X. Graduate Program - Department of Biological Sciences, San Jose ...


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X. Graduate Program


Centrality to Mission


Mission and Goals of Program

The mission of the graduate programs in Biological Sciences (Microbiology &
Molecular Biology, Physiology, Conservation Biology & Ecology, and General Biology) is
to prepa
re graduates for employment in their chosen field (or for further doctoral
training or professional schools) and to provide them with a rigorous scientific environment
in which they can develop the observational, technical, and deductive reasoning sk
required for a successful career in the biological sciences. The specific program goals are to
provide limited remedial upper
division coursework in the biological and physical sciences;
provide advanced academic instruction and laboratory or field t
raining; offer the degree
options of coursework only (MA) or coursework and research thesis (MS) and the curricular
flexibility to best meet the needs of the student and societal needs for graduate
training; raise student awareness of issues in profe
ssional ethics, science
based public
policy, and to teach effective communication of scientific ideas; offer core masters
courses along with a selection of elective courses which allow graduates to learn
fundamental concepts in their chosen disciplin
e while gaining experience in related and
complementary fields; and provide students and faculty with adequate teaching and research
laboratory space, supplies, and equipment in order to foster an environment conducive to
effective teaching, learning, and


Program Contributions to the Mission of SJSU

The graduate program in Biological Sciences provides its students with advanced
intellectual and practical skills required for successful careers in molecular biology,
microbiology, genetics,

cell biology, anatomy, physiology, conservation biology, botany,
zoology, or entomology and gives them a broad
based understanding of how these
disciplines, and science in general, can be applied to meet societal needs.


Needs Analysis for the Program


Societal Needs for the Program

MA and MS graduates from the program are in demand for research, development,
quality control, and manufacturing for the biotechnology, pharmaceutical, and food
industries (Microbiology & Molecular Biology); research
in human and veterinary drug
metabolism, diseases, and medical devices (Physiology); ecological analysis of the effects
of development, pollution, and land management on plant and animal wildlife (Conservation
Biology & Ecology); and post
graduate training

in medicine and other health
related fields.

Student Demand Trends in the Major

According to the latest SJSU Statistical Abstract, the total graduate population in
Biological Sciences has ranged from approximately 70
100 over the past five years.
owever, a recent census within the Department indicates 122 actively enrolled graduate

an all
time high. The Statistical Abstract numbers may accurately reflect the


numbers of students officially enrolled in the individual graduate concentratio
ns, but they
significantly underestimate the numbers of students pursuing degrees in those areas. This
may be due to a large number of students who enter as conditionally classified (and are
therefore considered to be in the General Biology category) but
do not officially change to a
specific concentration until they are nearly finished. For example, nearly half (60) of all our
'00 graduate students are known to be in the Microbiology & Molecular Biology
program, but as of Spring '99 the Statistical A
bstract showed only nine!

The enrollments from the Departmental graduate census indicate the following as of Spring

Graduate Concentration





Microbiology & Molecular Biology





ation Biology & Ecology










General Biology





Department totals:





The increase (>20%) in total number of graduate stu
dents in the past few years can be
attributed to an increase in the number of MA students accepted into the Microbiology &
Molecular Biology concentration. This was a deliberate decision based on the increased
need in the biotechnology industry for employ
ees trained at the Masters level.


Program Interdependence at SJSU

Although each graduate concentration provides its own required courses, several graduate
courses in the Microbiology & Molecular Biology program are popular electives outside of
the c
oncentration and Department. Advanced Molecular Techniques (Bio 205), Advanced
Immunology (Bio 233), and several of the Advanced Seminars in Biology (Bio 255M) are
taken by many biochemistry graduate students and occasionally by advanced seniors in the

Molecular Biology concentration as major electives. Bio 205 is also taken by a few
Conservation Biology & Ecology MS graduate students who need molecular training for
their population genetics research projects.


