Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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1. Cover page
Hope College HHMI Faculty/Students Collaborative Research Grant Proposal
Title of the Proposal: Exploring the Association of Rapid Diversification of Maple Lineages
and the Diversity of Protective Pigments
Principal Investigators
Jianhua Li (Biology Department, Hope College)
Kenneth Brown (Chemistry Department, Hope College)
Airat Bekmetjev (Mathematics Department, Hope College)
Current undergraduate research students: Kaleb Skinner and Parker Bussies (Jianhua Li,
Airat Bekmetjev), Gerardo Ochoa and Tanweer Ismail (Kenneth Brown)
Dear HHMI Steering Committee,
We write to submit a faculty/students collaborative research proposal titled “Exploring the
association of rapid diversification of maple lineages and the diversity of protective pigments.”
Maples are one of the most important trees in the Northern Hemisphere, and have been
divided into 19 subgroups (sections) based on morphological traits. The RD (rapid
diversification) hypothesis states that maple sections may have diversified rapidly within a short
time span by the Mid-Eocene. Maples are famous for colorful foliage due to the presence of
various pigments, which protect plants from damages of the sunlight and/or herbivores. Thus, we
hypothesize that the pigment diversity underlines the rapid diversification of maple lineages. In
the proposed research we will work together with students to explore the association between the
pigment diversity and the rapid radiation of maple lineages using quantitative statistical analyses
and a solid phylogenetic framework to be constructed with plastid genome sequence data.
We have worked out the detailed protocol of plastid genome sequencing technology and
obtained plastid genome data from five maple species using the IonTorrent PGM Sequencing
Machine Biology Department has recently acquired via a NSF MRI (major research
instrumentation) grant. We have also secured sources of plant samples for the project and
designed a protocol for determining the diversity of the protective pigments. Therefore, we are
confident that the proposed research will be implemented with great success. The results will be
presented in professional meetings and published in peer-reviewed journals. We will also use the
results in a collaborative research proposal to be submitted to NSF in collaboration with
Michigan State University and Oregon State University.
With the HHMI grant support, we will establish an interdisciplinary research area with a
focus on the quantitative analyses of interactions of plants, insects, and chemicals, train students
to become research leaders in the STEM fields, and develop materials for a research-based,
interdisciplinary course based on the results from the proposed research.
We are excited about the opportunity to work across different disciplines and sincerely hope
you will grant the application serious consideration.
Sincerely yours,
Jianhua Li, Ken Brown, and Airat Bekmetjev
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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2. Abstract
Maples are an important tree group in the Northern Hemisphere with the center of diversity
in China, and several unique species in Europe, the Middle East, Japan, and North America.
Albeit with a long history of study, our understanding of the natural history of maples remains
limited; many fundamental questions have not been answered with satisfaction. For example,
where and when did maples originate? how did maples migrate throughout the Northern
Hemisphere? what are the evolutionary relationships among major groups of maples? and what
are the temporal patterns of and causes for the diversification of maple lineages? Studies of the
fossil records have led to the RD (rapid diversification) hypothesis that maple lineages may
have diversified rapidly within a short time span by the Mid-Eocene. Recent molecular analyses
using less than 5,000 data points have not provided enough information to establish a wellsupported phylogenetic framework. The lack of the framework hampers our ability to test the RD
hypothesis. Therefore, the first objective of the proposed research is to establish the phylogenetic
framework using plastid genome sequences with over 100,000 data points. Maples are well
known for their beautiful foliage in the spring and fall due to the presence of colorful pigments
(xanthophylls and anthocyanins). Because of their protective function against environmental
factors (e.g., drought, excessive sunlight, and herbivores), the pigments provide adaptive
advantages to plants, thus promoting lineage RD. Based on this, we propose the CP (colorful
pigments) hypothesis that colorful pigments may have played an important role in the rapid
radiation of maple lineages. In the proposed research, we will test the CP hypothesis based on
chemical determination of the pigment diversity and quantitative analysis of the association
between the diversity of colorful pigments and the lineage diversification. The solid phylogenetic
framework will also provide answers to the other fundamental questions about the natural history
of maples in the world. The interdisciplinary project will for the first time examine the potential
association of pigment production and adaptive radiation of maples in the world. We will crosstrain students in biology, chemistry, and mathematics. The successful implementation of the
project will provide materials and protocols for developing a research-based, interdisciplinary
course. In addition, we will present our results to the scientific communities via professional
meetings and peer-reviewed publications as well as to the general public via talks and websites.
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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3. Project Description
3.1. Background Information and Significance of the Proposed Work
Acer is the largest tree genus in the broad-leaved deciduous forests of the Northern
Hemisphere (Wolfe and Tanai 1987) and includes well-known and horticulturally important
species such as sugar maple (A. saccharum), red maple (A. rubrum), Japanese maple (A.
palmatum), and Norway maple (A. platanoides). Many species are also important sources of
commercial products, e.g., maple syrup from Acer saccharum and construction timber from Acer
saccharum, A. rubrum, and A. pseudoplatanus (van Gelderen et al. 1994).
