Advanced Mass Spectrometry Core
D. Eric Anderson, Ph.D.
The Advanced Mass Spectrometry Core assists the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) investigators with a wide range of mass spectrometry applications, including basic quality control, general problem solving during the development of complex experimental approaches, and discovery work. In each application, mass spectrometers are involved directly in obtaining important project answers.
Mass spectrometry detects molecules without specialized molecule-specific reagents. This makes it an unbeatable tool for rapid and tailored problem solving.
The types of analyses we perform are diverse and can include activities ranging from intact mass measurements of small molecules to proteins over 100kD. Peptide-centric experiments involving protein identification and isotope-aided, relative quantitative comparisons can be used to observe differences in protein abundance or a post-translational state between two or more samples containing hundreds or thousands of proteins. However, “off-menu” solutions to unique problems brought to us by principal investigators are among our most exciting puzzles, and such problems are especially sought. We use minimal cost recovery for the NIDDK to make analysis sustainable. Non-NIDDK federal projects with cost recovery, which is very competitive with outsourcing, are also possible. The first step of consideration for any analysis is to contact staff before samples are created.
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Elizabeth C. Wright, Ph.D.
The Biostatistics Program provides advice to both extramural and intramural NIDDK staff on the design and feasibility of proposed research studies and the conduct of ongoing studies. Dr. Wright and her staff perform research on statistical methods and conduct educational seminars. They attend Data and Safety Monitoring Board meetings for extramural projects and provide analytical services for intramural research projects.
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Joseph Shiloach, Ph.D.
The Biotechnology Core specializes in large-scale production and purification of biological materials from various sources to advance research in fields such as vaccine development, drug development, and structural biology. To achieve this goal, the laboratory integrates two main functions: (1) production of biologics, conducted in a multipurpose, state-of-the-art production facility, and (2) research and process development related to solving biological production issues by utilizing physiological, molecular biology, and technical approaches.
The lab has successfully solved a variety of production challenges. These include growing large amounts of different microorganisms, mammalian cells, and insect cells, and obtaining bulk and purified proteins from large amounts of media and biomass. Scientists achieved this by utilizing physiological, molecular biology, and technical approaches specific to each producer and product. Examples of molecule production for structural studies include the following: (1) toll-like receptor 3 by transiently infected insect cells, (2) G protein-coupled neurotensin receptor (NTS1) from recombinant E. coli and from stably transfected HEK 293 cells, and (3) capsular polysaccharides of Neisseria meningitidies from E. coli. Examples of production of molecules, microorganisms and cells for therapeutic and vaccine studies include cell wall and peptydoglycan from Bacillus anthracis, Shigella, and recombinant malaria transmission blocking vaccine Pfs 25h. The laboratory conducts research on modifying adhesion properties of mammalian cells (for virus production) and on improving the growth properties of recombinant E. coli strains (for recombinant protein production).
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Clinical Laboratory Core
Mary Walter, Ph.D.
Scientists in the Clinical Laboratory Core collaborate with investigators from across the Clinical Research Program to provide sensitive, inexpensive, and reproducible analyses. We also develop new assays and support a wide range of clinical studies in the fields of endocrinology, hepatology, nephrology, and metabolism. These analyses include measurement of gut hormones, adipokines, oxidative stress markers, cytokines, and other biomarkers in biologic fluids that are related to diabetes, endocrine, and metabolic research. The Laboratory has added new hormone assays to reflect the current research trends, as well as the Luminex technology, which has greatly expanded our analytical capabilities. The Laboratory performs extensive validation of all assays before conducting routine sample analyses of clinical specimens. After assay validation, the Laboratory coordinates with clinical research investigators to establish a charge-back fee structure. This structure supports ongoing and routine specimen analyses, charging for the cost of supplies only. Additionally, the Laboratory works to reduce costs of assays by centralizing the purchase of common supplies used in specimen analyses and by taking advantage of bulk purchasing discounts. This approach yields savings that are passed along to the investigators utilizing the Laboratory’s services. Assays are uniquely tailored to meet the needs of the investigator, thus saving on sample volume and promoting cost efficiency in all cases.
The Clinical Laboratory Core also provides a service that allows for simple access to human sample acquisition, processing, tracking, and storage in accordance with current legislation. The acquisition process involves preparation of tubes for blood draw to achieve the lowest levels of degradation. Samples are processed within 1 hour of blood collection to ensure thermal preservation. The Laboratory recently purchased a new specimen-tracking database. This web-based tool is customizable and provides quick, reliable, and accurate accounting for clinical specimens stored with the Clinical Laboratory Core.
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Clinical Mass Spectrometry Core
Peter J. Walter, Ph.D.
The Clinical Mass Spectrometry Core collaborates with investigators from across NIDDK’s Intramural Research Program to conduct stable isotope tracer studies in both human and mammalian subjects. Clinical studies using stable isotopes involve administering a subject with substances labeled with rare, non-radioactive, stable isotopes; collecting samples; and monitoring production or decay in the isotopic ratio of the labeled product. Stable isotopes are advantageous for clinical studies because they are chemically and physically indistinguishable from the predominant natural isotope of the same element but they are readily distinguished and quantitated by isotope-ratio mass spectrometers. The most commonly used stable isotopes are hydrogen (2H), oxygen(18O) and carbon (13C), and, to a lesser extent, nitrogen (15N) and sulfur (34S).
The doubly labeled water (DLW) method was developed to measure total energy expenditure. A person or animal is administered a dose of water enriched in deuterium (D) and 18oxygen. Labeled hydrogen can only be lost through water, whereas oxygen can be lost as water or carbon dioxide. Calculating the rate of carbon dioxide production then yields a measure of total energy expenditure.
