|
Date |
Speaker and title of seminar |
09/06/06 |
Speaker:
Dr.
Stephen W. Schaeffer- Department of Biology
Title: Chromosomal
Rearrangement during the Evolution of Drosophila Genomes
Abstract: Seven
of the 12 Drosophila genomes that have recently been
sequenced provide an opportunity to understand the process of
chromosomal rearrangement because substantial changes in gene
order have taken place. This talk will focus on the method of
linkage chain analysis to infer the number of chromosomal
inversion occurring on various Drosophila lineages. This
method examines the information at conserved linkage group
boundaries to link breakpoints that have been involved in
paracentric inversions. The distribution of breakpoints within
linkage chains provide a more accurate estimate of the total
number of inversions that have occurred down different
Drosophila lineages. The use of breakpoint information from
outgroup species allows the ancestral states of each inversion
breakpoint to be determined between a pair of species. The
ancestral states can then be used to infer the gene order of the
common ancestral species. As an example, a complete linkage chain
analysis of the six chromosomes between D. melanogaster and
D. pseudoobscura will be presented. The data show that
while there is not a significant difference in the rate of
rearrangement between the two species, several chromosomes show
significant differences in inversion rates. Simulations of the
rearrangement process show that breakpoints are nonrandomly
re-used. I will briefly discuss the implications of genomic
comparison data between D. pseudoobscura and D.
persimilis to models of chromosomal speciation.
References:
RICHARDS,
S.,
Y.
LIU,
B.
R.
BETTENCOURT,
P.
HRADECKY,
S.
LETOVSKY,
R.
NIELSEN,
K.
THORNTON,
M.
A.
TODD,
R.
CHEN,
R.
P.
MEISEL,
O.
COURONNE,
S.
HUA,
M.
A.
SMITH,
H.
J.
BUSSEMAKER,
M.
F.
V. BATENBURG,
S.
L.
HOWELLS,
S.
E.
SCHERER,
E.
SODERGREN,
B.
B.
MATTHEWS,
M.
A.
CROSBY,
A.
J.
SCHROEDER,
D.
ORTIZ-BARRIENTOS,
C.
M.
RIVES,
M.
L.
METZKER,
D.
M.
MUZNY,
G.
SCOTT,
D.
STEFFEN,
D.
A.
WHEELER,
K.
C.
WORLEY,
P.
HAVLAK,
K.
J.
DURBIN,
A.
EAGAN,
R.
GILL,
J.
HUME,
M.
B.
MORGAN,
Y.
HUANG,
L.
WALDRON,
D.
VERDUZCO,
K.
P.
BLANKENBURG,
H.
ROBERTSON,
I.
DUBCHAK,
M.
A.
F.
NOOR,
W.
W.
ANDERSON,
K.
WHITE,
A.
G.
CLARK,
S.
W.
SCHAEFFER,
W.
M.
GELBART,
G.
WEINSTOCK
and R.
A.
GIBBS,
2005 Comparative genome sequencing of Drosophila pseudoobscura:
Chromosomal, gene and cis-element evolution. Genome Res.
15: 1-18.
NOOR,
M.
A.,
K.
L.
GRAMS,
L.
A.
BERTUCCI
and J.
REILAND,
2001 Chromosomal inversions and the reproductive isolation of
species. Proc. Natl. Acad. Sci. USA 98: 12084-12088.
PEVZNER,
P.,
and G.
TESLER,
2003 Human and mouse genomic sequences reveal extensive breakpoint
reuse in mammalian evolution. Proc. Natl. Acad. Sci. USA 100:
7672-7677.
SANKOFF,
D.,
and P.
