Vanderbilt Institute For Integrative Biosystems Research And Education

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GlucoseVanderbilt Institute for IntegrativeBiosystemsResearch and EducationLactateGlycolysisNAD NADHAcidificationThird-YearCO2 Review of Academic Venture Capital Fund InitiativesGlycogenDecember, 2004TCA CycleO-2NADPHOxidaseNADHNAD OxidativePhosphorylationJohn P. Wikswo, DirectorFranz J. Baudenbacher, Deputy DirectorOxygenHeat

EXECUTIVE SUMMARYThe Vanderbilt Institute for Integrative Biosystems Research and Education, VIIBRE,was created in December, 2001 with a 5.1 million, five-year grant from the VanderbiltAcademic Venture Capital Fund (AVCF) to help move Vanderbilt University to a leadership rolein basic research, technological development, and the delivery of advanced education in thebiophysical sciences and bioengineering, particularly in areas involving the application of microand nanotechnologies to biology and medicine. The VIIBRE mission is to 1) strengthen andbroaden our existing foundation of basic research in the biophysical sciences andbioengineering; 2) develop enabling technologies that span these disciplines; 3) provide closearticulation of the biophysical and biochemical sciences and bioengineering with ourundergraduate, graduate, and postgraduate educational programs in biology and medicine; and4) foster programs of outreach to industry, government, and other educational institutions.Taking advantage of Vanderbilt’s existing strengths in the biological and physicalsciences, medicine, engineering, and education, VIIBRE is creating on-campus collaborations inresearch areas that include instrumenting and controlling the single cell, therapeuticbioengineering, biological applications of nanosystems, and cellular/tissue bioengineering andbiotechnology. VIIBRE has also contributed to University initiatives in biomedical imaging andbioengineering education technologies. VIIBRE has gathered a highly qualified and diverse setof investigators from twenty-one departments in four schools at Vanderbilt. Ten Senior FacultyFellows, thirty Faculty Fellows, and ten External Associates comprise the core of VIIBRE.Thirty-nine other faculty members have participated in the submission of grant proposals.VIIBRE has participated in the training of eighteen postdoctoral research associates, thirtyseven graduate students, two high school teachers, forty-four undergraduates, and one highschool student. VIIBRE works with investigators from six other universities, three companies,and two federal laboratories. VIIBRE has been directly involved with 216 individuals.As of June 30, 2004, VIIBRE has spent approximately 40% of its AVCF grant and is ontrack with its original budget. The core research program for VIIBRE has been funded in part bya 2 million, three-year DARPA grant and two smaller NIH SBIR grants that preceded the formalstart of VIIBRE. A million-dollar grant from the Whitaker Foundation with comparable matchingby VIIBRE allowed the addition of two new tenure-track faculty members to the Department ofBiomedical Engineering. In addition VIIBRE has been the primary contributor to the startupcosts of one faculty member in Physics & Astronomy, and a secondary contributor to two inBiomedical Engineering and two in Chemistry. VIIBRE and VIIBRE-related grants and contractshave supported eleven postdocs, twenty-five graduate students, and thirteen undergraduates.VIIBRE faculty have created or revised nine courses in three departments.To date, fourteen peer-reviewed publications and twelve patent applications have beenmade possible by VIIBRE or VIIBRE-related funding. Sixty people from nine departments haveused the three VIIBRE-created microfabrication clean rooms dedicated to BiologicalMicroElectromechanical Systems (BioMEMS). VIIBRE is developing several laboratories thatare well-equipped for cellular instrumentation and control and tissue engineering.Since it began officially in December, 2001, VIIBRE has been involved in 52 proposalsfor funding this new endeavor. VIIBRE faculty have led or contributed to eleven research grantsand contracts that have been funded for a total of over 20 million. Thirteen proposals arepending, with a total potential value of about 29 million. Seven proposals are being preparedfor resubmission, with a potential value in excess of 18 million. Eighteen proposals weresubmitted to be declined or withdrawn, for a total value of more than 36 million. VIIBRErecognizes fully the need to obtain grants, contracts, and gifts that provide several million dollarsannually to continue its research program beyond the initial funding of the AVCF.The short-term challenges facing VIIBRE are providing adequate space for a growingnumber of VIIBRE projects and personnel, and obtaining adequate staff support for grantsaccounting and for the submission of large, multi-investigator proposals. The long-termchallenge is to obtain funding to support the research programs after June 30, 2006, to institutea fee-for-services structure, and devise a means by which VIIBRE members can continue todevelop and launch new programs and proposals that are beyond existing grants and contracts.2