Availability of Instructional Alte

Other Bay Area universities (UCSC, UC
Berkeley, UCSF, Stanford, SFSU, and Hayward
State) offer graduate training in biological sciences. Of the two nearby CSU campuses,
SFSU has a Masters program similar in scope and size to our program while Ha
yward State
is smaller. The UC schools and Stanford usually offer a Masters degree as a consolation
prize to unsuccessful Ph.D. students. The geographical area that our graduate program
serves ranges from Santa Cruz and Gilroy to the south and Palo Alto
and Fremont to the




Summary of Future Student Demands

The need for entry
level molecular biologists, microbiologists, and physiologists has
risen steadily over the past several years due to the explosive growth of the biotechnology
and related

health care industries. The demand is especially heavy in the Bay Area which
has the highest concentrations of these kind of companies in the entire world. Currently,
demand for well
trained entry
level employees is greater than the supply, and as long
as the
positive economic conditions prevail we expect our Microbiology & Molecular Biology and
Physiology programs to be in heavy demand. As San Jose and other urban areas continue
their sprawl, there has been more interest by local and state agencies to
document the
ecological impact of development on wildlife habitat. Graduates of the Conservation
Biology & Ecology program will continue to be employed by government agencies (Water
Districts, Fish and Game, etc.) and environmental consulting firms for th
is purpose.


Analysis of Program Quality


Quality of Instruction

One of the strengths of our graduate program is our cadre of "bridge" faculty who have
expertise in more than one program area and have developed interdisciplinary curricula and
earch projects. For example, Bio 218 (Evolution) is team
taught by faculty members in

Microbiology & Molecular Biology area along with Conservation Biology & Ecology
faculty. This brings together students and faculty from both concentrations who woul
otherwise never take or teach classes together. The Conservation Genetics Laboratory has
been a meeting place in the Department where molecular genetics and conservation biology
MS students can learn from each other to work on projects involving locally

endangered and
threatened species of wildlife. Another strength is the depth and currency of our graduate
laboratory offerings. Biology 227 (Physiology and Pharmacology) is the only course of its
kind in the region and is intensely sought after by our P
hysiology graduate students.
Further, all of the graduate courses in each concentration are taught by faculty with research
expertise in the field. Our graduate faculty in Conservation Biology are practicing
conservation biologists who do contract work f
or government agencies and, on occasion,
private companies. Many of our faculty in the Physiology area have been funded through
NIHAU grants which provide stipend for students. With the recent acquisition of state
art instrumentation (DNA sequence
r, digitizing fluorescent microscope, cell bioreactor,
thermal cycler, scanning spectrophotometers) the Microbiology & Molecular Biology
graduate program can improve upon its traditional strength in laboratory instruction. As a
way of improving the gradua
te curriculum even further, the department decided a few years
ago to offer at least six Advanced Biology Seminars (Bio 255) per year

one each semester
from each of the three graduate areas. These special topic seminars (e.g., Gene Therapy,

in the 21st Century, Space Physiology, Physiology of Vision,
Pathophysiology, etc.) have greatly enhanced the traditional lecture/laboratory curriculum.


Contributions to an Academic Field

The goal of all MS student thesis projects is the advancemen
t of scientific knowledge in


their discipline. Whenever possible thesis projects are published in peer
reviewed journals
with students as co
authors. Many student research projects are presented as poster sessions
at local, regional, or national professi
onal meetings. Research faculty spend several hours
per week with individual graduate students discussing research strategies and teaching them
the skills required to further their projects. A number of our faculty have national
reputations in their rese
arch field, publish regularly, attend and present papers at
conferences, collaborate on projects with industry colleagues, are invited speakers at
symposia, sit on panels and advisory boards, and provide expert testimony at trials
(Appendix X).


fits to Students and Other Stakeholders

Graduates of this program have been extremely successful in the job market and in
gaining entry to medical, graduate and other professional schools. In the Microbiology &
Molecular Biology concentration all of our

recent graduates are currently employed in their
discipline, and even those who dropped out or were academically disqualified from the
concentration have been able to find good jobs in the biotechnology industry based on the
skills they learned at SJSU!
Employers have been pleased with our graduates due to their
superior laboratory skills, sense of responsibility, and work ethic compared to students from
other more prestigious Bay Area institutions. Students from the Conservation Biology &
Ecology gradua
te program are in very high demand by local and state agencies and by
environmental consulting firms. Graduates of our Physiology program have been successful
in gaining entry to the best medical schools and graduate schools in the country. They have

been very successful in the job market. And many of our graduates are on the faculty
of local community colleges (appendix).