TRINH,
2005 Chromosomal breakpoint reuse in genome sequence
rearrangement. J Comput Biol 12: 812-821. |
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09/13/06 |
Speaker:
Dr. Mark Shriver- Department of Anthropology
Title: The
Genetic Architecture of Normal Variation in Human
Pigmentation: An
Evolutionary Perspective and Model
Abstract: Skin
pigmentation varies substantially across human populations in a
manner largely coincident with ultraviolet radiation intensity. This
observation suggests that natural selection in response to sunlight
is a major force in accounting for pigmentation variability. We review
recent progress in identifying the genes controlling this
variation with a particular focus on the trait's evolutionary past and
the potential role of testing for signatures of selection in aiding
the discovery of functionally important genes. We have analyzed SNP data
from the International HapMap project in 77 pigmentation candidate
genes for such signatures. Based on these results and other
similar work, we provide a tentative three population model
(West Africa, East Asia and North Europe) of the
evolutionary-genetic architecture of human pigmentation. These results suggest a
complex evolutionary history with selection acting on different gene
targets at different times and places in the human past. Some candidate
genes may have been selected in the ancestral human population,
others in the 'out of Africa' proto European-Asian
population, while most
appear to have selectively evolved solely in either Europeans or
East Asians separately despite the pigmentation similarities between
these two populations. Selection signatures can
provide important
clues to aid gene discovery. However, these should be viewed as
complements, rather than replacements of, functional studies including
linkage and association analyses, which can directly
refine our
understanding of the trait.
References:
STILL IN PRESS
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09/20/06 |
Speaker:
Dr. Jamie Blair- Plant Pathology - CANCELLED
Title:
Abstract:
References: |
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09/27/06 |
Speaker:
Dr. Helen Piontkivska- Department of Biology
-Kent State University
Title: "Host-pathogen
interactions and sequence changes: evolution of CTL and
antibody epitopes in
Human Immunodeficiency Virus (HIV-1)"
Abstract: In
human immunodeficiency virus (HIV), mutations that escape from
cytotoxic T-lymphocyte (CTL) recognition have been documented, and
sequence analyses have provided indirect support for the
hypothesis that natural selection has favored CTL escape mutants
within an infected host. Similarly, neutralization of virus
particles by antibodies may also be contributing factor shaping
the evolution of the virus. However, the relative contribution of
these two aspects of the host immune response to selection on
proteins of HIV-1 and related viruses remains unclear. Our
analyses of sequence data from the nine protein-coding genes of
HIV-1 showed striking differences in evolutionary pattern between
epitopes for host neutralizing antibodies (Ab) and epitopes for
CTL. Our results showed that the greatest median amino acid
residue diversity was seen at sites that formed part of Ab
epitopes, but not of CTL epitopes. By contrast, sites belonging to
CTL epitopes but not to Ab epitopes showed reduced median amino
acid sequence diversity not only in comparison to sites in Ab
epitopes but also in comparison to non-epitope sites. Further, Ab
epitopes that did not overlap CTL epitopes showed the highest
frequency of comparisons in which the rate of nonsynonymous (amino
acid-altering) nucleotide substitution exceeded that of synonymous
nucleotide substitution, supporting the hypothesis that much of
the diversity at Ab epitopes results from positive selection
exerted by the host immune system. Though less frequent than that
at Ab epitopes, there was evidence of such selection at certain
CTL epitopes as well; and amino acid differences between sister
pairs of sequences in CTL epitopes were more likely to be
convergent than those in Ab epitopes. The pattern seen at CTL
epitopes may represent the result of conflicting pressures
favoring conservation of the amino acid sequence for functional
reasons and amino acid replacements for reasons of CTL escape.
References:
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10/04/06 |
Speaker:
Dr.
Cooduvalli Shashikant ~ Dairy and Animal Science Depart.
Title: "Comparative
cis-regulatory analysis of a vertebrate Homeobox gene"
Abstract:
The
Hoxc8 early enhancer
is a 200 bp cis-regulatory region that controls initiation and
establishment phase of Hoxc8
expression
during mouse embryonic development. The
Hoxc8 early enhancer
comprises nearly a dozen elements identified by comparative
studies and mutational analysis in transgenic mouse embryos.
Comparative study shows a remarkably plasticity in the
Hoxc8 early enhancer
activity. Species specific variation in its sequence and elemental
composition is reflected in differences in their enhancer
activities when assayed in transgenic mouse embryos. The
Hoxc8 early enhancer
determines reporter gene expression by two distinct mechanisms.
One that determines tissue-specific expression and a second
determines the anterior extent of expression. Transcription
factors that are likely to regulate
Hoxc8 expression
include members of the Cdx,
forkhead, Lef1/Tcf, Smad and
Hox families. Among
these, Cdx2 is a
strong candidate to regulate
Hoxc8 early enhancer activity.
