THIS INITIATIVE IS BEING REPLACED BY Molecular Cell Biology Strategic Academic Vision – Round Two (MAY 2, 2014)

A.  Introduction:  The MCB Unit in the School of Natural Sciences is currently comprised of faculty whose research is focused in four main interdisciplinary areas:  1) Biochemistry, Physiology and Molecular Biology, 2) Cell and Developmental Biology, 3) Microbiology and Immunology and 4) Neurobiology.  We currently serve the majority of undergraduate and graduate students in the School of Natural Sciences:  an estimated 1084 undergraduate students in the Biological Sciences (BIO) major in these emphasis tracks:  Human Biology, Developmental Biology, Microbiology/Immunology, and Molecular and Cell Biology; and 45 masters and doctoral students in the Quantitative and Systems (QSB) Graduate Group, and we have proposed a new Molecular and Cell Biology Graduate Group (under review).  We anticipate that the BIO major will continue to be popular, but we require additional faculty and graduate students to achieve our research goals for 2020.  Here, we present our Strategic Academic Vision for the MCB Unit, in which we strategize for our growth to 29 research track faculty and 3 L(P)SOE faculty members.  To improve the quality of the BIO major, we propose to cap the number of BIO majors at its current number, which will improve student: faculty ratios and allow for the development of more teaching laboratory courses and undergraduate research opportunities.  The addition of 2 new L(P)SOE faculty members will help to facilitate this UG program.  At the same time, we propose to aggressively increase graduate student recruitment, as we grow our research faculty across the core MCB disciplines at a rate of about 2 per year until 2020.  In addition to the human resources, MCB research requires addition physical spaces for new teaching labs, new faculty research labs and offices, core facilities, and collaboration spaces. 

B. Our Vision: 

 

The 2009 Strategic Academic Vision included “Human Health” as a major research theme, with 3 objectives:  1) to establish the Health Sciences Research Institute (HSRI), which now exists, 2) establish a School of Medicine, and 3) evaluate the potential for a School of Public Health.  Basic research in the biological sciences has been a primary driver for these initiatives at UC Merced.  As we progress forward to 2020, we envision that the Molecular and Cell Biology (MCB) Unit’s research foci will continue to feed into the development of these objectives, through its research strengths in the core disciplines of biochemistry, cell biology, microbiology and immunology, molecular biology, neurobiology, and physiology.  

 

There are several “grand challenge” research questions in MCB, such as:

• What are the biochemical mechanisms that control cellular metabolism and is dysregulation of  these mechanisms the cause of obesity, cardiovascular disease and diabetes?
• How can we identify and manipulate the genes that control stem cell differentiation to regenerate diseased tissues and organs?
• How do microbes communicate with each other to form communities, and during fungal infections can we use this knowledge to prevent biofilm contamination in medical devices?
• What are the molecular and cellular mechanisms that control immune cell recognition and response to viral, bacterial and fungal pathogens, and do these mechanisms also initiate autoimmune disease?
• Can we predict the evolution of antibiotic and antiviral resistance and use this knowledge to design novel vaccines and chemical inhibitors to prevent and treat infection?
• What are the molecular and cellular processes that are affected in brain cells to cause mental disorders such as autism, addiction, and dementia?

 

These grand challenge questions are likely to be best answered using an interdisciplinary approach, contextualized in these broader questions:  What are the evolutionary and systems-level causes of diseases like cancer, cell fate decision pathways, and other questions in the organization and dynamics of cells, molecular networks and cellular networks?

 

The composition of the current MCB faculty provides unique and key opportunities for intellectual contributions by combining their personal expertise in the core disciplines and applying them to these grand challenge questions.   All MCB faculty research to date has made significant impacts in their respective core disciplines (as demonstrated through our publications and research grants, which are key indicators of the development of a successful institutional program).  In addition, we already have examples of interdisciplinary collaborations within the MCB Unit, as well as between the MCB Units and other research groups (such as QSB, COGS).

