Date: 12/3/10 To: Dr. Steven Castillo, Provost; Dr. John Poate, VPRTT From: Biosciences Strategy Committee, Prof. David Marr (chair), Prof. Matt Posewitz, Prof. Mike Kaufman, Prof. John McCray, Prof. Anthony Petrella Committee Charge: With a mission specific to earth, energy, and the environment, Mines must develop an institution-wide strategy in the biosciences to better prepare our students and perform cutting-edge research in each of these areas. Examine and catalog the current portfolio of expertise in the biosciences at Mines. Provide an analysis of the portfolio in terms of the range of bioscience expertise that should be present to support Mines’ mission and vision at both graduate and undergraduate levels. Provide a set of recommendations and potential strategies including programmatic, structural, and/or partnering-based approaches, that if implemented over a five-year period, would best support Mines’ vision of becoming the leading university in earth, energy and the environment. Expertise Portfolio & Analysis: During the last 135 years, CSM has built a global reputation as one of the foremost institutions of higher education in the world dealing with effective and responsible use of the earth and its resources. Throughout its history, the emphasis has been on engineering and applied science and the institution is now entering an exciting time where it is applying this expertise in relatively new areas. Biology is certainly one of these, as it has become comparable to chemistry, physics, and math as an important component of an engineering education. CSM attracts the top engineering students in Colorado and surrounding states and these students have pushed strongly to increase the biology-related opportunities available to them at both educational and research levels. To address this need, the university has strengthened its efforts to provide a solid foundation for biology and related technologies and has expanded in this area with targeted cluster hiring in multiple departments. Note here that hiring has occurred at both the tenure-track level to support research growth as well as at the lecturer level to support the growing undergraduate interest and need for ABET accreditation in some majors. It is apparent from Table 1 that, leveraging CSM’s traditional strength in engineering and applied science, the overarching expertise at Mines is clearly one of biotechnology, with emphasis on biomedical, bioenergy, and bioremediation. Market Analysis: Research: According to the National Science Foundation, in FY09 the majority of the $55 billion in academic science & engineering expenditures was in the life sciences (including agricultural at $3 billion, biological at $10.2 billion and the medical sciences at $18.2 billion) followed by engineering with $8.7 billion1. To better serve our students at all levels and grow our research to broaden our financial base, an effort needs to be made to capitalize on our available expertise and better tap into such funding. We have shown with our expertise portfolio and the corresponding increase in bio-related research performed on campus (Figure 1) that bio-related research can lead to significant funding on the CSM campus. Education: In the 3 years since inception, the Chemical and Biochemical Engineering degree has grown to 210 students with an average 49% women in the program. This percentage is roughly double that for CSM as a whole and provides a clear message that growing the bio-oriented opportunities on campus will attract higher numbers of women in our admissions process. In our marketing, a broader interpretation of “Earth” to include “Earth and its inhabitants” could greatly increase our reach to these students (see Figure 2 and header above). The Issues: With significant and growing efforts in both research (Figure 3) and teaching, what are the impediments to the strength and future growth of bio on campus? These are various but can be summarized as a lack of a locus in which to focus equipment, resources, and intellectual effort – a sense of community. Until this is in place, future growth will simply be impeded. This has impacted the school in both the research lab (and volume) and the undergraduate classroom (and recruitment) in a variety of ways (Table 2). Recommendation: To address these issues, the committee has considered various options including the status quo, moving BELS into its own unit, creation of a cross-departmental bioengineering program, and establishing a new department/division. Our recommendation recognizes that, to create this identity and locus, a physical relocation of some faculty, students, and instructional resources will be necessary. To

