoclonal antibodies as research tools and theranostics, and to conduct biomarker discovery research in the areas of metabolic disorders, infectious diseases and oncology. Following the conclusion of his doctoral studies, he completed two years of postdoctoral training at the City of Hope National Medical Center (Duarte, Calif.), where he worked on the development of HLA A*0201-restricted peptide vaccines for HIV and CMV. Dr Simms then entered the private sector, where he worked for CTL ImmunoTherapies Corp. and MannKind Corp. from 2001 until 2005. His research included the pre-clinical development of HLA-restricted DNA vaccines for chronic infectious diseases and cancer, evaluating the clinical potential of novel biotherapeutics, and the immunotoxicological evaluation of an inhalable insulin formulation currently undergoing Phase III clinical trials. Dr Simms has published several articles relating to vaccine design and immunology in the area of infectious diseases and is a co-inventor on three U.S. patent applications.
Selected Publications for John Simms
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