We hope you are enjoying (finally!) this season of warm weather and road repair, here in Madison. We are writing now to touch base and summarize our recent activities at the UW Biotechnology Center. As you may be aware, the UWBC has expenditures of ca. $16 million per year and ca. 154 employees, with activities focused on our three main missions:
- Establishment and support of core facilities in basic research services (e.g., DNA sequencing and other genomic profiling technologies),
- Faculty research and innovation in genomic sciences within the UW Genome Center, a ‘center within the center’.
- Outreach and education of K-12 and the general public and government leaders, in biotechnology.
Since our previous ‘letter to the community’ was sent out in the fall of 2011, we will focus here on what has transpired within the past two years. We encourage you to visit our website at http://www.biotech.wisc.edu for complete details. As always we welcome your feedback about our current activities and possible future directions for the Biotechnology Center.
BIOTECHNOLOGY CORE FACILITIES
The Bioinformatics Resource Center (BRC) was created on July 1, 2012 with the recruitment as Director of Dr. Xiao-yu Liu from the Mayo Clinic. It provides computational support for high-throughput DNA and RNA sequencing data and project-specific advanced bioinformatic analysis. In addition to data analysis service, the BRC provides consulting services for pre-experimental project design, post-sequencing data analysis strategy, and grant proposals. A wide variety of techniques are supported, including genome re-sequencing and comparison, variant identification, quantification of the relative abundances of mRNA and small RNA transcripts, and studies of the binding sites for DNA-binding proteins. Additionally, a computer lab with high-end computing hardware and specialized software is maintained for the benefit of researchers wishing to perform their own data analyses. UWBC has continued to add to its IT infrastructure and staffing to support these activities, and now has over ½ petabyte of data storage and several hundred processing cores of compute power.
BRC has hired two additional highly skilled bioinformaticians, Dr. Fenglou Mao (U. of Georgia) and Dr. Derek Pavelec (Prevention Genetics, Marshfield, WI), to meet the campus’ increasing demands. Several automated data analysis pipelines, including DNA resequencing and ChIPseq analysis, have now been developed for fast and reliable data analysis. BRC has also created NGS data analysis workshops for researchers to learn data analysis techniques and to fully utilize the BRC computing resources. On Jan. 1, 2013 a collaborative effort with the Waisman Center started in which BRC operates an outreach post at the west campus to provide on site support for their investigators. Close collaborations with other colleges, centers and departments are being actively sought. Dr. Liu is available to provide half hour or hour long seminars to any units on campus interested in meeting and learning more about the BRC service and capabilities.
Contact: Dr. Xiao-yu Liu, email@example.com.
DNA Sequencing and Synthesis Facilities. Thanks to the generous support of five campus groups, several next generation DNA sequencing platforms are now operating at the UWBC DNA Sequencing Facility/Gene Expression Center. These include a Roche GS FLX Plus, two Illumina HiSeq 2000s, an Illumina MiSeq, an Ion Torrent PGM and an Ion Torrent Proton. Howard Hughes investigators on campus (with thanks to Judith Kimble, Paul Ahlquist and Sean Carroll!) obtained funding for a GAIIx followed by an upgrade arrangement that resulted in our first HiSeq 2000. Our second HiSeq was obtained partly through WID support (with thanks to John Denu and WID!). We also thank Phil Simon and his USDA campus colleagues for providing financial resources to acquire a Roche Next Gen DNA Sequencing platform and Mei Baker in the State Lab of Hygiene for housing her Illumina MiSeq in our facility and making it available to campus when not being used for her own projects. We have just recently placed an order for an Illumina HiSeq 2500 (an instrument that can provide much faster turnaround service, days rather than weeks), and a second MiSeq which provides a much smaller amount of sequence (tens of millions rather than hundreds of millions of reads) but at a lower cost of reagents and, like the HiSeq 2500, with a faster turnaround time.
With the introduction of the latest Illumina chemistry on this campus, our sequencing capacity grew to 120 billion bases per day on the HiSeq platform. Other platforms have also benefitted from advancement to their reagents and base calling algorithms. The Roche sequencing chemistry and software recently underwent improvements boosting read lengths to ~900 base pairs and the Illumina MiSeq read lengths are following suit with ten to twenty million 450 base pair reads now possible. As the number of instruments grows and our familiarity with their diverse applications and nuances increases, we have expanded our ability to provide high quality, cost effective sequencing options. Applications that we have already performed on campus include ChIP-Seq, mRNA-Seq, small RNASeq, resequencing of genomes, targeted sequencing (exome, gene panels), and de novo sequencing of small and large genomes. The purchase of a HiSeq 2500 and another MiSeq will enable us to provide more rapid turnaround of these services when grant deadlines loom.