accomplish this in a manner that best serves the faculty and students, we propose the establishment of a new department/division (D/D). Though resources are always necessary for the creation of something new, significant savings in terms of consolidation of teaching, instrumentation and lab efficiencies are anticipated. Structure: The Dept. or Division of Biotechnology or Bioengineering should be established with offices, teaching labs and research lab space. A steady-state size of 10 TT faculty and 5 lecturers could be seeded with 5-6 current TT faculty on campus (Table 1) and BELS instructors to provide the undergraduate teaching component. This will subsequently grow to the steady-state size with the hiring of additional TT faculty. Curriculum: A committee must be formed to discuss and define a curriculum in greater detail; however, given the current degrees offered within the state (Table 3) there appears to be significant opportunity for additional technology oriented offerings. At the undergraduate level this could include a minor (akin to the current BELS minor), a BS in Bioengineering (with 3 tracks focusing on the school strengths of Biomedical, Bioenergy, and Environmental), and/or an MS/PhD in Bioengineering. In this, there are opportunities for close partnership with other local institutions. CU and NREL could both tie into efforts in bioenergy and bioremediation and Anschutz and/or National Jewish could partner in our biomedical/premed efforts. Note here that new programs must be approved by the BOT; however, as long as new degrees are within the role and mission of the university (broadly interpreted as “Applied Science and Engineering”) then the CCHE should not be a significant hurdle. In general, a centralized body defining bio-based curricula and courses that most effectively meet undergraduate and graduate student needs is required. Here cost savings will come from elimination of topic redundancy offered by multiple departments. In addition, establishing curricula that are attractive to pre-med students, bio-engineers, and life science students wishing to pursue bio-based graduate education will attract elite graduate students and postdoctoral scientists interested in the biosciences. Implementation Strategy: To achieve the goals outlined here, we propose that either a DHDD be chosen from the pool of available bio-oriented faculty (Table 1) or a search be conducted for an external candidate. Initial faculty should then be chosen where the DH would work with potential faculty on deciding the best fit. Transitioning faculty will have a single office in the new structure, freeing space in their current department/division. Here, joint appointments may make sense to accommodate departmental needs (see Figure 3 for a proposed accelerated timeline); however, the committee felt that a single primary appointment is absolutely necessary. Budget: An estimated budget depends on the physical location of the new D/D and, with the move of PE to Marquez Hall, Alderson Hall provides one possible location (Table 4). With this assumption, necessary budget includes the office, research, and classroom lab renovation of Alderson Hall ($6.5m), the hiring of 5-6 new faculty over several years, and the addition of a support admin and technician (Table 5). Lab space of ~8000 ft2 is required and will be shared amongst faculty with “community” labs having specified research themes (to coordinate appropriate instrumentation). Collaboration here is encouraged by the seeding of shared laboratories with commonly used equipment (Table 6) some of which may already be available on campus. Such centralized facilities for analytical equipment supporting biological research will be used to reduce costly duplication of capital equipment leading to overall significant cost savings. Also, reduced duplication of topics in different departments may lead to savings on the teaching side. Any transitioning of faculty to the new D/D would also free up offices/labs in current departments for future growth. Examples could include chemistry lab space in the GRL and/or Coolbaugh, space in Hill for other programs, and space in Brown now used for BELS instruction. Signed, -The Biosciences Strategy Committee

Year Hired CSM Dept. TT FacultyExample publications Current research interest 1979 Chem Kent Vorhees2,3 Biodefense, biodetection 1981 ChemE Annette Bunge4,5 Dermal transport 1991 ESE Linda Figueroa6,7 Env. biotechnology 1995 ChemE David Marr8,9 Biomedical microdevices 1996 ESE Junko Munakata Marr10,11 Env. microbiology 2001 Engineering Joel Bach12,13 Biomechanics 2002 Physics Jeff Squier14,15 Biomedical microdevices 2003 LAIS Tina Gianquitto Evolutionary theory 2004 Chem Steven Boyes16,17 Polymers, drug delivery 2005 ESE John Spear18,19 Env. mol. microbiology 2006 Engineering Tony Petrella20,21 Comp. biomechanics 2007 MME Reed Ayers22,23 Biomaterials 2008 MME Hongjun Liang24,25 Biomaterial assembly 2008 ChemE Keith Neeves26,27 Biomedical microdevices 2008 Chem Matt Posewitz28,29 Algal microbiology, biofuels 2009 ESE Josh Sharp30,31 Env. microbiology 2009 ESE Christopher Higgins32,33 Env. toxicology 2010 ChemE Mark Maupin34,35 Comp. biochem., biofuels 2011 Engineering Anne Silverman36,37 Amputee biomechanics Lecturers 2004 ChemE John Persichetti Bioprocess engineering 2007 ChemE/BELS Paul Ogg PhD, cell biology, virology 2007 ChemE/BELS Hugh King MD/PhD, biology, math, CS 2008 ChemE/BELS Cynthia Norrgran MD, biology, biophysics

Table 1: Hiring in biotechnology at CSM.