 

These collaborations are fostered by the enthusiasm of our MCB faculty to build from a solid successful foundation in core disciplines, and then to combine their disciplinary strengths to create novel approaches to challenging scientific questions that seem impossible to tackle.  By supporting the growth of an interdisciplinary, quantitative and systems-oriented MCB Unit, our program will have a unique opportunity to benefit from and synergize with other units and programs to lead the MCB discoveries of tomorrow.  Interdisciplinary collaborations, both on and off campus, will play an important role in the continued success of the MCB program.  We envision that these interdisciplinary studies will not only help to solve these questions, but also contribute to the scholarly development of our faculty, and ultimately, to imbed this intellectual desire into our graduate trainees, as well as into our undergraduate curriculum.

 

UCM consists of a diverse group of collaborative individuals that appreciate considering diverse approaches to their research problems.  There are numerous opportunities for collaboration, including mathematical modeling, metabolic modeling, exploring microbial interactions with the immune system, exploring how cellular communities evolve, comparative studies across model organisms,  structure-function analyses .   This rich resource of colleagues gives us an advantage over other institutions, as we have the ability to more rapidly incorporate “higher-order” types of data analysis into our thinking and research plans.   Medical practitioners in the Central Valley are motivated and interested in contributing to research that investigates the causes and predicts disease progression within our community, which has been understudied. The MCB Unit is poised to take advantage of this community interest and is already providing lay seminars on our research and collaborating with local physicians to research medical issues within the community to foster this additional unique source of partnerships. 

 

Extramural funds are absolutely required to support our research.  Financial support for MCB faculty research comes from federal and state organizations (such as the National Institutes of Health, the National Science Foundation, California Institute for Regenerative Medicine), nonprofit and private sponsors (UC Cancer Research Coordinating Committee, American Heart Association, American Diabetes Association, National Kidney Foundation, Autism Speaks, Simons Foundation, American Cancer Society, Gates Foundation), local community research grants, industry partnerships, and philanthropists.  One of our faculty members is exploring “crowd funding” as an additional funding mechanism.   Interdisciplinary collaborations, both on and off campus, will play an important role in the continued success of the MCB program, especially if economic drivers of funding agencies are pushed to support a move from basic to translational research questions.

 

C.  Our Strategic Plan:    The following resources are needed for the MCB unit to realize these research goals by 2020:

a. Increase current number of MCB faculty from 16 to 30, with specific growth in experimentalists (i.e. “wet lab” scientists) in biochemistry, cell biology, developmental biology and metabolism, as well as target faculty recruitment for MCB growth in computational (i.e. “theoretical”, computational biology, bioinformatics) within all the MCB research subareas.  We are in major need of senior-level researchers with their strong scientific connections, mentoring capacity and general understanding/overview of our research programs. We envision that these scientists will also bring the capacity for more funding, are usually well-respected in their fields, and can facilitate invitations to renowned speakers to our research seminar series. Senior-level faculty can also elevate the overall quality of graduate programs by attracting the highest quality students and postdoctoral researchers to UCM.  We also see a need to add L(P)SOE faculty members to our unit to help manage and provide leadership in the improving the rigor and quality of the undergraduate BIO major.

b. Build new faculty research space.  We are currently in a deficit in terms of wet labs for experimentalists in MCB, and even with the opening of the new Science and Engineering-2 Building, all wet lab spaces will be full until an additional new building is constructed.  The lab spaces for current MCB faculty do not allow for adequate growth for the addition of appropriate numbers of graduate students (our target graduate student to faculty ratio is 3:1), postdoctoral trainees and research staff. New wet laboratories will require temperature and air control, gas and vacuum lines, tissue culture rooms, and common work areas for chemical handling, shared equipment, glassware and consumable storage, and electrical capabilities to handle power -20C and -80C freezers, refrigerators, centrifuges, incubators and microscopes.   Shared computing resources are currently constrained and MCB faculty will need access to central planning for computational resources, including server room space, time and staff support for research computing, and infrastructure to support servers, cloud computing, and sharing large data sets, and specialized computing (such as structural biology).  It is envisioned that MCB will participate in the proposed Center for Theory and Computation (CTC) to fulfill some of these needs.  To facilitate interdisciplinary collaborations, these labs would be co-housed in a building that is connected or in close proximity to faculty within the QSB program, which includes faculty researchers in biophysics, mathematical biology, and systems biologists.