DNA synthesis continues to be an active part of this facility and the group aims to provide the highest quality and inexpensive oligonucleotides including unique modifications. Recent protocol changes have improved yield, fidelity and purity. An extensive array of modifications are available. Contact: firstname.lastname@example.org.
The Gene Expression Center (GEC) offers a wide array of RNA based services ranging from cutting edge technology such as next generation sequencing (NGS), to robust/reliable microarray expression and genotyping, and quantitative PCR. In collaboration with the DNA Sequencing Facility, the GEC offers RNA library preparation services for mRNA and Small RNA Sequencing. Libraries prepared in the GEC are submitted to the DNA Sequencing Facility for sequencing. Microarray expression services using the Affymetrix GeneChip Instrumentation and the Illumina iScan System are available at a variety of level of services to meet campus needs. In addition, array based genotyping services are also available on the Illumina iScan platform. In collaboration with the DNA Sequencing Facility, a Laboratory Information Management System (LIMS) is being implemented for sample tracking and laboratory process management.
The Mass Spectrometry Proteomics and Metabolomics Facility has undergone significant changes in terms of new equipment, personnel and services available, over the past two years. In October 2010, Dr. Amy Harms left the facility to pursue new opportunities overseas and Dr. Greg Barrett-Wilt was appointed as the new Director. The mass spectrometry facility maintains a diverse group of mass spectrometers with unique capabilities to provide a broad spectrum of services to clients. These instruments include an AB Sciex 3200 QTRAP (acquired 2005), an AB Sciex 4800 MALDI TOF/TOF (acquired 2005), an Agilent Nanoflow LC/MSD Trap SL (acquired 2003), and Agilent LC/MSD TOF (acquired 2005), a ThermoFisher LTQ-Orbitrap XL with ETD (acquired 2008), a ThermoFisher Scientific TSQ Quantum Discovery Max (acquired 2012) and an AB Sciex 5500 QTRAP with Eksigent nanoflow ChipLC (acquired 2011). The ThermoFisher Scientific LTQ-Orbitrap XL continues to be an important instrument for the facility and has provided critical data. It is the primary platform for untargeted analysis of complex protein mixtures and is used for both label-free quantitation by spectral counting and through stable isotope metabolic labeling. It is also the go-to instrument for identification of proteins present at low levels from samples after in-gel digestion and for identifying and quantifying posttranslational modification sites, such as phosphorylation. The AB Sciex 5500 QTRAP instrument has recently been used extensively by researchers on campus for very high sensitivity protein quantitation experiments from complex biological matrices, with attomole sensitivity and a dynamic range of at least five orders of magnitude. The typical workflow for these experiments involves digestion of a complex protein mixture containing the proteins of interest using trypsin protease, spiking the resulting peptide mixture with synthetic, stable isotope-labeled forms of peptides to be used for protein quantitation, and acquisition of the data in single-reaction monitoring (SRM) mode. As many as 50 ‘targeted’ proteins can be quantified in a single LC/MS/MS analysis using this approach. The mixture of labeled synthetic is added to all the samples to be quantified in the same amount, and thus serves as an internal standard for comparison of target protein abundance across multiple samples. This approach has been applied to not only protein quantitation, but also to relative quantitation of phosphorylation events at specific sites in response to stimuli. Unlike the untargeted approach with the Orbitrap, the targeted SRM approach with the Sciex triple quad provides biologists with greater reliability in observing the same peptide in multiple experiments even with highly complex unfractionated samples.
A new major effort in the mass spectrometry facility is in conjunction with the Molecular Archaeology Group led by Prof. William Aylward in the Classics Department. Prof. Aylward is the newly appointed director of the joint archaeological expedition at the ancient city of Troy in Turkey. Greg Barrett-Wilt visited the site last August and has been working on devising techniques to analyze protein residue from pottery from the site. This work was featured on the cover of the Wisconsin State Journal on October 18, 2012. Dr. Barrett-Wilt, along with several other students, scientists, staff, and faculty from UW-Madison, will visit the site again in July - August 2013 to continue this work.
