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IMEG SEMINARS
Fall 2007
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| Previous IMEG
Seminars and Abstracts: |
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Date |
Speaker |
| 09/05/07 |
Speaker:
Dr. Ross Hardison- Department of Biochemistry & Molecular Biology Title:
ENCODE and Evolution:
What signatures of selection are associated with functional genomic
regions? Abstract: The
ENCODE project is a consortium supported by the National Human Genome
Research Institute that has as its goal to build an ENCyclopedia
Of functional DNA Elements. The aim is to
identify all the functional DNA sequences in the human genome, and a
new MOD-ENCODE has recently begun for model organisms. In the pilot
phase of ENCODE, a large number of high through-put biochemical assays
were run on 1% of the human genome (30 Mb in 44 different regions).
These included extensive transcript mapping, chromatin modifications,
and binding by transcription factors and components of transcription
complexes. Hybridization to high density microarrays of DNA enriched
for these various “functions” was a major technology employed. In
parallel, regions orthologous to the human ENCODE pilot regions were
sequenced (or extracted from existing sequences) for 28 species; these
were mostly mammals but they included vertebrates as distant as fish.
The sequences were aligned and evaluated for evidence of constraint.
Comparing the functional DNA segments (defined by the biochemical
assays) and the constrained DNAs led to these conclusions, which I
plan to discuss:
- About 60% of the “constrained bases” are associated with a known
function.
- Although functional regions tend to overlap with constrained
segments, not all the bases in the functional regions are under
constraint.
- “Surprisingly, many functional elements are seemingly unconstrained
across mammalian evolution. This suggests the possibility of a large
pool of neutral elements that are biochemically active but provide no
specific benefit to the organism. This pool may serve as a ‘warehouse’
for natural selection, potentially acting as the source of lineage-specfic
elements and functionally conserved but non-orthologous elements
between species.”
References:
The
ENCODE Project Consortium (2007) Identification and analysis of
functional elements in 1% of the human genome by the ENCODE pilot
project. Nature 447: 799-816
Full text available from
http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html
David C. King, James Taylor, Ying Zhang, Yong Cheng, Heather A.
Lawson, Joel Martin, ENCODE groups for Transcriptional Regulation and
Multispecies Alignment, Francesca Chiaromonte, Webb Miller, and Ross
C. Hardison (2007) Finding cis-regulatory elements using comparative
genomics: some lessons from ENCODE data. Genome Research 17
: 775-786.
Full text available from
http://www.genome.org/cgi/content/full/17/6/775
|
| 09/12/07 |
Speaker:
Dr. Masafumi Nozawa- Department of Biology Title:
Genomic drift and
copy number variation of sensory receptor genes in humans
Abstract: The
number of sensory receptor genes varies extensively among different
mammalian species. This variation is believed to be caused partly by
physiological requirements of animals and partly by genomic drift due
to random duplication and deletion of genes. If the contribution of
genomic drift is substantial, each species should contain a
significant amount of copy number variation (CNV). We therefore
investigated CNVs in sensory receptor genes among 270 human
individuals by using published CNV (i.e., relatively large insertion
and deletion) data. The results indicated that olfactory receptor
(OR), taste receptor type 2, and vomeronasal receptor type 1 genes
show a much larger extent of CNVs than the average for all annotated
genes. However, there was no significant difference between functional
and nonfunctional OR genes in the extent of CNVs. If OR pseudogenes
have evolved in a neutral fashion, this suggests that functional OR
genes also have evolved in a similar manner with respect to copy
number change in humans. In addition, we found that the ratio of
interspecific copy number divergence to intraspecific copy number
polymorphism is much higher than the corresponding ratio for human
populations, indicating that copy number difference has increased with
time. We therefore conclude that genomic drift is an important factor
for generating intra- and interspecific CNVs.
References:
Gilad Y et al. (2004)
Loss of olfactory receptor genes coincides with the acquisition of
full trichromatic vision in primates. PLoS Biol 2: e5.
Redon R, et al.
(2006) Global variation in copy number in the human genome. Nature
444: 444-454.