Table of ContentsEXECUTIVE SUMMARY . 2I. Intellectual thrust . 5A.Research direction. 6B.Changes, if any, in direction since project inception . 6II. Funding (AVCF) – Expenditures as of 6/30/2004 and for the future . 7III. Accomplishments to date . 7A.Research. 7B.Publications and Underlying Science . 8C.Patents and Licensing . 9D.Grants . 9E.Faculty Recruitment . 9F.Curriculum. 10G.Cellular Instrumentation Laboratory Training Program . 11H.Facilities. 131. Renovation Strategy . 132. VIIBRE Clean Room Facilities. 133. VIIBRE Laboratories and Shops . 14I.Undergraduate, Graduate, and Postdoctoral Programs. 14J.Collaborations. 151. Vanderbilt Collaborations . 152. External Collaborations. 16K.Minority Support . 16L.Outreach . 161. Website . 162. Industry Interns. 173. Conferences . 174. Research Experience for Teachers . 17IV. Opportunities and obstacles in the days ahead. 17A.Unanticipated issues and events, if any, since initiative got under way . 17B.Prospects and plans for sustainability beyond AVCF seed funding. 17V. Organization of the initiative. 17A.Administrative structure. 171. Management Structure . 172. Staff Support . 18B.Decision-making protocols and processes . 181. Research directions. 182. Expenditures . 183. Other substantive issues . 19VI. Effect of institutional organization and tradition . 19A.Impediment to interdisciplinary/inter-school initiatives?. 19B.Suggestions . 19APPENDIX A – VIIBRE Publications . 20APPENDIX B – VIIBRE Patents and Disclosures . 213

APPENDIX C – VIIBRE Facilities . 221. Microfabrication Clean Rooms . 222. Cellular Instrumentation and Control Laboratory. 233. Microscopes . 244. Cell Culture. 245. Biomaterials, Drug Delivery, and Tissue Engineering Laboratory . 256. Tissue Electrophysiology Imaging Laboratory . 257. Electronics Shop . 268. Prototype Development Machine Shop . 269. General VIIBRE Laboratories. 26APPENDIX D – VIIBRE Research Projects . 27APPENDIX E – VIIBRE Core Faculty . 30APPENDIX F – VIIBRE Trainees . 33APPENDIX G – Faculty Participating in VIIBRE Proposals. 38APPENDIX H – Staff Supporting VIIBRE . 40APPENDIX I – Users of VIIBRE Facilities . 41APPENDIX J – VIIBRE Grants and Proposals. 44APPENDIX K – Images from VIIBRE Projects, Publications, and Proposals . 504

Vanderbilt Institute for Integrative Biosystems Research and EducationI. Intellectual thrustWe are witnessing a revolution in biology and medicine associated with the new-foundability to determine in detail the genome of humans and many animals and organisms used inbiomedical research. These findings have triggered major efforts to identify the structure andfunction of the hundreds of thousands of proteins and protein variants that are encoded by tensof thousands of genes. It is becoming increasingly clear that applications of genomics andproteomics are limited because the function of living systems is determined not only by genesand the structure and function of their individual proteins, but also by the marvelous complexityof protein-protein and other intra- and intercellular interactions. It is generally recognized thatthe greatest challenge facing biomedical science is the integration of genetic and molecularknowledge – generated at a bewildering rate for the last few years – into a systems knowledge.This in turn must map into an understanding of the basic processes of normal function anddisease, and into the design of effective, specific, controlled treatments. We envision that withinthe next decade there will be a major, international need for advanced research and training tosupport quantitative, post-proteomic, multiscale, dynamic integrative biology, often described as“systems biology.” We believe that the greatest progress in this area will be made by programsthat can bring great interdisciplinary and technological strength to bear on the problem.Chemists, engineers, mathematicians, and physicists who can work closely with biologists andphysicians will be able to make advances that would be impossible for one group working alone.Many of the problems amenable for examination by biophysical scientists and engineersare exquisitely complex and require the combined power of instrumentation development,experiment, and mathematical theory. For example, at Vanderbilt and elsewhere, dynamicprocesses are being investigated in many biological systems using a wide range ofsophisticated experimental and theoretical approaches, with an emphasis upon determiningcritical links between structure and function. Important biological processes span many ordersof magnitude in time, such as the femtosecond dynamics of electron transfer reactions to theyears time scale representative of the aging process.With increasing frequency incontemporary biomedical research, the spatial organization of systems is known with somecertainty. However, the factors that modulate this spatial organization are often not understood.Unraveling the time-dependent changes in biological structure and organization routinelyinvolves the use of sophisticated experimental and theoretical approaches, with the aim ofunderstanding the nature of a biological system, including the unifying principles that willgeneralize to related systems. Given this understanding, it will be possible to tailor and guidebetter therapies for specific disorders. The investigation of dynamical processes whose spatialscales span orders of magnitude provides an ideal forum for enhanced coupling betweenbiology, chemistry, engineering, mathematics, medicine, and physics.Given the anticipation of the ever-increasing need to integrate the flood of biologicalinformation, the Vanderbilt Institute for Integrative Biosystems Research and Education(VIIBRE) is concentrating on two kinds of integration – the integration of biological knowledgeinto a systems framework, and the integration of biomedical research and education. VIIBRE ispoised to address the challenges of research and education in systems biology. Our view isthat the full integration of the physical and engineering sciences with biology is an absoluteprerequisite for progress in post-reductionist biology, both in academe and industry. Thephysical and engineering sciences are rich in quantitative, systems approaches based uponfoundational information, and there is a long history of successful efforts in applying thisapproach at Vanderbilt. Vanderbilt, through VIIBRE and other efforts, is addressing theformidable current biological challenges with a dedicated interdisciplinary approach in researchareas such as cellular biosensors for chemical and biological warfare defense; infectiousdisease detection; single- and multi-cellular instrumentation and control; biological applicationsof nanosystems; biotechnology; cellular/tissue bioengineering; cell motility in embryonicdevelopment, angiogenesis, cancer, and wound healing; point-of-care diagnostics, andbioengineering education.5

