The University Senate of
Michigan Technological University
Proposal 6-12
(Voting Units: Academic)
“Proposal for a
non-departmental Ph.D. Program in Biochemistry and Molecular Biology (BMB)”
Submitted by the
Biochemistry and Molecular Biology Doctoral Planning Group
Contacts: P. Murthy
(Chemistry), R. Wusirika (Biological Sciences), C.P. Joshi (Forestry and
Environmental Sciences)
There is a
growing world-wide demand for scientists and engineers with advanced training
in biochemistry and molecular biology. In particular, there is a recognized
need for society to understand and respond to problems associated with human
health, medicine, forestry and agriculture at the biochemical and molecular
levels. Powerful new research tools for understanding these complex processes, such
as complete genomes (of humans, animals, crop plants and trees), multi-scale
computer models, and applications of “omics” technologies including pharmacogenomics
(designing specific therapies based on individual genomes) are being rapidly
developed. To successfully participate in these advanced research and development
endeavors students require graduate-level training in biochemistry and
molecular biology. Furthermore, these
research problems and the techniques used to address them are inherently
interdisciplinary in nature, and therefore span traditional departmental
boundaries.
Michigan Tech
has a long and rich history of research in the exciting field of biochemistry
and molecular biology. Recent conceptual and technological
advancements have widened the scope of what is possible to study in these
fields and correspondingly, many recent faculty hires in individual departments
and through the Strategic Faculty Hiring Initiative have increased the ranks of
those around campus (Biological Sciences, Chemistry, Forest resources and
Environmental Sciences, Chemical Engineering, Biomedical Engineering,
Mathematics) engaged in biomedical
research, plant genomics and other health-related biochemistry and molecular
biology studies. Our ability to carry
out cutting edge research in these areas will strongly benefit from greater
coherence and integrated graduate training. Here, we propose a new doctoral degree program
in Biochemistry and Molecular Biology (BMB) which would consolidate our
dispersed resources and expertise. This
would provide a more appropriate degree program for some of our current and
future graduate students as well as a stronger and more focused educational
experience for all students involved in molecular level investigations of life
processes. Items required by the
University Senate for proposing new academic programs (Proposal 108.1.1) are
detailed in this proposal.
This program would
be categorized within the one or both of the following two CIP codes:
· 26.0210 Biochemistry/Biophysics and Molecular Biology
· 26.0299 Biochemistry, Biophysics and Molecular Biology, Other
1. General description and characteristics of the program
A
growing number of faculty and graduate students at Michigan Tech are working in
the area of biochemistry and molecular biology. These include members of the
Departments of Chemistry, Biological Sciences, Chemical Engineering, Biomedical
Engineering and the School
of Forest Resources and
Environmental Sciences. Active research
programs, courses, and a growing number of graduate degrees based on work in
this area already exist. The current initiative is to build on the established
and emerging research programs by developing a new, coherent, non-departmental
Ph.D. program whose primary focus is the graduate education of students in the
interdisciplinary areas of biochemistry and molecular Biology (BMB).
A core group of 14 graduate
faculty members will be involved in the BMB Ph.D. program (Table 1). The BMB
Core Faculty are those who likely would advise Ph.D. students in the program,
teach relevant lecture and laboratory courses, serve on qualifying exam
committees, be elected to serve on the steering committee and otherwise perform
programmatic duties of graduate faculty. Current members are from the
Departments of Biological Sciences, Chemistry, and the School of Forest Resources
and Environmental Sciences.
The BMB program is open to
faculty and students with overlapping research and academic interests. Michigan Tech faculty with close research
interests include Drs. S. Bagley (BL), M.H. Song (BL), D. Shonnard (CM), C.-A.
Peng (CM), A. Minerick (CM), C. Heldt (CM), M. Frost (BE), R. Rajachar (BE) and
others. We expect that some of these
faculty members will be interested in participating in the BMB Ph.D. program by
joining the BMB Core Faculty group and participating in associated teaching and
service duties. Other faculty members
advise graduate students who will benefit from the new course offerings and other
educational activities resulting from this program as their research focus
needs a detailed understanding of biochemistry and molecular biology.
We anticipate that a coherent
program in BMB will help to attract future faculty with diverse expertise in
this area into the above departments as well as other department such as the
Departments of Chemical Engineering and Biomedical Engineering.
Table 1. BMB Core Faculty
Department of Biological Sciences
Rupali Datta, Ph.D.
Associate Professor
Plant
Biochemistry, Environmental Remediation, Plant-Microbe Interactions
Office: 530
Dow Environmental Sciences and Engineering
Building
Phone: (906)
487-1783; Email: rupadatta@mtu.edu
K. Michael Gibson, Ph.D., FACMG
Professor
Inherited human genetic disorders
Office: 740
Dow Environmental Sciences and Engineering
Building
Phone: (906)
487-2025; Email: kmgibson@mtu.edu
Michael Gretz, Ph.D.
Professor
Carbohydrate biochemistry
Office: 730 Dow Environmental Sciences and Engineering Building
Phone: (906) 487-3175; Email: mrgretz@mtu.edu
Wan Jin Jahng, Ph.D.
Assistant
Professor
Vision mechanism, retinal degeneration, functional proteomics
Office: 501 Dow Environmental Sciences and Engineering Building
Phone: (906) 487-2192; Email: wjahng@mtu.edu
Ramakrishna Wusirika, Ph.D.
Associate Professor
Plant Molecular Biology, Comparative Genomics, Bidirectional Promoters and
Transposons
Office 505 Dow Environmental Sciences and Engineering Building
Phone: (906) 487-3068; Email: wusirika@mtu.edu
Thomas Werner, Ph.D.
Assistant Professor
Evolution, Genetics, Toxicology, Developmental
Biology, Insect Immunology, Virology
Office 523, Dow Environmental Sciences and Engineering Building
Phone: (906) 487-1209; Email: twerner@mtu.edu
Department of
Chemistry
Tarun Dam, Ph.D.
Assistant
Professor
Glycobiology;
protein-glycan interactions in immune regulation and pathogen invasion
Office:
701C Chemical Science and Engineering
Building
Phone:
(906) 487-2940; Email: tkdam@mtu.edu
Pushpalatha
Murthy, Ph.D.
Professor
Phospholipid and Phosphoinositide metabolism and biochemistry
Office: 505 Chemical Science and Engineering
Building
Phone: (906) 487-2094; Email: ppmurthy@mtu.edu
Martin Thompson, Ph.D.
Associate Professor
Protein-protein interactions and design of small peptide-based inhibitors of
protein-interactions
Office: 510C Chemical Science and Engineering
Building
Phone: (906) 487-3522; Email: thompson@mtu.edu
Ashutosh Tiwari, Ph.D.
Assistant Professor
Protein misfolding diseases’ with special emphasis on
neurodegenerative diseases
Office: 402B Chemical Science and Engineering
Building
Phone: (906) 487-1840;
Email: tiwari@mtu.edu
School of Forest Resources and Environmental Sciences
Victor Busov, Ph.D.
Associate
Professor
Functional
genomics of woody development
Office: 185, Noblet Building,
School of Forest Resources and Environmental
Science
Phone: 906-487-1728; Email: vbusov@mtu.edu
Oliver Gailing, Ph.D.
Assistant
Professor
Ecological
genetics and genomics
Office: 167, Noblet Building,
School
of Forest
Resources and Environmental Science
Phone: (906-487-1615);
Email: ogailing@mtu.edu
Chandrashekhar Joshi,
Ph.D.
Professor
Development of fast growing bioenergy trees for
efficient cell wall deconstruction to biofuels
Office:
168 Noblet Building, School of Forest
Resources and Environmental Science
Phone:
906-487-3480; Email: cpjoshi@mtu.edu
Hairong Wei, Ph.D.
Assistant
Professor
Plant systems
biology and bioinformatics
Office: 176, Noblet Building,
School of Forest Resources and Environmental
Science
Phone:
906-487-1473; Email: hairong@mtu.edu
Organizational Structure and Administration
The Biochemistry Ph.D.
program, as an interdisciplinary, non-department program, will be administered
through the Graduate
School. Participating core faculty will elect a
three-member steering committee. The committee will elect a Graduate Program Director
who will work closely with the Dean of the Graduate School
and will be assisted by a staff member. Most
biochemistry and molecular biology grants are affiliated with the Biotechnology
Research Center (BRC) so the staff member of BRC, who is supported by overhead
returns, will provide some assistance.
The Graduate Program Director
and the Steering Committee, with the help of BMB Core faculty, will review
applications, make admission decisions, determine whether or not changes to the
program need to be made (e.g., changing the “approved” curriculum or adding or
removing faculty from participation). The home departments of the core courses are
committed to offering them on a regular basis. Students enrolled in the program
will be housed within the home department of their advisors. The home departments will provide office
space, computational resources, and necessary supplies and infrastructure
support, and will consider the students for departmental teaching
assistantships when appropriate and available. All such students will be
counted as members of their home departments for the purposes of internal
university accounting.
2. Rationale
The
new program responds to a national and international need for more researchers
to address problems in the areas of human health, disease treatment and
sustainable environment at a molecular level.
Advanced education in biochemistry, molecular biology and related fields
is essential for creative and productive approaches to these problems. This initiative is motivated by the
following:
·
This
program provides a mechanism for recruiting more highly qualified graduate
students by providing a degree that encompasses the interdisciplinary nature of
biochemical research better than existing programs within individual academic
departments. Currently, students interested
in BMB must apply to programs in Biological Sciences, Chemistry, or the School of Forest Resources and Environmental Studies,
which have their own curriculum and culture.
This new BMB program would attract additional Ph.D. students who wish to
have a broader interdisciplinary academic experience focused on biochemistry
and molecular biology.
·
The new
program builds on current strengths with a core group of 14 faculty in three different
departments committed to the BMB program. The program could be offered as soon as it is
approved. Several existing students are already
interested in entering the program.
·
Many graduate-level
biochemistry and molecular biology courses are currently offered at Michigan
Tech in separate departments and this program would streamline existing faculty
effort by helping to identify and eliminate redundancies and increase
enrollments in courses that are currently undersubscribed. New graduate courses will be added to address
existing deficiencies and serve the needs of students in several disciplines.
The new courses along with existing courses will be organized into a coherent
program.
·
The
Ph.D. in BMB is attractive to students as they will have a degree in their area
of interest. In addition, the area of
expertise of students will be obvious to academic and private sector employers because
it is not currently apparent to employers that Michigan Tech students educated
in Chemistry, Biological Sciences, or Forest Resources and Environmental Studies
have specialized Ph.D. – level training in biochemistry and molecular biology.
·
The new program would enhance interdisciplinary
research at Michigan Tech by bringing together graduate students and faculty
housed in different departments who are conducting related research.
·
The new
BMB program will be housed in the Graduate
School. It will be overseen by a Steering Committee
made up of BMB Core Faculty.
·
Research
in biochemistry and molecular biology is well funded and the new program could
help with efforts to increase external funding.
3. Discussion of related programs within the institution and at other
schools
There are currently three biochemistry
Ph.D. programs (The University of Michigan, Ph.D. in Biological Chemistry; Michigan State
University, Ph.D. in Biochemistry and
Molecular Biology; Wayne State University, Ph.D. in Biochemistry and Molecular
Biology) in the State of Michigan. The character of the biochemistry degree
programs vary depending on the research emphasis of the faculty. The faculty involved at Michigan Tech form a
unique and broad mix involving biological chemistry, molecular and cellular
biology, chemical biology, plant physiology, biomedical science and
engineering, biochemical engineering, biomechanical engineering, forest
molecular biology and genomic sciences. This
combination of subject areas spans the major sub-disciplines of biochemistry
and molecular biology. Job opportunities
for Ph.D. graduates in BMB are excellent and are expected to remain so as a
result of national and international priorities in medicine, health,
agriculture, forestry and bioenergy fields.
4. Projected enrollment
We
anticipate that 2-5 students will enter the program immediately and that within
five years the program will have between 15-20 students.
5. Scheduling plans
We are aiming for
implementation by Fall Semester 2012. Participating
departments have committed to offer core courses on a regular basis.
6. Curriculum design
Course requirements are designed to ensure
that all students have a firm understanding of the fundamentals of
biochemistry and molecular
biology, including the principles underlying biochemical structure, biochemical
dynamics, molecular biology, genomics and biotechnology. These principles will be covered in three
core courses BMB5010, BMB5020 and BMB5030. The set of core courses will be
offered annually. This ensures that students will be able to complete the core
courses and be prepared to take the qualifying examinations during their second
year.
6.1 Required Core Courses
Three6000-level courses (three
credits each), a seminar course (BMB6040; one credit), and doctoral research
(BMB6990) will form the core of the curriculum for the BMB doctoral program. The courses are BMB6010: Advanced Biochemistry,
BMB6020: Advanced Molecular Biology, and BMB6030: Modern BMB techniques, descriptions
in Section 7 below). These courses cover
the fundamentals of biochemistry and molecular biology. The three core courses will be developed and
team taught by the BMB core faculty from the departments of Biological Sciences,
Chemistry, and the School
of Forest Resources and
Environmental Sciences. These courses
will provide the necessary background in the areas of biochemistry and
molecular biology including genomics and biotechnology. The Departments of Chemistry and Biological
Sciences and the School
of Forest Resources and
Environmental Sciences have agreed to support the creation of these new
courses.
In addition to the nine core
course credits above, students, depending on their academic background, may be
required to take additional courses to provide the breadth and depth necessary
for graduate research. The necessary
courses will be suggested by the student’s Advisor in consultation with the Advisory
Committee. The courses may be at the
3000-, 4000-, 5000- or 6000-level. A
partial listing of relevant 5000-level courses is included below (7.2). Courses used to satisfy the requirements for
a degree will conform to Graduate
School policies regarding
required grades, overall GPA, and academic level.
Students will be required to
complete a seminar course (BMB6040, 1 credit).
Instead of duplicating seminar courses offered by other departments, BMB6040
may include elements of graduate level seminar courses currently offered by other
departments such as Biological Sciences (BL5503), Chemistry (CH5900) and the
School of Forest Resources and Environmental Sciences (FW5800) and others.
Students conducting research
will enroll in (BMB6990).
Students will need a total of
60 credits beyond a Bachelor degree or 30 credits beyond a Master degree, per Graduate School requirements.
6.2 Qualifying Examination
Each student must pass a
written qualifying exam followed by an oral exam no later than the end of the
second year of graduate study (Spring semester of second year). This examination will cover topics covered in
the core courses BMB6010, BMB6020 and BMB6030. The purpose of the examination
is to determine the student’s mastery of knowledge in biochemistry and
molecular biology and the ability to apply this knowledge. Each examination will be written by a
committee of four faculty members who have been involved in teaching BMB6010,
BMB6020 and BMB6030. All students in the
program will take the same qualifying exam.