Acer is most closely related to Dipteronia (2 species) and Aesculus (13 species) in the
family Sapindaceae (Judd et al. 1994; Gadek, Fernando et al. 1996). Within Acer, the most
important early monograph by Pax (1885, 1886, 1902) divided then 114 species into 13 sections.
Many authors have since adopted this system with some revisions (Rehder 1905; Koidzumi
1911; Nakai 1915; Pojarkova 1933; Hu and Cheng 1948; Momotani 1962; Fang 1966; Ogata
1967; de Jong 1976, 1994; Delendick 1981; Mai 1984; Huang et al. 2002). The most recent
taxonomic system of Acer (de Jong 2004) recognized 19 sections. Sections of Acer have also
been grouped in various ways based on different morphological characters. Although there have
been several molecular phylogenetic studies of maples (Hasebe et al. 1998; Suh et al. 2000; Tian
et al. 2002; Li et al. 2006), none have used a large amount of DNA sequence data from either
the plastid or nuclear genomes, and as a result relationships among sections of Acer remain
largely unresolved, which hampers our understanding of the natural history of maples in
the world. In addition, for morphologically unique species such as Acer carpinifolium and A.
spicatum, our ignorance of which species are their close relatives makes it difficult for directing
the plant breeding and conservation efforts. It is therefore urgently needed to establish a wellresolved phylogeny for the genus. The recent development of sequencing the entire plastid
genome holds great promises in resolving phylogenetic relationships among maple sections
because it can potentially provide nearly 100,000 data points (Atherton et al. 2010). It is possible
that the poor resolution of relationships among sections of Acer reflects a history of rapid
diversification (RD), as observed in many other groups of organisms (Morrison et al. 2004;
Soltis et al. 2005). The RD hypothesis seems to be consistent with the fossil history of Acer.
Fossil species of Acer first appeared in late Cretaceous and diversified during the Eocene, and by
the Mid-Eocene most lineages had evolved. Based on this, Wolfe and Tanai (1987) concluded
that there was a rapid diversification of Acer lineages in the Mid-Eocene. The solid
phylogenetic framework will help test the RD hypothesis.
If the RD hypothesis is true, what may have accounted for the successful rapid
diversification of maple lineages? Maples are well known for their beautiful spring and fall
foliage due to the presence of colorful pigments. The colorful pigments other than chlorophylls,
which are the key pigment for photosynthesis, function as a sunscreen to protect against damage
from excess solar energy (Field et al. 2001; Gould et al. 1995; Hoch et al. 2003) or as a warning
to potential herbivores (Archetti et al. 2009). Therefore, it is reasonable to hypothesize that the
colorful pigments (CP) may have played an important role in the successful diversification of
maples. In the proposed research we will test the CP hypothesis by exploring the association
between the pigment diversity and the rapid radiation of maple lineages with the reference to the
close relatives of maples, which have low species diversity.
The proposed research will for the first time establish a solid phylogenetic framework for
maple sections in the world based on plastid genome data, which will in turn provide new
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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insights into the natural history of maples in the world. It will provide the first quantitative test
for the RD hypothesis and for the newly proposed CP hypothesis. The positive association of RD
and CP in maples may be tested in other plant groups to see whether it can be generalized.
Students will be cross-trained in biology, chemistry, and mathematics. The successful
implementation of the project will also provide materials and protocols for developing a
research-based, interdisciplinary course.
3.2. Objectives of the Project
The main goals of the proposed project are dual: 1) to establish a robust phylogeny of all section
and series of Acer and test the RD hypothesis that maple lineages diversified rapidly in the MidEocene, and 2) to determine the diversity of colorful pigments in maples and relatives and test
the CP hypothesis that there is an association between the pigment diversity and the
diversification of maple lineages.
3.3. Materials and Methods
3.3.1. Species to be included in the project
We will obtain plastid genome data from 26 species, 20 of which are maples representing
all sections and series, and the other three species represent close relatives of Acer (Table 1).
Table 1. Species to be included. Boldface indicates species that we have recently completed the
PCR amplification of the plastid genome.
Classification (de Jong 2004)
Species
Source
Section Parviflora
A. nipponicum
Section Spicata
A. spicatum
Section Palmata
A. palmatum
Section Wardiana
A. wardii
Section Macrantha
A. pensylvanicum
Section Glabra
Section Arguta
A. glabrum
A. argutum
Section Negundo
A. negundo
A. henryi
Section Indivisa
A. carpinifolium
Section Acer
Section Pentaphylla
A. saccharum
A. pentaphyllum
Section Trifoliata
A. triflorum
RBGE
19795193
Arnold Arb.
359-79*D
Arnold Arb.
585-88*C
Yunnan. Li
4890
Arnold Arb.
1331-79*B
Aaron Liston
Arnold Arb.