Figure 1: Recent growth in biotechnology research volume at CSM.

Issue Potential positives with recommendation Potential negatives What is the appropriate home for BELS? How does it grow and maintain support.

Provide a home for undergraduate biology service courses for both majors and minors (premed, for example).

Leaving BELS within ChemE may provide a stronger supporting environment even if direct interactions are not present.

Core BELS courses are currently offered by non-TT faculty. TT instruction outside of BELS performed with few provided resources.

Better integration of core and non-core BELS courses and delivery could provide additional opportunities for bio-oriented students to take courses.

It is less expensive to provide instruction with non-TT faculty.

We need to dramatically increase the enrollment of female students.

A bio themed D/D would likely aid recruiting of female undergraduate students.

Is it better to simply grow those departments (such as CE) with higher current female enrollments?

Into what department should we be recruiting high school students broadly interested in bio and engineering?

A new D/D, different from other programs and departments in the state, would aid recruiting.

Would CSM be able to compete for these students? Is there a desire to?

Only one available degree at the undergraduate level with bio flavor

A new D/D would create new opportunities for undergraduates

Chemical and Biochemical Engineering may be enough.

How do we support pre-med undergraduate students?

An undergraduate track in a new D/D could provide clear opportunities for premeds, including undergraduate research or working directly with partner institutions.

Do we want to encourage premed students to attend CSM? Would this be in their best interest?

There are currently no degrees offered at the graduate level in a bio-related discipline.

Potential D/D would provide an appropriate home for new graduate degrees.

Is there a need/market for such degrees? Can we recruit graduate students into this major? Can it be a top-25 program?

No critical bio- mass yet in any one unit.

Potential D/D would provide scholarly bio-community that supports strong grad student interactions and effective mentoring for young faculty.

Move of any faculty from a current unit will be politically difficult.

With uncoordinated research efforts, common required resources are unavailable or spread out and difficult to use.

Potential D/D would provide a physical home for appropriate laboratory facilities.

Move of current equipment/resources may be disruptive.

Without a clear home/identity, seeking resources from some agencies are hindered.

Potential D/D would provide a focus for inter-unit research/resource acquisition efforts. Would also provide a physical home for coalescing campus characterization/research tools. Would also provide a clear biotech presence within and outside CSM for recruiting/seeking resources. Would allow coordination of large-scale proposals for bio-related equipment.

Is seeking of external resources zero-sum? How do we know a new D/D will catalyze resource acquisition efforts?

Growing disciplines where we could be a big player are not well represented.

The new D/D could provide the clear biology support structure to make this feasible.

Will creating a new unit help us in this regard?

Interactions/partnerships with local institutions are minimal and operate primarily at the faculty-faculty level.

New D/D could provide the framework to establish partnerships with local institutions. This could create clear educational/research opportunities for students at all levels.

Are partners willing? Does CSM provide something of benefit to them?

Table 2: Common issues and potential solutions considered

Institution Degrees offered Comments University of Colorado, Boulder

BS degree in biology in MCDB Molecular, Cellular and Developmental Biology, EBIO Ecology and Evolutionary Biology, IPHY Integrative Physiology, and BCHM (Biochemistry), Department of Chemistry and Biochemistry.

No separate department of Bioengineering at CU, various arrangements are available for augmenting degrees obtained in Aerospace, Chemical and Biological, Electrical, Mechanical, and Civil and Environmental Engineering. Has two biology departments: Molecular, Cellular and Developmental Biology (MCDB) and Ecology and Evolutionary Biology (EEB). CU (all campuses) research expenditures at $648 million.

Colorado State University

College of Engineering – BS in Chemical and Biological Engineering, degrees in Biomedical Engineering (below) College of Applied Human Sciences – “People-oriented” professions School of Natural Sciences – BS, MS, PhD in Biochemistry, BS in Biology, Botany, Zoology. MS/PhD in Botany, Zoology. School of Biomedical Engineering – a minor, a dual BS degree (5 years), ME, MS, and PhD degrees

School of Biomedical Engineering established in 2007 (http://www.engr.colostate.edu/sbme). Now has a new building under construction (http://www.bmes.org/aws/BMES/pt/sd/news_article/37130/_PARENT/layout_details/false). CSU Research expenditures at $302.8 million in FY10.

