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IMEG
SEMINARS
FALL 2004
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Previous
IMEG Seminars and Abstracts: |
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Date |
Speaker and title of seminar |
09/08/04 |
Speaker:
Dr. Zhi-Chun Lai - Department of Biology
Title: Notch
Regulation and Cell Fate Control
Abstract:
Cellular signaling activities must be
tightly regulated for proper cell fate control and tissue
morphogenesis. We have previously shown that the Drosophila leucine-rich
repeat (LRR) transmembrane glycoprotein Gp150 plays a critical role in
regulating Notch signaling in the developing eye and other tissues.
Gp150 is co-localized with Delta, a ligand of the Notch receptor, in
intracellular vesicles. More recently, gp150 is shown to
synergistically interact with scabrous (sca) to regulate Notch
signaling. Genetic analysis indicated that gp150 and sca function in
a common pathway and gp150 is required for all activities of sca.
Immunostaining experiments revealed that Gp150 concentrated Sca
protein in late endosomes. A model is proposed in which endosomal Sca
and Gp150 promote Notch activation in response to Delta.
References:
Li, Y., Fetchko, M., Lai, Z.-C. and Baker, N. E. "Scabrous and Gp150
are endosomal proteins that regulate Notch activity," Development,
130: 2819-2827, 2003.
Fetchko, M., Huang, W., Li, Y. and Lai, Z.-C. "Drosophila Gp150
is Required for Early Ommatidial Development through Modulation of
Notch Signaling," The EMBO Journal,21: 1074-1083, 2002.
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09/15/04 |
Speaker:
Dr. Jan Klein
- Department of Biology
Title: The
Place of the Human Species in Nature
Abstract: The belief that humans are special and hence that
they have special rights, which include domination and mastery of
nature, is widespread. It is based on three illusions (physical,
psychological, and biological) people have about their position in
nature. The consequences of this belief are unrestrained growth of
human population, disproportionate usurpation of territory by our
species, uncurbed exploitation of Earth' resources, befouling of our
planet, and unrestrained extermination of other species. I will argue
that molecular evolutionary biology provides no justification for the
view that we are special and that a large gap separates our species
from our nearest relative. I will discuss rules of rational ethical
behavior which follow from the study of evolution.
Reference:
Klein, J. 2002. Where do we come from? New York, Springer-Verlag.
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09/22/04 |
Speaker:
Liying Cui
- Department of Biology
Title: Estimating
gene number from cDNA libraries of developing flowers
Abstract:
The flowering plants are the most successful
group of land plants with unique reproductive organs -- flowers.
Molecular phylogeny studies elucidate the group of the most early
branching flowering plants, or basal angiosperms, including water
lilies (Nuphar and Nymphea ), Amborella (a shrub
from New Caledonia) and several other woody plants. The Floral Genome
Project (FGP) aims at sequencing 10,000 ESTs from cDNA libraries of
young flower buds from selected species of basal angiosperms . Several
questions arise in EST sequencing. We would like to know how many
genes are expressed in a underlying cDNA library with a few thousand
EST sequences. We also want to predict the sequence redundancy in
future EST sequencing. The statistical model of cDNA libraries was
developed to address these questions. I present a simple estimate
based on log ratio plots described by Mao and Lindsay. A web-based
software, ESTstat, is developed to correct EST clustering errors and
to estimate the number of genes in a given cDNA library.
Reference:
Wang, J. P., B. G. Lindsay, J. Leebens-Mack, L. Cui, K. Wall, W. C.
Miller, and C. W. DePamphilis. 2004. EST clustering error evaluation
and correction. Bioinformatics.
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09/29/04 |
Speaker:
Dr. Hongzhi Kong
- Department of Biology
Title: Rapid Birth-and-Death
Evolution in the SKP1 Gene Family
Abstract: Skp1 (S-phase kinase-associated protein 1) is a core
component of SCF ubiquitin ligases and mediates protein degradation,
thereby regulates eukaryotic fundamental processes such as cell cycle
progression, transcriptional regulation, and signal transduction.