640-77*B
Holland, MI
Arnold Arb.
164-83*A
Arnold Arb.
10959*B
Holland, MI
Quarryhill
Arb.2001.430B
Arnold Arb.
DNA
number
Li 4045
Li 6444
Li 6451
Li 4890
Li 6446
Li 4275
Li 6445
Li 4041
Li 6450
Li 6443
Li 6439
Li 4262
Li 6442
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
Section Lithocarpa
A. diabolicum
Section Macrophylla
A. macrophyllum
Section Plantanoidea
Section Pubescentia
Section Ginnala
A. platanoides
A. stenolobum
A. tataricum
Section Rubra
Section Hyptiocarpa
A. saccharinum
A. laurinum
Aesculus
A. glabra
Aesculus
A. chinensis
Aesculus
A. hippocastanum
Aesculus
Dipteronia
A. californica
D. sinensis
Dipteronia
D. dyerdiana
1217-25*A
Arnold Arb.
2625*A
Morton Arb.
31-86
Holland, MI
De Jong, P.
Arnold Arb.
1302-80*A
Holland, MI
Tian 2079,
XSBN Bot.
Gard.
Arnold Arb.
1221-79*A
Arnold Arb.
156-2001
Arnold Arb.
12648
UBC Bot. Gard.
Liu; NACPEC
08003
Tian
page
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Li 6447
Li 4240
Li 6440
Li 5646
Li 6449
Li 3521
Li 3353
Li 6448
Li 6075
Li 3363
3.3.2. Plastid genome amplification using Phusion PCR and primer walking method
The circular plastid genome of plants has four major regions: the large single copy region
(LSC), small single region (SSC), and two inverted repeats (IRa and IRb) situated between LSC
and SSC. We have used 73 pairs of primers to amplify the three regions (IRa and IRb are
identical to each other) from 13 species (12 maples and 1 Aesculus). We will use the same
method to amplify the plastid genome of the remaining species (see Table 1).
3.3.3. DNA library construction and sequencing
We will use Life Technologies’s Ion Xpress Plus gDNA fragment library preparation kits to
construct library for each of the amplified plastid genomes. The template will be prepared using
Ion OneTouch 200 Ion Sphere particles, which will then be enriched using an Ion OneTouch ES
station. The enriched ISPs will be sequenced with an IonTorrent PGM sequencing machine. The
DNA sequences of ca. 200 bp will be assembled de novo using the IonTorrent Assembler. And
the contiguous sequences will be aligned against known plastid genomes in a SEQUENCHER
program.
3.3.4. Phylogenetic analysis and testing the RD hypothesis
Plastid sequences of all species will be aligned using MUSCLE program and a maximum
likelihood method will be used to reconstruct the phylogenetic tree using MEGA program
(Tamura et al., 2011). Reliable fossils of maples and relatives with known ages will be used to
estimate the times of divergence of different lineages (sections) of maples under the Bayesian
theorem as implemented in the BEAST program (Drummond et al., 2012). Statistical analysis
will be conducted to test the RD hypothesis based on the reconstructed phylogenetic framework.
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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3.3.5. Determination of pigment diversity and its association with species diversity
Tools from analytical chemistry (e.g., HPLC) will be used to determine the diversity of
xanthophylls and anthocyanins in the leaves of the selected species (Table 1). The association of
species diversity and the diversity of the pigments will be analyzed using independent contrasts
method by comparing maples and their relatives (Dipteronia and Aesculus) as well as the pairs of
sections in the phylogeny with differential diversity of pigments and number of species (Garland
1992).
3.4. Expected Outcomes
Li has confirmed the sources of all the plant materials for this project with botanical gardens
and arboreta and has successfully obtained the plastid genome data from five maple species and
one species of Aesculus. Brown has worked out the detailed protocol of determining the diversity
of pigments. Bekmetjev has compared different statistical methods for testing the RD and CP
hypotheses within a phylogenetic framework. Therefore, we expect to implement the proposed
research successfully within the timetable without serious difficulties. The results will be
presented in local, national, and international conferences and published in peer-reviewed
journals. Three students will be cross-trained in chemistry, biology, and mathematics through the
project. The project will provide materials and protocols for developing a research-based,
interdisciplinary course or case study. Dr. Li was one of the PIs on a preliminary collaborative
research proposal submitted via Michigan State University to the NSF on January 23, 2013 with
a focus on the species diversity of maples in Europe, North America, and Asia. The results from
the HHMI project will be used as preliminary data for the full proposal if the preliminary
proposal passes the NSF panel review.
3.5. How the Project will Connect to Other HHMI 2012 Programs
The proposed project will strengthen the other HHMI 2012 programs. First, students trained
via the project will gain a deeper understanding of the interdisciplinary nature of scientific
research and become well-trained research leaders in any STEM fields. Second, successful
implementation of the project will lay a foundation for designing a research-based
interdisciplinary course involving biology, chemistry, and mathematics. Third, students in the
project will be actively engaged with students involved in other HHMI-supported projects (such
as course-based research experience program).