Overall Indicators of Program Quality

Ultimately, the best indicator of program quality is the ability of our graduates t
compete successfully in the job market and go on to fulfilling careers in their chosen
discipline or gain entry to professional schools. By that indicator, our graduate program has
been remarkably successful. The strength of the economy over the past f
ive years has
certainly helped our graduates in the job market, but even when the economy took a turn for
the worse 10 years ago, our students were still very competitive. An interesting fact
concerning the Microbiology & Molecular Biology area is that th
e MA graduates (course
work only) seem to be as successful in gaining employment as the MS students who have
the experience of a research project. We attribute this to the intensive hands
on training that
all the Masters students in that area receive in
the laboratory. This holds for the other
graduate concentrations, as well. Students in the Physiology concentration get a tremendous
amount of small animal handling experience which sets them apart from graduates of other
institutions. Students in the C
onservation Biology & Ecology area spend untold hours in the
field honing their observational and data collecting skills. Practical training in school means
less on
job training at work.


Summary Statement of Program Quality

Overall, the graduate

program in the Department of Biological Sciences is in very good
shape. Nearly all of the graduates in the three concentrations have gone on to careers in
their chosen areas. The addition of several new faculty over the past five years has


increased the

amount of graduate research and modernized the curriculum. Infrastructure
constraints and the loss of laboratory space to other expanding departments are the only
issues on the horizon that may have a negative impact on program quality.


Program Resource


Sources of Program Funding

Nearly all of the funding for instructional materials in the graduate program is provided
by the Department. The Department’s equipment budget is far too low, so high
laboratory instrumentation must come from

other sources (College of Science, Lottery,
outside grants, or donations). Over $150,000 of College and Lottery funds were spent on
molecular biology instrumentation in the ‘99
’00 academic year as part of the overall
biotechnology enhancement effort by
the University, and approximately $60,000 worth of
used equipment was donated to the Department from biotechnology companies. For
graduate research projects, the Department allocates between $10,000
20,000 per year from
endowed scholarship funds to the Gr
aduate Research Fellowship program. Many faculty
have obtained outside funding to support graduate research (NIH, private companies, local
government agencies). One major concern that has been precipitated by acquiring new
equipment is the high
cost of s
ervice contracts. Much of our new equipment cannot be
serviced by our own technicians and the cost of service contracts can be $5000 to $10,000
per year per item.

Year Historical Summary of Resource Use

See department’s summary of resource us

The Department decided almost five years ago to allow the graduate program to
grow to a point where a slightly larger variety of graduate courses could be given. As
the number of graduate students has increased from approximately 85 to almost 125,
number of students accepted as Plan A, or thesis, students has declined. In the
mid 1990’s we had close to 75 percent of our students as MS students; today it is
slightly less than 50 percent. This shift has allowed the program to grow without
greatly incr
easing the resources needed by the program. It has grown, however to a
point where the time and energy demands of the faculty have reached a level that the
faculty has more
less agreed to keep the number of graduate students level for
some time.

lysis of Resource Stability and Impacts on Program Effectiveness

Organismal biology students (i.e. those interested in ecology, field aspects,
environmental problems) do much of their work off campus. A considerable amount
of those student’s support comes

from faculty research contracts often for research
for state and federal agencies. In the last five years income from those sources has
amounted to more than 1.5 million dollars (See Appendix

Molecular and microbiology graduate students, however,
either work in our labs
(most of them) or in off campus industrial labs. The needs of the on campus students
are similar to and usually greater than the upper division undergraduate molecular
biology and microbiology students. Approximately a quarter of ou
r Department’s


graduate students are MS students in this very expensive area of research. We have
difficulty keep our equipment up
date and functioning properly as well as
supplying the often very expensive materials and supplies needed in their researc
We have industry support and students get various small grants but we need much
more support in this area, the area most applicable to the biotech industry
surrounding us.

Summary of Future Resource Needs by Category

Repeated here are the items fro
m the
Molecular Biology and Microbiology

as they are as applicable to the graduate program as to those undergraduate


Higher electrical capacity and emergency power


Replacement of aging autoclaves and incu

need for a bacterial fermentor to enhance both the

instructional and research programs. Replacement of aging

centrifuges; acquisition of a chemiluminescent image analyzer (to

obviate the need for radioisotope use in teaching labs).


One more tenure tract hire within two years.

For the Physiology Concentration


Upgrade present laboratory instrumentation and acquire

new, state
art equipment.


One more tenure track hire within two years.

For the Organismal Biology, Conservation and Ecology Concentration


One more tenure track hire within one year.