The committee will grade the qualifying exam and conduct the oral
examination. On the basis of the
student’s performance, the committee will decide whether or not each student
passes; a student will pass if a majority of committee members vote in the
affirmative. Students who do not pass
the examination will be allowed a second attempt. Failure to pass the Qualifying examination in
two attempts will result in dismissal from the Ph.D. program; both attempts
must be completed by the end of the second year.
6.3 Proposal defense
The student will present a proposal
followed by an oral defense of the research plan to his/her Advisory Committee.
The proposal should be submitted within one year of successfully completing the
qualifying examinations above (6.2) and no later than the completion of the
third year in the Ph.D. program. The
student's advisory committee must unanimously agree that the research plan is
acceptable. The oral proposal is open to the University community.
6.4 Doctoral dissertation and final oral examination
The research conducted by the
student will be presented to the Advisory Committee as a written dissertation. An oral presentation of that dissertation will
be made following the completion of the written work. The committee will
consist of at least four members of the graduate faculty. At least one of these
will be from outside the student's administrative home department or school. The dissertation is acceptable if the
advisor and at least two of the remaining three members of the Advisory
Committee concur on its acceptance. The oral defense is open to the University
community.
7. New course descriptions
In order to meet the needs of
graduate students for graduate level courses in biochemistry and molecular
biology, departments periodically offered courses such as, Special topics in
biochemistry and molecular biology, Protein folding, Enzymology, Bioorganic
chemistry, and others. We anticipate
that the following core courses, which will be offered regularly, will replace
many of the previous offerings
BMB6010 Advanced
Biochemistry This course
will focus on the relationships between structure and function of proteins,
nucleic acids lipids and carbohydrates.
Specific topics include enzyme catalysis, binding and allosterism,
protein-protein interaction and protein-nucleic acid interaction, membrane
function and signal transduction.
Classic and current papers may accompany the lecture material.
Foundations in basic biochemistry and
molecular biology are required for this course.
Credits: 3.0. Lec-Rec-Lab: (3-0-0). Semesters Offered: Fall.
BMB6020 Advanced Molecular
Biology This course will focus on the gene
structure, gene duplication gene expression, gene regulation, DNA
recombination, DNA repair and transposition.
Comparison between prokaryotes and eukaryotes will be drawn. Genomics and modern biotechnology methods
will be discussed. Classis and current
papers may accompany the lecture material.
Foundations in basic biochemistry and molecular biology are required for
this course. Credits: 3.0. Lec-Rec-Lab: (3-0-0).
Semesters Offered: Fall.
BMB6030 Modern BMB Laboratory This is an intensive laboratory course that
focuses on protein chemistry, nucleic acid chemistry, genomics and
biotechnology. Students will rotate
between research labs of four faculty where they will gain in-depth laboratory
experience in modern biochemistry and molecular biology. Credits: 3.0. Lec-Rec-Lab: (0-0-3). Semesters
Offered: Spring.
BMB6990 Doctoral Research Original research that culminates in
a PhD dissertation. Credits: Variable
to 12.0.May be repeated; Graded Pass/fail only.
Semesters offered: Fall/Spring.
Restrictions: Permission of instructor required. Must be enrolled in one of the following
level(s): Graduate
7.1 Courses currently offered in Biochemistry and
Molecular Biology at the 5000 level
- BL5030 - Molecular
Biology Molecular biology of
gene structure, expression and regulation. Molecular techniques and their
application to biotechnology and genomes are covered. Credits: 3.0. Lec-Rec-Lab: (3-0-0).
Semesters Offered: Fall; Restrictions: Must be enrolled in one of the
following Level(s): Graduate.
- BL 5035 – Bioimaging Current concepts in light and electron
microscopy and scanning probe techniques. Theory and practice of
fluorescence (including confocal and multi-photon), atomic force, scanning
and transmission electron, and video microscopy as applied to biological
specimens with an emphasis on sample preparation. Emphasis will be placed
on application of advanced techniques. Half semester course. Credits: 2.0. Lec-Rec-Lab: (0-4-0). Semesters Offered: Fall - Offered
alternate years beginning with the 2010-2011 academic year. Restrictions: May not be enrolled in one
of the following Class(es): Freshman, Sophomore, Junior
- BL 5042 - Scanning
Electron Microscopy of Biological Specimens Hands-on training in operation of the scanning
electron microscope (SEM). Students prepare biological specimens of their
choice for observation. Emphasis will be placed on application of advanced
techniques. Successful completion of course is prerequisite to becoming a
certified SEM operator in the ACMAL. Half semester course. Credits: 2.0 Lec-Rec-Lab: (0-2-6) Semesters Offered: Fall - Offered
alternate years beginning with the 2010-2011 academic year Restrictions:
May not be enrolled in one of the following Class(es): Freshman,
Sophomore, Junior. Pre-Requisite(s):
BL 5035
- BL 5052 - Fluorescence
and Video Microscopy of Biological Sciences Hands-on training in fluorescence microscopy
and video microscopy. Students prepare biological specimens of their
choice for observation. Emphasis will be placed on application of advanced
techniques. Half semester course. Credits: 2.0 Lec-Rec-Lab: (0-2-6) Semesters
Offered: Spring - Offered alternate years.
Restrictions: May not be enrolled in one of the following
Class(es): Freshman, Sophomore, Junior .
Pre-Requisite(s): BL 5035
- BL 5062 - Transmission
Electron Microscopy of Biological Specimens Hands-on training in operation of the
transmission electron microscope (TEM). Students prepare biological
specimens of their choice for observation. Emphasis will be placed on
application of advanced techniques. Successful completion of course is
prerequisite to becoming a certified TEM operator in the ACMAL. Half
semester course. Credits: 2.0 Lec-Rec-Lab:
(0-2-6). Semesters Offered: Spring
- Offered alternate years. Restrictions:
May not be enrolled in one of the following Class(es): Freshman,
Sophomore, Junior. Pre-Requisite(s):
BL 5035
- BL 5145 -
Plant-Microbe Interactions Interactions between
plants and microorganisms in the environment. Topics include microbial
virulence, signaling, gene expression, beneficial interactions and disease
resistance in plants. Laboratory will focus on plant biochemical and
microbiological methods as they relate to environmental problems. Credits: 3.0 Lec-Rec-Lab: (2-0-2) Semesters Offered: Fall Restrictions: May not be enrolled in one
of the following Class(es): Freshman, Sophomore, Junior
- BL 5503 - Graduate
Research Seminar Seminar is designed to facilitate
critical discussions of student research projects at various stages of
their development. The presenter will provide a seminar on their project
and research goals, which will establish the foundation for the discussion
thereafter. Credits: 1.0; May be
repeated. Lec-Rec-Lab: (0-1-0). Semesters Offered: Fall
- CH 5110 -
Pharmaceutical Chemistry: Drug Action
Focuses
on structural and mechanistic approaches to pharmaceuticals and drug action. General principles of
absorption, distribution, action, metabolism, and toxicity of drugs will
be presented followed by action of drug classes such as antibiotics,
cardiovascular, and anti-inflammatory drugs. Credits: 3.0. Lec-Rec-Lab: (3-0-0).
Semesters Offered: Spring.
Restrictions: Must be enrolled in one of the following Level(s): Graduate
- CH 5120 -
Pharmaceutical Chemistry: Drug Design
Focuses
on the important concepts in the design and synthesis of drugs. Rational
basis for drug design including synthetic, computational, and biochemical
concepts will be discussed. Topics include structure-activity
relationships, synthesis and reaction mechanism, and case studies of
drugs. Credits: 3.0 Lec-Rec-Lab: (3-0-0) Semesters Offered: Fall Restrictions: Must be enrolled in one of
the following Level(s): Graduate
- CH 5210 - Analytical
Separations Covers theory and
applications of modern gas chromatography, high performance liquid
chromatography, and ion chromatography as well as instrumentation for
these techniques. Studies trace organic analysis and environmental
problems. Credits: 3.0 Lec-Rec-Lab: (3-0-0) Semesters Offered: Spring. Restrictions: May not be enrolled in one
of the following Class(es): Freshman, Sophomore, Junior
- CH 5230 - Mass
Spectrometry and Fluorescence Fundamentals and applications of gas
chromatography-mass spectrometry, liquid chromatography-mass spectrometry
and fluorescence spectroscopy. Credits:
3.0. Lec-Rec-Lab: (3-0-0). Semesters Offered: On Demand Restrictions: May not be enrolled in one
of the following Class(es): Freshman, Sophomore, Junior
- CH 5570 - Advanced
Biophysical Chemistry A discussion of
experimental techniques and applications of physical chemistry principles
to the study of the structure, dynamics, and chemical reactions of
proteins, nucleic acids, and other biopolymers. Credits: 3.0. Lec-Rec-Lab: (3-0-0). Semesters
Offered: On Demand. Pre-Requisite(s): CH 3520
- FW 5070 - Developmental and Ecological
Genetics Course will provide current knowledge on signal perception,
transduction and response pathways in higher eukaryotes with most examples
primarily from but not limited to plants in a lecture and colloquium
format. Topics will cover major developmental pathways, and molecular
bases of adaptation to biotic and abiotic factors. Credits: 3.0 Lec-Rec-Lab:
(1-2-0) Semesters Offered: Fall Pre-Requisite(s): BL
5030
- FW 5076 - Molecular Techniques in
Ecology The course provides knowledge on molecular techniques used in
ecology, population biology, and evolutionary studies. Credits: 3.0;
Graded Pass/Fail Only Lec-Rec-Lab: (3-0-0) Semesters Offered: Fall
- Offered alternate years beginning with the 2010-2011 academic year
- FW 5082 – Gene Expression Data Analysis
Students
will learn statistical methods and skills for analyzing large-scale gene
expression data resulting from high-throughput technologies, become
familiar with various bioinformatics tools and resources, and develop
useful working knowledge of how to analyze genetic data. Credits: 3.0
Lec-Rec-Lab: (3-0-0) Semesters Offered: Spring - Offered
alternate years beginning with the 2010-2011 academic year
- FW 5089 - Tools of Bioinformatics Computer applications
in molecular biology. Hands-on experience with using popular computer
programs for DNA, RNA and protein sequence analysis, database management,
data editing, assembly, and organization, multiple sequence comparisons,
protein structural analysis, evolutionary relationships of genes, use of
Internet for data retrieval, comparison and analysis. Credits: 4.0 Lec-Rec-Lab:
(2-1-2) Semesters Offered: Fall - Offered alternate years
beginning with the 2011-2012 academic year Restrictions: Must be
enrolled in one of the following Level(s): Graduate
- FW 5413 - Sustainable Biomass Production and
management systems involving biomass for bioenergy and biofuels
applications in native forests and energy plantations. Emphasis on
integration across systems and values in the context of environmental
sustainability. Credits: 3.0 Lec-Rec-Lab: (2-1-0) Semesters
Offered: Fall - Offered alternate years beginning with the 2010-2011
academic year Restrictions: May not be enrolled in one of the
following Class(es): Freshman, Sophomore, Junior
- FW 5413 - Sustainable Biomass Production and
management systems involving biomass for bioenergy and biofuels
applications in native forests and energy plantations. Emphasis on
integration across systems and values in the context of environmental
sustainability. Credits: 3.0 Lec-Rec-Lab: (2-1-0) Semesters
Offered: Fall - Offered alternate years beginning with the 2010-2011
academic year Restrictions: May not be enrolled in one of the
following Class(es): Freshman, Sophomore, Junior
- FW 5800 - Master's Graduate Seminar Presentation by
students of current forest resource- related problems and research. Some
instruction on presentation skills. Credits: 1.0 Lec-Rec-Lab: (0-1-0)
Semesters Offered: Fall, Spring Restrictions: Must be
enrolled in one of the following Level(s): Graduate
- FW 5850 - Effective Grantsmanship
Workshop Ability to write successful grant application is an important part
of graduate education. Students will learn basic techniques of grant
writing for federal, industrial, and international funding agencies and
will submit a well-organized proposal for peer review in the class. Credits:
2.0 Lec-Rec-Lab: (1-1-0) Semesters Offered: Spring Restrictions:
May not be enrolled in one of the following Class(es): Freshman,
Sophomore, Junior
7.2 Potential
additional courses
New
courses will be offered based on the needs of graduate students and the expertise
and availability of affiliated faculty. Potential
new courses include, Bioremediation; Cancer/tumor metabolism; and Metabolic
impact of pollutants.
8. Library and other learning resources
The program builds on existing resources, so it is
not anticipated that new library or other learning resources will be required.
9. Computing
Access Fee
Initially
each student will pay the Computing Access Fee appropriate to the advisor's
home department. The program will revisit this issue as circumstances
dictate.
10. Faculty
resumes
Attached below.
11. Description of available/needed equipment
Faculty
listed in Table 1 have fully functioning laboratories with the necessary
equipment and computers. No new
equipment is required to startup this program.
12. Program
costs
No new
resources are requested, and costs associated with recruiting and other program
administration will be handled through the Graduate
School and the departments of
Biological Sciences, Chemistry, and Forest
resources and environmental sciences and the BRC.
13. Space
No new space
is required14. Policies, regulations and rules
Described in
Section 1 (faculty participation) and Section 6 (curriculum requirements) above.
15. Accreditation
requirements
Not
applicable
16. Internal
status of the proposal
Approved by
the Department Chairs and the Deans of the College
of Sciences and Arts and the School of Forest Resources and Environmental Sciences
(See attached signature sheet). Preliminary
review by the Dean of the Graduate
School completed. Reviews
by the Provost, Dean’s Council, Graduate Faculty Council, and University Senate
are pending.
17. Planned
implementation date
There are
students currently attending Michigan Tech who are interested in the BMB PhD
program so we are aiming for implementation by Fall Semester 2012.
Biographical
Sketch
Victor B. Busov
Associate Professor
Michigan Technological University
School of Forest Resource Environmental Science
185 Horner Hall
Phone:906-487-1728
Fax:906-487-2915
Houghton, MI 49931
E-mail: vbusov@mtu.edu
Education
Oregon State University Molecular biology Post-doc., 2004
North Carolina State University Genetics Ph.D.,2001
Southern Illinois University Forestry M.S., 1996
Bulgarian Higher Forestry
Institute Forestry B.S., 1990
Appointments
05/08-present Associate Professor. Michigan Technological University. Functional genomics of adaptation and development in trees.
03/04–05/08 Assistant Professor. Michigan Technological University. Functional genomics of adaptation and development in trees.
12/01—01/04 Post-doctoral Research Associate, Oregon State University
Activation tagging for gene discovery in poplar.
08/96--12/01 Graduate Research Assistant. North Carolina State University.
Microarray analysis of auxin-regulated gene expression in loblolly pine.
08/94--01/96 Graduate Research Assistant, Southern Illinois University
Allozyme analysis of diversity and genetic structure of black walnut in central U.S.
01/96--06/96 Intern (during M.S. work), Westvaco Corporation (now MeadWestvaco)
Clonal propagation of loblolly pine and cottonwoods.