3.6. Plans for External Funding to Continue Work
We will seek external funding from NSF to expand our species sampling in each of the
sections and series within Acer to gain more comprehensive insights into the association of
species diversification and the diversity of protective pigments in plant species.
3.7. Timeline
The project will be conducted from June 1, 2013 through May 31, 2014. Plant materials will
be collected in June 2013 from various arboreta and botanical gardens (see Table 1), and DNA
and chemical extraction will be completed in the summer of 2013. We will focus on gathering
DNA sequence and colorful pigment data and testing various statistical methods in the first 9
months of the project. In the last three months of the project we will concentrate on data analyses
and writing manuscripts based on the results.
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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4. Literature cited
APG. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and
families of flowering plants: APG III. Bot. J. Linnean Soc. 161, 105–121.
Archetti, M. et al. 2009. Unraveling the evolution of autumn colors: an interdisciplinary
approach. Trends Eco. Evol. 24: 166-172.
Atherton, R.A., B.J. McComish, L.D.Schepherd, L.A. Berry, N.W.Albert, and P.J. Lockhart.
2010. Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII
platform. Plant Methods 6: 22.
de Jong, P. C. 1976. Flowering and sex expression in Acer L. A biosystematic study.
Mededelingen Landbouwhogeschool Wageningen Nederland 76: 1-201.
de Jong, P. C. 2004. World maple diversity. International Maple Symposium, Westonbirt
Arboretum and Royal Agricultural College in Gloucestershire, England.
Delendick, T. 1981. A systematic review of the Aceraceae. New York, City University of New
York.
Drummond AJ, Suchard MA, Xie Dong, Rambaut A. 2012. Bayesian Phylogenetics with
BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969-1973.
Fang, W.-P. 1966. Revisio Taxorum Aceracearum Sinicarum. Acta. Phytotax. Sin. 11: 139-189.
Field, T.S., N.M. Holbrook, and D.W. Lee. 2001. Why leaves turn red in autumn. The role of
anthocyanins in senescing leaves of red-osier dogwood. Plant Physiology 127: 566-574.
Gadek, P. A., E. S. Fernando, et al. 1996. Sapindales: Molecular delimitation and
infraordinal groups. Amer. J. Bot 83(6): 802-811.
Garland, T., P.H. Harvey, and A. R. Ives. 1992. Procedures for the analysis of comparative data
using phylogenetically independent contrasts. Syst. Biol. 41: 18-32.
Gould, K.S., D.N.Kuhn, D.W.Lee, and S.F.Oberbauer. 1995. Why leaves are sometimes red.
Nature 378: 241-242.
Hasebe, M., T. Ando, et al. 1998. Intrageneric relationships of maple trees based on the
chloroplast DNA restriction fragment length polymorphisms. J. Pl. Res. 111(1103): 441-451.
Hoch, W.A., E.L. Singsaas, and B. H. McCown. 2003. Resorption protection. Anthocyanins
faciliate nutrient recovery in autumn by shielding leaves from potentially damaging light levels.
Plant Physiology 133: 1296-1305.
Hu, H. H. and W. C. Cheng. 1948. New and noteworthy species of Chinese Acer. Bull. Fan
Mem. Inst. of Biol., New Ser. 1(2): 199-212.
7
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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Judd, W. S., R. W. Sanders, et al. 1994. Angiosperm family pairs: preliminary
phylogenetic analyses. Harvard Pap. Bot. 5: 1-51.
Koidzumi, G. 1911. Revisio Aceracearum Japonicarum. Journ. Coll. Sci. Univ. Tokyo 32: 1-75.
Li, J., J. Yue, et al. 2006. Phylogenetics of Acer (Aceroideae, Sapindaceae) based on nucleotide
sequences of two chloroplast non-coding regions. Harvard Pap. Bot. 11: 101-115.
Mai, D. H. 1984. Die endokarpien bei der Gattung Acer L. (Aceraceae) - eine
biosystematische studie. Gleditschia 11: 17-46.
Momotani, Y. 1962. Taxonomic study of the genus Acer, with special reference to the seed
proteins III. System of Aceraceae. Mem. Coll. Sci. Univ. Kyoto, ser. B. 29: 177-189.
Morrison, C. L., R. Rios, et al. 2004. Phylogenetic evidence for an ancient rapid radiation of
Caribbean spone-dwelling snapping shrimps (Synalpheus). Mol. Phylog. Evol. 30: 563-581.
Nakai, T. 1915. Flora Sylvatica Koreana.
Ogata, K. 1967. A systematic study of the genus Acer. Bull. Tokyo Univ. Forest. 63: 89-206.
Pojarkova, A. I. 1933. Botanico-Geographical survey of the maples in USSR, in
connection with the history of the whole genus. Acta Inst. Bot. Acad. Sci. USSR, ser. 1 1: 225374.