The Peptide Synthesis Facility now offers a microwave based system for ‘do-it-yourself’ users, in addition to the Symphony and Prelude automated peptide synthesizers, which can create smaller synthesis scales (at decreased cost) and Absolute QUAntification (AQUA) peptides for highly sensitive mass spectrometric based measurements of proteins and their modifications. Routine peptides frequently have a quick turnaround time.
The Transgenic Animal Facility (TAF) has introduced new molecular biology services which now include gene targeting in C57BL/6 embryonic stem cells and re-deriving genetically modified mouse strains for importation into the new pathogen free animal facilities on campus. The sperm cryopreservation and in vitro fertilization programs are also new services. Recently they have generated knockout mice by the microinjection of zinc finger nucleases, a technology which enables the generation of knockouts in rats and in mice of many different genetic backgrounds. In April 2012, they welcomed a new staff member, embryologist Xiao Huang, to the animal services team.
The Targeted Genome Editing Facility (TGEF) was created October 2011. This new facility designs and constructs Transcription Activator-Like EffectorNucleases (TALEN)forgenomeediting. The Facility will also provide different levels of characterization ofTALENs to suit your specific researchneeds. This facility is completing the beta phase within the coming month and hopefully will be in full production by summer of 2013.
THE GENOME CENTER OF WISCONSIN (GCW)
The Genome Center of Wisconsin (GCW), founded a decade ago by Genetics Professor Fred Blattner, has continued to thrive and develop over the past two years, under the leadership of Chemistry Dept Professor Lloyd Smith. The GCW, which is a ‘center within the center’ at UWBC, serves as home for several prominent ongoing and new faculty collaborative and individual research programs and training grants:
The National Library of Medicine Computation and Informatics in Biology and Medicine (CIBM) Training Program, which provides 9 predoctoral and 9 postdoctoral training slots to the UW Madison community, has recently undergone a change in leadership. Mark Craven has taken over duties from George Phillips as PI for the program, as George has moved back to Rice University. The program was competitively renewed for five more years last July. The NHGRI Genomic Sciences Training Program (GSTP) which provides 10 predoctoral and 4 postdoctoral training slots to the UW Madison community, continues to thrive under the leadership of PI David Schwartz, and was also competitively renewed for five more years starting July 2013. The National Human Genome Research Institute funded Center of Excellence in Genomic Sciences is a collaboration with the Medical College of Wisconsin, co-directed by Lloyd Smith (UW) and Michael Olivier (MCW), with Madison co-P.I.’s Joshua Coon and Audrey Gasch, and is now entering its fifth year of funding. A W.M. Keck Foundation Award was recently awarded to Aseem Ansari, Parmesh Ramanathan, Jennifer Reed, and David Schwartz to build “Genome Foundries.” More details at: http://www.news.wisc.edu/20951
In addition to these efforts, our GCW members continue their remarkable success in securing new individual and joint research grants. Some of these include:
- Josh Coon: NIH R01 “A GC/FTMS for Ultra-High Accuracy Metabolite Identification”; NIH R01 “Regulation of Mitochondrial Metabolism by Post-Translational Modifications”, with co-PI Dave Pagliarini.
- Mark Craven: NSF grant “Active Learning with Rich Query Types on Networks and Trees”, with collaborators Audrey Gasch and Paul Ahlquist.
- Colin Dewey: Co-PI for ENCODE Computational Analysis Grant with SunduzKeles (PI) and Emery Bresnick (Co-PI).
- Audrey Gasch: NIH R01 “Functional Genomics of Stress in Yeast”.
- David Page: NIH R01 “Secure Sharing of Clinical History & Genetic Data: Empowering Predictive Personalized Medicine”; NIH R01 “Machine Learning for Identifying Adverse Drug Events”; NIH R01 co-PI for “Informatics Techniques to Optimize Mammography for Aging Populations” (PI Burnside).
- Bret Payseur: NIH R01 “Genetics & Evolution of Extreme Body Size”.
- Lloyd Smith: NIH U54:”QPASS: Quantitative Parallel Aptamer Selection System”, Co-PI with James
- James Thomson and Tom Soh (UC Santa Barbara, Department of Mechanical Engineering); NIH R01 “A Mechanical Nanomembrane Detector for Time-of-Flight Mass Spectrometry” with Co-PI Robert Blick.
- James Thomson: NIH UH2 “Human iPS/ES Cell-based Models for Predictive Neural Toxicity and Teratogenicity” with UW Collaborators David Page and William Murphy.
Promotions: Audrey Gasch and Colin Dewey were promoted to Associate Professor; Josh Coon and Nicole Perna were promoted to Full Professor.