Among the four components of the SCF complexes, Rbx1 and Cullin form a
core catalytic complex, F-box protein acts as a receptor for target
proteins, and Skp1 serves as an adaptor that links one of the variable
F-box proteins to Cullin. Whereas protists, fungi and some vertebrates
have a single SKP1 gene, many animal and plant species possess
multiple SKP1 homologs which have evolved at highly
heterogeneous rates. The slowly evolving members are relatively
conserved in structure and expressed widely and/or at high levels and
serve the most fundamental function(s), while the rapidly evolving
ones are structurally more diverse and usually expressed at low
levels, in specific tissues, or possibly under specific conditions,
suggesting that they may have lost their original function(s) and/or
acquired new function(s). In addition, the relationships of the most
slowly evolving Skp1 proteins from different species tend to follow
the organismal phylogeny, but the moderately and rapidly evolving
genes appear to be members of species-specific clades. Orthologous
relationships could not be easily observed even when SKP1 genes
from the closely related species were compared. dN/dS
analysis further indicated that the vast majority of the moderately
and rapidly evolving SKP1 genes have evolved under relaxed or
altered constraint. All this suggests that the SKP1 gene family
has experienced a rapid birth-and-death process.
Reference:
Kong H., Leebens-Mack J., Ni W., dePamphilis C. W., Ma H., 2004.
Highly heterogeneous rates of evolution in the SKP1
gene family in plants and animals: Functional and evolutionary
implications. Molecular Biology and Evolution 21: 117-128
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10/06/04 |
Speaker:
Richard Meisel
- Department of Biology
Title:
Reexamining a Classic
Genetic System: What can laboratory crosses tell us about the
maintenance of paracentric inversions in natural populations of
Drosophila pseudoobscura?
Abstract:
Drosophila pseudoobscura
is polymorphic for over 30 different arrangements of the third
chromosome distinguished by single paracentric inversions. Surveys of
natural populations, experimental studies, and sequence analysis
(Schaeffer et al. 2003) all suggest that natural selection plays a
role in maintaining this polymorphism. It is hypothesized that
suppressed recombination between karyotypes maintains coadapted
alleles within inversions so that favorable combinations are held in
cis. Early studies (e.g., Dobzhansky and Epling 1948) confirm
that recombination is highly suppressed in inversion heterozygotes,
but the data suggest a possible meiotic drive mechanism that has been
overlooked in the literature for over a half of a century. Due to the
paucity of markers used in these early studies it is difficult to
quantify the degree that recombination is suppressed by inversions.
Also, these studies relied on phenotypic markers that may cause
decreased fitness of certain phenotypic classes. To gain a more fine
scale understanding of recombination in inversion heterozygotes and to
overcome the problems associated with phenotypic markers in studying
meiotic drive, we propose using microsatellite markers to study both
of these phenomena.
References:
Dobzhansky, T., and C. Epling. 1948. The suppression of crossing over
in inversionheterozygotes of Drosophila pseudoobscura. Proc.
Natl. Acad. Sci. USA 34:137-141.
Schaeffer, S. W., M. P. Goetting-Minesky, M. Kovacevic, J. R. Peoples,
J. L. Graybill, J. M. Miller, K. Kim, J. G. Nelson, and W. W.
Anderson. 2003. Evolutionary genomics of inversions in Drosophila
pseudoobscura: evidence for epistasis. Proc. Natl. Acad. Sci. USA
100:8319-8324.
