Keck Biotechnology Resource Lab Offers Wide Range of Technologies
How to Charge the Cost of Analyses and Syntheses to Grants
- For $10,000 or less in services annually, it is usually best to request funding in the “Other Expenses” category. Services should be clearly delineated (number of samples, cost per sample) and well justified in terms of achieving the proposed specific aims.
- For $20,000 or more in services annually, the best approach is to request funding for the actual Keck staff effort, supplies, and instrument maintenance/repair rather than on a service charge basis.
- For annual services in the $10,000 to $20,000 range, either approach may be used. Letters of support in all three cases are usually not required but are available on request.
Biomedical research is increasingly dependent on highly sophisticated instrumentation. For Yale investigators, the Keck Biotechnology Resource Laboratory provides access to one of the largest academic biotech laboratories of its kind. Keck’s 150 technologies are organized into three genomic, three proteomic, and three multidisciplinary resources, providing a wide range of syntheses and analyses that includes gene expression and SNP genotyping using microarray and bead technologies; oligonucleotide and peptide synthesis; DNA and protein sequencing; biophysical analysis of proteins and other biopolymers; biostatistical and bioinformatics analyses; mass spectrometry; protein profiling; and high-performance computing.
Keck offers a number of technologies not often found in academic core labs. Its proteomics capabilities include amino acid analysis; peptide/protein sequencing using the Edman degradation; large-scale peptide synthesis using t-BOC chemistry to synthesize and purify custom synthetic peptides; and biophysics facilities. Keck’s Basic Protein Identification service has been streamlined to offer investigators lower prices and a quick turnaround. Samples are digested with trypsin and analyzed by LC-MS/MS on a Thermo Scientific LTQ Orbitrap, then searched against the NCBinr or UniProtkb/Swiss-Prot databases.
The development of two robust LC-MRM assays for human red blood cell membrane and mouse post-synaptic density fractions now enables Keck to quantify 57 and 119 proteins respectively. The resource is also performing small-molecule quantitation, in particular looking at creatinine levels in urine using mass spectrometry, which allows for increased accuracy compared to older methods.
One example of an innovative project involving Keck’s resources is the work being done in collaboration with Chirag Parikh, M.D., Ph.D., and Lloyd Cantley, M.D., on a targeted proteome assay for urine to identify biomarkers of polycystic kidney disease and acute kidney injury (AKI). “The current traditional methods of diagnosis are outdated, not accurate, and delayed,” said Parikh, associate professor of medicine (nephrology). Until now, most work in this area has been done in animal models. Parikh and his colleagues have taken it to the next level, enrolling 2,000 subjects from 11 institutions to obtain random human samples of individuals with and without AKI. Instead of testing one protein at a time, technology at the Keck lab has allowed Parikh and Cantley to test multiple proteins at the same time; they currently have a list of 200 proteins they’re targeting. Parikh, who had not worked with Keck previously, said that the experience has been rewarding. “It’s a new technology and the Keck people have been very supportive,” he said. “Identifying that magic protein that will help us with either recovery, early diagnosis, or prognosis would be a home run, but the journey so far looks very productive.”
Keck’s genomics technologies include Sanger sequencing, microarray, and oligonucleotide synthesis. Microarray, now located at the Yale Center for Genome Analysis, is winding down as investigators turn to sequencing for identifying genes associated with disease. The oligo synthesis resource provides rapid turnaround and a wide variety of high-quality and complex specialty syntheses.
Keck’s high-performance computing (HPC) resource has about 275 active users from 60 Yale laboratories and is accessible at no cost, thanks to two NIH Shared Instrumentation Grants. HPC is supported by staff with appointments in computer science and an extremely high level of expertise. A number of faculty have purchased their own nodes and/or storage; and new queuing software is expected to allow “common” sharing of idle computing nodes by hundreds of users when these owners are not using them. “You can do high computing,” said Kenneth Williams, Ph.D., co-director of Keck, pointing out that HPC creates almost 200 accounts for new users each year.