c. Core research facilities:  UCM currently has an excellent vivarium, facilities for flow cytometry, confocal microscopy and genomics.  However, additional core facilities are needed.  These cores need to be sustained and be located within close proximity to the faculty research labs that utilize them.  Future core facilities should include:

 

• Protein engineering/biochemical analysis core:  one room for a mass spectrometer and another room for equipment for N-terminal sequencing, amino acid analysis, and for making new antibodies; space for proteomic and metabolomic analyses
• Bioinformatics core:  space for a core of 3-5 bioinformaticians and biostatisticians (staff, not to be confused with the tenure-track faculty) dedicated to assisting faculty with experimental planning and data processing (especially for large RNA-sequencing);
• Histology core:  space for cryostat/microtome, large sink and fume hood for histological analysis of tissue specimens, and possibly a human tissue repository to store human tissue samples from healthy and diseased individuals. 
• Machine shop for creating custom equipment.
• Transgenic mouse facility to be housed in the vivarium, including space for equipment of microinjection of cells and mouse embryos to create transgenic, knockin and knockout mice, collection of gametes and their cryopreservation
• Animal behavior core:  various cognitive tests, locomotor activity, motor performance tests, etc.)
• Extended imaging facility: laser microdissection microscope, stereology, and real-time, in vivo functional imagery
• Expanded genomics core: to house current DNA sequencing and genomics core, and add oligonucleotide synthesis service and next-generation sequencing equipment
• Standalone BSL2+ to BSL3 facilities for the study of pathogens that could cause severe or lethal human disease.   Such facilities are usually confined to a specific area of a building with appropriate positive air pressure controls, ventilation, equipment for decontamination and biological safety cabinets. 
• Robotics core consisting of useful equipment for high throughput experiments, such as genetic and small molecule screens.  Some examples of equipment in this core could be liquid handling robots like the Beckmann Fx, cell analyzers, plate readers, bulk liquid dispensers, plate washers and dispensers like the Biotek EL406, and colony plating robots.

 

d. Common physical spaces that promote interactions and collaborations, such as a dedicated large amphitheater/lecture hall for the seminars for the School of Natural Sciences outside of the main buildings that house the faculty labs.  Reorganization and renovation of existing labs to shared spaces between faculty to promote efficiency through the use of shared equipment and facilities, as well as promote close interaction among collaborating labs, and laboratory safety.

 

e. Increase graduate student recruitment. Currently, most of the graduate students in MCB faculty labs are recruited within the QSB Graduate Group.  We have proposed the formation of a new additional graduate group (MCB) that we anticipate will permit for the growth and strengthening of graduate education at UCM.   We aim to reach a goal of 3 graduate students to each faculty member by 2020.

 

e. Physical spaces to promotion of the scientific work ethic and culture that is required for scientific success.  Biological research does not follow the traditional “9 to 5” business hours. Secure spaces on campus within science buildings that encourage and support students for round-the-clock experiments and intensive study are necessary (such as a science library, with graduate student library/lounge with kitchenette, couches, coffee, and workstations/wireless internet access).

 

f. Research funding:  NIH, NSF, Department of Defense, Army, DOE, UC internal funds, state and federal agencies, philanthropic donors, professional societies, international government funds (such as JSPS, UCMEXUS)  industrial biomedical industry.  Funding for interdisciplinary/multidisciplinary research is very difficult to obtain, institutional resources such as the Research Development Services could be leveraged to make UCM more competitive in this area to provide administrative support for faculty in grant preparation, and to maintain an updated database and search for UCM-specific funding opportunities.  Given the current low funding climate, bridge funding programs to sustain faculty research progress as they work to re-establish extramural funding need to be established.  This bridge funding program is also important for faculty retention at UCM. 

 

D. Targeted faculty recruitment strategy:  We are committed to reaching our goal of 30 tenure-track faculty by 2020.   However, after the 2013-14 academic year, we will be unable to hire faculty that require experimental wet labs without allocation of space in SE2 or construction of new buildings.  Table 1 shows the current MCB faculty by subdiscipline, and planned hires for each type.  Table 2 shows the space needs for our proposed recruitment plan.