Cdx2 protein can bind
to two distinct elements within the enhancer. Its spatiotemporal
expression pattern is consistent with the early phase of
Hoxc8 expression.
Comparison of Hoxc8
and Cdx2 regulation
suggests that they both respond to posteriorizing signals.
Furthermore, cis-regulatory analysis of
Cdx2 reveals the
presence of positive-negative regulatory elements that control
Cdx2 expression.
Taken together these studies will present a model for a posterior
determination mechanism active during mouse embryonic development.
References:
Shashikant C.S.,
S.A. Bolanowski,
S. Anand, and S.M. Anderson. Comparisons of diverged vertebrate
Hoxc8 early
enhancer activities reveal modification of regulatory interactions
at conserved cis-acting elements
Submitted.
Wang,
W.C.H. and C.S. Shashikant.
Evidence for positive and negative regulation of the mouse Cdx2
gene. Submitted.
Shashikant C.,
S.A. Bolanowski, J. Danke, and C.T. Amemiya. Hoxc8
early enhancer of the Indonesian coelacanth,
Latimeria menadoensis.
J.Exp.Zool. Mol.Dev.Evol.
302, 557-563, 2004.
Wang, C.H.W.,
S. Anand, D.R. Powell, A.B. Pawashe, C.T. Amimiya, and C.S.
Shashikant.
Comparative cis-regulatory analysis identify new elements of the
mouse Hoxc8 early enhancer.
J.Exp.Zool. Mol.Dev.Evol. 302, 436-445, 2004. |
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10/11/06 |
Speaker:
Dr. Kazuhiko Kawasaki - Department of Anthropology
Title: Gene
duplication and the evolution of vertebrate skeletal
mineralization
Abstract:
The mineralized
skeleton is a critical innovation that evolved early in vertebrate
history. The tissues found in dermal skeletons of ancient
vertebrates are similar to the dental tissues of modern
vertebrates; both consist of a highly mineralized surface hard
tissue, enamel or enameloid, more resilient body dentin, and basal
bone. These tissues all form on distinct sets or compositions of
protein matrix. Many genes coding these proteins are
evolutionarily related and form the secretory calcium-binding
protein (SCPP) gene family. We hypothesize here the duplication
histories of these SCPP genes, and their common ancestors,
SPARC and SPARCL1. At around the same time that
Paleozoic jawless vertebrates first evolved mineralized skeleton,
SPARCL1 arose from SPARC by whole genome
duplication. Then both before and after the split of ray-finned
fish and lobe-finned fish, tandem gene duplication created two
types of SCPP genes, each residing on the opposite side of
SPARCL1 on the same chromosome. One type of these genes was
subsequently used in surface tissue and the other in body tissue.
In the tetrapod lineage after the divergence from amphibians,
these two types of SCPP genes were separated by intrachromosomal
rearrangement. Subsequently, SCPP genes were co-opted for use by
milk, saliva, and eggshell. While new SCPP genes arose by
duplication, some old genes were eliminated from the genome. As a
consequence of this birth-and-death process, phenogenetic drift
can occur: while mineralized skeleton is maintained by natural
selection, the underlying genetic basis has drifted. The
different genes used for mineralized tissues may partly explain
the variation of ancient mineralized tissues. Many SCPP genes
present in our genome today arose as redundant genes that survived
and diversified through the adaptive evolution of vertebrate
mineralization.
References:
Kawasaki, K. and Weiss,
K. M. Evolutionary genetics of
tissue mineralization: the origin and evolution of the secretory
calcium-binding phosphoprotein family. J. Exp. Zool.
(Mol. Dev. Evol.) 306B, 295-316, 2006.
Kawasaki, K., Suzuki, T., and
Weiss, K. M. Phenogenetic drift in evolution: the changing
genetic basis of vertebrate teeth. Proc. Natl. Acad.
Sci. USA. 102, 18063-18068,
2005.
Kawasaki, K., Suzuki,
T., and Weiss, K. M. Genetic basis for the evolution of
vertebrate mineralized tissue. Proc. Natl. Acad. Sci. USA.