Keck At a Glance
|Genomics||Shrikant Mane, Ph.D.|
|DNA sequencing||Nancy daSilva, Ph.D.||Individual tube sequencing, high-volume plate sequencing, PCR purification, fragment analysis, ready-to-run service|
|Microarray||Guilin Wang, Ph.D.||Expression, genotyping, methylation, miRNA, gene expression, CGH|
|Oligonucleotide synthesis||Joe DeLuca||Wide variety of complex specialty syntheses|
|Proteomics||Erol Gulcicek, Ph.D.|
|Biophysics||Ewa Folta-Stogniew, Ph.D.||Resources to study the oligomeric state of biomolecular assemblies and the thermodynamics and kinetics of macromolecular interactions|
|MS/Proteomics||Chris Colangelo, Ph.D.
TuKiet Lam, Ph.D. (FTICR/MS)
|Amino acid analysis||Myron Crawford||Amino acid composition of peptides and proteins|
|Protein/peptide sequencing||Myron Crawford||Amino-terminal sequencing|
|Small-scale peptide synthesis||Janet Crawford||FMOC peptide synthesis (25-100 µmol)|
|Large-scale peptide synthesis||James I. Elliott, Ph.D.||t-BOC peptide synthesis (0.5 mmol)|
|Bioinformatics||Mark Gerstein, Ph.D. and Hongyu Zhao, Ph.D.
||Support of software provided by core; consultation on DNA/protein sequence, microarray, protein structure, pathway analysis; collaboration on bioinformatics projects|
|Biostatistics||Hongyu Zhao, Ph.D.||Statistical and computational analysis of such various types of data as gene expression, genotyping, mass spectrometry, next-generation sequencing, and many others|
|High-performance computing||Robert Bjornson, Ph.D. and Nicholas Carriero, Ph.D.
||Analysis and interpretation of data resulting from Keck technologies|
Advantages of Working with Keck
“One of the ways by which Keck seeks to achieve its goal of maximizing its contribution to biomedical research is by balancing services with grant support,” said Williams. This approach enables the lab to provide better and more analytical services at lower cost. NIH-funded and other centers closely associated with Keck carry out research that results in new and improved technologies, which are then made available to the more than 1,000 investigators from 300 institutions who use Keck’s services each year. For example, Keck’s NIDA Neuroproteomics Center Grant enables the 26 investigators in the Neuroproteomics Center to utilize MS/proteomics technologies at no charge while at the same time allowing Keck to offer a range of proteome analyses on a service-charge basis to other investigators.
Keck’s bioinformatics and biostatistics resources stand ready to help users interpret the often huge amounts of data that result from the high-throughput analyses it provides. In close collaboration with the Center for Medical Informatics, Keck has built the Yale Protein Expression Database (YPED), an integrated Web-accessible software system that addresses the storage, retrieval, and integrated analysis of high-throughput proteomic and small-molecule analyses. The YPED interface supports sample submission, project management, sample tracking, data import, sample administration, and user billing. It also contains a repository for public access to protein identification experimental data and serves as a peptide spectral library for all of Keck’s protein database search identification results. “We believe that few if any other academic core labs provide their users with similar databases to help fully leverage their analyses,” said Williams.
The Keck Lab is one of the oldest academic core labs built on a service-charge model. While Keck’s facilities are open to both Yale and non-Yale users, Yale investigators receive priority and benefit from lower rates. Most analyses and syntheses are provided on a full-service basis. The backlog of non-Yale requests helps maintain high productivity and low service charges when Yale demand is below capacity. The backlog also increases the ability of the Keck lab to compete for grants. For example, Keck has been awarded 25 NIH Shared Instrumentation Grants (sigs); the current NIH sig provided $600K for Keck’s LTQ Orbitrap Elite Mass Spectrometer and was supported by 52 faculty members at 10 universities across the country. Keck’s ability to attract requests from approximately 600 investigators and more than 300 institutions each year is a testament to the high quality of the services it offers.
Sample submission forms, drop-off hours and locations can found online at http://medicine.yale.edu/keck/index.aspx; or call 203-737-2206 for more information.