Metabolic studies with stable isotopes cover a vast range of investigations. Currently, we are developing the use of D- or 13C-labeled glucose as a measure of glucose metabolism and labeled free fatty acids.
Across all of these efforts, the core advises, develops, and validates novel research assays in support of ongoing clinical research projects and actively seeks new areas for collaboration with staff members from across the NIH.
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John A. Hanover, Ph.D.
Harold Smith, Ph.D. — Illumina sequencing services and bioinformatics
Weiping Chen, Ph.D. — Bioinformatics
Chithra Keembiyehetty, Ph.D. — Affymetrix array services
The services we provide in the Genomics Core Facility include next-generation sequencing, genome-wide microarrays, quantitative PCR, bioinformatics infrastructure and support, and data management and security.
The facility currently offers microarray screening using the Affymetrix GeneChip platform and massively parallel sequencing (also known as “next-generation sequencing”) using the Illumina HiSeq2000. These services are available to all National Institutes of Health (NIH) investigators, although NIDDK samples have first priority. The user provides samples to the facility for processing (including quantification and quality control) and receives datasets with basic statistical and bioinformatic analyses. Front-end support includes assistance with experimental design and advice on sample preparation. Users also have access to several data analysis software packages. Additional bioinformatic support is available from the facility’s staff members on a collaborative basis. The facility also provides access to real-time Polymerase Chain Reaction (PCR) for target validation.
NIH staff members are encouraged to contact any of the individuals listed above to discuss the application of Genomics Core Facility services to their research programs or to visit the facility in person at Building 8, Room 1A11.
The Genomics Core Facility was created in January 2003 within the NIDDK Office of the Director to provide investigators with innovative, genome-scale technologies in gene expression and DNA sequencing.
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Human Energy and Body Weight Regulation Core
Kong Y. Chen, Ph.D.
The mission of the Human Energy and Body Weight Regulation Core is to collaborate with investigators from across the NIDDK, clinical research programs at the NIH, and other institutions by performing metabolic and physiological phenotyping measurements in healthy volunteers as they relate to obesity, physical activity, and energy metabolism, and in patients with metabolic disorders as they relate to specific metabolic dysregulations.
The Core supports the collection of highly sensitive, continuous measurements of whole-body energy metabolism. We use standard bedside indirect calorimetry measurements of resting energy expenditure and whole-room indirect calorimeters (metabolic chambers) over a 24-hour period. We measure sleep, post-prandial, resting, exercise, recovery, and spontaneous movement periods; substrate oxidation rates over 24 hours; physical activity during free living; heart rate and heart-rate variability; and skin and core body temperatures.
The Core also provides standardized measurements of cardio-respiratory fitness (maximum and submaximum tests performed using upright, recumbent, and treadmill) and body composition (collected using dual energy x-ray absorptiometry [DXA], air-displacement plethysmography [BodPod], bioelectrical impedance, and anthropometry). In addition, staff members advise and consult with clinical research teams to optimize measurement selection and protocol design. Finally, Core members coordinate and provide measurement services, perform routine equipment calibrations and maintenance, and manage related data.
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Laboratory of Animal Sciences Section
Mark B. Foster St. Claire, D.V.M.
The Laboratory of Animal Science Section (LASS) provides support and guidance to the NIDDK’s intramural researchers for all phases of laboratory animal experimentation, including:
- advising staff members about practices for the proper housing, handling, care, and use of research animals to ensure compliance with guidelines issued by the HHS, the U.S. Department of Agriculture, and the Association for the Assessment and Accreditation of Laboratory Animal Care;
- managing animal care facilities in order to maximize the use of animals, animal room space, and animal care resources;
- implementing and coordinating animal disease monitoring, investigation, prevention, and treatment;
- providing guidance on animal-study proposal submission; and
- training animal care personnel.
The LASS is responsible for the housing and care of research animals and for enhancing their well-being. The LASS provides technical animal research services to researchers and surgical support. The section’s facilities and services are available to all NIDDK researchers who have been approved to conduct animal research by the Institutional Animal Care and Use Committee.
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Mouse Knockout Core
Chuxia Deng, Ph.D.
The laboratory supports the NIDDK’s intramural researchers and outside collaborators in their efforts to
- design targeting constructs;
- culture embryonic stem (ES) cells;
- carry out transfection and identify specific targeted clones;
- perform microinjection to create new mouse lines; and
- answer any questions related to gene targeting.
The NIDDK Mouse Knockout Core was established in 1995. Since then, more than 100 knock-out (and knock-in) mouse lines have been generated in the laboratory.
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Mouse Metabolism Core
Oksana Gavrilova, Ph.D.
Ruifeng Teng, M.D., Ph.D., Staff Scientist/Contractor
Tanyana Chanturiya, B.S., Research Assistant
Mouse models of obesity and diabetes contribute greatly to a better understanding of how environmental and genetic factors affect metabolism. The Mouse Metabolism Core Laboratory supports NIDDK’s intramural investigators by characterizing and analyzing phenotypes of metabolic disease in genetically modified mice.
We analyze the following: body composition (MRI and Echo Medical Systems), body temperature (Mini-Mitter telemetry), activity (Accuscan Open Field), feeding behavior (BioDAQ, Research Diets), energy expenditure (Oxymax CLAMS and Columbus Instruments), glucose metabolism (insulin tolerance, glucose tolerance, first phase insulin secretion tests, and euglycemic-hyperinsulinemic clamps), and lipid metabolism ( triglyceride clearance and production and fatty-acid oxidation in whole animals and in isolated muscle). We also assist in the isolation of pancreatic islets, perform transplantation of islets under the kidney capsule, and measure concentrations of major metabolites and hormones in mouse plasma.
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