11/90--08/94 Research Associate. Bulgarian Academy of Sciences
Breeding, propagation and conservation of Fagus species in southeastern Europe.
Selected Publications
1)Gou, J., Strauss, S.H.,
Tsai, C.J., Fang, K., Chen, Y., Jiang, X., and Busov, V.B. (2010) Gibberellins
Regulate Lateral Root Formation in Populus through Interactions with Auxin and
Other Hormones. Plant Cell 22:623-639.
2)Busov, VB, Yordanov, Y
Gou, J, Meilan, R, Ma, C, Regan, S and Steven Strauss
(2010) Activation tagging is an effective gene tagging system in Populus. Trees Genetics and Genomes. DOI: 10.1007/s11295-010-0317-7
3)Xiaoqi Cui, Tong
Wang, Huann-Sheng Chen, Victor Busov and Hairong Wei (2010) TF-finder: A
Software Package for Identification of
Transcription Factors Involved in a Biological Process Using Microarray Data
and Existing Knowledge. Bioinformatics. 11: 425
4)Katherine M. Han,
Palitha Dharmawardhana, Renee´ S. Arias, Cathleen Ma, Victor Busov and Steven
H. Strauss. (2010) Gibberellin-associated cisgenes modify growth, stature and
wood properties in Populus. Plant
Biotech J. p 1–17.
4)Busov VB, Brunner AM,
Strauss SH. 2008. Genes for control of plant stature and form. New Phytologist 177: 589-607.
5)Tuskan GA,
…Busov V et al.. 2006. The genome of
black cottonwood, Populus trichocarpa
(Torr. & Gray). Science. 313, 1596-1604.
6)Busov VB, Brunner A,
Meilan R, Filichkin, S, Ganio, L, Gandhi, S, Strauss, SH. 2005. Genetic transformation: A powerful tool for
dissection of adaptive traits in trees. New Phytologist.167: 9-18.
7)Brunner, AM, Busov VB,
and Strauss SH. 2004. The Poplar Genome
Sequence: Functional Genomics in a Keystone Plant Species. Trends in Plant Science 9: 49-56
8)Busov VB, Meilan R,
Pearce DW, Ma C, Rood SB, Strauss SH. 2003. Activation tagging of a dominant
gibberellin catabolism gene (GA 2-oxidase)
from poplar that regulates tree stature. Plant
Physiology. 132: 1283-1291.
Synergistic Activities
1)Member of IUFRO Working
Party S3. 02-03
2)Member of American
Society of Plant Biologist
3)American
Association for the Advancement of Science (AAAS)
4)Namkoong’s Family
Fellowship for Academic and Teaching Excellence, 2000
5)North Carolina Biotechnology Consortium
Travel Award, 2001.
6)Ad Hoc reviewer: NSF Multiple Directorates and Programs,
USDA-NRI Competitive Grants Program.
7)Ad Hoc manuscript reviewer: Transgenic Research, Plant Science, Tree Physiology, Plant Molecular
Biology, New Phytologist.
8)Invited participant in
the Populus genome sequence
annotation jamboree. Dec 6-10, 2004, Joint Genome Institute, Walnut Creek, CA
Collaborators
Allen, N., NCSU; Brunner,
A.M., OR State U; Davis, J., DOE; DiFazio, S.P., DOE, ORNL; Garcia, C., NCSU;
Goldfarb, B., NCSU; Johannes, E., NCSU; Kung, F., S. Illinois U.; LeBude, A.,
NCSU; Pearce, D., U. of Lethbridge, CAN; Pregitzer, K., MTU; Rink, G., U.S.
Forest Service; Rood, S.B., U. of Lethbridge, CAN; Sambeek, J.V., U.S. Forest
Service; Sederoff, R.R., NCSU; Spiker, S.L., NCSU; Strauss, S.H., Oregon State
U.; Sun, Y., NCSU; Swain, S., CSIRD, Austrailia; Tsai, C.-J., MTU;
Tschaplinski, T.J., ORNL Oakridge, TN; Tuskan, G.A., ORNL, Oakridge; Whetten,
R.W., NCSU; Woeste, K.E., Purdue University
Graduate and Post-Doctoral Advisors
M.S. Advisor: Kung,
F., Southern Illinois
University
Ph.D. Advisor: Goldfarb,
B., NC State University;
Spiker, S.L., NC State
University
Post-doctoral Advisor: Strauss, S.H., Oregon State
University
Advisor and Postgraduate-Scholar Sponsor
Hao Wei (OSU); Rewati
Potkar (MTU); Zhan Ye (MTU); Trisha Colling (MTU); Chamini Geethenjalee (MTU);
Shiv Thammannagowda (MTU); Fuyu Xu (Ph.D., MTU); Christine Zawaski (MTU);
Elizabeth Etherington (OSU); Rama Joshi (MTU) Mahita Kadmiel (MTU); Rajinikanth
Mohan (MTU)
Biographical
Sketch
Tarun K. Dam
Assistant Professor
Department of Chemistry
Michigan Technological University
1400 Townsend
Drive, Houghton,
MI 49931
Phone: 906 487 2940
Email: tkdam@mtu.edu
Education
University of Calcutta,
Calcutta, India Protein Biochemistry Ph.
D. 1994
Indian Institute of Science, India Protein Biochemistry Trainee, 1993-1995
Albert Einstein College of Medicine, NY Protein
Biophysics Postdoc,
1996-2000
Appointments
2010- Assistant Professor, Michigan
Technological University, MI
2000-2010 Instructor (Full
time Faculty), Albert Einstein College of Medicine, NY
Selected publications
1)
Dam, T. K. and Brewer, C. F., Maintenance
of cell surface glycan density by lectin-glycan
interactions:
a homeostatic and innate immune regulatory mechanism. Glycobiology 20,
1061
1064 (2010). http://glycob.oxfordjournals.org/content/20/9/1061.full.pdf+html
2)
Dam, T. K. and Brewer, C. F., Lectins
as pattern recognition molecules: the effects of epitope density in innate
immunity Glycobiology 20, 270-279 (2010).
http://glycob.oxfordjournals.org/cgi/content/full/20/3/270?view=long&pmid=19939826
3) Dam, T.
K., Gerken, T. A. and Brewer, C. F. Thermodynamics of multivalent carbohydrate-lectin
cross-linking interactions: importance of entropy in the bind and jump
mechanism. Biochemistry, 48, 3822-3827
(2009). http://www.ncbi.nlm.nih.gov/pubmed/19292456
4)
Dam, T. K., Torres, M., Brewer, C. F. and Casadevall, A., Isothermal titration
calorimetry reveals differential binding thermodynamics of variable
region-identical antibodies differing in constant region for a univalent
ligand. J. Biol. Chem. 283, 31366-31370 (2008).
http://www.jbc.org/content/283/46/31366.long
5)
Dam, T.
K., and Brewer, C. F., Effects of clustered epitopes in multivalent ligand-receptor
interactions. Biochemistry, 47, 8470-8476 (2008).
http://pubs.acs.org/doi/abs/10.1021/bi801208b
6)
Dam, T. K., Gerken, T. A., Cavada, B. S., Nascimento, K. S., Moura, T. R., and
Brewer, C. F., Binding studies of -GalNAc specific lectins to the -GalNAc (Tn-antigen) form of
porcine submaxillary mucin and its smaller fragments. J. Biol. Chem. 282, 28256-28263
(2007).
http://www.jbc.org/content/282/38/28256.long
7) Dam, T. K. and Brewer, C. F.
Fundamentals of lectin-carbohydrate interactions, in Comprehensive
Glycoscience, (Kamerling, J. P., ed.), Elsevier Ltd., Vol. 3, pp. 397-452
(2007).
http://www.sciencedirect.com/science?_ob=RefWorkIndexURL&_idxType=TC&_cdi=48257&_refWorkId=3687&_explode=5584000008,5584000010&_alpha=&_acct=C000050221&_version=1&_userid=10&md5=48905b7cd1c795793063a99d0dce51b6&refID=5584000010#5584000010
8)
Dam, T. K., Gabius, H.-J., André, S., Kaltner, H., Lensch, M., and Brewer, C.
F. Galectins bind to the multivalent glycoprotein asialofetuin with enhanced
affinities and a gradient of decreasing binding constants. Biochemistry, 44,
12564-12571 (2005).
http://pubs.acs.org/doi/abs/10.1021/bi051144z
9)
Dam, T. K., Oscarson, S.,
Roy, R., Das, S. K., Page, D., Macaluso, F. and Brewer, C. F. Thermodynamic, kinetic and
electron microscopy studies of concanavalin A and Dioclea grandiflora lectin cross-linked with synthetic divalent
carbohydrates. J. Biol. Chem. 280, 8640-8646 (2005). http://www.jbc.org/content/280/10/8640.long
10) Dam, T. K.
and Brewer C. F. Carbohydrate-lectin cross-linking interactions: structural,
thermodynamic, and biological studies. Methods in Enzymology (Recognition of
Carbohydrates in Biological Systems; Y.C. Lee & R. T. Lee, ed.), 362,
455-486 (2003).
http://www.ncbi.nlm.nih.gov/pubmed/12968382
11) Hegde, S.
S., Dam, T. K., Brewer C. F. and Blanchard, J. S. (2002), Thermodynamics of
aminoglycoside and acyl-coenzyme A binding to the Salmonella enterica
AAC(6’)-Iy aminoglycoside N-acetyltransferase. Biochemistry 41, 7519-7527
(2002).
http://www.ncbi.nlm.nih.gov/pubmed/12044186
12) Dam, T. K.
and Brewer, C. F. Thermodynamic studies of lectin-carbohydrate interactions by
isothermal titration calorimetry. Chemical Reviews 102, 387-429 (2002).
http://pubs.acs.org/doi/abs/10.1021/cr000401x
13) Dam, T.
K., Roy, R., Page, D. and Brewer, C. F. Negative cooperativity associated with
binding of multivalent carbohydrates to lectins. Thermodynamic analysis of the
“Multivalency Effect”. Biochemistry 41, 1351-1358 (2002).
http://www.ncbi.nlm.nih.gov/pubmed/11802737
14) Dam, T. K., Roy, R., Das, S. K., Oscarson, S.
and Brewer, C. F. Binding of multivalent carbohydrates to concanavalin A and Dioclea grandiflora lectin.
Thermodynamic analysis of the “Multivalency Effect”. J. Biol. Chem. 275, 14223-14230 (2000).
http://www.jbc.org/content/275/19/14223.long
15) Dam, T. K., Bachhawat, K., Rani, P. G. and
Surolia, A. Garlic (Allium sativum) lectins bind to high mannose
oligosaccharide chains. J. Biol. Chem. 273, 5528-5535 (1998).
http://www.jbc.org/content/273/10/5528.long
Synergistic Activities
1) Received
Young Scientist Award for “outstanding accomplishments
and contributions in the field of microcalorimetry” given at
‘Biocalorimetry 2001 Conference: Philadelphia,
PA.
2) Developed
educational materials, which have been published in several books, such as Animal Lectins: A Functional
View, (Vasta and Ahmed ed., Taylor
and Francis);
Comprehensive Glycoscience, (Kamerling, J. P., ed., Elsevier Ltd) and Lectins:
Analytical Technologies, (Nilsson, C., ed., Elsevier B.V. Elsevier B.V).
3)
Reviewed manuscripts for scientific journals, namely, The Journal of Biological Chemistry,
Biochemistry, Biophysical Journal, Proceedings of the National Academy of
Sciences, Biochimica et Biophysica Acta, Glycobiology, Glycoconjugate Journal,
Journal of the American Chemical Society, European Journal of Biochemistry,
Phytochemistry, Analytical Biochemistry.
4)
Published a book review in the journal
Carbohydrate Research. 325, 233-234 (2000).
5)
Received invitation to deliver oral presentation at national scientific
meetings and universities.
Collaborators
Thomas Gerken (Case Western Reserve University, Ohio)
Arturo Casadevall, John
Blanchard (Albert Einstein College
of Medicine, New York)
Benildo Cavada
(FederalUniversity of Ceará,
Brazil)
Marit Sletmoen (The
Norwegian University of Science andTechnology, Norway)
Hans-J Gabius (Ludwig-Maximilians-University,
Germany)
René Roy (Université du Quebec à Montréal, Canada)
Stefan Oscarson (Stockholm University, Sweden)
Membership
Society for
Glycobiology
American
Chemical Society
American Society
for Biochemistry and Molecular Biology
Biographical
Sketch
Rupali
Datta
Assistant professor
Department of Biological Sciences
Michigan Technological University
1400 Townsend Drive, Houghton,
MI-49931
Phone: (906) 487-1783
Email: rupdatta@mtu.edu
Education
Osmania University, India
Biology and Chemistry B.S.,
1987
University of Hyderabad, India Life
Sciences M.S.
1989
University of Hyderabad, India, Life
Sciences Ph.D.
1997
Appointments
2008-present Associate Professor, Department of
Biological Sciences, Michigan Technological University,
Houghton, Michigan
2004-2008 Assistant Professor, Department of Earth and Environmental
Sciences, University of Texas at San Antonio, San Antonio, Texas
2003-2004 Research Assistant Professor and Senior Lecturer, Earth
and Environmental Science Department, University of Texas at San Antonio,
2002-2003 Post-doctoral Fellow and Lecturer-I, Earth and
Environmental Science Department, University of Texas at San Antonio, San
Antonio, Texas
1998-2001 Post-doctoral Associate, Plant Pathology Department, University of Florida,
Gainesville, Florida
1997-1998 Visiting Research Fellow, Japanese Society for Promotion
of Science Fellowship) Niigata University, Niigata,
Japan
Honors
1991-96 Junior
and Senior Research Fellowships from the University Grants Commission, Govt. of
India
1992 American Society for Plant
Physiologists (ASPP) fellowship for Plant Biochemistry course at the University of California,
San Diego
1994 Young Scientist Fellowship by 16th
International Union of Biochemistry and Plant
Molecular Biology Congress
1996-97 Senior
Research Fellowship in project funded by Department of Science and Technology
(Govt. of India)
1997-98 JSPS Research Fellowship by the
Japanese Society for Promotion of Science
2004 Outstanding Young Scientist Award,
2004 Association of Agricultural Scientists of Indian Origin (AASIO)
2005 University of Texas
at San Antonio
Faculty Research Award.