101, 11356-11361, 2004.
Kawasaki, K. and Weiss,
K. M. Mineralized tissue and vertebrate evolution: The secretory
calcium-binding phosphoprotein gene cluster. Proc. Natl. Acad.
Sci. USA. 100, 4060-4065, 2003. |
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10/18/06 |
Speaker:
Dr.
Paula McSteen -
Department of Biology
Title: Genetic
and hormonal regulation of inflorescence development in maize
Abstract:
Unlike
animals, which make organs during embryogenesis, plants make
organs throughout their lifetime through the action of meristems.
My lab focuses on axillary meristems, which give rise to branches
and flowers and therefore play a fundamental role in plant
architecture and reproduction. We aim to understand how
axillary meristems initiate using maize which is a model system as
it produces multiple types of axillary meristem in the
inflorescence.
We have shown that auxin (a plant growth hormone) is required for
axillary meristem initiation in maize as treatment of plants with
inhibitors of auxin transport blocks initiation of axillary
meristems. The phenotype of plants treated with auxin transport
inhibitors bears striking resemblance to a large class of mutants
in maize, called “barren inflorescence”. We have taken a genetic
approach to identify the genes regulating auxin transport and
perception by characterizing and cloning the mutants in this
class. One of these mutants is barren inflorescence2 (bif2)
which makes fewer branches, spikelets and ear shoots due to
defects in the initiation of axillary meristems. The bif2
gene encodes a serine/threonine protein kinase which is conserved
in monocots and dicots. We are identifying additional genes
required for axillary meristem initiation by identifying proteins
that interact with BIF2. One of the proteins BIF2 interacts with
and phosphorylates is a transcription factor which is specific to
monocots. Therefore, although bif2 sequence and expression
are conserved between monocots and dicots, at least one of its
putative downstream targets may have diverged.
References:
P. McSteen (2006)
Branching out: The ramosa pathway and the evolution of
grass inflorescence morphology. Plant Cell, 18: 518-522.
P. McSteen, O. Leyser
(2005) Shoot branching. Annual Review of Plant Biology, 56:
353-374. |
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10/25/06 |
Speaker:
Kerr Wall -
Department of Biology
Title:
Ultrahigh-throughput transcriptome tagging using pyrosequencing
technology
Abstract: Over the last year, pyrosequencing technology has
been used to sequence
microbial and
organelle genomes, as well as small RNA libraries. A first
study has recently
been reported using this same technology to sequence cDNA
libraries. We report
results from several plates of pyrosequenced
transcripts from a
model plant species, Arabidopsis thaliana, and a
non-model basal
eudicot, Eschscholzia californica (California poppy). We
also discuss the
implications of this new technology for transcriptome
sequencing as well as
the advantages and disadvantages over traditional
capillary-based cDNA
sequencing.
References:
Margulies et al
(2005). Genome sequencing in microfabricated high-density
picolitre reactors.
Nature. Sep 15;437(7057):376-80.
Bainbridge et al
(2006). Analysis of the prostate cancer cell line LNCaP
transcriptome using a
sequencing-by-synthesis approach. BMC Genomics. Sep
Moore et al (2006).
Rapid and accurate pyrosequencing of angiosperm plastid
genomes. BMC Plant
Biol. Aug 25;6:17.
Goldberg et al
(2006). A Sanger/pyrosequencing hybrid approach for the
generation of
high-quality draft assemblies of marine microbial genomes.
PNAS. Jul
25;103(30):11240-5.
Poinar et al (2006)
Metagenomics to paleogenomics: large-scale sequencing of
mammoth DNA. Science.
Jan 20;311(5759):392-4.
Lu C et al (2006).
MicroRNAs and other small RNAs enriched in the
Arabidopsis
RNA-dependent RNA polymerase-2 mutant. Genome Res.
Oct;16(10):1276-88.
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11/01/06 |
Speaker:
Dr. Veronica Hinman- Department of Biology,
Carnegie Mellon University
Title: Regulatory
Gene Network Evolution in Echinoderms
Abstract:
We
are undertaking an evolutionary comparison of the gene regulatory
network (GRN) architectures that control specification in sea
urchin and sea star embryos. The extensive analysis of a GRN in
sea urchins has provided a unique opportunity for a comparative
investigation to elucidate mechanism of evolution at this level.