Rehder, A. 1905. The maples of eastern continental Asia. Trees and Shrubs. C. S. Sargent: 131181.
Renner, S. S., G. W. Grimm, et al. 2008. Rooting and Dating Maples (Acer) with an
Uncorrelated-Rates Molecular Clock: Implications for North American/Asian Disjunctions. Syst.
Biol. 57(5): 795-808.
Soltis, D. E., P. S. Soltis, et al. 2005. Phylogeny and evolution of angiosperms. Sunderland,
Sinauer Associates.
Suh, Y., K. Heo, et al. 2000. Phylogenetic relationships of maples (Acer L.; Aceraceae) implied
by nuclear ribosomal ITS sequences. J. Pl. Res. 113(1110): 193-202.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular
evolutionary genetics analusis using maximum likelihood, evolutionary distance, and maximum
parsimony methods. Mol. Biol. Evolution 28: 2731-2739.
Tian, X., Z. H. Guo, et al. 2002. Phylogeny of Aceraceae based on ITS and trnL-F data sets. Acta
Bot. Sin. 44(6): 714-724.
van Gelderen, D. M., P. C. de Jong, et al. 1994. Maples of the World. Portland, Timber Press.
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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Wolfe, J. A. and T. Tanai. 1987. Systematics, phylogeny, and distribution of Acer
(Maples) in the Cenozoic of western North America. Journ. Fac. Sci. Hokkaido Univ. ser. IV 22:
1-246.
5. Budget and justification
A total budget of $15,000 is requested for the proposed research covering two major areas:
1) Plastid genomic sequencing ($11,310)
The fund is for plant material acquisition ($500) and molecular kits ($10,810) for DNA
extraction, PCR amplification of plastid genome, PCR product cleanup, library construction,
enrichment, and genomic sequencing of 26 species of maples and close relatives (see Table 2 for
details).
2) Chemical determination of pigments ($3,690)
The fund is for supplies for testing types and concentrations of various pigments in maple
species.
Table 2. Budget items for each of the steps needed to obtain the plastid genome data for 26
samples. The fund will be spent on PCR and sequencing reagents and supplies. There are
generally two or three students working in our labs during the semester for research credits.
Reagent or kit
Phusion PCR master mix kit
Qiaquick PCR purification kit
Pippin Prep Kit 2010
Ion XpressTM Plus Fragment
Library Kit
Ion PGMTM 200 Xpress
Template Kit (replaces PN
4471253
Ion SphereTM Quality Control
Kit
Ion PGMTM 200 Sequencing
Kit (replaces PN 4471258
Ion 314 Chip Kit
Total:
Vendor &
Catalog#
NEBL M0531L
Qiagen 28104
Invitrogen 4472170
Invitrogen 4471269
Unit
price
$435
$105
$450
$750
Cost
Invitrogen 4474280
$1250
2 x $1250 = $2,500
Invitrogen 4468656
$350
2 x $350 = $700
Invitrogen 4474004
$1000
3 x $1,000 = $3,000
Invitrogen 4462923
$792
2 x $792 = $1,584
2 x $435 =$870
$105
3 x $450 = $1,350
2 x $750 = $1,500
$10,810
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
page 10
6. Biographical sketches
6.1. Jianhua Li
PROFESSIONAL PREPARATION
Postdoc, Plant Molecular Systematics, 1998, Harvard University
Ph.D., Plant Biology, 1997, University of New Hampshire
M.S., Botany, 1987, Huazhong Normal University
B.S., Biology, 1984, Henan Normal University
APPOINTMENTS
2009-present: Associate Professor of Biology, Hope College, MI.
2005-present: Adjunct Professor, Zhejiang University, Hangzhou, China
2005-2009: Senior Research Scientist, Arnold Arboretum of Harvard
University
1999-2004: Botanical/Horticultural Taxonomist, Arnold Arboretum
1999: Putnam Postdoctoral Fellow, Harvard University Herbaria
1993-1997: Graduate Assistant, University of New Hampshire
1992: Visiting Researcher, Institute of Botany, Academia Sinica, Beijing
1989-1991: Assistant Professor, Department of Biology, Henan Normal
University
1987-1988: Assistant Professor, Department of Geography, Henan University
RECENT SYNERGISTIC ACTIVITIES
Selected Awards and Honors
Adjunct Professor (Henan Agricultural University (2001-); Member of the Editorial
Committee of Arnoldia (2003-2009), and Associate Editor of the Journal of Systematics
and Evolution (2007-present); Adjunct Professor (Zhejiang University, Henan
Agricultural University, Nanyang Teachers College).
Selected Invited Seminars:
Harvard University, University of New Hampshire, Zhejiang University, Zhongshan
University, South China Agricultural University, Northwest University, Beijing Institute
Botany, Henan Agricultural University, Guizhou University, New England Botanical
Club, Michigan Botanical Club.
Manuscript Reviews:
Rhodora, HortScience, American Journal of Botany, Molecular Phylogenetics and
Evolution, Systematic Biology, Systematic Botany, International Journal of Plant
Sciences, Journal of Systematics and Evolution.