 

Table 1. Current and Proposed Future MCB Faculty by Subdiscipline

Biochem/Mol Bio/ Physiology	Cell and Development	Microbiology and Immunology	Neurobiology	Computational, Bioinformatics
Choi	Cleary	Barlow	Cleary	Ardell
Filipp	Hoyer	Choi	Kitazawa	Barlow
Liwang	Manilay	Garcia-Ojeda (LPSOE)	Saha	Huerta-Sanchez
Ortiz	Oviedo	Hoyer	Wolf	AY13-14: Molecular Sys Bio
Recruit: AY16-17 Metabolism	Recruit:  AY17-18 cancer cell biologist	Manilay	Recruit:  AY17-18 Genomics	AY14-15: Computational Cell Biologist
Recruit: AY16-17 Structural biochemist	Recruit: AY18-19 Developmental biologist	Nobile	Recruit:AY18-19: Neurobiology	AY14-15: Bioinformatics#1
		Ojcius		AY14-15: Bioinformatics#2
		AY13-14 Immunologist
Recruit AY15-16: LPSOE (Human Biology BIO major and develop teaching labs in biochemistry
Recruit AY18-19:LPSOE (Cell and Development, Neurobiology)

 

Table 2.  Proposed MCB Recruitment Plan with Space Needs*

Recruitment Year	Type of recruitment	Space needs
2013-14	1) Immunology 2) Molecular Systems Biology	Wet Wet/Dry
2014-15	1) Computational Cell Biologist 2) Bioinformatics #1 3) Bioinformatics #2	Dry Dry Dry
2015-16	1) L(P)SOE No research hires (we need new wet lab space to be under construction)	Office
2016-17	1) Structural biochemist 2) Metabolism	Wet Wet
2017-18	1) cancer cell biologist 2) genomics	Wet Wet
2018-19	1) L(P)SOE 2) developmental biologist	Office

*this is a proposed plan based on current space constraints; our preference is to grow dry and wet labs simultaneously

 

E.  The Potential Impact of our Vision and Strategic Plan:    In our plan, we have included projections of faculty and graduate student growth through AY2020 (please see the attached “MCB Impact Metrics Worksheet”).  In addition, we have proposed to cap the number of BIO majors as lectures are currently impacted, and teaching laboratories are currently scarce.  We wish to improve the quality of our undergraduate major by the creation of new upper division specialized lab courses to complement our junior and senior level courses and to provide specialized experiential learning and practical skills to our BIO majors within their disciplinary emphases.  We have added 2 LPSOE positions to our plan to enhance faculty support to the undergraduates.  As is shown in the Impact Metrics, this reduces the undergraduate: MCB faculty ratio to 36:1 by AY2020, (currently at 77:1).  Clearly, more will have to be done to reduce this to the target ratio of 24:1.  We have projected graduate student enrollment to grow with faculty recruitment to achieve a graduate: MCB faculty ratio of 3:1 as early as AY17-18, although we would like this to increase to 4:1.

F. Peer Institutions:  The following peer institutions were selected using data collected by the National Research Council: http://sites.nationalacademies.org/PGA/Resdoc/.  The research programs of the peer institutions mirror what we wish to achieve for UC Merced MCB by 2020.

Table 3. Realistic Peer Institutions
Institution	Number of faculty	Number of grad students	Website
Rice University Wiess School of Natural Sciences Biochemistry and Cell Biology	21	60	http://natsci.rice.edu/ShowContent.aspx?id=800
UC Santa Barbara Molecular Cellular and Developmental Biology	26 faculty, 3 lecturers	52	https://www.mcdb.ucsb.edu/research
UC Santa Cruz Molecular Cellular and Developmental Biology	26	46	http://mcd.ucsc.edu/faculty/index.html

 

Table 4. Aspirational Peer Institutions
Institution	Number of faculty	Number of grad students	Website
Caltech – Biology	30	77	http://biologyoption.caltech.edu/people/index.html
Cornell University Graduate Field of Biochemistry, Molecular and Cell Biology	52	91	http://bmcb.cornell.edu/program/index.html
UC Irvine Cellular and Molecular Sciences	139	??	http://cmb.uci.edu/