University of Colorado, Denver/Anschutz

MS and PhD degrees in Bioengineering

Department of Bioengineering founded in 2010 with a “clinical + engineering” focus with significant radiology expertise. Other than chair (Robin Shandas), no dedicated faculty but instead draws upon Boulder, UCD, and Anschutz (http://bioengineering.ucdenver.edu).

Colorado School of Mines

BS degree in Chemical and Biochemical Engineering

Research expenditures of $55 million with approximately 15% biotech related.

Table 3: Lay of the land – Colorado bio and biotech programs.

Location Size (ft2) Possible Use AH 281/219 3321 BELS instructional (includes two large labs and a small classroom) 286/288 542 Research lab - 2 smaller rooms could be combined for lab 290 572 Research lab 294 572 Research lab 287 555 Research lab 279 326 Research lab – smaller/no windows – perhaps support (microscopy) 190 1192 Current shop – could be converted to large communal lab 194 592 Current shop – could be converted to large communal lab 188 196 Current tissue culture 186 303 Current bioreactors 182 537 Current bioprocessing/bio field session teaching lab 191 1695 Current high bay (could be partially converted to shop space)

Table 4: Current space in Alderson Hall.

Figure 2: Expansion of “Earth, Energy, and the Environment” to include biorelated concepts

Figure 3: “Accelerated” timeline.

Figure 1: Alderson Hall 1st and 2nd floors – Current CE space in lavender.

Cost Comments Renovation of 1st and 2nd floors of Alderson Hall

$6.5 million (includes ~$1.5m in soft and contingency costs)

Based on 2400 ft2 of office space ($240k), 4350 ft2 of classroom space ($540k), 6600 ft2 of lab space on the 2nd floor ($2m) and 7250 ft2 of lab space on the 1st floor ($2.2m).

1 Administrative Assistant + 1 junior technician

New faculty Shared equipment (Table 6) $1.5 million Startup costs $300k startup for newly hired faculty,

$100k for transferring faculty

Library $100k first year, $50k in subsequent years.

Table 5: Budget.

$75000 FPLC for protein purification work w/ columns

75000 HPLC for quantitative metabolite research

85000 Typhoon imaging system for Southern/Northern/Western blotting

100000 Ultra-centrifuge with rotors

40000 -80 Freezers for cryopreservation

100000 High-capacity autoclaves

50000 Small-capacity autoclaves

50000 Floor centrifuges

45000 High end general applications microscope

15000 UV/vis

50000 Basic protein purification infrastructure (french press, sonicator, gels, power supplies)

50000 Basic DNA cloning infrastructure

100000 High capacity Milli-Q water system

100000 Floor incubators

75000 Plate incubators w and w/o CO2

50000 Human cell line incubators

10000 Sterile transfer hoods large capacity BSL-II

30000 Thermal cyclers

50000 Real time-PCR thermal cycler

75000 Plate reader w/ fluorescence capacity

50000 Cell counters

40000 PCR clean hoods

50000 Incubation ovens and rollers for blotting

50000 Semi-dry blotting system

50000 Liquid N2 storage Dewar for cell lines

40000 DNA/protein gel documentation system

Table 6: Suggested shared equipment with approximate costs.

REFERENCES 1 National Science Foundation, Science Resources Statistics,

<http://www.nsf.gov/statistics/infbrief/nsf10329/nsf10329.pdf> (2010). 2 Beverly, M. B., Voorhees, K. J., Hadfield, T. L. & Cody, R. B. Electron monochromator mass

spectrometry far the analysis of whole bacteria and bacterial spores. Analytical Chemistry 72, 2428-2432 (2000).

3 Madonna, A. J., Voorhees, K. J., Taranenko, N. I., Laiko, V. V. & Doroshenko, V. M. Detection of cyclic lipopeptide biomarkers from Bacillus species using atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 75, 1628-1637, doi:10.1021/ac020506v (2003).