Selected Research Support United States Environmental Protection Agency, 2002, $391,473/2y (Total): Biogeochemistry of arsenic in contaminated
soils of Superfund sites
National Institutes of Health
1) 2007, $414,550 (Direct): Novel Remediation Methods to Lower Human Health Risk from Exposure to Arsenic-Enriched Soils
2) San Antonio Life Sciences Institute - REF, 2004-05, $199,990 (Direct): A multi
disciplinary approach to reduce human bioavailability and carcinogenicity of soil arsenic
3) Department
of Housing and Urban Development - Lead Technical Studies Program, 2004 - 2006,
$372,767 (Total): A novel phytoremediation method using vetiver grass to cleanup
lead-based paint-contaminated soils (Joint-PI)
4)Department
of Defense – Small Business Innovative Research, Phase-I, 2006-2007, $100,000
(Total): A new method to clean up chromium and metal enriched stormwater in
Naval shipyards (Principal)
5) Department
of Defense – Small Business Innovative Research, Phase-II, 2008-2010, $750,000
(Total): A new method to clean up chromium and metal enriched stormwater in
Naval shipyards (Principal)
Selected Refereed Publications (out of >160 refereed publications):
1) Sarkar, D. and R. Datta (2003). A modified in-vitro method to assess bioavailable
arsenic in pesticide-applied soils. Environ. Polln. 126: 263-266.
2) Sarkar, D.
and R. Datta (2004) Health Risk from Soil Arsenic: Does one size fit all. Arch.
Environ. Health, 59(7): 337-341.
3) Datta, R.
and D. Sarkar (2005) Consideration of soil properties in assessment of human
health risk from exposure to arsenical pesticide appl. soils. Integr. Env.
Assess. Mgmt. 1 (1): 55-59.
4) Sarkar, D.,
R. Datta, and S. Sharma (2005) Fate and
bioavailability of arsenic in organo-arsenical pesticide applied soils. Part-I.
Incubation Study. Chemosphere, 60: 188-195.
5) Sarkar D.,
R. Datta, S. Sharma and K. Sand (2006) Arsenic biogeochemistry and human health
risk assessment in organo-arsenical pesticide applied acidic and alkaline soils
- Incubation study. Sci. Total Environ. 372 (1): 39-48.
6) Makris K.C., D.
Sarkar and R.
Datta (2006) Evaluating a waste by-product as a
novel sorbent for arsenic. Chemosphere 64(5): 730 – 741.
7) Makris K.C., S. Quazi, R. Nagar, D. Sarkar, and R.
Datta and V.L.
Sylvia (2008) In-vitro model improves prediction of soil arsenic bioavailability: Worst-case scenario.
Environ. Sci. Technol. 42: 6278-6284.
8) Nagar R., K.
Makris, D. Sarkar, R. Datta and Sylvia V (2009)
Bioavailability and
Bioaccessibility of arsenic in a soil amended with drinking water treatment residuals. Arch.
Environ. Contamin. Toxicol.
57(4): 755-766.
9) Andra S,
Datta R, Sarkar D, Bach S, Mullen C (2010) Synthesis of phytochelatins in
vetiver grass upon lead exposure in the presence of phosphorus. Plant and Soil
326: 171-185.
10) Das P,
Datta R, Makris K, Sarkar D (2010). Vetiver grass is capable of removing TNT
from soil in the presence of urea. Environmental Pollution 158: 980-983.
11) Makris K,
Sarkar D, Salazar J, Punamiya P, and Datta R (2010) Alternative amendment for
soluble phosphorus removal from poultry litter. Environ. Sci. Pollut. Res.
17(1):195-202.
12) Nagar R,
Sarkar D, Makris K, and Datta R (2010) Effect of solution chemistry on As
sorption by Fe- & Al-based drinking-water treatment residuals. Chemosphere.
78(8): 1028-1035.
13) Andra S,
Datta R, Sarkar D, Bach S, Mullen C (2010). Synthesis of phytochelatins in
vetiver grass upon lead exposure in the presence of phosphorus. Plant &
Soil. 326(1-2): 171-185.
14) Das, P.,
Datta, R., Makris, K., and Sarkar, D. (2010). Vetiver grass is capable of
removing TNT from soil in the presence of urea. Environ. Pollut. 158(5):
980-983).
15) Andra S,
Sarkar D, Saminathan S, and Datta R. (2010) Predicting potentially
plant-available lead in contaminated residential sites. Environ. Monitor.
Assess. DOI 10.1007/s10661-010-1559-4 (E-publication ahead
of print).
Biographical Sketch
Oliver Gailing
Assistant
Professor of Ecological Genomics
School of Forest Resources and Environmental Science
Michigan Technological University, Houghton,
MI 49931
Tel: 906-487-1615, email: ogailing@mtu.edu
Web Page: http://forest.mtu.edu/faculty/gailing/
Professional preparation
M. Sc. (Botany), University of Bochum, Germany, 1994
Ph.D. (Genetics), University of Halle, Germany, 2000
PostDoc (Genetics),
Leibniz Institute IPK-Gatersleben, Germany, 2002-2002
Post lecturer
qualification (Habilitation, Forest Genetics), University of Goettingen, Germany,
2009
Appointments
2009-present Assistant Professor, Michigan Tech
University
2008-2009 Research Scientist, Goettingen University, Germany
2002-2008 Assistant Professor (“Wiss.
Assistent”) , Goettingen
University
2000-2002 Research Scientist (PostDoc),
Leibniz Institute IPK-Gatersleben,
Germany
1996-2000 Research Scientist (Ph.D), Leibniz
Institute IPK-Gatersleben, Germany
1994-1996 Research Scientist, Bochum University, Germany
Five recent publications most closely related to the
proposed project:
Gailing, O., Vornam,
B., Leinemann, L.L & R. Finkeldey. 2009. Genetic and genomic approaches to
assess adaptive genetic variation in plants: forest trees as a model.
Physiologia Plantarum 137:509-519. doi: 10.1111/j.1399-3054.2009.01263.x.
Curtu, A. L., Gailing, O. & R. Finkeldey.
2009. Patterns
of contemporary hybridization inferred from paternity analysis in a
four-oak-species forest. BMC Evolutionary Biology. 2009, 9: 284,
doi:10.1186/1471-2148-9-284.
Gailing, O., Langenfeld-Heyser, R. Polle, A. & R. Finkeldey.
2008.
QTL loci affecting stomatal density and growth in a Quercus robur
progeny: implications for the adaptation to changing environments. Global
Change Biology 14:1934-1946. doi:10.1111/j.1365-2486.2008.01621.x
Gailing, O. 2008. QTL
analysis of leaf morphological characters in a Quercus robur full-sib
family (Q. robur x Q. robur subsp. slavonica). Plant
Biology 10: 624-634. Doi: 10.1111/j.1438-8677.2008.00063.x
Curtu, A. L., Gailing, O. & R. Finkeldey. 2007. Evidence for
natural hybridization within a species-rich oak (Quercus spp.)
community. BMC Evolutionary Biology 7:218. Doi:10.1186/1471-21-48-7-218.
Five
additional significant publications:
Durand , J., E., Bodenes , C., Chancerel, Frigerio, J.-M., Vendramin,G., Sebastiani, F., Buonamici, A., Gailing, O., Koelewijn, H.P., Villani F., Mattioni, C., Cherubini, M., Goicoechea,
P.,Herran, A., Ikaran, Z., Cabane,
C., Ueno, S., de Daruvar, A., Kremer, A. & C. Plomion. 2010. SSR mining in oak ESTs and bin mapping of 256 loci
in a Quercus robur L. full-sib
pedigree. BMC Genomics 11:570.
Gailing, O., Wachter, H., Heyder, J., Schmitt H.-P,
& R. Finkeldey. 2007. Chloroplast DNA analysis in oak stands (Quercus robur L.)
in North Rhine-Westphalia with presumably Slavonian origin: Is there an
association between geographic origin and bud phenology? Journal of Applied
Botany and Food Quality 81: 165-171.
Curtu, A.L., Gailing, O., Leinemann, L. & R. Finkeldey. 2007. Genetic variation and differentiation within a
natural community of five oak species (Quercus spp.). Plant Biology
9:116-126.
Mottura,
M.C, Finkeldey, R., Verga, R.A. & O. Gailing. 2005. Development and
characterization of microsatellite markers for Prosopis chilensis and P.
flexuosa and cross-species amplification. Mol. Ecol. Notes 5: 487-489.
Gailing, O., Kremer, A., Steiner, W., Hattemer, H.H. & R.
Finkeldey. 2005. Results on quantitative
trait loci for flushing date in oaks can be transferred to different
segregating progenies. Plant Biology 7: 516-525.
Synergistic
activities
1) Ad
hoc reviewer for international Journals (e.g. BMC Plant Biology, BMC genomics,
Conservation Genetics, Molecular Ecology, New Phytologist, Plant Biology,
Physiologia Plantarum, Plant Cell and Environment, Plant Systematics and
Evolution)
2) Ad
hoc reviewer for Agence Nationale de la Recherche (France); ERANET, European
Union's 6th Framework Program for Research
3)
Session Chair in international conferences, (AOX symposium, 2009, Evora, Portugal,
Fagaceae Genomic conference (Raleigh November 10
-13, North Carolina)
4) Ph.D. Committees: Klaus Richter (University Kassel, 2009), Jerome Durand (University of Bordeaux,
December 2009)
5) Developed a new class in Ecological Genomics
Honors and
Awards
1/2009: Habilitation (Post Lecturer Qualification) for
Forest Genetics and Forest Tree Breeding at
the Georg-August University of Göttingen
7/2000 Luther certificate of the University Halle / Wittenberg for the PhD
thesis
Graduate and
Postdoctoral advisors:
Prof. Dr. Reiner Finkeldey, Prof. Dr. Konrad Bachmann,
Prof. Dr. Thomas Stuetzel
Thesis Advisees:
PhD (co-supervisor): Indrioko Sapto (2005), Pandey Madhav (2005), Cao Cuiping (2006), Curtu Alexandru Lucian (2006), Mottura Martin (2006), Derero Abayneh (2007), Ayele Bekele Taye (2008), Akinnagbe Akindele (2008), Nuroniah Hani (2009), Nguyen Nga (2009), Richter Klaus (2009), Rachmayanti
Yanti (2009)
Master
(co-supervisor): Duyen Ngo Thi (2004), Pandey Madhav (2004), Villarin Randy (2007), Gauli Archana (2007), Min Yazar (2007), Desta Demissew Sertse (2008)
Bachelor
(co-supervisor): Nesemann Kai (2004), Hesse Katrin (2007), Maschek Daniela (2007), Gottwald Christoph (2008),Hinrichsen Julia (2008), Hess Bastian (2008)
Biographical Sketch
Gibson, K. Michael
Professor and Chair
Department of Biological Sciences
Michigan Technological University
1400 Townsend Drive, Houghton,
MI-49931
Phone: (906) 487-2025
Email: kmgibson@mtu.edu
Education
University of California, Riverside,
CA Biochemistry B.S.
1977
University
of Colorado, Boulder, CO Chemistry
M.S. 1979
University of California, San
Diego, CA Chemistry Ph.D. 1983
Appointments, Honors, Awards
1984
- 1986 Postdoctoral
Fellow, Dept. Pediatrics, University of California, San Diego, La Jolla, CA
1985
- 1986 Bank
of America-Giannini Foundation Fellow
1986
- 1988 Assistant
Research Biochemist, Dept. Pediatrics, Univ. of California, San Diego, La
Jolla, CA
1988
- 1998 Senior
Research Scientist, Institute for Metabolic Disorders, Baylor University
Medical Center
and Baylor Research
Institute, Dallas, Texas
1991
- 1992 Alexander
von Humboldt Foundation Research Fellow, Heidelberg,
Germany
1989
- 1994 Assistant
Professor of Biomedical Studies, Baylor
University, Waco, Texas
1989
- 1995 Adjunct
Assistant Professor of Biological Sciences, Southern Methodist
University, Dallas, TX
1994
- 1998 Associate
Professor of Biomedical Studies, Baylor
University, Waco, TX
1995
- 1998 Adjunct
Associate Professor of Biological Sciences, Southern Methodist
University, Dallas, TX
1995
- 1998 Adjunct
Associate Professor/Neurology, Univ. Texas
Southwestern Medical School, Dallas,
TX
1998
- 2001 Associate
Professor, Depts. of Molecular and Medical Genetics and Pediatrics, Oregon Health
& Science
University, Portland, Oregon
1998
- 2005 Director,
Biochemical Genetics Laboratory, Oregon
Health & Science University, Portland,
OR
1999
- 2009 Board
Certified Clinical Biochemical Geneticist, American College
of Medical Genetics
2001
- 2005 Professor,
Dept. Molecular and Medical Genetics, Oregon Health & Science
University
2004- Komrower Memorial Lecturer,
Annual Meeting, Society for Study of Inborn Errors of
Metabolism,
Amsterdam,
August 31 - September 4, 2004
2005- 2009 Director,
Biochemical Genetics Laboratory, Children’s Hospital of Pittsburgh
of UPMC
2005
- 2009 Professor,
Pediatrics, Pathology, Human Genetics, University
of Pittsburgh School of Medicine
2009- Pres
Professor and Chair, Biological Sciences, Michigan Technological University
2008 NIH
Site Visit, PDEGEN (Program in Developmental Endocrinology/Genetics), March
26-28.
Selected Publications (from 258)
1) Harding CO, Gibson KM (2010) Therapeutic liver
repopulation for phenylketonuria. J
Inherit Metab Dis May 22. [Epub ahead of print] PMID: 20495959
2) Skvorak KJ, Hager EJ,
Arning E, Bottiglieri T, Paul HS, Strom SC, Homanics GE, Sun Q, Jansen EE,
Jakobs C, Zinnanti WJ, Gibson KM
(2009) Hepatocyte transplantation (HTx) corrects selected neurometabolic
abnormalities in murine intermediate maple syrup urine disease (iMSUD). Biochim Biophys Acta
1792:1004-10. PMID: 19699299
3) Skvorak KJ, Paul HS,
Dorko K, Marongiu F, Ellis E, Chace D, Ferguson C, Gibson KM, Homanics GE, Strom SC (2009) Hepatocyte transplantation
improves phenotype and extends survival in a murine model of intermediate maple
syrup urine disease. Mol Ther
17:1266-73. PMID: 19436271
4) Vardya I, Drasbek KR, Gibson KM, Jensen K (2010) Plasticity
of postsynaptic, but not presynaptic, GABA(B) receptors inSSADH deficient
mice. Exp Neurol June 4 [Epub ahead of
print] PMID: 20570675
5) Dósa Z, Nieto-Gonzalez
JL, Korshoej AR, Gibson KM, Jensen K
(2010) Effect of gene dosage on single-cell hippocampal electrophysiology in a
murine model of SSADH deficiency (gamma-hydroxybutyric aciduria).
Epilepsy Res 90:39-46.
PMID: 20363598
6) Acosta MT, Munasinghe
J, Pearl PL, Gupta M, Finegersh A, Gibson
KM, Theodore WH (2010) Cerebellar atrophy in human and murine succinic
semialdehyde dehydrogenase deficiency. J
Child Neurol May 5 [Epub ahead of print] PMID: 20445195
7) Zhang GF, Kombu RS,
Kasumov T, Han Y, Sadhukhan S, Zhang J, Sayre LM, Ray D, Gibson KM, Anderson VA, Tochtrop GP, Brunengraber H (2009) Catabolism
of 4-hydroxyacids and 4-hydroxynonenal via 4-hydroxy-4-phosphoacyl-CoAs. J Biol Chem 284:33521-34. PMID: 19759021
8) Pearl PL, Gibson KM, Cortez MA, Wu Y, Carter
Snead O 3rd, Knerr I, Forester K, Pettiford JM, Jakobs C, Theodore WH (2009)
Succinic semialdehyde dehydrogenase deficiency: lessons from mice and men.