Niimura Y, and Nei M
(2007) Extensive gains and losses of olfactory receptor genes in
mammalian evolution. PLoS One 2: e708. |
| 09/19/07 |
Speaker:
Dr. Sabyasachi Das- Department of Biology
Title:
Evolution of immunoglobulin
VH multigene families in vertebrates
Abstract: Immunoglobulin
heavy chains are polypeptides encoded by four gene segments: variable
region (VH), joining (JH ),
diversity (D), and constant (CH) gene
segments. The number of VH gene segments varies from
species to species. To understand the evolution of the VH
multigene families, we identified and analyzed the VH
sequences from sixteen vertebrate species. The results show that the
numbers of functional and nonfunctional VH are
highly correlated among different species. The number of VH
gene segments is relatively stable in teleosts, but the intragenomic
sequence variation is generally higher in teleosts than in tetrapods.
The VH gene segments in tetrapods can be classified
into three phylogenetic groups (I, II, and III). The group III and/or
II gene segments are relatively abundant, whereas group I gene
segments exist in small numbers or are absent in most species. The
genomic organization of group I, II, and III VH gene
segments varies considerable among species, but the entire VH
region seems to be conserved in the subtelomeric or near-centromeric
region of chromosome. The presence or absence of specific VH
group members and the lineage-specific expansion and
contraction of VH gene segments indicate that the
VH region continues to evolve in a species-specific
manner. Our results suggest that the evolution of VH
gene segments is more complex than previously thought and that several
factors may act synergistically for the development of antibody
repertoire.
References:
|
| 09/26/07 |
Speaker:
Eleca Dunham-
Department of
Biology - CANCELLED
Title: Molecular
evolution and population demography of the swine H1N1 influenza A
viruses
Abstract:
A comparative analysis of the
classical swine H1N1 and European swine H1N1 influenza A viruses
reveals both convergent evolution and differential population
dynamics. Our analyses of the European swine virus indicate that the
classical H1N1 lineage suffered substantial population bottlenecking
during its introduction into Europe in the late 1970s. Coalescent
models confirm that the European swine lineage arose from a Eurasian
avian ancestor in the late 1970s and that the diversity of the virus
population is increasing over time. The classical swine lineage arose
sometime in the 1920s in North America from the 1918 Spanish H1N1
influenza A pandemic strain. Analysis of the amino acid profiles of
both lineages (classical and European) indicate similarities, but the
genomes of these two lineages are evolving differently. In line with
previous studies, we find that antigenic drift is much more pronounced
in the European swine lineage than it is in the classical swine
lineage.
References:
Brown, I, et al. (1997)
Antigenic and genetic analysis of H1N1 influenza A viruses from
European pigs. J. Gen. Virol. 78: 553-562.
Schultz, U, et al. (1991) Evolution of pig influenza viruses. Virol.
183: 61-73.
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10/03/07 |
Speaker:
Zhenguo Lin-
Department of
Biology
Title:
The sound of silence: non-neutral evolution at synonymous sites in
mammalian Hox genes
Abstract:
The discovery of the Hox
gene cluster uncovered a general universal principle of genetic
control of development. Hox genes encode homeodomain-containing
transcription factors which determine the body plan along
anterior-posterior axis in bilaterian animal. Hox genes are arranged
on the chromosomes in the same order as they are expressed along the
anterior-posterior axis in developing embryo. In this study, we found
some mysterious phenomena about the evolutionary dynamics of so call
silent mutation, synonymous mutation. The levels of synonymous
mutation in Hox genes have strong correlation with their position on
the cluster in mammals. Furthermore, many ultraconserved coding
regions were identified with completely depleted synonymous
substitution over 100 million years. Evolutionary analysis indicates
that the selection forces are mainly specific to placental mammals.
Our study suggests that these synonymous sites in Hox genes may play
active roles during mammalian embryo development.
References:
McGinnis, W., and Krumlauf,
R. (1992). Homeobox genes and axial patterning. Cell 68, 283-302.
Zhang, J., and Nei, M.
(1996). Evolution of Antennapedia-class homeobox genes. Genetics 142,
295-303. |
| 10/10/07 |
Speaker:
Fabia Battistuzzi-
Department of
Biology Title: Prokaryote
evolution and a terrestrial ancestry for most species
Abstract: The
relationships and timescale of prokaryote evolution are unresolved.