4 Bunge, A. L. Release rates from topical formulations containing drugs in suspension. J. Control. Release 52, 141-148 (1998).

5 McCarley, K. D. & Bunge, A. L. Pharmacokinetic models of dermal absorption. J. Pharm. Sci. 90, 1699-1719 (2001).

6 Hemsi, P. S., Shackelford, C. D. & Figueroa, L. A. Modeling the influence of decomposing organic solids on sulfate reduction rates for iron precipitation. Environ. Sci. Technol. 39, 3215-3225, doi:Doi 10.1021/Es0486420 (2005).

7 Biesterfeld, S., Figueroa, L., Hernandez, M. & Russell, P. Quantification of nitrifying bacterial populations in a full-scale nitrifying trickling filter using fluorescent in situ hybridization. Water Environment Research 73, 329-338 (2001).

8 Oakey, J., Allely, J. & Marr, D. W. M. Laminar Flow-Based Separations at the Microscale. Biotechnology Progress 81, 1555 (2002).

9 Terray, A., Oakey, J. & Marr, D. W. M. Microfluidic Control Using Colloidal Devices. Science 296, 1841 (2002).

10 Albert, J. M., Munakata-Marr, J., Tenorio, L. & Siegrist, R. L. in Environ Sci Technol Vol. 37 4554-4560 (2003).

11 Hopkins, G. D., Munakata, J., Semprini, L. & McCarty, P. L. Trichloroethylene Concentration Effects on Pilot Field-Scale In-Situ Groundwater Bioremediation by Phenol-Oxidizing Microorganisms Environ. Sci. Technol. 27, 2542-2547 (1993).

12 Eckhoff, D. G., Dwyer, T. F., Bach, J. M., Spitzer, V. M. & Reinig, K. D. 43-50 (Journal Bone Joint Surgery Inc).

13 Keir, P. J. & Bach, J. M. Flexor muscle incursion into the carpal tunnel: A mechanism for increased carpal tunnel pressure? Clin. Biomech. 15, 301-305 (2000).

14 Applegate Jr., R. W. et al. Optically-Integrated Microfluidic Systems for Cellular Characterization and Manipulation. Journal of Optics A: Pure and Applied Optics 9, S122-S128 (2007).

15 Applegate Jr., R. W., Squier, J., Vestad, T., Oakey, J. & Marr, D. W. M. Optical Trapping, Manipulation, and Sorting of Cells and Colloids in Microfluidic Systems with Diode Laser Bars. Optics Express 12, 4390-4398 (2004).

16 Rowe, M. D. et al. Tuning the Magnetic Resonance Imaging Properties of Positive Contrast Agent Nanoparticles by Surface Modification with RAFT Polymers. Langmuir 25, 9487-9499, doi:Doi 10.1021/La900730b (2009).

17 Rowe, M. D., Thamm, D. H., Kraft, S. L. & Boyes, S. G. Polymer-Modified Gadolinium Metal-Organic Framework Nanoparticles Used as Multifunctional Nanomedicines for the Targeted Imaging and Treatment of Cancer. Biomacromolecules 10, 983-993, doi:Doi 10.1021/Bm900043e (2009).

18 Spear, J. R., Walker, J. J., McCollom, T. M. & Pace, N. R. Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proceedings of the National Academy of Sciences of the United States of America 102, 2555-2560, doi:Doi 10.1073/Pnas.0409574102 (2005).

19 Walker, J. J., Spear, J. R. & Pace, N. R. Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434, 1011-1014, doi:Doi 10.1038/Nature03447 (2005).

20 Halloran, J. P. et al. Verification of Predicted Knee Replacement Kinematics During Simulated Gait in the Kansas Knee Simulator. Journal of Biomechanical Engineering-Transactions of the Asme 132, -, doi:Doi 10.1115/1.4001678 (2010).

21 Laz, P. J., Stowe, J. Q., Baldwin, M. A., Petrella, A. J. & Rullkoetter, P. J. Incorporating uncertainty in mechanical properties for finite element-based evaluation of bone mechanics. Journal of Biomechanics 40, 2831-2836, doi:Doi 10.1016/J.Jbiomech.2007-03-013 (2007).