J Inherit Metab Dis 32:343-52. PMID: 19172412
9) Pearl PL, Gibson KM, Quezado
Z, Dustin I, Taylor J, Trzcinski S, Schreiber J, Forester K, Reeves-Tyer P,
Liew C, Shamim S, Herscovitch P, Carson R, Butman J, Jakobs C, Theodore W
(2009) Decreased GABA-A binding on FMZ-PET in succinic semialdehyde
dehydrogenase deficiency. Neurology 73:423-9. PMID: 19667317
10) Nylen K, Velazquez JL,
Sayed V, Gibson KM, Burnham WM,
Snead OC 3rd (2009) The effects of a ketogenic diet on ATP
concentrations and the number of hippocampal mitochondria in Aldh5a1(-/-)
mice. Biochim Biophys Acta 1790:208-12.
PMID: 19168117
11) Jansen EE, Struys E, Jakobs C, Hager E, Snead
OC, Gibson KM (2008)
Neurotransmitter alterations in embryonic succinate semialdehyde dehydrogenase
(SSADH) deficiency suggest a heightened excitatory state during
development. BMC Dev Biol 8:112. PMID:
19040727
12) Drasbek KR, Vardya I,
Delenclos M, Gibson KM, Jensen K
(2008) SSADH deficiency leads to elevated extracellular GABA levels and
increased GABAergic neurotransmission in the mouse cerebral cortex. J Inherit
Metab Dis 31:662-8. PMID: 18696252
13) Stewart LS, Nylen KJ,
Persinger MA, Cortez MA, Gibson KM,
Snead OC 3rd (2008) Circadian distribution of generalized
tonic-clonic seizures associated with murine succinic semialdehyde
dehydrogenase deficiency, a disorder of GABA metabolism. Epilepsy Behav 13:290-4. PMID: 18514581
Nylen K, Velazquez JL,
Likhodii SS, Cortez MA, Shen L, Leshchenko Y, Adeli K, Gibson KM, Burnham WM, Snead OC 3rd (2008) 14) A
ketogenic diet rescues the murine succinic semialdehyde dehydrogenase deficient
phenotype. Exp Neurol 210:449-57. PMID:
18199435
15) Hager EJ, Tse HM,
Piganelli JD, Gupta M, Baetscher M, Tse TE, Pappu AS, Steiner RD, Hoffmann GF, Gibson KM (2007) Deletion of a single
mevalonate kinase (Mvk) allele yields a murine model of hyper-IgD
syndrome. J Inherit Metab Dis 30:
888-95. PMID: 18008182
Biographical
Sketch
Michael
R. Gretz
Biotechnology Research Center
Department of Biological Sciences
Michigan Technological University
Houghton, MI 49931-1295
Telephone: (906)487-3175,
Email: mrgretz@mtu.edu
www.desmids.mtu.edu
A. Professional Preparation:
Ph.D. 1981, Arizona State
University; Botany (Plant
Biochemistry)
B.Sc., 1977, Central Michigan
University; Chemistry
& Biology
B. Appointments:
2010-present: Director, Biotechnology Research Center, Michigan
Technological University
2007-2008: Visiting Scholar, Scripps Institution of Oceanography,
UCSD
1999-present: Professor of Biological Sciences, Michigan Technological University
1993-1999: Associate Professor of Biological Sciences, MTU
1992-1993: Associate Professor of Biology (Tenured), George Mason
University
1989-1992: Director, Shared Research Instrumentation Facility, GMU
1988-1989: Co-Director, Center
for Basic and Applied Research, GMU
1986-1991: Assistant Professor of Biology, GMU
1984-1986: Postdoctoral Research Assoc., Univ.
of Texas, Austin with R. Malcolm Brown
1981-1984: Postdoctoral Research Fellow, McMaster University
with E. L. McCandless
C.
Publications:
FIVE
SELECTED PUBLICATIONS RELATED TO PROPOSED PROJECT:
Bellinger, B.J., Gretz, M.R.,
Domozych, D, Kiemle, S and Hagerthy, S. 2010. The composition of extracellular
polymeric substances from periphyton assemblages in the Florida Everglades.
Journal of Phycology 46:674-678.
Bellinger, B.J., Underwood, G.J.C.,
Ziegler, S.E. and Gretz, M.R. 2009. The significance of diatom-derived polymers
in carbon flow dynamics within estuarine biofilms determined through isotopic
enrichment. Aquatic Microbial Ecology 55:169-187.
Domozych, D.S., Elliot, L, Kiemle,
S.N. and Gretz, M.R. 2007. Pleurotaenium trabecula, a desmid of wetland
biofilms: The extracellular matrix and adhesion mechanisms. Journal of
Phycology 43:1022-1038.
Hanlon, A.R.M., Bellinger, B.J.,
Xiao, G., Haynes, K, Ball, A.S., Osborn, M, Gretz, M.R., and Underwood, G.J.C.
2006. Dynamics of EPS production and loss in an estuarine, diatom-dominated
microalgal biofilm over a tidal emersion-immersion period. Limnology &
Oceanography 51:79-93.
Bellinger, B.J., Abdullahi, A.S.,
Gretz, M.R. and Underwood, G.J.C. 2005. Biofilm Polymers: Relationship between
carbohydrate biopolymers from estuarine mudflats and unialgal cultures of
benthic diatoms. Aquatic Microbial Ecology. 38:169-180.
OTHER PUBLICATIONS (last five years):
Domozych, D.S.,. Lambiasse, L., Kiemle, S.N.. and Gretz, M.R. 2009. Structure and biochemistry of
charophycean cell walls. II. Cell wall development and bipolar growth in the
desmid Penium margaritaceum. Asymmetry in a symmetric world. Journal of
Phycology 45:894-897.
Domozych, D.S., Serfis, A., Kiemle,
S. and Gretz, M.R. 2007. The structure and biochemistry of charophycean cell
walls. I. Pectins of Penium margaritaceum. Protoplasma 230:99-115.
Kiemle, S.N., Domozych, D.S. and
Gretz, M.R. 2007. The exopolymers of desmids: Chemistry, structural analysis
and implications in wetland biofilms. Phycologia 46:617-627.
Apoya, M.D., Yin, L., Underwood,
G.J.C. and Gretz, M.R. 2006. Movement modalities and responses to environmental
changes of the mudflat diatom Cylindrotheca closterium. Journal of Phycology
42:379-390.
Abdullahi, A.S., Underwood, G.J.C.,
and Gretz, M.R. 2006. Extracellular matrix assembly in diatoms (Bacillariophyceae).
V. Environmental effects on polysaccharide synthesis in the model diatom
Phaeodactylum tricornutum. Journal of Phycology 42:363-378.
D. Synergistic Activities:
Elected Treasurer, Phycological
Society of America 2004-2006
AAAS Section G Committee
representative 2006-2008
Organized NSF funded “Modern
Methods” workshop at International Botanical Society meeting 2002
Patents:
Magnetic alteration of cellulose during it's biosynthesis (with R. M.
Brown, Jr. and D. B.
Folsom). United States Patent No. 4,891,317, January 1990. Foreign
counterparts
E. Collaborators (last 48 mo.):
Ziegler, Sue. Memorial University of Newfoundland, Canada
Liepman, Aaron. Eastern Michigan University
Hildebrand, Mark. Scripps
Institution of Oceanography
Roberts, Alison, University of Rhode Island
Delwiche, Chuck, University of Maryland
Domozych, David. Skidmore College
Willats, William, University of Copenhagen
Hagerthey, Scot. South Florida
Water Management District
Hotchkiss, Arland. USDA ERRC
Wyndmoor
Pauly, Markus, Michigan
State University. – DOE Lab
Spaulding, Sarah. EPA, Colorado
Underwood, Graham. University of Essex, UK
Handler, Robert. Michigan Technological University
Graduate and Post-doctoral Advisors of M. Gretz:
Aronson, Jerome. Arizona State
University
Sommerfeld, Milton. Arizona State University
Brown, R. Malcolm, Jr. University
of Texas, Austin
McCandless, Esther. McMaster University, Ontario,
Canada
Graduate Students:
Erin McKenney, M.S. expected 2012.
Sarah Kiemle, Ph.D. 2010.
Melba Apoya, Ph.D. 2006.
Brent Bellinger, Ph.D. 2006.
Abass Abdullahi, Ph.D. 2006.
Yan Wang, Ph.D. 2000
Jingjie Lu, Ph.D. 1999
Brandon Wustman, Ph.D. 1998
Yalin Wu, Ph.D. 1993
Carla Kinslow, M.S. 1999
Postdoctoral Fellows Hosted:
Sarah Kiemle, 2010-11, MTU
Utpal Adhikari, 2009-10, University of Burdwan, India
Ash Haeger, 2008-10, University of Leeds, UK
Eric Koh, 1998-99, University of Otago, NZ
Jean-Claude
Mollet, 1993-95, UC Riverside
Biographical Sketch
Wan Jin
Jahng
Assistant Professor
Department of Biological Sciences
Michigan Technological University
1400 Townsend Drive, Houghton,
MI-49931
Phone: (906) 487-2192
Email: wjahng@mtu.edu
Education
Korea University, Seoul, Korea
Agricultural
Chemistry B.S.
1986-1990
Korea University, Seoul, Korea Organic
Chemistry M.S.
1990-1992
University of Nebraska,
Lincoln, NE
Organic
Chemistry Ph.D.
1995-2000
Harvard Medical School, Boston,
MA Biochemistry, Proteomics Postdoc 2001-2003
Harvard Medical School, Boston,
MA Biochemistry, Proteomics Research
Associate 2004-2005
Appointments
Professional Experience
2009-present Assistant Professor, Department of Biological
Sciences, Michigan
Technological University
2006-2009 Assistant
Professor, Department of Ophthalmology, Adjunct Assistant Professor,
Department of Pathology, Microbiology,
and Immunology, School of Medicine, University of South Carolina
2001-2005 Research Fellow,
Research Associate, Department of Biological Chemistry and Molecular
Pharmacology, Harvard
Medical School
1995-2000 Research and teaching assistant,
Department of Chemistry, University
of Nebraska-Lincoln
1994 Instructor, Department of Chemistry, Korea University
1990-1992 Research and teaching assistant,
Department of Chemistry, Korea
University
2010- Institutional Animal Care and Use Committee, Michigan Technological
Unversity
2009- Graduate Committee, Biology Department, Michigan
Technological University
2007-9 Proteomics Committee, University of South Carolina
2007- Scientific Advisory Board, Center for
Molecular Dynamics-Nepal (Nonprofit NGO)
2006- Principal Organizer,
Nepal Trauma Center Project
2003
Symposium Organization: Principal Organizer, U.S.-Korea
Bioscience-Biotechnology Conference
2003 President, New England
Bioscience Society (NEBS)
2003- Member, Association for Research in
Vision and Ophthalmology (ARVO)
2001
Editor-in-Chief, New England Bioscience Society (NEBS)
1998 Nebraska Chapter President, Korean-American
Scientists and Engineers Association (KSEA)
1996- Member, American Chemical Society (ACS)
1992-4 Republic of Korea Navy
1992- Life
member, Korean Chemical Society (KCS)
Honors
2010 Research
Excellent Fund, Michigan
Technological University, MI
2007 New Investigator Award, International Foundation, Korea
2003 Appreciation Award for the service of the
20th President, New England Bioscience Society, Boston, MA
2001 Appreciation Award for Annual Conference
Editor-in-Chief. New England Bioscience Society, Boston, MA
2000 Outstanding Research Award. Department of
Chemistry, University of Nebraska-Lincoln
1999 Outstanding Teaching Award. Department of
Chemistry, University of Nebraska-Lincoln
1997 Distinguished Teaching Award. College of
Arts and Sciences, University of Nebraska-Lincoln
1992 Seok
Lim Korea
University Alumni Faculty Scholarship,
Graduate School, Korea University
Publications
Five related
1)
Lee, H., Chung, H, Hunt, R.C., Lamoke, F., Arnouk, H., Wood, P.A., Hrushesky,
W. J. M. and Jahng, W. J. (2010) Cleavage of the retinal pigment epithelium-specific
protein RPE65 under oxidative stress, International Journal of Biological
Macromolecules, in press.
2)
Zhang, Z., Hrushesky, W. J. M., Wood, P.A., Hunt, R. C., and Jahng, W. J.
(2010) Melatonin reprogrammes proteomic profile in light-exposed retina in
vivo, International Journal of Biological Macromolecules, in press.
3)
Chung, H., Lee, H., Lamoke, F.,
Hrushesky, W. J. M. Wood, P. A., and Jahng, W. J. (2009) Neuroprotective
Role of Erythropoietin by Anti-apoptosis in the Retina, Journal of Neuroscience
Research, 87, 2365-2374.
4)Xue,
L., Jahng, W. J., Gollapalli, D., Rando, R. R. (2006) The Palmitoyl Transferase
Activity of Lecithin Retinol Acyltransferase, Biochemistry 45, 10716-10718.
5)
Xue, L., Gollapalli, D., Maiti, P., Jahng, W. J., and Rando, R. R. (2004) A
Palmitoylation Switch Mechanism in the Regulation of the Visual Cycle,
Cell 117, 761-771.
Five
others:
6)
Hamirally, S., Kamil, J. P.,
Ndassa-Colday, Y. M., Lin, A. J., Jahng,
W. J., Baek, M. C., Noton, S.,
Simpson-Holley, M., Knipe, D. M., Golan, D. E., Marto, J. A., and Coen, D. M.
(2009) Viral Mimicry of Cdc2/Cyclin-Dependent Kinase 1 Mediates Disruption of
Nuclear Lamina During Human Cytomegalovirus Nuclear Egress, PLoS Pathogene,
2009 Jan; 5(1): e1000275 Epub 2009 Jan23.
7)
Karukurichi, K. R., de la Salud-Bea, R., Jahng, W. J., Berkowitz, D. B. (2007)
Examination of the New -(2’ Z-Fluoro)vinyl Trigger with Lysine
Decarboxylase : The Absolute Stereochemistry Dictates the Reaction Course,
Journal of the American Chemical Society 129, 258-259.
8)
Kim, J., Jahng, W. J., Vizio, D. D., Lee, J., Rubin, M. A., Shisheva, A., and
Freeman, M. R. (2007) The Phosphoinositide Kinase PIKfyve Mediates EGF Receptor
Trafficking to the Nucleus, Cancer Research 67, 9229-9237.