The poor fossil record of these organisms does not provide sufficient
information to outline their evolutionary history. Hence, phylogenetic
and molecular clock methods are fundamental to clarifying their
evolution and relating that to events in early Earth history. This
study uses genomic sequence data to reconstruct the phylogeny of
prokaryotes and estimate the divergence times of major groups.
Multiple methods and data sets are applied and compared to gain a more
general and robust result compared with previous studies that were
narrower in scope. The timeline of prokaryotes obtained was used to
infer evolutionary patterns in types of metabolism, such as the origin
of phototrophy, and the colonization of land. In general, a more
robust phylogeny of prokaryotes is established, with high-level groups
previously unrecognized. Archaebacteria and Eubacteria are found to
have rapidly evolved in the mid- to late-Archean (3.3-2.6 billion
years ago) in relation to the colonization of new environments such as
mesophilic photic zones and terrestrial habitats. We also traced a
terrestrial ancestry for most prokaryote species.
References:
Ciccarelli, F.D. et al.
Toward automatic reconstruction of a highly resolved tree of life.
Science 311, 1283-1287 (2006). |
|
10/15/07
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Speaker:
Dr. Sean Carroll -
Professor
of Molecular Biology and Genetics University of Wisconsin- Marker
Lecture
5:30 PM 112 Kern Bldg.
Title: The Making of the Fittest: DNA and
Evolution in Action
Abstract:
Every change or new trait,
from the gaudy colors of tropical birds to our color vision through
which we admire nature's diversity. is due to changes in DNA that
biologists can now trace in exquisite detail. We can now see not just
that the fittest survive, but how they are made. n this
lecture, Dr. Carroll will examine the massive DNA record of evolution
and what that tells us about how some fascinating creatures have
adapted to life on a changing planet.
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10/16/07
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Speaker:
Dr. Sean Carroll -
Professor
of Molecular Biology and Genetics University of Wisconsin- Marker
Lecture
4:00 PM Berg
Auditorium, Life Science Bldg.
Title: Endless Flies Most Beautiful: The Role of
cis-Regulatory Sequences in the Evolution of Animal Diversity
Abstract:
Changes in animal form arise
through changes in development, but for a very long time biologists
have wanted to understand just how new structures and patterns arise?
Contrary to expectations, the evolution of new genes has played a much
lesser role in the evolution of form than has the evolution of gene
regulatory sequences. In this lecture, Dr. Carroll will examine the
role of cis-regulatory sequences in the evolution of animal form.
|
| 10/24/07 |
Speaker:
Dr. Claude dePamphilis -
Department of
Biology
Title: Palaeopolyploidy
and the genomes of the flowering plants
Abstract: This
talk will review several completed and current plant genome
sequencing projects. While Arabidopsis thaliana was selected for
genome sequencing in part because of its small diploid genome, the
Arabidopsis genome proved to include large amounts segmental
duplication tracing to at least two distinct time points, suggesting
at least two rounds of ancient genome duplication ["paleopolyploidy]'
in Arabidopsis' history. The rice and poplar genomes also show
evidence of likely ancient polyploidy. Although complete genome
sequences are in progress for many plant species, smaller scale
studies of the relative age distribution of duplicate genes suggest
that most if not all flowering plant lineages have a likely
polyploid history. Surprisingly, the recently published genome of
Vitis [grapevine] shows no such evidence, which helps to
identify the likely dates of genome scale duplication events in
angiosperms. Here, I will compare some of the evidence for
polyploid events in the history of flowering plants and attempt to
summarize the current state of our understanding. Numerous current
and and future genome sequencing projects will address a host of
questions about the implications of these genome-wide events.
Reference
Arabidopsis Genome
Initiative (2000). Analysis of the genome sequence of the flowering
plant Arabidopsis thaliana. Nature 408: 796-815.
Simillion, C., Vandepoele, K., Van Montagu, M., Zabeau, M. & Van de
Peer, Y. (2002). The hidden duplication past of Arabidopsis
thaliana. Proceedings of the National Academy of Science of the USA
99: 13627-13632.