SELECTED PUBLICATIONS (* denotes an undergraduate student)
Li, Q., W.Liao, W.Guo, J.Macklin, and J. Li. 2012. Generic limits of Pyrinae:
insights from ribosomal DNA sequences. Botanical Studies 53: 151-164.
Li, J., B. Goldman-Huertas, J. DeYoung*, and J. Alexander. 2012. Phylogenetics
and diversification of Syringa inferred from nuclear and plastid DNA sequences.
Castanea. 77: 82-88.
Du, Y., Q. Dai, L. Zhang, Y. Qiu, J. Li, and C. Fu. 2012. Development of
Microsatellite Markers for the Dove Tree, Davidia involucrata (Nyssaceae), a Rare
Endemic From China. American Journal of Botany, Volume 99 (1): E-206-E-209.
Li, J., J. Corajod*, H. Vander Stel*, and A. Homkes*. 2011. The mycorrhizal system of
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
page 11
Pterospora andromedea (pine-drops) in West Michigan inferred from DNA sequence
data. The Michigan Botanist 50: 131-138.
Li, J. 2011. Phylogenetic evaluation of series delimitations in section Palmata (Acer, Aceroideae,
Sapindaceae) based on sequences of nuclear and chloroplast genes. ALISO. 29: 43-49.
Li, J. and Z. Zhang. 2010. Sequences of 72 plastid genes support the early divergence of
Cornales in the asterids. Journal of Systematics and Evolution 48(6): 426-434.
Li, J., J. Corajod*, and J. DeYoung*. 2010. Host preferences of Beechdrops (Epifagus): evidence
from chloroplast DNA sequence data. The Michigan Botanist 49: 79-84.
Zhang, Z. and J. Li. 2010. Conflicting phylogenies of section Macrantha (Acer, Aceroideae,
Sapindaceae) based on chloroplast and nuclear DNA. Syst. Bot. 35(4): 801-810.
Li, M., J. Jiang, C. Fu, W. Judd, and J. Li. 2009. Phylogenetics and biogeography
of Pieris (Lyonieae, Ericaceae) inferred from sequences of nuclear and chloroplast
genomes. Systematic Botany 34 (3): 553-560.
Zhang, Z, C. Li, and J. Li. 2009. Phylogenetic placement of Cynomorium in Rosales inferred
from sequences of the inverted repeat region of the chloroplast genome. Journal of
Systematics and Evolution 47 (4): 1–8.
Theis, N., M. J. Donoghue, and J. Li. 2008. Phylogenetics of the Caprifolieae and Lonicera
(Dipsacales) based on nuclear and chloroplast DNA sequences. Systematic Botany
33(4): 776-783.
Li, J. 2008. Phylogeny of Catalpa (Bignoniaceae) inferred from sequences of
chloroplast ndhF and nuclear ribosomal DNA. Journal of Systematics and Evolution 46:
341-348.
Li J. 2008. Sequences of low-copy nuclear gene support the monophyly of
Ostrya and paraphyly of Carpinus (Betulaceae). Journal of Systematics and Evolution 46:
333-340.
Yue, J., H. Sun, J. Li, Al-Shehbaz, I. A. 2008. A synopsis of an expanded Solms-Laubachia
(Brassicaceae), and the description of four new species from western China. Annals of
Missouri Botanical Garden 95: 524-554.
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
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6.2. Kenneth Brown
A. Professional Preparation
Oral Roberts University
Oklahoma State University
Chemistry
Chemistry
B.S., 1993
Ph.D., 1999
B. Appointments
Associate Professor of Chemistry, Hope College, 2006-Present.
Assistant Professor of Chemistry, Hope College, 2002-2006.
Assistant Professor of Chemistry (Term Position), Hope College, 1999-2002.
Teaching Assistant, Department of Chemistry, Oklahoma State University, 1995-1999.
Research Assistant, Dowell Schlumberger, 1994-1995.
Analytical Chemist, Lab One Analytical, 1993-1994.
C. Recent Significant Publications (* indicates undergraduate authors)
1. K. Klunder*, F.A. Hekman, K.L. Brown, and G.F. Peaslee, “A Study of Dissolved Gas
Dynamics in Mixed Stream Electrolyzed Water,” Electrochemistry: The Electrochemical
Society of Japan, 2012, 80(8), 1-4.
2. K.L. Brown, X. Hou*, O. Banks*, K.A. Krueger*, J. Hinson*, G.F. Peaslee, P.A. DeYoung,
S.A. Alger*, J. Benzer*, and T.L. Neils, ”Characterization of Tris(5-amino-1,10-phenanthroline)
Ruthenium(II/III) Polymer Films Using Cyclic Voltammetry and Rutherford Backscattering
Spectrometry,” International Journal of Chemistry, 2011, 3(4), 12-19.