9)Berkowitz,
D. B., de la Salud-Bea, R., Jahng, W. J. (2004) Synthesis of Quaternary Amino
Acids Bearing a (2’Z)-Fluorovinyl alpha-Branch: Potential PLP Enzyme
Inactivators. Organic Letters 6,
1821-1824.
10)
Furukawa, N., Ongusaha, P., Jahng, W. J., Choi, C. –S., Kim, H.-J., Araki, K.,
Lee, Y. H. Kaibuchi, K., Kahn, B. B., Masuzaki, H., Kim, J. K., Lee, S. W.,
Kim, Y.-B. (2005) Role of Rho-kinase in Regulation of Insulin Action and
Glucose Homeostasis, Cell Metabolism, 2, 119-129.
Synergistic Activities
1) 2007
Development of new teaching course: Systems biology, functional proteomics
(2008 Spring semester), USC
2) 2007-9 Proteomics Center Committee member,
Development of Differential 2D Electrophoresis, USC
3) 2006- Principal Organizer, Nepal Trauma Center Project
4) 2006 Director, Science Summer Camp for middle and
high school students in South
Carolina
5) 2003 Principal Organizer, U.S.-Korea
Bioscience-Biotechnology Conference, Harvard
Medical School
Selected Collaborators & Other Affiliations
Dr. Heywon Chung,
Department of Ophthalmology, Asan Medical Center,
Seoul, Korea. Project: Retina
Degeneration-Apoptosis
Prof. Donald M. Coen, Department of Biological
Chemistry and Molecular Pharmacology,
rvard Medical School,
Boston, MA
02115. Project: Human
Cytomegalovirus Phosphorylation Signal Transduction
Graduate Advisors and Postdoctoral Mentor
M.S.: Prof. Bong Rae Cho,
Department of Chemistry, Korea University, Seoul,
Korea
Ph.D.: Prof. David B.
Berkowitz, Department of Chemistry, University
of Nebraska, Lincoln, NE
Postdoc.: Prof. Robert R.
Rando, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School
Biographical
Sketch
Chandrashekhar
P. Joshi
Professor of Plant Molecular Genetics
Biotechnology Research Center
School of Forest Resources and Environmental Science
Michigan Technological University, Houghton,
MI 49931
Tel: 906-487-3480 Fax:
906-487-2915
email: cpjoshi@mtu.edu
Web page: http://forest.mtu.edu/faculty/joshi/
Current Research
Interests:
Biotechnological
improvement of lignocellulosic materials in poplars for better bioenergy
production
Education
Ph.D. University of Poona, India
Biochemistry 1982
M.Sc. University of Poona, India Botany 1977
B.Sc. University of Poona, India Botany 1975
Appointments:
2010-present WCU Visiting Professor, Chonnam
National University,
Gwangju, S. Korea
2008-present Professor, Michigan
Tech University,
Houghton, MI
2007-2009 Director, Biotechnology Research Center, Michigan
Tech University
2004-2009 Director, SFRES graduate programs, Michigan Tech University
2004-2008 Associate Professor, Michigan Tech University,
Houghton
1999-2004 Assistant
Professor, Michigan
Tech University,
Houghton
1996-1999 Research Assistant Professor, Michigan Tech University,
Houghton
1990-1996 Research Scientist, Texas Tech University, Lubbock
1988-1990 Research Associate, Ohio State University, Columbus
1985-1988 Scientist, National Chemical
Laboratory, Pune, India
1983-1985 Visiting Scientist, Max Planck
Institute, Cologne, Germany
1980-1983 Scientist, National Chemical
Laboratory, Pune, India
1979-1980 Research Student, National Chemical
Laboratory, Pune, India
1977-1979 Lecturer in Botany, S.P. College,
Pune, India
Some selected
recent and significant publications:
1) Zhu X, Pattathil S, Mazumdar K, Brehm A, Hahn MG, Dinesh-Kumar, SP and Joshi CP.: VIGS offers a functional genomics platform for studying plant cell wall
formation. Molecular Plant 3: 818-833, 2010.
2) M. Kumar, S.
Thammannagowda, V. Bulone, V. Chiang, K-H Han, C P. Joshi, S. D. Mansfield, E. Mellerowicz, B. Sundberg, T. Teeri,
and B. E. Ellis: An update on the nomenclature for the cellulose synthases
genes from Populus. Trends in Plant Science 14: 248-254,
2009.
3) C. P. Joshi, Brunner A, Busov V, Meilan R, Thammanagowda
S, and Tsai C.: Poplars. In: The
Transgenics: Compendium of transgenic crop plants: Transgenic forest tree
species. C. Kole and T. Hall (eds). Blackwell Publishing, Oxford, UK.
PP. 1-34, 2008
4)C.P. Joshi and S.D. Mansfield: The cellulose paradox: simple
molecule, complex biosynthesis. Current
Opinion in Plant Biology 10: 220-226, 2007.
5)
C. P. Joshi: Genomics of Wood development. In
6) Tuskan GA, … Joshi C, et al The genome of black cottonwood, Populus
trichocarpa (Torr. & Gray). Science 313: 1596 –1604, 2006.
7) Suchita Bhandari,
Takeshi Fujino, Shiv Thammanagowda, Dongyan Zhang, Fuyu Xu, and C P. Joshi: Coordinate expression of
tension stress-responsive and secondary cell wall-associated KORRIGAN
endoglucanase and three cellulose synthase genes in aspen trees. Planta 224: 828-837, 2006.
8)
Chandrashekhar P. Joshi, S. Bhandari,
P. Ranjan, U. C. Kalluri, X. Liang, T. Fujino, and A. Samuga: Genomics of
cellulose biosynthesis in poplars. New
Phytologist 164: 53-61, 2004
9) L. Wu, C.P. Joshi,
and V.L. Chiang: A xylem-specific cellulose synthase gene from aspen (Populus tremuloides) is responsive to
mechanical stress. Plant Journal 22(6): 495-502, 2000
10) K. Osakabe, C-C. Tsao,
L. Li, J. L. Popko, T. Umezawa, D. T. Carraway, R. H. Smeltzer, C. P. Joshi,
V. L. Chiang: Coniferyl aldehyde 5-hydroxylation and methylation direct
syringyl lignin biosynthesis in angiosperms. Proceedings of National Academy of Sciences,
USA, 96
(16): 8955-8960, 1999.
Synergistic activities
1) Spearheaded
establishment of M. S. and PhD degrees in Forest Molecular Genetics at Michigan
Tech
2) Currently editing two
books on poplar genomics and bioenergy; author of three approved US patents
3) Director of
Biotechnology Research Center 2007-2009, MTU
4) Current member of
Research Advisory Council and Chair of the Institutional Biosafety Committee,
MTU
5) Graduate Program
Director, 2004-2009, SFRES, MTU
6) Faculty judge: Western
Upper Peninsula Science Fair (Grades 4-9) and Graduate Poster competitions
7) Ad hoc reviewer for
numerous International journals and NSF, USDA and DOE proposals;
8) Panel service: NSF
(2005, 2006 & 2007); DOE (2006), USDA-NRI (2008)
9) Distinguished Teaching
Award Finalist, Assistant Professor Category, MTU, 2004; fellow of SFI, 2010
10) PI on a successful US
Department of Education grant for establishing transatlantic dual degree
program in Forest Resources and Biotechnology
11) PI or Co-PI on over $6
million grants from national and international agencies at Michigan Tech
Collaborators
Coauthors and
Collaborators (Last 48 months)(Our Science 2006 paper has over 100 coauthors)
Arioli
Tony, Bhandari Suchita, Chiang Vincent,
Crasta Oswald, Davis Mark, Festucci-Buselli R, Fei Z, Fujino Takeshi, Haigler Candace, Harding Scott, Jiang Y, Kalluri Udaya,
Li Laigeng, Liang Xiaoe, Liu,
Yunxia, Lu, S, Mansfield Shawn, Otoni
W, Podila Gopi, Ranjan Priya, Samuga
Anita, Tsai Chung-Jui,
Thammanagowda Shiv, Turner Simon, Williamson R, Xu Fuyu, Yi, X, Zhang Dongyan
Graduate and Postdoctoral Advisors
Dr. P.K. Ranjekar, Late Prof. Otto Schieder, Prof. Desh Pal Verma, Prof. Henry Nguyen
Thesis and Postdoc
Advisees
PhD: Chen-Chung Tsao
(1998), Udaya Kalluri (2003),
Anita Samuga (2003), Priya Ranjan (2005), Shivegowda Thammanngowda
(2007), Fuyu Xu (2009)
MS:
Zihao Wang (2003), Siau Voo (2006), Asha Lakkavaram (2006), Rajesh Chavli (2000), John Saida (2008), Jake Ladd (2010), Aparupa Sengupta (2009)
Postdocs and other staff:
Xiaoe Liang, Shanfa Lu, Yihua Zhou, Takeshi Fujino, Suchita Bhadari,
Dongyan Zhang, Yunxia Liu, Ramesh Thakur, Xiaohong Zhu
Undergraduate Research Advisors
Marie Wilkening, Hwee Chi Tay, James Wee, Katherine
Kieckhafer, Laura Kluskens, Katie Kruger, Ellen Brenna, Ashley Sharp, Megan
McQuillan, Jill Recla, Kristina Flesher, Eric Koronka, Ayushi Kawatra, Ian
Bonner, Sandra Orlowski, Nathan Fettinger, Eric Hollender, Justeen Beaune, and Josh
Papacek
Biographical
Sketch
Pushpalatha P. N. Murthy
Professor
Department of
Chemistry
Michigan Technological University
Houghton,
MI-49931
Tel:
906-487-2094; Fax:906-487-2061
E-mail:
ppmurthy@mtu.edu
Education
Miranda House, Delhi
University, Delhi, India
Chemistry B.Sc. (Hons) 1972
Indian Institute
of Technology, Kanpur, India
Chemistry M.Sc.
1974
Brown University, Providence, RI Bioorganic Chemistry Ph.D. 1979
The Univ. of Mich., Ann
Arbor, MI Bioorganic Chemistry
1979-1980
The Univ of Michigan,
Ann Arbor, MI Neuroscience 1980-1982
Appointments
Sept.99 - present: Professor,
Dept. of Chemistry, Michigan
Technological University, Houghton,
MI
Feb. 06 - May 06: Sabbatical leave at CSIRO
Canberra, and CAMBIA, Canberra,
Australia
Aug. 01 - July 04: Chair, Dept. of Chemistry, Michigan
Technological University, Houghton
Aug. 00 - Aug.01: Interim Chair, Dept. of
Chemistry, Michigan Tech. University,
Houghton, MI
Sep. 91 ‑ Aug. 99: Associate
Professor, Dept.of Chemistry, Michigan Tech.
Univ., Houghton, MI
Mar. 93 - May 93: Visiting
Assoc. Prof (on sabbatical leave), Biotechnology Dept., Cornell
University,
Ithaca, NY
Sep. 92 - Dec. 92: Visiting
Assoc. Prof (on sabbatical leave), Michigan
State University,
East
Lansing, MI
Sept. 86 - Aug. 91 Assistant Professor, Department
of Chemistry, Michigan
Technological
University,
Houghton, MI
Sept. 85 - Aug. 86 Visiting Asst. Professor,
Department of Chemistry and Chemical Engineering,
Michigan Technological University, Houghton, MI
Aug. 82 - Jan. 85: Research Chemist, Stauffer
Chemical Company, Dobbs Ferry,
NY.
Selected Publications
1) S.C.
Johnson, M.Yang, P.P.N. Murthy (2010) Heterologous expression and functional
characterization of a plant alkaline phytase in Pichia pastoris. Protein
Express. Purif. 74, 196-203.
2) C. Xue, S.
Velayudhan, S. C. Johnson, R. Saha, A. Smith#, W. Brewer, P.P.N. Murthy, ST. Bagley, Haiying Liu (2009)
Highly water –soluble, fluorescent, conjugated fluorine-based glycopolymers
with poly(ethylene glycol)-tethereed spacers for sensitive detection of Escherichia coli. Chem.
Eur. J. 15, 2289-2295.
3) Pushpalatha
P.N. Murthy (2007) Identification of inositol phosphates by NMR spectroscopy:
unraveling structural diversity. In
Proceedings of the Bouyoucos conference on Biogeochemical interaction of
inositol phosphates in the environment, B.L. Turner, A.E. Richardson, and E.J.
Mullaney (Editors), CB international, Cambridge, MA, pp 7-22
4) Ping Yang, Bernard Spiess, Pushpalatha P.N. Murthy,
Richard E. Brown (2007) Influence of metal cations on the intramolecular
hydrogen-bonding network in phosphorylated compounds. J.
Phys. Chem. 111, 3602-3612
5) Cuihua Xue,
Sonali P. Jog, Pushpalatha P. N. Murthy, and Haiying Liu (2006) Synthesis of highly water-soluble fluorescent
conjugated glycopoly(p-phenylene)s for lectin and Escherichia coli. Biomacromolecules, 7, 2470-2474
6) Bakul Dhagat Mehta, Sonali P.
Jog, Steven C. Johnson and Pushpalatha P.N. Murthy (2006) Lily pollen alkaline
phytase is a histidine phosphatase similar to mammalian multiple inositol
polyphopsphate phosphatase (MINPP), Phytochemistry, 67, 1874-1886.
7) B.G. Garchow, S.P. Jog, B. D. Mehta, J.M. Monosso
(posthumous), P.P.N. Murthy (2006) Alkaline phytase from Lilium longiflorum: purification and structural characterization. Protein Express. Purif. 46, 221-232.
8) P. P. N. Murthy (2006)
Structure and nomenclature of inositol phosphates, phosphoinositides,
and glycosylphosphatidylinositols.
Subcellular Biochemistry series: Volume 39, (Eds. ), Plenum Publishing Co. Ltd., London, pp
1-20.
9) P. Yang,
P.P.N. Murthy, R.E. Brown (2005) Synergy of intramolecular hydrogen bonding
network in myo-inositol-2-phosphate: theoretical investigation s into the
electronic structure, proton transfer and pKa.
J. Amer. Chem. Soc. 127,
15848-15861.
10) S.P. Jog,
B. G. Garchow, B. D. Mehta, P.P.N. Murthy (2005) Alkaline phytase from lily
pollen: Investigation of biochemical properties. Archives
of Biochemistry and Biophysics 440, 133-140
11) G.
Pliska-Matyshak, B. Narasimhan, R. Kinnard, S. Carstensen, M.Ritter #, L. von Weymarn #, and
P.P.N. Murthy (1997) Novel phosphoinositides in barley aleurone
cells, additional evidence for the
presence of phosphatidyl-scyllo-inositol. Plant
Physiol. 113,
1385-1393.
# Undergrad student
Synergistic Activities
1) Developing a
new inquire-based lab course “Research methods in Biomolecular Chemistry”. This project is funded by the NSF-CCLI
program.