Paterson, A.H., Bowers, J. E., Van de Peer, Y. & Vandepoele, K.
(2005). Ancient duplication of cereal genomes. New Phytologist 165:
658-661.
Cui, L., P.K. Wall, J.H. Leebens-Mack, B.G. Lindsay, D.E. Soltis,
J.J. Doyle, P.S. Soltis, J.E. Carlson, K. Arumuganathan, A. Barakat,
V.A. Albert, H. Ma, and C.W. dePamphilis. 2006. Widespread genome
duplications throughout the history of flowering plants. Genome
Research 16: 738-749. (cover)
Tuskan, G.A. and many others (including PSU group K. Wall, J.
Leebens-Mack, J. Carlson, and C.W. dePamphilis). 2006. The genome of
black cottonwood, Populus trichcarpa (Torr. & Gray ex
Brayshaw). Science, 313:1596-1604.
Jaillon, O. and many others [2007]. The grapevine genome sequence
suggests ancestral hexaploidization in major angiosperm phyla.
Nature 449, 463-46.
|
| 10/31/07 |
Speaker: Dr.
Daniel Cosgrove -
Department of
Biology
&
Dr. Nikolas Nikolaidis - Department of Biology
Title:
Expansin diversions: plant, pollen and plant pathogens
Abstract:
Expansins are plant cell
wall loosening proteins that function in plant cell enlargement, fruit
softening, abscission and various other developmental processes. Land
plants possess 30-60 or more genes, which are readily divided into two
large families (EXPA and EXPB), with ~20% identity at the protein
sequence level. Sequence-based phylogenetic analysis was combined with
microsynteny analysis to reconstruct the history of gene births and
deaths in this family since the divergence of the rice/Arabidopsis
lineages. The EXPB family has grown considerably, perhaps because of
coincidence changes in cell wall structure in grasses. One subset of
the EXPB family in grasses gave rise to two novel classes of noxious
pollen allergens. We have begun to reconstruct the evoution of this
pollen allergen clade. Crystal structure of the maize EXPB pollen
allergen has not only revealed aspects of the protein structure and
its likelly mechanism of interaction with the cell wall, but also
focussed interest on a group of distantly related bacterial proteins.
These have only 5-15% amino acid identity with plant expansins, but
their protein structures superimpose on each other amazingly well,
indicating homology. We will present our ideas on the possible origin
and function of the bacterial homologs.
References:
Yennawar,N.H., Li, L-C.,
Dudsinski,D.M., Tabuchi,A., Cosgrove, D.J. (2006). Crystal structure
and activities of EXPB1 (Zea m 1), a
 -expansin
and group-1 pollen allergen from maize. PNAS 103:14664-14671.
J. Sampedro and D. J. Cosgrove. The expansin superfamily. Genome Biol.
6 (12):242, 2005.
http://www.bio.psu.edu/expansins/ |
|
11/07/07 |
Speaker:
Dr. Chris
House -
Department of
Geosciences
Title:
Genome-wide Gene Order Distances Support a United Gram-Positive
Bacteria
Abstract:The
pair-wise distance between 143 prokaryotic genomes was determined
using a simple monte carlo method to estimate the conservation of gene
order. The method was based on repeatedly selecting six non-adjacent
random orthologs from each of two genomes and determining if the
chosen orthologs were in the same order. The raw distances were then
corrected for gene order convergence using an adaptation of the
Jukes-Cantor model. We have compared the distances found to those of
ortholog gene content and small subunit ribosomal RNA (rRNA). The
gene order distances are reasonably well correlated with the
divergence of rRNA (R2 = 0.24), especially at rRNA Jukes-Cantor
distances of less than 0.2 (R2 = 0.52). Overall, gene content is only
weakly correlated with rRNA divergence (R2 = 0.04), however, it is
especially strongly correlated at rRNA Jukes-Cantor distances of less
than 0.1 (R2 = 0.67). Using the gene order distances, the relations
of prokaryotes (tree of life) were studied using neighbor joining,
agreement subtrees, and a new proposed hierarchical tree building
strategy that relies on the fact that shorter distances are known with
higher confidence than longer distances. Consistently, our trees show
the Actinobacteria as a sister group to the bulk of the Firmicutes. In
fact, the level of gene order support was found to be considerably
greater for uniting these two phyla than for uniting any of the
proteobacterial classes together. The results are supportive of the
idea that the Actinobacteria and Firmicutes are a monophyletic group,
which in turn implies a single origin for the gram-positive cell.