3. K.L. Brown, and S.B. Gray*, “Cyclic Voltammetric Studies of Electropolymerized Films
Based on Ruthenium(II/III)Bis(1,10 phenanthroline)(4-methyl-4’vinyl-2,2’-bibyridine),”
International Journal of Chemistry, 2010, 2, 2, 3-9.
4. D.J. Gonthier*, T.J. Sullivan, K.L. Brown, B. Wurtzel*, R. Lawal*, K. VandenOever*, Z.
Buchan*, and T.L. Bultman, “Stroma-forming endophyte Epichloe glyceriae provides woundinducible herbivore resistance to it grass roots”, Oikos, 2008, 177, 629-633.
5. J.S. Pinter*, K.L. Brown, P.A. DeYoung, and G.F. Peaslee, “Amperometric Detection of
Hydrazine by Cyclic Voltammetry and Flow Injection Analysis Using Ruthenium Modified
Glassy Carbon Electrodes,” Talanta, 2006, 71, 1219-1225.
6. Brown, K.L.; Pinter, J.S*.; Ewing, K.*; Ruch, T.R.*; Ambrose, M.* and
Hesselsweet, I.*; “Amperometric Detection of Glucose Involving Electropolymerized
Tetraaminophthalocyanine and Ferrocene Films.” Analytical Letters, 2005, 38(5), 769-780.
7. Brown, K.L.; Shaw, J.*; Ambrose, M.* and Mottola, H.A. “Voltammetric, Chronocoulometric and Spectroelectrochemical Studies of Electropolymerized Films Based on
Co(III/II)-and Zn(II)-4, 9, 16, 23-Tetraaminophthalocyanine: Effect of High pH.”
Microchemical Journal, 2002, 72, 285-298.
8. Brown, K.L. and Mottola, H.A. “Voltammetric, Chronocoulometric, and Spectroelectrochemical Studies of Electropolymerized Films Based on Cu(II/I)- 4, 9,16, 23Tetraaminophthalocyanine.” Langmuir, 1998, 14(12), 3411-3417.
D. Synergistic Activities
(i) Talks
1. Kenneth L. Brown, “The Development of New Electrochemical Probes: Three
Dimensional Macroporous Electrodes,” Gentex Corporation, April 20, 2010.
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
page 13
2. Kenneth L. Brown, “Research Opportunities at Hope College: From Electrochemistry to
Plant Physiology and Beyond,” Harold Washington College, March 2, 2007.
3. "Fungi, Alkaloids, and Differential Equations: A Multidisciplinary Undergraduate Program
at Hope College,” Council on Undergraduate Research, Depauw University, Greencastle, IN,
2006.
4. "Developing the Next Generation of Scientific Leaders Through a Dynamic Trio: Mentoring,
Research, and Education, " PEW Capstone Experiences Workshop, Chicago, March 4, 2006.
5. Kenneth L. Brown, “Cyclic Voltammetric Studies of Metal(II) Tetraaminophthalocyanine
Polymer Thin Films: Electrochemistry at Hope College,” Calvin College, December 2, 2004.
E. Collaborators and other Affiliations
Professor Tom Higgins (Harold Washington College, Chicago, IL)
Professor Tom Neils (Grand Rapids Community College)
Dr. Marc Wirtz (PPG Industries, Electrochemical Group, Pittsburgh, PA)
Professor Phillip Buhlman (University of Minnesota)
Professor Graham Peaslee (Hope College)
Professor Thomas Bultman (Hope College)
Dr. Jeffrey Hendricks (Biotectix, LLC)
Dr. Sarah Richardson-Burns (Biotectix, LLC)
Dr. Elizabeth M. Sanford (Hope College)
F. Graduate Advisor
Horacio A. Mottola (Oklahoma State University-Retired)
G. Undergraduate Students Supervised: 45
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
page 14
6.3. Airat Bekmetjev
PROFESSIONAL PREPARATION:
Institution
Major
Degree & Year
Moscow State University, Moscow, Russia
Applied Mathematics B.S. 1991
Arizona State University, Tempe, AZ
Mathematics
Ph.D. 2002
APPOINTMENTS:
Associate Professor of Mathematics, Hope College, 2009 – present
Assistant Professor of Mathematics, Hope College, 2003 - 2009.
Assistant Professor, Gettysburg College, 2002 - 2003.
Teaching Assistant/Graduate Student, Arizona State University, 1996-2002
Scientist/Researcher, Center for Computing and Applied Mathematics, Moscow, Russia, 1991-1995
SELECTED PUBLICATIONS:
1. A. Bekmetjev, D. Van Bruggen*, B. McLellan*, B. DeWinkle B, E. Lunderberg*, Tintle
N.L. “Reclassification as a cost-effective method of estimating disease prevalence.”
PLoS One. 2012. 7(2):e32058.