2) Developed a
new course for chemistry majors interested in teaching high school chemistry:
Design and Operation of a High School Chemistry Laboratory. I worked with local high schools to develop
this course. The aim of the course is to address topics necessary for the
design and introduction of a chemistry laboratory in high schools including
ordering, storage, tracking, and disposal of chemicals, safety issues,
developing new lab experiments and demonstrations, preparation of reagents on
large scale, and internships in local high schools. The need for such a course
was identified by a workshop organized by the American Chemical Society on
Secondary Chemical Education curriculum and our own alumni. This course is now offered every other year.
3) Worked on a
curriculum for two new degree programs now offered in the Department – BS in
Biochemistry and Molecular Biology and BS in Pharmaceutical Chemistry
4) Developed a
new course for the BS in Pharmaceutical Chemistry program - Pharmaceutical
Chemistry I – Mechanism of Drug Action.
This course is now offered every year.
5) Finalist for Outstanding Teacher of the Year award for
1989-90 in Assistant Professor category.
Collaborators and Other Affiliations
Dr. Richard Brown, Dept. of Chemistry, Michigan
Technological University
Dr. Haiying Liu, Dept of Chemistry, Michigan Technological University
Dr. Victor Raboy, USDA,
Aberdeen, Idaho
Graduate Advisors and Postdoctoral
Sponsors
Ph.D. Advisor: Prof. David Cane, Brown University
Postdoctoral sponsor:
Prof. Masato Koreeda, Univ of
Michigan, Ann Arbor, MI
Postdoctoral sponsor:
Prof. Bernard Agranoff, Univ of
Michigan, Ann Arbor, MI
Thesis Advisor (Ph.D.)
Dr. Laura Barrientos, Center for Disease Control,
Atlanta; Dr. Bhuvaraha Murthy, Ohio State University, Columbus, Ohio; Dr. Barry
Garchow, Univ of Pennsylvania; Dr. Sonali Jog, Univ of Southern
California; Dr. Bakul Dhagat Mehta, Univ
of Missouri, Columbia; Dr. Gay Pliska-Matyshak, Henry Ford Hospital, Detroit,
Dr. Steven Johnson, Univ of Illinois, Urbana-Champaign
Biographical
Sketch
Ashutosh
Tiwari
Assistant Professor
Department of Chemistry,
Michigan Technological University,
1400 Townsend
Drive, Houghton,
MI 49931
Phone: (906)
487-1840(Work)
Fax:(906) 487-2061
Email:tiwari@mtu.edu
Web page: http://www.chemistry.mtu.edu/pages/faculty/faculty.php?fac=tiwari
Current research
interests
‘Protein misfolding
diseases’ with special focus on neurodegenerative diseases.
Education
Jawaharlal
Nehru University
(JNU), New Delhi, India Biotechnology
Ph.D.
1999
Jamia Millia Islamia, New Delhi, India Biosciences M.Sc. 1993
All-India Institute of Medical Sciences
(AIIMS),New Delhi India Human Biology, specialization in biophysics 1991 B.Sc.(Hons)
Appointments
2009 – Assistant
Professor, Department of Chemistry, Michigan
Technological University, Houghton,
MI.
2009 – Adjunct
Research Assistant Professor, Department of Neurology, University of
Massachusetts Medical School (UMMS), Worcester, MA.
2005 – 2009 Research Assistant Professor,
Department of Neurology, UMMS,
MA.
2003 – 2005 Instructor,
Department of Neurology, UMMS,
MA.
2000 – 2003 Post-Doctoral Fellow, Department of
Neurology, UMMS, MA.
1999 – 2000 Post-Doctoral Fellow, Department of
Neurology, Massachusetts General Hospital, Boston,
MA.
1995 – 1999 Senior Research Fellow, Center for
Biotechnology, JNU, New Delhi,
INDIA.
1993 – 1995 Junior Research Fellow, Center for
Biotechnology, JNU, New Delhi,
INDIA.
Five recent
publications
1) Molnar KS, Karabacak NM, Johnson JL, Wang Q, Tiwari A,
Hayward LJ, Coales SJ, Hamuro Y, and Agar JN.
A common property of amyotrophic lateral sclerosis-associated variants:
Destabilization of the Cu/Zn superoxide dismutase electrostatic loop. J
Biol Chem. (2009) 284(45):
30965-30973.
2) Tiwari A, Liba A, Sohn SH,
Seetharaman SV, Bilsel O, Matthews CR, Hart PJ, Valentine JS, and Hayward LJ. Metal deficiency increases aberrant hydrophobicity
of mutant superoxide dismutases that cause amyotrophic lateral sclerosis. J
Biol Chem. (2009) 284(40): 27746–27758.
3)
Karabacak NM, Li L, Tiwari A, Hayward
LJ, Hong P, Easterling ML, and Agar JN.
Sensitive and specific identification of wild-type and variant proteins
from 8 to 669 kDa using top-down mass
spectrometry. Mol Cell Proteomics. (2009)
8(4): 846-56.
4) Cao X, Antonyuk S,
Seetharaman SV, Whitson LJ, Taylor AB, Holloway SP, Strange RW, Doucette PA,
Valentine JS, Tiwari A, Hayward LJ,
Padua S, Cohlberg JA, Hasnain SS, and Hart PJ. Structures of the G85R variant of
SOD1 in familial ALS. J
Biol Chem. (2008) 283(23): 16169-77.
5) Shaw BF, Lelie
HL, Durazo A, Nersissian AM, Xu G, Chan PK, Gralla EB, Tiwari A, Hayward LJ,
Borchelt DR, Valentine JS, and Whitelegge JP. Detergent-insoluble aggregates associated
with amyotrophic lateral sclerosis in transgenic mice contain primarily
full-length, unmodified superoxides dismutase-1. J Biol
Chem. (2008) 283(13):
8340-8350.
D)
Five additional significant publications:
1) Tiwari A and Bhat R. Stabilization
of yeast hexokinase A by polyol osmolytes: Correlation with physicochemical
properties of aqueous solutions. Biophys
Chem. (2006) 124(2):
90-99.
2) Tiwari A, Xu Z, and Hayward
LJ. Aberrantly increased hydrophobicity
shared by mutants of Cu/Zn superoxide dismutase in familial amyotrophic lateral
sclerosis. J Biol Chem. (2005) 280(33):
29771-29779.
(Featured in August 19,
2005 issue of the Journal of Biological Chemistry as ‘Paper of the Week’
(J Biol Chem. (2005) 280: e99939)).
3) Rodriguez
JA, Shaw BF, Durazo A, Sohn SH, Doucette PA, Nerissian AM, Faull KF, Eggers DK,
Tiwari A, Hayward LJ, and Valentine
JS. Destabilization of apoprotein is
insufficient to explain Cu,Zn-superoxide dismutase-linked ALS
pathogenesis. 4) Proc Natl Acad Sci USA. (2005) 102(30): 10516-10521.
Chacko B, Qin BY, Tiwari A, Shi G, Lam S, Hayward LJ,
deCaestecker M, and Lin K. Structural
Basis of Heteromeric Smad Protein Assembly in TGF-b Signaling. Mol Cell. (2004) 15(5): 813-23.
5) Tiwari A and Hayward
LJ. Familial ALS Mutants of Cu/Zn
Superoxide Dismutase are Susceptible to Disulfide Reduction. J
Biol Chem. (2003) 278(8):
5984-5992.
Synergistic activities
1) Ad-hoc reviewer for
Biophysical Journal, Journal of Neuroscience Research, and Cellular and
Molecular Life Sciences.
2) Member of ‘Graduate
Admissions and Recruiting Committee’ for Chemistry department at MTU.
3) Member of ‘Biochemistry
Curriculum Committee’ for Chemistry department at MTU.
4) Member of ‘University
Animal Care Committee’ and ‘Institutional Biosafety Committee’ at MTU.
Collaborators
Robert Brown (UMMS),
Lawrence Hayward (UMMS), Zuoshang Xu (UMMS), Hoi Pang Low (UMMS), Robert
Matthews (UMMS), Jeffrey Agar (Brandeis University); John Hart (UTHSCA), Joan
Valentine (UCLA), Patricia Heiden (MTU), Haiying Liu (MTU), Rudy Luck (MTU).
Supervising and advising of students and trainees
At UMMS:
Brian Mitchell Haas (summer student, Harvard
University, MA);
Benoy M. Chacko (graduate student, UMMS); Charusheila Ramkumar (graduate
rotation student, UMMS) and Laura Baldassari (summer student, Worcester
Polytechnic Institute, MA).
At MTU: Kyrie Pappas (project CH471, Spring 2010);
Claire Drom (CH4995, Fall 2010).
Research technicians
supervised: At UMMS: Hongru Zhou (UMMS);
Kumudini Misra (UMMS).
Biographical
Sketch
Martin Thompson
Associate
Professor
Department
of Chemistry Tel: (906) 487-3522
Michigan Technological
University Fax: (906) 487-2061
1400 Townsend Drive Email:
thompson@mtu.edu
Houghton, MI 49931
Education
Arizona State University,
Tempe, AZ.
Ph.D. Chemistry Ph.D.
2000
Dissertation “Synthesis and
Characterization of the Photophysical and Photochemical Properties of Sequence
Specific DNA-Binding Probes,” Advisor: Neal Woodbury
Arizona State University,
Tempe, AZ.
Chemistry,
with a Concentration in Biochemistry B.S.
1995,
Appointments
2009-present Associate Professor, Department of
Chemistry, Michigan Technological University Assistant Professor,
Department of Chemistry, Michigan Technological University (2003-2009)
2004 Visiting Scientist, Department of
Biological Chemistry, University
of Michigan Medical
Center
2002-2003 Postdoctoral Fellow, Department of
Biological Chemistry, University
of Michigan
2000-2002 Postdoctoral Assistant, Howard Hughes Medical
Institute, University
of Michigan
Other
Activities
2010-present Councilor,
Upper Peninsula Section of the American Chemical Society
2007 Panel Member, National Institutes of
Health, Center for Scientific Review, Study Section ZRG1 GGG-F(90) 2006-2009 Chair, Upper
Peninsula Section of the American Chemical Society
Reviewer for: FEBS
Letters, Protein Expression and Purification, Journal of Medical &
Biological Sciences
Professional
Affiliations
American Chemical Society,
Biophysical Society, Council on Undergraduate Research
Research Interests
Fluorescence-based bioanalytical
methods and biosensors; quantification of modification-dependent
protein-protein interactions associated with transcription; development of assays
for drug discovery; molecular recognition; cell-specific targeting using
peptidomimetics;
Five Significant Publications
1) Thompson, M. (2010) Thermodynamic and Kinetic Analysis of
Bromodomain–Histone Interactions. Vol 466, Biothermodynamics, Part B. Methods
in Enzymology, pp.383-407
2) Thompson, M. (2009) Polybromo-1: The chromatin targeting subunit of
the PBAF complex. Biochimie 91, 309-319.
3) Thompson, M., and
Chandrasekaran, R. (2008) Thermodynamic analysis of the acetylation dependence
of bromodomain-histone interactions. Anal. Biochem. 374, 304-312.
4) Kupitz, C., Chandrasekaran,
R., and Thompson, M. (2008) Kinetic analysis of acetylation-dependent Pb1
bromodomain-histone interactions. Biophys. Chem. 136, 7-12.
5) Chandrasekaran, R., and Thompson,
M. (2007) Polybromo-1 bromodomains bind histone H3 at specific acetyl-lysine
positions. Biochem. Biophys. Res. Comm. 355, 661-666.
Additional
Significant Publications
1) Thompson, M. (2007) Spectral properties and DNA targeting features
of thiazole orange-peptide bioconjugates. Biomacromolecules 8, 3628-3633.
2) Thompson, M. (2006) Synthesis, photophysical effects, and DNA
targeting properties of oxazole yellowpeptide bioconjugates, Bioconjugate
Chemistry 17, 507-513.
3) Chandrasekaran, R., and Thompson, M. (2006) Expression, purification
and characterization of individual bromodomains from human Polybromo-1, Prot.
Expr. Purif. 50, 111-117.
4) Babendure, J., Liddell, P. A., Bash, R., LoVullo, D., Schiefer, T.
K., Williams, M., Daniel, D. C., Thompson, M., Taguchi, A. K. W., Lohr, D., and
Woodbury, N. W. (2003) Development of a fluorescent probe for the study of
nucleosome assembly and dynamics, Anal. Biochem. 317-327, 1-11.
5) Thompson, M., and Woodbury, N. (2001) Thermodynamics of Specific and
Non-specific DNA-binding by Cyanine Dye Labeled DNA-binding Domains, Biophysical
J. 81, 1793-1804.
Recent
Collaborators
Sarah Green (MTU), Haiying Liu
(MTU), Lanrong Bi (MTU), Shiyue Fang (MTU), Kedmon Hungwe (MTU), Pushpalatha
Murthy (MTU), Justin Carlson (Chemotrope)
Graduate and Postgraduate Advisees
Current graduate students:
Katrina Bugielski
Past graduate students: Renu
Chandrasekaran, Jon Maxwell, Renee Kerr, Mark Parmley, Wendy VanAken, Joshua
Bailey
Undergraduate students: Talisha
Sutton, Sam Stam, Christopher Kupitz, Andrew Spaeth, Kelli Whelan, Kirk Koebke,
Jesus Fransisco Glaus Garzon, Marie Wilkening, Joshua Bailey
Postdoctoral Advisees: Alexis Black, Momoko Tajiri
Biographical
Sketch
Hairong Wei
Assistant Professor of Systems Biology & Molecular
Biology
School of Forest Resources and Environmental Science
Michigan Technological University
1400 Townsend
Drive, Houghton,
MI 49931
Email: hairong@mtu.edu Phone: (906) 487-1473 Fax: (906) 487-2915
http://forest.mtu.edu/faculty/wei/index.htm
Current Research Interests
Systems Biology: Gene
network constructions & gene function prediction
Bioinformatics and
Genomics on tree growth & wood development
Biological database design
and development
Impact of CO2
and abiotic stress on gene network
New
algorithm/software/pipeline development
Education
Beijing Forestry
University, P.R. China Agricultural Sci. BS
& 4 years
Beijing Forestry
University, P.R. China Plant Genetics MS
& 3 years
University of Hawaii at Manoa Plant Mol. Biol Ph.D.
& 5 years
University of Chicago Computer Sci. MS
& 1.5 years
University
of Minnesota Bioinformatics Post-doc
& 1.5 years
University of Alabama at Birmingham Biostatistics Post-doc
& 1 year
Appointments
2008~Present Assistant Professor, Michigan
Technological University, Houghton,
MI
2006~2008 Bioinformatics Developer, Wicell
Research Institute, Inc., Madison, WI
2005~2006 Bioinformatics Scientist, Operon
Biotechnologies, Inc., Huntsville, AL
2004~2005 Postdoc, Biostatistics, University of Alabama,
Birmingham, AL
2003~2004 Postdoc, Bioinformatics, University of Minnesota,
Minneapolis, MN
1996~2001 Res. Assistant, Plant Mol. Biology, University of Hawaii,
Honolulu, HI
1995~1996 Res. Assistant, Plant Genetics, University of Hawaii,
Honolulu, HI
1989~1995 Assistant Professor, and Lecturer,
Forestry Genetics, Beijing
Forestry University
Some selected publications
1) Cui, X, T. Wang, H.S.