References: NO REFERNCES |
| 11/14/07 |
Speaker:
Yogeshwar Kelkar - Department of Biology Title: The
Genome-Wide Determinants of Human and Chimpanzee Microsatellite
Evolution
Abstract: Mutation
rates of microsatellites vary greatly among loci. The causes of this
heterogeneity remain largely enigmatic, yet are crucial for
understanding numerous human neurological diseases and genetic
instability in cancer. In this first genome-wide study, the relative
contributions of intrinsic features and regional genomic factors to
the variation in mutability among orthologous human-chimpanzee
microsatellites are investigated with resampling and regression
techniques. As a result, we uncover the intricacies of microsatellite
mutagenesis as follows. First, intrinsic features (repeat number,
length, and motif size), which all influence the probability and rate
of slippage, are the strongest predictors of mutability. Second,
mutability increases non-uniformly with length, suggesting that
processes additional to slippage, such as faulty repair, contribute to
mutations. Third, mutability varies among microsatellites with
different motif composition likely due to dissimilarities in secondary
DNA structure formed by their slippage intermediates. Fourth,
mutability of mononucleotide microsatellites is impacted by their
location on sex chromosomes vs. autosomes and inside vs.
outside of Alu repeats, the former confirming the importance of
replication and the latter suggesting a role for gene conversion.
Fifth, transcription status and location in a particular isochore do
not influence microsatellite mutability. Sixth, compared to intrinsic
features, regional genomic factors have only minor effects. Finally,
our regression models explain ~90% of variation in microsatellite
mutability and can generate useful predictions for the studies of
human diseases, forensics, and conservation genetics.
References:
Ellegren, H. 2000.
Heterogeneous mutation processes in human microsatellite DNA
sequences. Nat Genet 24: 400-402.
Ellegren, H. 2004. Microsatellites: simple sequences with complex
evolution. Nat Rev Genet 5: 435-445.
Lai, Y. and F. Sun. 2003. The relationship between microsatellite
slippage mutation rate and the number of repeat units. Mol Biol Evol
20: 2123-2131.
Pearson, C.E., K. Nichol Edamura, and J.D. Cleary. 2005. Repeat
instability: mechanisms of dynamic mutations. Nat Rev Genet 6:
729-742.
Webster, M.T., N.G. Smith, and H. Ellegren. 2002. Microsatellite
evolution inferred from human-chimpanzee genomic sequence alignments.
Proc Natl Acad Sci U S A 99: 8748-8753.
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| 11/21/07 |
NO IMEG
SEMINAR~ THANKSGIVING HOLIDAY
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|
11/28/07 |
Speaker:
Dimitra Chalkia -
Department of
Biology
Title:
"Origin and evolution of the
Formin gene family"
Abstract:
Molecular innovations of
eukaryotes are fundamental for understanding the dramatic changes that
have contributed to the advent of the eukaryotic cell. Actin, one of
the principal components of the cytoskeleton, was classified as a
molecular innovation of eukaryotes, but recent studies have revealed
that it is not a genuine eukaryotic innovation, since actin homologs
have been identified in prokaryotes. On the other hand, eukaryotes
possess four actin-filament assembly factors, but whether these
factors have precursor molecules in prokaryotes remains unknown. In
this study we focused on formin, one of the known actin-filament
assembly factors, and addressed the question of formin origin and
evolution. Our results showed that formin constitutes an authentic and
ancient eukaryotic innovation. Formin multi-gene family has followed a
gene birth-and-death mode of evolution and has experienced multiple
lineage-specific gene rearrangement events that led to domain gain
and/or loss. Moreover, our analyses showed that formin proteins from
deeply diverged eukaryotes possess similar motifs, which can be
attributed to independent amino acid replacement events. Thus, this
study provides insights into how eukaryote-specific molecular
regulators of the cytoskeleton diversified, which may be beneficial
for understanding not only the eukaryotic scaffolding apparatus, but
also the eukaryotic phylogenetic patterns and the functional
attributes of early eukaryotes.