2. A. Bekmetjev, C. Cusack, “Pebbling Algorithms in Diameter Two Graphs,” SIAM
J. Discrete Math., 23(2), 634-646, 2009.
3. A. Bekmetjev, G. Hurlbert “The Pebbling Threshold of the Square of Cliques”, J.
of Discrete Math, 308/19 (2008) pp. 4306-4314.
4. A. Bekmetjev, G. Brightwell, A. Czygrinow and G. Hurlbert “Thresholds for
families of multisets, with an application to graph pebbling”, Discrete Math. 269
(2003), no.1-3, pp. 21-34.
5. Borchers, B.*, Brown, M.*, McLellan, B.*, A. Bekmetjev, Tintle, N.L.
“Incorporating duplicate genotype data into linear trend tests of genetic association:
methods and cost effectiveness” Stat. Appl. in Genetics and Molecular Biology, 2009.
OTHER PUBLICATIONS
1. A. Petersen*, A. Sitarik*, A. Luedtke*, S. Powers*, A. Bekmetjev, N. Tintle
“Evaluating methods for combining rare variant data in pathway-based tests of genetic
association” BMC Proceedings. 5(9):S48. (http://www.biomedcentral.com/17536561/5/S9/S48), 2012
2. Luedtke A*, Powers S*, Petersen A*, Sitarik A*, Bekmetjev A, Tintle NL (2011)
“Evaluating Methods for the Analysis of Rare Variants in Sequence Data.” BMC
Proceedings, 5(9):S119 (http://www.biomedcentral.com/1753-6561/5/S9/S119)
3. N.L. Tintle, A. Bekmetjev, Borchers, B.*, Brown, M.* “Comparing gene set
analysis methods on SNP data from GAW16.” (2009) Proceedings of Genetic Analysis
Workshop 16, St. Louis, MO. BMC Proceedings, 3(Suppl 7):S96.
(http://www.biomedcentral.com/1753-6561/3/S7/S96)
4. A. Bekmetjev,T. Pennings and T. Swanson “Do Dogs Know Calculus? A
Statistical Investigation”, STATS, 41 (2005), pp. 10-13.
5. A. Bekmetjev, “The influence of fines on the behavior of Ramsey type Model”,
Moscow State University Press, Vol. 15, no. 3, pp. 53-57
* undergraduate students
SYNERGISTIC ACTIVITIES:
o Undergraduate research advisor. Every summer I participated as an undergraduate research
advisor in projects funded by NSF REU and NIH AREA15 programs
o Actuarial career. Participated in the development of a pre-professional program in actuarial
science through the Crossroads Project at Hope College
Li, Brown, Bekmetjev HHMI Research Grant Proposal, February 14, 2013
page 15
REACH (Research Experience Across Cultures at Hope College). Participated in Hope College’s
REACH program by being an advisor of a summer research team of high school students The
goal of the program for high school students and teachers is to create opportunities for students
and teachers to engage in research projects with Hope's science and math faculty.
o Conferences and workshops Participated in organization of several students research conferences
such as Spring Undergraduate Conference at Gettysburg College, Undergraduate Research
Session at Pennsylvania MAA meeting, Undergraduate Research Conference at Moravian
College. Participated as an invited speaker at Pew New Faculty Workshop at Hope College.
o Publications Review. Reviewer of publications for journals Ars Combinatoria and College
Mathematics Journal.
COLLABORATORS & OTHER AFFILIATIONS:
Collaborators:
Graham Brightwell (London School of Economics)
Charles Cusack (Hope College)
Andrzej Czygrinow (Arizona State University)
Glenn Hurlbert (Arizona State University)
Tim Pennings (Hope College)
Todd Swanson (Hope College)
Nathan Tintle (Hope College)
Graduate and Post Doctoral Advisors:
Glenn Hurlbert (Arizona State University)
o
7. Current and pending support
7.1. Jianhua Li. Pending from MSGC grant. $5000. Unraveling the differential speciation rates of
eastern Asian and eastern North American disjunct plant genera based on plastid genome data.
Match fund: $9569 from Hope College DNAS and Biology Department.
7.2. Airat Bekmetjev. Pending. Course-based research experiences HHMI grant. $12,000.
Integrating Research and Statistical Investigation in a First Year Seminar.
7.3 Kenneth Brown
Collaborative Research: Testing Mutualism Theory Using Endophytic Fungi and Their Host
Grass, NSF-CRUI; DEB-Pop & Community Ecol. Cluster, $280,290, Co-PI with Thomas
Bultman. Status: Current
Kenneth Brown, Graham Peaslee, and Elizabeth Sanford. REU Site: Professional Excellence
and Development Through Undergraduate Research, NSF-REU CHEM, $185,000, Status:
Current
Kenneth Brown, Graham Peaslee, and Elizabeth Sanford. REU Site: Achieving the Next
Level—Research Experiences for Underserved Populations, NSF-REU CHEM, $285,732,
Status: Pending
Kenneth Brown and Elizabeth Sanford. GOALI: Probing Interfaces—A Collaboration Between
Academics and Industry, NSF-Polymers, $446,816, Status: Pending