Chen, V. Busov and H. Wei. 2010
TF-finder: A software package for identifying transcription factors involved in
biological processes using microarray data and existing knowledge base. BMC Bioinformatics, 11:425
2) Ming, R., S. Hou,…, H. Wei, …, M. Alam. 2008. The draft genome sequence of transgenic
papaya, Carica papaya. Nature, Vol. 452, No.
7190:991-996.
3) Wei, H., P. F. Kuan, S. Tian, C. Yang, J. Nie, S. Sengupta, V.
Ruotti, G. Jonsdottir, S. Keles, J. Thomson and R. Stewart. 2008. A study of the relationships between
oligonucleotide properties and hybridization intensity in NimbleGen platform. Nucleic Acids Research, Vol. 36,
No. 9:2926-2938.
4) Pan, G., S. Tian, J.
Nie, C. Yang, V. Ruotti, H. Wei,
G. Jonsdottir, R. Stewart, and J. Thomson.
2007. Whole genome analysis of
Histone H3 lysine 4 and lysine 27 methylation in human embryonic stem
cells. Cell Stem Cell, Vol.
1, No 3:299~312.
5) Wei, H, S. Persson, T. Mehta, V. Srinivasasainagendra, L. Chen, G.
Page, C. Somerville, A. Loraine. 2006.
Transcriptional coordination of the metabolic network in Arabidopsis
thaliana. Plant Physiology. 142(2):76274.
6) Persson, S., H. Wei, J. Milne, G. Page, C.
Somerville. 2005. Identification of
genes required for cellulose synthesis by regression analysis of public microarray
data sets. Proc Natl Acad Sci USA,
102: 8633-8638. (Faculty 1000 evaluation).
7)
Wei, H., Y. Kaznessis. 2005. Inferring gene regulatory relationships by
combining target-target pattern recognition and regulator-specific motif
examination. Biotechnology and
Bioengineering. Vol.
89, No1: 53-77.
8)
K.M.,
S. Bhawan, T. Majima, H. Wei, V.
Kumar. 2003. Cutting Edge: The NK cell receptor 2B4 augments Ag-specific CTL
activity through CD48 ligation on neighboring T cells. Journal of Immunology. Vol.170, No 10: 4881
9) Albert, H and H. Wei. Sugarcane Ubi9 gene promoter and methods of
use thereof. 2004, U.S. Patent
No. 6706948 | Promoter of the sugarcane Ubi9 gene. 2004. U.S. Patent No. 6686513 B1 | Promoter
of the sugarcane Ubi4 Gene. 2003. U.S.
Patent No. 6638766 (http://www.uspto.gov).
Teaching
FW4099 Programming
Skills for Bioinformatics Fall
2009, 2011
FW5082 Gene Expression Data Analysis Fall
2010, 2012
CS2321 Data
Structure in Java Spring
2011
FW4500 Experimental Design and Data
Analysis for Natural Science
Spring 2012
Recent Synergistic Activities
1)
Grant Proposal Reviews: NSF Organism and
Environment Interaction. 2010
2) Grant Proposal Reviews:
NSF of China
Forestry Biotechnology, 2010.
3) Invited speaker: International Conference on Sustainable Management
of Multi-purpose Poplar Plantations, IUFRO, China, 2010
4) Invited speaker: Plant
and Animal Genome XIX Conference, Jan 2011, San Diego, California.
Collaborators &
Collaborators & Other Affiliations (within last 48 months)
Co-authors and
Collaborators: Xiaoqi Cui,
Huann-sheng Chen, Victor, Busov, Pei-Fen Kuan, Guangjin Pan, Ron Stewart, James
Thomson, Shulan
Tian, Chuhu Yang, Jeff Nie, Srikumar Sengupta, Victor Ruotti, Gudrun Jonsdottir, Sunduz Keles. Vinodh Srinivasasainagendra, Chuhu Yang, and Ray Ming, Shaobin Hou, Yun Feng et al 82
co-authors of the article in Nature,
Vol. 452, No. 7190:991-996, 2008
Advisor
Fang Ruan, Ph.D. student
in Systems Biology, Spring, 2010 to Present
Yang Li, Master student in Genomics.
Fall, 2009 to Present
Hang Zhang, Master student
in Computer Science, Spring, 2010 to Present
Biographical
Sketch
Thomas
Werner
Assistant Professor
Department of Biological Sciences
DOW 523, 1400 Townsend Drive
Michigan Technological University
Houghton, MI 49931
Phone: (906)
487-1209
FAX: (906)
487-3167
E-mail:
twerner@mtu.edu
Education
2005 Ph.D., Cell and Molecular Biology, Umeå Center
for Molecular Pathogenesis, Umeå
University, Umeå, Sweden.
1997 M.Sc., Biology, Jena University, Jena,
Germany.
Appointments
2010 - present Assistant
Professor, Department of Biological Sciences, Michigan
Technological University,
Houghton, MI.
2005 - 2010 Post-Doctoral
Research Associate, Department of Molecular Biology, University
of Wisconsin-Madison, Madison,
WI.
Honors and Awards
2005 - 2008 Postdoctoral
Long-term fellowship, Human Frontier Science Program
2005 - 2007 Postdoctoral
Long-term fellowship, European Molecular Biology Organization (declined in
favor of the HFSP fellowship)
1998 – 2000 Graduate
fellowship Umeå University
1990 Special
Award at the National Youth Science and Technology Competition “Jugend Forscht”
(“Youth researches”) , Mainz, Germany.
Peer Reviewed Publications
1) Werner T., Koshikawa
S., Williams T.M., Carroll S.B. (2010) Generation of a novel wing color pattern
by
the Wingless morphogen. Nature,
Vol. 464, pp. 1143-1148. (Cover article)
2) Rebeiz M., Ramos-Womack M., Jeong S.,
Andolfatto P., Werner T., True J., Stern D.L., Carroll S.B.
(2009) Evolution of the tan
Locus Contributed to Pigment Loss in Drosophila santomea: A Response to
Matute et al. Cell, Vol.
139, pp. 1189-1196.
3) Williams T.M. , Selegue
J.E., Werner T., Gompel N., Kopp A., and Carroll S. B. (2008) The Regulation
and Evolution of a Genetic
Switch Controlling Sexually Dimorphic Traits in Drosophila. Cell, Vol. 134, pp.
610–623.
4) Jeong S., Rebeiz M.,
Andolfatto P., Werner T., True J., Carroll S.B. (2008) The Evolution of Gene
Regulation Underlies a
Morphological Difference between Two Drosophila Sister Species. Cell, Vol. 132,
pp. 783-93.
5) Werner T., Borge-Renberg K., Mellroth P.,
Steiner H. and Hultmark D. (2003) Functional diversity of the
Drosophila PGRP-LC gene
cluster in the response to LPS and peptidoglycan. J Biol Chem, Vol. 278, Issue
29, pp. 26319-22.
6) Choe K.M., Werner T.,
Stoven S., Hultmark D, Anderson
K.V. (2002). Requirement for a Peptidoglycan
Recognition Protein (PGRP)
in Relish Activation and Antibacterial Immune Responses in Drosophila.
Science, Vol. 296, Issue
5566, pp. 359-62.
7) Werner, T., Liu, G.,
Kang, D., Ekengren, S., Steiner, H. and Hultmark, D. (2000). A family of
peptidoglycan recognition
proteins in the fruit fly Drosophila melanogaster. Proc Natl Acad Sci USA,
Vol.
97, Issue 25, pp. 13772-7.
Memberships
Michigan Tech Biotechnology Research
Center (BRC)
Current Collaborations
Sean B. Carroll and Shigeyuki Koshikawa, University of Wisconsin-Madison, WI.
Advisors
M.Sc. Advisor: Dr. Andreas Henke, Jena
University, Jena, Germany
Ph.D. Advisor: Dr. Dan Hultmark, Umeå
Center for Molecular Pathogenesis, Umeå University,
Umeå, Sweden.
Postdoctoral Advisor: Dr. Sean B. Carroll, University of Wisconsin-Madison, WI.
Present Undergraduate Students
Bryant Kollie, Roger Yeager
Biographical
Sketch
Ramakrishna Wusirika
Associate PRofessor
Department of Biological Sciences
DOW 505, 1400
Townsend Drive
Michigan Technological University
Houghton, MI 49931
Phone: (906) 487-3068
FAX: (906) 487-3167
E-mail: wusirika@mtu.edu
Web site:
www.bio.mtu.edu/faculty/rwusirika.htm
Education
National Chemical
Laboratory, and University of Pune, Pune,
India Biochemistry Ph.D., 1995
University of Hyderabad,
Hyderabad, India Biochemistry M.Phil., 1990
University of Hyderabad,
Hyderabad, India Biochemistry M.Sc., 1988
Osmania University, Hyderabad, India Biology B.Sc., 1986
Appointments
2009 – present Associate Professor Department of Biological Sciences, Michigan Technological
University, Houghton, MI.
2003 - 2009 Assistant Professor Department
of Biological Sciences, Michigan Technological
University, Houghton, MI.
1999 - 2003 Post-Doctoral Research Fellow Department of Biological Sciences, Purdue University,
West Lafayette, IN.
1997 - 1999 Post-Doctoral Research Fellow Department of Horticulture, Purdue University,
West Lafayette, IN.
1995 - 1997 Post-Doctoral Research Fellow Division of Biochemical Sciences,
National Chemical Laboratory, Pune,
India.
Recent Publications
1) Wusirika R, Li K,
Bennetzen JL, Phillips RL (2010) Zea. In: Kole C (ed) Wild Crop Relatives:
Genomic and Breeding Resources. Vol 1: Wild Relatives of Cereals. Springer, Heidelberg, Berlin, New York (in press)
2) Krom, N., and
Ramakrishna, W. (2010) Conservation, rearrangement, and deletion of gene pairs
during the evolution of four grass genomes.
DNA Res doi:
10.1093/dnares/dsq022
3) Dhadi, S.R., Krom, N.,
and Ramakrishna, W. (2009) Genome-wide comparative analysis of putative
bidirectional promoters from rice, Arabidopsis
and Populus. Gene 429: 65-73.
4) Krom, N., and
Ramakrishna, W. (2008) Comparative analysis of divergent and convergent gene
pairs and their expression patterns in rice, Arabidopsis, and Populus. Plant Physiol. 147: 1763-1773.
5) Krom, N., Recla, J.,
and Ramakrishna, W. (2008) Analysis of genes associated with retrotransposons
in the rice genome. Genetica 134: 297-310.
6) Xu, Z., and
Ramakrishna, W. (2008) Retrotransposon insertion polymorphisms in six rice
genes and their evolutionary history. Gene
412: 50-58.
7) Oakley, R.V., Wang,
Y-S., Ramakrishna, W., Harding,
S.A., and Tsai,
C-J. (2007) Differential expansion and expression of α- and β-tubulin gene families in Populus. Plant Physiol.
145: 961-973.
8)Nagy, E., Lee, T-C.,
Ramakrishna, W., Xu, Z., Klein, P., SanMiguel, P., Cheng, C-P., Li, J., Devos,
K., Schertz, K., Dunkle, L., and
Bennetzen, J. (2007) Fine mapping of the Pc
locus of Sorghum bicolor, a gene controlling the reaction to a fungal
pathogen and its host-selective toxin. Theor.
Appl. Genet. 114: 961-970.
9) Yan, L., Loukoianov,
A., Blechl, A., Tranquilli, G., Ramakrishna, W., SanMiguel, P., Bennetzen,
J.L., Echenique, V., and Dubcovsky, J.
(2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.
Science 303: 1640-1644.
20) Bennetzen, J.L.,
Coleman, C., Liu, R., Ma, J., and Ramakrishna, W. (2004) Consistent
over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7: 732-736.
11) Lai, J., Ma, J.,
Swigonova, Z., Ramakrishna, W., Linton, E., Llaca, V., Tanyolac, B., Park,
Y.J., Jeong, O.Y., Bennetzen, J.L., and Messing, J. (2004) Gene loss and
movement in the maize genome. Genome Res.
14: 1924-1931.
12) Swigonova Z, Lai J, Ma
J, Ramakrishna W, Llaca V, Bennetzen JL, and Messing J. (2004) Close split of
sorghum and maize genome progenitors. Genome
Res. 14: 1916-1923.
13) Ramakrishna W, Deng Z,
Ding CK, Handa AK, Ozminkowski RH Jr. A novel small heat shock protein gene,
vis1, contributes to pectin depolymerization and juice viscosity in tomato
fruit. (2003) Plant Physiol. 131:
725-735.
Synergistic Activities
1) Member, American
Society of Plant Biologists
2) Coordinator, Bioinformatics Program, Michigan Tech University
3) Ad hoc reviewer for
several international journals and funding agencies (NSF, US-Israel BARD and
U.S. Civilian Research and Development Fund)
4) Chief editor for a
special issue of International Journal of Plant Genomics
Collaborators
Jeffrey Bennetzen (U.
Georgia, GA), Phillip SanMiguel (Purdue
Univ, IN), Jianxin Ma (Purdue
Univ, IN), Ramanjulu Sunkar (Oklahoma State Univ, OK), Chung-Jui Tsai
(U. Georgia, GA), Erich Grotewold (Ohio State Univ, OH), Sastry Jayanty
(Colorado State Univ, CO), Rupali Datta (MTU), Wan Jin Jahng (MTU), Charles
Kerfoot (MTU)
Graduate and Postdoctoral
Advisors
PhD Advisor: Prabhakar
Ranjekar, National Chemical Laboratory, Pune,
India
Postdoctoral Advisor:
Jeffrey Bennetzen, University of Georgia, Athens, GA, Avtar Handa, Purdue
University, West Lafayette, IN, Prabhakar Ranjekar, National Chemical
Laboratory, Pune, India
Thesis Advisor
Current Ph.D.
Surendar Reddy Dhadi,
Kefeng Li and Sheikh Rafi
Past Ph.D./M.S.
Nicholas Krom, Zijun Xu,
Deepak Kumar and Patience Tenney
Curren Visiting Scientist
Zhiying Dou
Past Visiting Scientist
Bashir Yusuf (Ahmadu Bello University, Nigeria)
Undergraduate Students Advised
Nari Kang, Matt Ogg,
Sulagna Gupta, Katie Kruger, Megan McQuillan, Jill Recla, Benjamin Baer and
Holly Grunst
Introduced to Senate: 19 October 2011
Approved by Senate: 02 November 2011
Approved by Administration: 11 November 2011
Approved by BOC: 09 December 2011
Approved by State: 20 January 2012