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10/13/04 |
Speaker:
Dietmar Schwarz
- Department of Biology
Title:
Speciation via
hybridization in a specialist insect is triggered by the shift to a
new host
Abstract:
Hybridization has long been regarded as an important
source of evolutionary novelty in plants. Zoologists, in contrast,
have regarded hybridization merely as an artifact of incomplete
reproductive isolation. Especially the formation of new animal species
via hybridization has been deemed highly unlikely (unless it results
in parthenogenetic, polyploid taxa). Here I present the first case of
hybridization in an insect that has resulted in an isolated, diploid
and bisexually reproducing population. I discovered the infestation of
invasive honeysuckle, Lonicera spp., by flies belonging to the
R. pomonella species complex (Diptera: Tephritidae). Because
all members of this species complex are native to North America, the
infestation of Lonicera has to be the result of a recent host
shift. Multilocus nuclear genotypes and mitochondrial DNA sequences
suggested that the Lonicera Fly originated via hybridization
between the blueberry maggot R. mendax and the snowberry maggot
R. zephyria. I tested a hybrid origin of the Lonicera
Fly against the competing hypotheses of a single species host shift
and incomplete lineage sorting. The same data also provide indirect
evidence for the reproductive isolation of the Lonicera Fly
from its parent taxa.This unique combination of host shift and
hybridization suggests sympatric speciation via host shift as the
mechanism by which the hybrid Lonicera Fly formed. I discuss
how the increased phenotypic variability of hybrid origin populations
could facilitate adaptive speciation. Based on the example of the
Lonicera Fly I propose the concept “biological metaspecies,” that
describes a group of sibling species that are connected by some degree
of hybridization. While under most circumstances gene flow between the
taxa of the metaspecies is of little consequence, hybridization can
provide novel genetic variation to adapt to a change in the
environment, such as the introduction of a new host plant.
Reference:
Vie, S. 2001. Sympatric speciation in animals: the ugly duckling grows
up. Trends Ecol. Evol.16:381-390.
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10/20/04 |
Speaker:
Dr. Claude dePamphilis
- Department of Biology
Title: Origin and diversification of the floral regulators in
the earliest angiospersms
Abstract: The
sudden appearance of flowers in the fossil record about 100 million
years ago represents a great mystery that has long puzzled
evolutionary biologists. Among the many key questions surrounding
the origin diversification of flowers include: Did the ancestral
flower possess the full complement of genetic information needed to
assemble a modern flower? Are there genes that have conserved
functions throughout much of flowering plant history? What components
of genetic diversity cause the important variation in flower diversity
that we see today? Recent studies in plant developmental genetics and
genomics have identified more than 100 genes with specific roles in
flower development in Arabidopsis and other model organisms,
and any other genes with critical roles may remain undiscovered,
largely because of functional redundancy or lethality of loss of
function mutations.
The Floral Genome Project (www.floralgenome.org)
was initiated to address these questions by identifying the origin and
studying the evolutionary diversification of floral regulators
throughout the major lineages of flowering plants. Our study was
designed to capture large numbers of genes expressed during early
flower development in phylogenetically critical lineages of flowering
plants and gymnosperms, and to determine their expression patterns at
several levels of resolution. We then link the sequences and
expression patterns through phylogenetic analysis to infer the gene
sets and expression patterns that may have been present in the
earliest angiosperm lineages. This talk will summarize some of the
results coming from over 70,000 EST sequences that tag homologs of
most genes known to be important in flower development. Among our
observations to date: 1) The floral transcriptome is similarly large,
and estimated to contain over 10,000 expressed genes, in basal as well
as more derived dicot and monocot model organisms. 2) Most key genes
playing known roles flower development have homologs present in basal
angiosperm lineages and may be inferred to be part of the ancestral
floral transcriptome. 3) genome doubling (polyploidy) appears to be
a common process in plant genomes, including these most basal
lineages, meaning that uniquely orthologous genes may be relatively
uncommon, 4) consistent with the above, specific genes of known
function are often the product of one or more gene duplications that
separate basal lineages from more derived eudicot and grass models.
I will illustrate these findings with a summary of several case
studies involving MADS box genes, which are critical regulators of
flower form, as well as several other gene families with genes
important in flower development.