We would like to answer questions such as, which features of a
regulatory network are conserved, how are changes incorporated
into a GRN, and how do these changes relate to the evolution of
morphology? The sea star Asterina miniata has been
developed as an ideal experimental model for this analysis.
Gametes are readily available and gene transfer and perturbation
of gene products have been performed. Sea stars last shared a
common ancestor with sea urchins around 500 million years ago, in
the Upper Cambrian. They appear to be at an ideal evolutionary
distance for meaningful comparisons since they share many
conserved aspects in their development and yet there exist
specific morphological differences.
We have previously shown that a common
developmental feature of sea star and sea urchin GRNs is the use
of an orthologous three gene positive regulatory feedback loop
that serves to ‘lock down’ gene expression required for the
specification of the endoderm and thus to drive development
forward. The conservation of this feature across the immense
period of evolutionary time such as separates these echinoderms
demonstrates the indispensable nature of this process in their
development. Several differences were also noted in the GRN
architecture. For example, tbrain (tbr) is
incorporated into the endomesoderm-specification network in the
sea star while it is involved in skeletal lineage specification in
sea urchins.
The comparative GRN
analysis has been continued by asking how (in terms of GRN
reorganization) tbr has been co-opted for use in
skeletogenesis in sea urchins. In this analysis it was shown that
the otx gene, although conserved in expression and
function, is regulated by Tbr in the sea star but not the sea
urchin. As a logical extension of this work, an extensive
comparison of the cis regulatory control module of the
otx gene in the two taxa was performed. We are able to
demonstrate how the evolution of function of the tbr gene
is encoded in the cis regulatory module of a target gene.
These new data will be discussed.
References:
Larroux, C., Fahey, B., Liubicich, D., Hinman, V. F., Gauthier,
M., Gongora, M., Green, K., Worheide, G., Leys, S. P. and Degnan,
B. M. (2006)Developmental expression
of transcription factor genes in a demosponge: insights into the
origin of metazoan multicellularity. Evol. Dev. 8(2):150-173.
Otim,
O., Hinman, V. F., and Davidson, E. H.
(2005)Expression of AmHNF6, a sea star
orthologues of a transcription factor with multiple distinct roles
in sea urchin development. Gene Expr Patterns. 5:381-386.
Hinman,
V. F., Nguyen, A. T., Cameron, R. A. and Davidson, E. H.
(2003). Developmental gene regulatory network architecture across
500 million years of echinoderm evolution. Proc Natl Acad Sci U
S A 100, 13356-61.
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11/08/06 |
Speaker:
Dr. Masafumi Nozawa
- Department of Biology
Title: Evolutionary
stability of the number and the repertoire of olfactory receptor
genes in Drosophila species
Abstract: Olfactory
receptor (OR) genes play an important role in olfaction and are
essential for animals to find desirable items and to avoid
dangers. We have identified all OR genes in the draft genome
sequences of 12 Drosophila species by bioinformatic methods
and investigated their evolutionary dynamics using phylogenetic
analysis. The results have shown that there have been frequent
gene gain and loss events during the Drosophila evolution,
suggesting birth-and-death evolution. Many recent gene
duplication events occurred in tandem, indicating that unequal
crossing over would be a major mechanism for gene duplication. On
the other hand, chromosomal rearrangements and translocations have
contributed to establish the genome-wide distribution of OR genes,
since the chromosomal positions of orthologous genes were
substantially different among distantly related species. In spite
of these gene gain and loss events, all species examined have a
similar number (51-66 genes) and repertoire of functional OR
genes. Estimating the numbers of OR genes in ancestors for these
species, we found that the ancestral species also had similar
numbers of OR genes compared to the extant species. In addition,
all clades defined in a phylogenetic tree already existed in the
ancestral species. These results suggest that the number and the
repertoire of OR genes have been stable during the Drosophila
evolution, which is in contrast to the evolutionary dynamics of
the mammalian OR genes. Mechanisms that keep the number and the
repertoire of Drosophila OR genes small and stable will be
discussed.