A. Research directionInvestigators with rigorous training in the physical, engineering, chemical, andcomputational sciences are essential for continued progress on the interdisciplinary fronts thatare the hallmark of modern biology. However, experience dictates that a fundamentalunderstanding of the biological system and extensive interaction with investigators from thebiological sciences are essential for trainees and faculty in the physical sciences andengineering to make substantial research contributions to biophysical and bioengineeringresearch. With this in mind, the VIIBRE was created in 2001 with a 5.1 million, five-year grantfrom the Vanderbilt Academic Venture Capital Fund. The vision and mission of VIIBRE, andthe strategy to achieve it, are as follows.Vision: VIIBRE will help move Vanderbilt University to a leadership role in basicresearch, technological development, and the delivery of advanced education in the biophysicalsciences and bioengineering, particularly in areas involving the application of micro- andnanotechnologies to biology and medicine.Mission: VIIBRE will: 1) strengthen and broaden our existing foundation of basicresearch in the biophysical sciences and bioengineering; 2) develop enabling technologies thatspan these disciplines; 3) provide close articulation of the biophysical sciences andbioengineering with our undergraduate, graduate, and postgraduate educational programs; and4) foster programs of outreach to industry, government, and other educational institutions.Strategy: VIIIBRE has made the strategic decision to bring to Vanderbilt new researchcapabilities that can support fledgling research efforts in the biological application of micro- andnanofabrication, which in turn should grow into self-sustaining research programs. We haveidentified four themes for which Vanderbilt has a potential strategic advantage: Instrumentingand Controlling the Single Cell, Therapeutic Bioengineering, Biological Applications ofNanoSystems, and Cellular/Tissue Bioengineering and Biotechnology. Given the lack ofexpertise in these areas at Vanderbilt, VIIBRE launched a major effort, in the form of thirtyprojects listed in Appendix D, to obtain sufficient preliminary data (Appendix K) to support thesubmission of over fifty research and training proposals (Appendix J) to NIH, DOD, NSF andother agencies and foundations. VIIBRE is bringing together existing junior and senior faculty,recruiting a small number of additional faculty members, and constructing as economically aspossible the specific facilities and instrumentation (Appendix C and I) required to support thesethemes and ensure that the investment will bring immediate, concrete return in the form of newcollaborations, grant support, and training opportunities. It is expected that these themes willmature and lead to external funding so that new themes can take their place within VIIBRE.As a part of this process, VIIBRE has strengthened the connections between theDepartments of Biochemistry, Biomedical Informatics, Biomedical Engineering, Cancer Biology,Chemistry, Chemical Engineering, Civil & Environmental Engineering, Electrical Engineering &Computer Science, Mathematics, Mechanical Engineering, Medicine, Microbiology &Immunology, Molecular Physiology & Biophysics, Pathology, Pediatrics, Pharmacology, Physics& Astronomy, Plastic Surgery, Radiology, Radiation Oncology, and Surgery (Appendices D, E,and G). VIIBRE has contributed to the recruiting of faculty in biomedical engineering,chemistry, and physics. VIIBRE has funded new graduate students in Physics, BiomedicalEngineering, Chemistry, and Chemical Engineering, and supported others through both VIIBREand VIIBRE-related grants and contracts (Appendix F). VIIBRE has led the development ofnew courses in cellular instrumentation, bioelectricity, tissue engineering, and biophysicalmeasurements. VIIBRE is supporting the efforts of the Vanderbilt-Northwestern-TexasHarvard/MIT (VaNTH) Engineering Research Center in Biomedical Engineering Education.B. Changes, if any, in direction since project inceptionNature of Changes: There have been remarkably few changes in VIIBRE since itsinception. More effort than anticipated was required to complete and instrument the cleanrooms, but the College of Arts & Science agreed to support some of the costs of buildingrenovation, and our staff (Appendix H) managed to produce a highly effective facility on arestricted budget and a tight time line. We have focused on specific projects that were notenvisioned when VIIBRE was proposed, but these projects are completely consistent with the6