References:
Ma,
H. and C. W. dePamphilis. 2000. The ABCs
of flower evolution. Cell 101:5-8.
The Floral Genome Project Research Group. 2002. Missing
Links: The genetic architecture of the flower and flower
diversification. Trends In Plant Science 7:22-31.
Baum, D. A., J. Doebley, V. F. Irish, E. M. Kramer. 2002.
Response: Missing links: the genetic architecture of flower and
floral diversification. Trends in Plant Science 7: 31-33.
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10/27/04 |
Speaker:
Jongmin Nam
- Department of Biology
Title:
Evolution of homeobox gene
family controlling fundamental processes of animal development.
Abstract: Homeobox genes are important transcription factors
regulating various processes of animal development. Therefore, study
of the evolution of homeobox genes is helpful for understanding the
evolutionary changes of morphological and physiological characters. To
this end we compiled 1699 homeodomain sequences from 11 completely or
almost completely sequenced genomes (humans, rodents, frogs, fishes,
tunicates, insects, and nematodes). We then performed a phylogenetic
analysis of these sequences and studied the increase and decrease of
the number of homeobox genes in the evolutionary process. Our analysis
showed that there were at least 71 homeobox genes in the most recent
common ancestor (MRCA) of all of the 11 species. Our further
phylogenetic analysis suggested that (1) the number of the descendents
of these 71 genes increased substantially in the vertebrate lineage,
but the increase was moderate in other lineages such as nematode,
insects, and tunicate, (2) the gene number increase was most dramatic
in the early stage of insect and vertebrate evolution, (3) although
the total number of descendents of 71 ancestral genes increased in
each genome, a substantial number of genes were lost in all
evolutionary lineages, (4) in contrast to the unequal rate of increase
of gene number among different evolutionary lineages, the numbers of
losses of descendents of the 71 ancestral genes were similar among the
11 species, and (5) at least 20 ~ 30 genes out of 71 ancestral genes
were lost in each genome. We also studied the increase and decrease of
gene number for different groups of homeobox genes and found that most
groups show similar patterns of increase and loss of genes, though
there are several exceptions. Biological implication of these
evolutionary changes of homeobox genes will be discussed.
References:
Wagner G. P., Amemiya C., Ruddle F. (2003) Hox cluster
duplications and the opportunity for evolutionary novelties. Proc.
Natl. Acad. Sci. USA. 100(25):14603-6.
Banerjee-Basu S., Baxevanis A. D. (2001) Molecular evolution of the
homeodomain family of transcription factors. Nucleic Acids Res.
29(15):3258-69.
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11/03/04 |
Speaker:
Indrani Halder
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Department of Biology
Title: Analyzing
individual BioGeographical ancestry and Admixture structure in human
populations
Abstract:
Understanding genetic variation in populations and how this variation
contributes to differences in disease risk among populations is an
important area of research. We have typed a panel of 11,555 SNP
markers in three resident US populations, (African Americans, Puerto
Ricans and European Americans) in an effort to analyze patterns of
genetic variability. The first two are considered admixed populations
with varying levels of BioGeographical ancestry (BGA), while the
European Americans are assumed to be more homogeneous. Putative
ancestral populations were chosen from among a panel of twelve world
populations typed for the same markers. Using a maximum likelihood
based method and a separate Bayesian method we show that individual
BGA estimates vary within all groups. Assuming a trihybrid model of
admixture between Europeans, West Africans and Native Americans we
observed large variations in individual BGA levels in both the
African-American and Puerto Rican samples, while the European
Americans are more tightly clustered. Additional simulation studies
were done to check the reliability of the estimates under the
specified model. Simulations further indicate that the choice of
ancestral population and its sample size both affect individual BGA
estimates. To test for stratification within the population samples we
have used the Individual Ancestry Correlation (IAC) test, where
markers are split into two non-overlapping subsets and ancestry is
estimated separately with both sets. Correlation between estimates
obtained with the different marker sets indicates presence of genetic
structure. While both the African-American and the Puerto Rican
samples show admixture stratification as expected, we also detected
evidence for stratification within the European-American sample.