V. Program Plan for the Future

Summary of Program Strengths, Challenges and Opportunities

See the similar sections of the r
eviews of the Molecular Biology and Microbiology
majors; they are almost totally applicable to the graduate programs in those areas. Those
concentrations and the Physiology Concentration are the “natural” fit with the biotech
environment around use. The mo
lecular biology and microbiology areas have the greatest
potential for growth but by far cost the most. How much we grow, how well we do will
be dependent or increase state support and increased industrial support and collaboration.
While the undergraduate

enrollment in the Organismal Biology, Conservation and


Ecology area have declined along with most of the majors on campus, the graduate area
continues to produce a steady stream of master’s degree students who find home and
favor in environmental consulti
ng, doctoral programs, agency work, and industry. The
number of graduate students in this latter area have gone up rather than down in the last
five years and the amount of money generated by faculty in the area to support those
graduate students exceeds $
1.5 million, no small amount of money in hard times
environmentally speaking. The recent passage of environmental support bonds in the
Spring 2000 elections bode well for future support of students through continued grants
and contracts to our faculty. Cu
rrently, conservation biology consulting companies are
heavily recruiting fisheries biologist with expertise in salmon biology. All of our
graduate programs suffer from smaller classes and heavy work loads for faculty. We have
lost a considerable amount o
f FTES in our General Education program. The Department
continues to work at the balancing act between large classes and the diversity of classes
needed to support our diverse graduate program.

Planned Direction of the Program for the Last Five Years

e plan to keep our graduate enrollment at about Spring 2000 levels for the near
future even though the graduate program could grow considerably in the face of
increased demand. Our decreased share of General Education FTES as well as a general
of our undergraduate majors will not support any increase in this area.
Several of the molecular/microbiology faculty will offer a continuing education program
in the DNA technology field but those workshops and short courses will be taught outside
of our
regular offerings. We are attempting to serve the needs of DNA technology
community in this way but such efforts, as laudatory as they are, come at a price, that of
increased overall work loads on the part of several of our most talented professors. We
ect grant and contract support for the organismal biology graduate students to stay
steady or increase in the next few years. Again how many Plan A students we can support
in this interesting and important area will depend on the resilience and enthusiasm
of an
increasing smaller group of professors in the Organismal Biology, Conservation and
Ecology Area.


1. Program Goals

aa) to prepare graduates for employment in their chosen field (or for further doctoral

training, teaching,

or professional schools)

bb) provide them with a rigorous scientific environment in which they can develop the

observational, technical, and deductive reasoning skills required for a successful

career in the biological sciences

cc) provide limi
ted remedial upper
division coursework in the biological and physical

dd) provide advanced academic instruction and laboratory or field training

ee) offer the degree options of coursework only (MA) or coursework and research thesis

(MS) an
d the curricular flexibility to best meet the needs of the student and

societal needs for graduate
level training


ff) raise student awareness of issues in professional ethics, science
based public policy, and

teach effective communication of sci
entific ideas

gg) offer core masters
level courses along with a selection of elective courses which allow

graduates to learn fundamental concepts in their chosen discipline while gaining

experience in related and complementary fields

hh) provid
e students and faculty with adequate teaching and research laboratory space,

supplies, and equipment in order to foster an environment conducive to effective

teaching, learning, and scholarship.

2. Performance Outcomes for Majors

AA) to have

an in
depth knowledge of a subdiscipline of biology

BB) to be able to solve biological problems, design experiments, formulate and

hypotheses, analyze data, and critically discuss research results

CC) to have quantitative, critical thinking,

oral and written communication skills consistent with a

level education

DD) to be able to do a thorough literature review

EE) to be prepared for employment in their chosen field (or for

level training or professiona
l schools)

DD) have advanced academic knowledge and laboratory skills beyond that

obtained through an undergraduate degree and consistent with the

expectations of a individual with a Master’s degree

3. Assessment Techniques

The knowledge

and skills of Master of Arts students are assessed in individual classes via
exams, seminar presentations, formal oral presentations, writing assignments, and
evaluation of their laboratory skills. In addition, MA students have a culminating
experience w
hich consists of an oral and or written exam.

The knowledge and skills of Master of Science students are assessed in individual classes
via exams, seminar presentations, formal oral presentations, writing assignments, and
evaluation of their laboratory s
kills. The progress of these students in accomplishing
program goals is also continually assessed by their research advisors and other members of
their thesis committee. In addition, MS students have a culminating experience which
consists of a written M
aster’s thesis and an oral presentation of their research to the faculty
of the Department of Biological Sciences.

4. Timelines (Tentative)

Fall 2002: The Graduate Committee will develop a mechanisms by which to determine
when changes in the program
need to be made based on results from the assessment
described above.