References:
Goode, B.L., and Eck, M.J.
(2007). Mechanism and function of formins in the control of actin
assembly. Ann. Rev. Biochem 76: 32.1-32.35.
Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W.,
Pearlman, R.E., Roger, A.J., and Gray, M.W. (2005). The tree of
eukaryotes. Trends Ecol. Evol 20: 670-676.
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| 12/05/07 |
Speaker: Dr.
Sarah Melissa Witiak - Department of Plant Pathology
Title:
Insect galls as fruits and
seeds ? was Darwin right again?
Abstract:
Galls have long captured the
curiosity of scientists, including Darwin who noted their
morphological resemblance to fruits. Produced only in response to an
insect stimulus, galls are highly varied and complex structures with
distinct tissues. Insect galls typically contain specialized nutritive
inner tissue that accumulates carbohydrates and seed-specific
proteins, and outer tissue with high levels of secondary metabolites
analogous to many fruits and seeds. In conjunction with studies on the
evolution of galling systems and floral organs, these observations led
us to hypothesize that the same genetic pathway that controls normal
fruit and seed development is also induced by galling insects during
gall development. To test this hypothesis, we examined
the hormonal characteristics and the expression of fruit and seed
developmental genes in the galls of an aphid-like insect, phylloxera,
and of a cecidomyiid fly elicited on wild grapevine leaves. We found
that a specific subset of plant genes involved in normal floral, furit,
and seed development is also expressed in gall tissues, supporting the
hypothesis that insect galls are developmentally related to fruits and
seeds. These results raise interesting questions about the
relationships between the evolution of galling insects, their plant
hosts, and gall structure and complexity.
References: NO REFERENCES
|
| 12/12/07 |
Speaker: Rubing
Chen -
Department of
Biology
Title:
Molecular
Evolution of Influenza Viruses
Abstract:
Influenza viruses have three
types (A, B, C). Influenza A viruses infect a variety of hosts,
including birds, human and other mammals, and are responsible for the
vast majority of disease in humans, including all three major
pandemics in the twentieth century. Some subtypes (H5 and H7) of
avian influenza virus can also cause epidemics when introduced to
poultry. However, despite the intensive study of human influenza A
viruses and H5N1 avian influenza viruses, many aspects of their
evolution are not clearly understood. In particular, it is not clear
how influenza A viruses evolve, persist and spread in their nature
reservoir, wild aquatic birds. To address this question we utilized an
expansive data set of complete genome sequence data to examine the
evolutionary pattern, global distribution and transmission of avian
influenza virus in wild birds. Our research reveals a rapid rate of
evolutionary change in avian influenza virus (running counter to the
theory of ‘evolutionary stasis’), with some evidence for positive
selection in the HA, NA and NS genes. We also found frequent
reassortment events, which play an important role in the maintenance
of genetic diversity in avian influenza virus. Interestingly,
although there are few genetic exchanges between birds resident in the
North American and Eurasian/Australian flyways, both contain most of
the subtypes detected so far. In the second part of my seminar I will
consider influenza B virus. Although type B virus shares great
similarities with type A virus both genomically and phylogentically,
it only causes milder respiratory disease and local epidemics in
humans. To investigate the underlying mechanism and driving force of
influenza B evolution, we traced its evolutionary history using
complete genome sequence data. This led us to propose a model in
which the shift of dominant viral strains through time is the result
of changes in herd immunity, with reassortment continuously generating
novel genetic variation. Finally, we suggest that the interaction
with influenza A virus may be central in shaping the evolutionary
dynamics of influenza B virus.
References:
Chen R & Holmes EC (2006)
Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol
Evol 23: 2336-2341.
Olsen B, Munster VJ, Wallensten A, Waldenstro¨m J, Osterhaus ADME,
Fouchier RAM (2006) Global Patterns of Influenza A Virus in Wild
Birds. Science 312:384-388.
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