Additional simulations showed that individual BGA estimates differed
when only a subset of informative markers was used as opposed to
including all markers.
References:
Bonilla C, Shriver MD, Parra EJ, Jones A, Fernandez JR. Ancestral
proportions and their association with skin pigmentation and bone
mineral density in Puerto Rican women from New York City.
Hum Genet. 2004 Jun;115(1):57-68.
Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM. Design
and analysis of admixture mapping studies. Am J Hum Genet. 2004
May;74(5):965-78.
Halder I; Shriver M.D. Measuring and using admixture to study the
genetics of complex diseases. Human Genomics, November 2003, vol. 1,
no. 1, pp. 52-62(11).
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11/10/04 |
Speaker:
Dr.
Kazuhiko Kawasaki
- Department of Anthropology
Title: Molecular
evolution of vertebrate mineralized skeleton.
Abstract:
Mineralized skeleton is a critical innovation for the adaptive
evolution of vertebrates. Paleozoic jawless fish developed extensive
body armor consisting of three tissue layers: surface enameloid
(enamel-like hard tissue), dentin, and basal bone. Three similar
tissues are seen in mammalian teeth, suggesting their ancient origin.
We have revealed that eight mammalian genes for enamel, dentin, and
bone matrix proteins arose by gene duplication from an ancestral gene,
SPARC. In addition, mammalian milk caseins, salivary proteins,
and an avian eggshell protein are also the relatives of these
proteins, and all form the secretory calcium-binding phosphoprotein (SCPP)
family. Notably, our analysis suggested that most SCPPs arose during
the evolution of the lobe-finned fish. This suggests that the
mechanism of tissue mineralization was considerably modified by
parallel functional specialization of duplicated SCPP genes
facilitating adaptive evolution in our lineage after the divergence of
rayfins and lobefins.
References:
Kawasaki, K. and Weiss, K. M. 2003.
Mineralized tissue and vertebrate evolution: The secretory
calcium-binding phosphoprotein gene cluster. Proc. Natl. Acad. Sci.
USA. 100: 4060-4065.
Kawasaki, K., Suzuki, T., and Weiss, K. M. 2004. Genetic basis for the
evolution of vertebrate mineralized tissue. Proc. Natl. Acad. Sci.
USA. 101: 11356-11361.
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11/17/04 |
Speaker:
Dimitra Chalkia
- Department of Biology
Title: Phylogenetic
Analysis of the Formin Homology 2 Domain in Metazoa
Abstract:
Formins are multidomain
proteins which are implicated in a wide range of actin-based
processes, including cell polarization, cytokinesis, and embryonic
development in all eukaryotic species studied so far. The most
conserved segment of formins is the formin homology-2 (FH2) domain,
which is crucial for actin nucleation. FH2 domain can be divided in
five subdomains, namely lasso, linker, knob, coiled-coil, and post.
Athough, six different formin protein subfamilies have been so far
described, there is no comprehensive understanding of the actual
number of genes encoding for the FH2 domains in different metazoan
genomes. Here, we describe several novel proteins containing FH2
domains from 13 metazoan species and investigate their evolutionary
relationships.
Our results show that metazoan formins can be classified into eight
monophyletic groups. Two novel groups, form4 and form5, were
identified, which are chordate-specific and nematode-specific,
respectively. All the metazoan formins evolved sequentially from a
common ancestor following the model of divergent evolution. Post
subdomain is highly conserved, while linker is the least conserved
region both within and between the eight formin groups. Amino acid
residues that directly or indirectly have been implicated in the
function of formins are conserved in all groups, suggesting that all
proteins most likely function in a similar manner. The remaining
residues show group-specific conservation, which could imply
functional specificity. Our analyses predict that metazoan formins
should share the same mechanism of function and furthermore that the
different groups might show functional specificity. The latter could
also be true for some of the paralogous sequences.