22 Ferguson, V. L., Ayers, R. A., Bateman, T. A. & Simske, S. J. Bone development and age-related bone loss in male C57BL/6J mice. Bone 33, 387-398, doi:10.1016/s8756-3282(03)00199-6 (2003).

23 High, W. A., Ayers, R. A., Chandler, J., Zito, G. & Cowper, S. E. Gadolinium is detectable within the tissue of patients with nephrogenic systemic fibrosis. J. Am. Acad. Dermatol. 56, 21-26, doi:10.1016/j.jaad.2006.10.047 (2007).

24 Liang, H. J., Whited, G., Nguyen, C. & Stucky, G. D. The Directed Cooperative Assembly of Proteorhodopsin into 2D and 3D Polarized Arrays. Proceedings of the National Academy of Sciences of the United States of America 104, 8212-8217 (2007).

25 Yang, L. et al. Self-Assembled Virus-Membrane Complexes. Nature Materials 3, 615-619 (2004). 26 Neeves, K. B. et al. Microfluidic focal thrombosis model for measuring murine platelet deposition and

stability: PAR4 signaling enhances shear-resistance of platelet aggregates. Journal of Thrombosis and Haemostasis 6, 2193-2201 (2008).

27 Okorie, U. M., Denney, W. S., Chatterjee, M. S., Neeves, K. B. & Diamond, S. L. Determination of surface tissue factor thresholds that trigger coagulation at venous and arterial shear rates: amplification of 100 fM circulating tissue factor requires flow. Blood 111, 3507-3513, doi:10.1182/blood-2007-08-106229 (2008).

28 Grossman, A. R. et al. Novel metabolism in Chlamydomonas through the lens of genomics. Current Opinion in Plant Biology 10, 190-198, doi:Doi 10.1016/J.Pbi.2007.01.012 (2007).

29 Posewitz, M. C. et al. Hydrogen photoproduction is attenuated by disruption of an isoamylase gene in Chlamydomonas reinhardtii. Plant Cell 16, 2151-2163, doi:10.1105/tpc.104.021972 (2004).

30 Sharp, J. O. et al. An inducible propane monooxygenase is responsible for N-nitrosodimethylamine degradation by Rhodococcus sp strain RHA1. Applied and Environmental Microbiology 73, 6930-6938, doi:Doi 10.1128/Aem.01697-07 (2007).

31 Sharp, J. O. et al. Structural Similarities between Biogenic Uraninites Produced by Phylogenetically and Metabolically Diverse Bacteria. Environ. Sci. Technol. 43, 8295-8301, doi:Doi 10.1021/Es901281e (2009).

32 Higgins, C. P., Paesani, Z. J., Chalew, T. E. A. & Halden, R. U. Bioaccumulation of Triclocarban in Lumbriculus Variegatus. Environmental Toxicology and Chemistry 28, 2580-2586 (2009).

33 Higgins, C. P., Mcleod, P. B., Macmanus-Spencer, L. A. & Luthy, R. G. Bioaccumulation of perfluorochemicals in sediments by the aquatic oligochaete Lumbriculds variegatus. Environ. Sci. Technol. 41, 4600-4606, doi:Doi 10.1021/Es062792o (2007).

34 Maupin, C. M. et al. Effect of Active-site Mutation at Asn67 on the Proton Transfer Mechanism of Human Carbonic Anhydrase II. Biochemistry 48, 7996-8005, doi:Doi 10.1021/Bi901037u (2009).

35 Maupin, C. M., Wong, K. F., Soudackov, A. V., Kim, S. & Voth, G. A. A multistate empirical valence bond description of protonatable amino acids. Journal of Physical Chemistry A 110, 631-639, doi:Doi 10.1021/Jp053596r (2006).

36 Fey, N. P., Silverman, A. K. & Neptune, R. R. The influence of increasing steady-state walking speed on muscle activity in below-knee amputees. Journal of Electromyography and Kinesiology 20, 155-161, doi:Doi 10.1016/J.Jelekin.2009.02.004 (2010).

37 Silverman, A. K. et al. Compensatory mechanisms in below-knee amputee gait in response to increasing steady-state walking speeds. Gait & Posture 28, 602-609, doi:Doi 10.1016/J.Gaitpost.2008.04.005 (2008).