Other activities by GCW Faculty:
- Aseem Ansari has established a remarkable US-India scholar exchange program, called the Khorana program and its success has recently led to the establishment of a sister program, called the Bose program. These programs will permit us to bring in 50 of the best Indian undergraduate students to UW and the Khorana partner institutions. The Indian government willalso provide funds for 30 US undergraduate students (juniors or higher) to spend a summer doing research in India. Taken together, between Khorana and Bose, UW now hosts the second largest US-India scholar exchange program. See the following websites for more information: http://www.biochem.wisc.edu/faculty/ansari/khorana_program/ and http://www.biochem.wisc.edu/faculty/ansari/bose_scholars/bose.aspx
- Josh Coon’s research has been highlighted in two recent news reports, one in Proteomics News: “Analytical Trick May Accelerate Cancer Diagnosis.” and a second in NIGMS ‘Latest News’: “Analytical Trick Accelerates Protein Studies.”
- Jamie Thomson continues to receive international awards and recognition for his ground-breaking work in stem cells. He received the Albany Medical Center Prize and the King Faisal International Prize in Medicine in 2011, and The International Society for Stem Cell Research will present him with the McEwen Award for Innovation at their annual meeting in June 2013.
BioTrek is the public outreach program operated jointly by the UW-Madison Biotechnology Center together with UW-Extension Cooperative Extension. There were five main activities provided by Biotechnology Center Outreach Director Dr. Tom Zinnen and his staff:
- BioTrek Fieldtrips at UW-Madison Biotechnology Center. The program welcomes K12 students and other groups of visitors to our Outreach Teaching Lab where they explore the basics of DNA. Ourfieldtrip activities include extracting DNA from wheat, analyzing a purified sample of DNA, and performing gel electrophoresis. A specialcomponent of the fieldtrips is the opportunity to walk through UWBC labs so visitors get a chance to see firsthand research labs and to chat with UWBCscientists. We also partner with other groups, such as Grandparents University and the Operation Military Kids University, to support summertime programs that welcomefamilies and groups to campus.
- Plant Proteomics Outreach Project. Cheryl Redman is working with UWBC colleagues to develop a new series of hands-on activities that helps visitors connect key ideas about the interplay of DNA, RNA andproteins. She has actively engaged visitors by introducing them to the field of proteomics, using mass spectroscopy and informatics.
- Wednesday Nite @ The Lab. The Biotechnology Center hosts this public science series held every Wednesday night, 50 times a year. WN@TL audiences average roughly 40 people attending each seminar, and its reach isamplified by the webstream available both live and in archives at: biotech.wisc.edu/webcams. WN@TL reaches a statewide audience through Wisconsin Public Television'sUniversity Place series, which records most WN@TLs for later broadcasts.
- Building the UW-Madison Community of Science Outreachers. BioTrek staff launched and continue to convene and host the UW-Madison Science Alliance, composed of science outreachers from all across campus. Science Alliance organizes UW-Madison Science Expeditions, the annual three-day campus-wide science open house held every April. BioTrek staff maintain thescience.wisc.eduwebsite,which is UW-Madison's science outreach portal for the public. Science Alliance also supports a series of Family Science Nights organized by the Adult RoleModels in Science program and held in communities around Madison
- Programs Across Wisconsin. In 2012 BioTrek staff helped organize a new series of "UW Outreach Days" in various communities across the state, including UW Day at Dodge County, UW Day at Marinette and UW Day at the State Capitol. These are modeled after UW Day at the State Fair, an event for which BioTrek staff recruit UW-Madison science outreachers to staff 20 Exploration Stations. BioTrek also participates in the three-day Wisconsin Farm Technology days held every July.
Overall, in 2011 the UWBC outreach group connected face to face with 4394 learners through classroom visits, Field Trips and Tours at the Biotechnology Center and in 2012, they connected directly to 8108 learners through programs such as Wednesday Nite @ the Lab, Field Trips, and classroom visits. So far in 2013, they have reached out to 1935 learners. In addition, BioTrek reached many others outside campus by helping co-organize major events such as UW-Madison Science Expeditions and UW Day at the State Fair.
Michael R. Sussman, PhD, UWBC Director, and Bascom Class of 1933 Endowed Professor, Dept of Biochemistry; email@example.com, 608-262-8608
Charles Konsitzke, UWBC Assistant Director, firstname.lastname@example.org, 608-262-8607