References:
Niimura, Y., and
M. Nei. 2005. Evolutionary dynamics of olfactory receptor genes in
fishes and tetrapods. Proc. Natl. Acad. Sci. USA 102: 6039-6044.
Robertson, H.
M., and K. W. Wanner. 2006. The chemoreceptor superfamily in the
honey bee Apis mellifera: expansion of the odorant, but not
gustatory, receptor family. Genome Res. 16 In press. |
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11/13/06 |
Speaker:
Dan Hartl- Higgins Professor of Biology Harvard
University -Marker Lecture
8:00 PM 104 Keller Bldg.
Title: Overwhelming
odds against the less fit: Evidence for positive selection in
protein evolution.
Abstract:
Short description:
Analysis of DNA sequence variation within and between species
confirms that many amino acid polymorphisms are deleterious, that
some deleterious polymorphisms can become fixed, but that the
majority of amino acid replacements are probably driven by weak
positive selection. Some explanations are suggested.
References: |
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11/14/06 |
Speaker:
Dan Hartl- Higgins
Professor of Biology Harvard University- Marker Lecture
12:00 PM 117 HUB Auditorium
Title: Transcriptional
variation and plasticity in the yeast genome.
Abstract:
Transcriptional plasticity refers to changes in the level of
transcription that take place in response to changes in the
environment. Although a great deal is known about the
transcriptome of laboratory yeast (S. cerevisiae) and its
response to environmental changes, relatively little is known
about either transcriptional plasticity or GEI for transcriptional
plasticity among genetically diverse natural isolates. We have
studied genome-wide patterns of gene expression in six natural
isolates grown in each of four different environments representing
a continuum of rich and poor nutritional conditions. We have also
identified a single-gene difference segregating in natural
populations that is associated with increase in transcription of
about 150 genes and a decrease in transcription of about 200
genes. Evidence is presented that the polymorphism responsible for
these manifold physiological effects is in a gene that encodes a
major sensor of the external nutritional environment.
References: |
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11/22/06 |
Speaker:
THANKSGIVING HOLIDAY BREAK~ NO
SEMINAR
Title:
Abstract:
References: |
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11/29/06 |
Speaker: Yogeshwar Kelkar
-
Department of Biology
Title: Factors
affecting microsatellite mutability inferred from human-chimpanzee
genomic alignments
Abstract:
Microsatellites,
tandemly repeated nucleotide sequences of small motifs (1-6 bp),
are ubiquitous in eukaryotic genomes. They undergo rapid change in
their length due to insertion or deletion of one or multiple basic
repeat units. Though these repeats are simple, their mutational
mechanism is not very well understood. Microsatellite mutations
take place at very high rates, as high as 10-4 to 10-3 mutational
events per cell per replication in humans. Some of these repeats
are very unstable and responsible for more than 40 known
neurological, neurodegenerative, and neuromuscular disorders;
though only certain trinucleotide repeats are responsible for most
of these disorders.
It is now widely accepted that number of repeats in a
microsatellite is an important determinant of mutation rate in the
sense that longer microsatellites mutate faster, although there is
no clear consensus over the exact manner in which length affects
microsatellites. Also, the motif that makes up a microsatellite
determines mutability of microsatellite to a large extent.
There is a lot of variation in mutability of microsatellites. It
has been experimentally shown that two similar microsatellites can
mutate at very different rates if the context of their flanking
sequences is changed. Clearly, microsatellite mutation process is
a function of inherent sequence properties, local as well as of
large-scale genomic factors. A comprehensive model that
incorporates all known factors affecting microsatellite mutability
is needed. Here we are trying to correlate various local genomic
factors around microsatellites, with the mutability of
microsatellites, as well as to estimate the degree to which
microsatellite length and motif are important in determining
microsatellite mutability.
References:
Webster,
M.T., N.G. Smith, and H. Ellegren, Microsatellite evolution
inferred from human-chimpanzee genomic sequence alignments.
Proc Natl Acad Sci U S A, 2002. 99(13): p. 8748-53.
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12/06/06 |
Speaker:
Dimitria Chalkia -
Department of Biology
- CANCELLED
Title:
Abstract:
References: |
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