original choice of topics. The interactions with the Department of Physics & Astronomy haveproven less fruitful than expected, but growing collaborations within and between theDepartments of Biomedical Engineering, Chemistry, Molecular Physiology & Biophysics, andMicrobiology & Immunology have more than compensated.How changes were accommodated and implemented: The changes were in generalimplemented by discussions between VIIBRE management, VIIBRE fellows, and theappropriate department chairs and deans. The VIIBRE staff has proven to be remarkably selfreliant and able to accomplish a great deal in a short time.II.Funding (AVCF) – Expenditures as of 6/30/2004 and for the futureSpentFutureCategories 322,033 850,0001. Faculty salaries (Note 1) 598,595 396,4052. Faculty start-up (Note 2) 174,609 475,0003. Staff salaries 203,671 500,5004. Graduate student support 15,991 30,0005. Undergraduate student support 50,0005. Facilities (Note 3) 590,467 375,0006. Equipment 205,495 325,0007. Supplies 22,628 15,1688. Travel9. OtherTotal 2,133,489 3,017,073Total 1,172,033 995,000 649,609 704,171 45,991 50,000 965,467 530,495 37,796 5,150,562Notes: 1) Includes 150,000 (Years 1-3) of postdoc salary, plus fringe benefits. A larger number of postdocswill be supported in Years 4-5. 2) Funds spent towards a 280,000 guarantee of graduate student support tofaculty startups are listed under Graduate Student Support. 3) VIIBRE contribution to clean room constructioncosts is given under equipment, e.g., clean room fans, filters, curtains, lights and hardware.III. Accomplishments to dateTaking advantage of Vanderbilt’s existing strengths in the biological and physicalsciences, medicine, engineering, and education and the close physical proximity of Arts andScience, Medicine, and Engineering at Vanderbilt, VIIBRE is creating new on-campuscollaborations in research areas such as cellular instrumentation and control, biologicalapplications of nanosystems, and cellular/tissue bioengineering and biotechnology, and isstrengthening existing efforts in biomedical imaging and bioengineering education technologies.We are doing this through a combination of new research initiatives, aggressive proposalsubmission, faculty development, new courses, and industrial connections, all of which shouldbe considered “true signature accomplishments” that far exceed the capabilities of existingprograms at Vanderbilt. We are just now beginning to see scientific return on this investment.A.ResearchWhen we proposed VIIBRE to the University administration, we believed that biologyand medicine at Vanderbilt were poised to take advantage of many recent advances in microand nanofabrication, but we were lacking not only the requisite science and engineeringexpertise, but also the specialized instruments and devices and the facilities required to producethem. A timely strategic investment could propel Vanderbilt forward in the emerging field ofsystems biology. However, from the outset, we have recognized that for VIIBRE to bring alasting return on Vanderbilt’s considerable investment in VIIBRE, it would be necessary for us tocreate a self-sustaining research program that transcended a specific physical facility. Hencewe have been concentrating on developing new devices and measurements that supportspecific research programs in biology and medicine, and then immediately leveraging this effortby preparing research proposals for external funding of the now-enabled scientific enquiries.During this process, the students’ research leads to undergraduate and graduate degrees.7