References:
Wallar, B. J., and Alberts, A. S. 2003. The formins: active scaffolds
that remodel the cytoskeleton. Trends Cell Biol. 13,
435-446.
Xu, Y. Moseley, G. B., Sagot, I., Poy, F., Pellman, D., Goode, B. L.,
and Eck, M. J. 2004. Crystal structures of a formin homology-2 domain
reveal a tethered dimer architecture. Cell 116, 711-723.
Zigmond, S. H. 2003. Fomin-induced nucleation of actin filaments.
Curr. Opin. Cell Biol. 16, 1-7.
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11/24/04 |
NO SEMINAR - THANKSGIVING
HOLIDAY |
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12/01/04 |
Speaker:
Dr.
Nikolas Nikolaidis
- Department of Biology
Title: Origin
and evolution of the Ig-like domains present in mammalian leukocyte
receptors.
Abstract: In
mammals many natural killer (NK) cell receptors encoded by the
leukocyte receptor complex (LRC) regulate the cytotoxic activity of NK
cells and provide protection against virus-infected and tumor cells.
To investigate the origin of the Ig-like domains encoded by the LRC
genes, a subset of C2-type Ig-like domain sequences was compiled from
mammals, birds, amphibians, and fish. Phylogenetic analysis of these
sequences generated several monophyletic groups. Two main conclusions
can be drawn from the phylogenetic relationships between the major
groups. First, the two groups of mammalian LRC sequences must diverged
before the separation of the avian and mammalian lineages. Second, the
mammalian LRC sequences are most closely related to the Fc receptor
sequences and these two groups diverged before the separation of birds
and mammals.
References:
Dennis G Jr, Kubagawa H, Cooper MD (2000) Paired Ig-like receptor
homologs in birds and mammals share a common ancestor with mammalian
Fc receptors. Proc Natl Acad Sci U S A 97:13245-13250
Hao L, Nei M (2004) Rapid expansion of Killer Cell Immunoglobulin-like
Receptor genes in primates and their coevolution with MHC Class I
genes. Gene in press.
Hughes AL, Nei M (1988) Pattern of
nucleotide substitution at major histocompatibility complex class I
loci reveals overdominant selection. Nature 355:167-170.
Martin AM, Kulski JK, Witt C, Pontarotti P, Christiansen FT (2002)
Leukocyte Ig-like receptor complex (LRC) in mice and men. Trends
Immunol 23:81-88
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12/08/04 |
Speaker:
Jill Ricker
- Department of Biology
Title: Strong
evidence for expression pattern shifts driving the maintenance of
duplicated regulatory genes in Arabidopsis
thaliana
Abstract:
Whole genome duplication is common in flowering plants,
with at least one detectable genome duplication in 50-70% of species.
This study examines the frequency of expression pattern shifts
representing subfunctionalization and/or neofunctionalization in
maintained duplicated regulatory genes. 280 paralogous pairs in
Arabidopsis were identified using phylogenetic trees of
Arabidopsis and rice amino acid sequences for 91 regulatory gene
families. A two-way ANOVA was performed to identify significance of
gene, tissue, and gene by tissue interaction effects within each
paralogous pair using microarray data from six wild-type tissues.
Results indicate that 85% of paralogous pairs have statistically
significant gene by tissue interactions; this is indicative of
subfunctionalization and/or neofunctionalization. Ka/Ks
analyses for global protein constraint indicate that there is no
relationship between the Ka/Ks ratio and a
significant gene by tissue interaction. We conclude that expression
pattern shifts drive maintenance of duplicated genes in Arabidopsis
regulatory gene families.
References:
Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y. L. &
Postlethwait, J. (1999) Genetics 151, 1531-1545.
Blanc, G. & Wolfe, K. H. (2004) Plant Cell 16, 1679-1691.
Makova, K. D. & Li, W. H. (2003) Genome Research 13, 1638-1645.
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