Our program in experimental, quantitative systems biology is focused on high-bandwidth(i.e., rapid temporal response) in vitro studies of membrane, single-cell, and multi-cellphysiology.VIIBRE is using soft-lithographic MEMS (microelectromechanical systems)fabrication techniques to create silicone-based elastomeric NanoPhysiometers andPicoCalorimeters that will eventually measure simultaneously from a small population ofcultured cells in a sub-nanoliter cell-culture chamber the following extracellular quantities: heatgeneration, oxygen consumption, extracellular pH, glucose consumption, lactate production,and the release of specific hormones and chemicals; and intracellular quantities such asoxidation/reduction potential, transmembrane potential, calcium concentration, and theexpression of selected genes. Active picopumps are being developed to maintain long-term cellhealth in the highly restricted nanoliter culture volumes. The small size of our culture chambers(sub-nanoliter rather than milli- or microliter), the small number of cells being measured (1 to100 versus 104 to 106), and the small size and proximity of our electrochemical sensors to thecells (microns versus millimeters) provide an unprecedented 10 to 100 ms dynamical response(i.e., wide bandwidth) to biochemical events that are at present studied with temporal resolutionof many seconds or even minutes.The combined use of our BioMEMS control systems and real-time numerical modeling ofnonlinear cellular events will allow us to explore the nature of cellular control mechanisms anddiscern the complexities of the role of specific proteins in cellular function in a manner notpossible with conventional instrumentation. The VIIBRE cellular instruments are being createdusing state-of-the-art multichannel potentiostats, inverted microscopes, computer-controlledmicropumps, and high-speed CCD and photodiode fluorescence imaging systems. Suchdevices are already being used by VIIBRE graduate and faculty fellows to study the pancreaticislet metabolism and the signaling and response for insulin release; physiological effects ofbiowarfare agents; thermal changes associated with protein denaturation; the electrophysiologyof single cardiac cells; the activation of T cells; the tractile forces developed by cells duringchemotaxis; and predator-prey relationships in bacterial-protozoan bioremediation.B. Publications and Underlying ScienceThe new VIIBRE research initiatives are beginning to bear fruit in the form ofpublications in peer-reviewed journals, which are listed in Appendix A. As a brief summary, thework on the Multiananalyte MicroPhysiometer1-3 is being directed by David Cliffel, an AssistantProfessor of Chemistry, and has been funded by a grant from the Defense Advanced ResearchProjects Agency (DARPA). This system provides, for the first time, the ability to recordsimultaneously the dynamics of glucose and oxygen consumption and lactate release andacidification of populations of 105 cells in 2 µL chamber with a 30 s temporal resolution andrapidly discriminate between different biotoxins. The NanoBioreactor,4,5 funded by NIH throughan SBIR subcontract from NanoDelivery, Inc., is directed by Franz Baudenbacher, a VIIBRErecruited Assistant Professor of Biomedical Engineering; this project provided the basis forsubsequent funding by DARPA/AFOSR and Pria Diagnostics, Inc. The NanoPhysiometer6,7,being developed by Franz Baudenbacher and his group, provides the capabilities for dynamicmultianalyte measurements on single cells. The development of this device has been funded byDARPA and will be incorporated into future biodefense platforms, the Pria systems, and ananticipated major cardiac initiative. The PicoCalorimeter8, being developed by Baudenbacherand Wikswo with support from NIH through an SBIR subcontract from Hypres, will allowunprecedented sensitivity and temporal response for thermal measurements of protein bindingand cellular metabolism. A VIIBRE- and Medical-Center-funded research associate workingwith Owen McGuinness and David Piston of the Department of Molecular Physiology &Biophysics, has developed a microfluidic device that allows spatial control of the perfusion of asingle pancreatic islet and has led to a clearer understanding of the intra-islet synchronizationand communication associated with the calcium oscillations and insulin release.9 A projectdirected by John Wikswo is examining the spatiotemporal properties of gradient mixers10 and isleading the development of devices that allow dynamic control of chemokines for cancerresearch. Franz Baudenbacher has led a group that has developed a NanoSQUID11-14Magnetic Microscope that has unprecedented spatial resolution and sensitivity, and has the8

capability of recording the magnetic fields from action currents in isolated cardiac tissue, frommagnetic inclusions in Lunar and Martian rocks, and from a single magnetically labeledmicrosphere. We anticipate a rapid increase in publications from these and other projects.C. Patents and LicensingThe creative effort that has been driving the proposals and development of prototypedevices has led to the submission of a number of patent disclosures and the filing of twelvepatents, listed in Appendix B. Licenses have been negotiated with Tristan Technologies for theSQUID microscope developed by Professor Franz Baudenbacher and his group. Researchlicenses have been obtained from both Harvard University and Caltech to allow VIIBRE to utilizethe soft lithographic techn

EXECUTIVE SUMMARY The Vanderbilt Institute for Integrative Biosystems Research and Education, VIIBRE, was created in December, 2001 with a 5.1 million, five-year grant from the Vanderbilt . Venture Capital Fund (AVCF) to help move Vanderbilt University to a leadership role in basic research, technological development, and the delivery of .

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