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IMEG
SEMINARS
FALL 2003
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Previous
IMEG Seminars and Abstracts: |
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Date |
Speaker and title of seminar |
09/03/03 |
Speaker:
Dr. Seogchan Kang, Dept. of Plant Pathology, Penn State Univ.
Title: Plant pathogen database: Cyber-infrastructure to capture and
visualize the structure and dynamics of plant pathogens in the
context of agroecosystems
Abstract: Crop losses from diseases pose a serious threat to global
food/fiber/feed security. Considering the importance of agriculture,
concerted efforts should be committed to developing a comprehensive
risk management decision support system to effectively deal with any
future crop disease outbreaks whether accidental or deliberate. This
project aims to achieve the following goals:
(i) To link pathogen genotypes to their phenotypes
(ii) To develop an integrated set of data analysis and
visualization tools to examine complex disease interactions
(iii)
To build a cyber-infrastructure linking community research
(iv)
To provide rapid, sensitive and accurate diagnostic tools for
high-risk pathogens at both the species and population levels
References:
Kang et al. (2002) The Internet-based
fungal pathogen database: A proposed model. Phytopathology 92:232-236.
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09/10/03 |
Speaker:
Dr. Laura Zahn, Dept. of
Biology, Penn State Univ.
Title:
Comparative analyses of Poppy MADS-box genes expressed during
flower development
Abstract: The Type II MIKC MADS-box genes play critical roles in controlling
flower development and specifying floral organ identity in plants.
Although homologs of many MADS-box genes have been analyzed from
both eudicots and monocots, it is not clear how conserved these
genes are among divergent angiosperm lineages, particularly in the
basal eudicots. Studies of the phylogenetic placement and
expression of 4 MADS-box genes isolated from a pre-meiotic floral
library of the California poppy demonstrate that these genes share
homology with genes in Arabidopsis. The expression patterns
of these genes in the basal Eschscholzia are both similar and
divergent to their homologs from the more derived Arabidopsis.
Based on this we can hypothesize that ancestral gene function has
both been conserved and diverged in these 4 MADS-box genes.
References:
Ma H., dePamphilis C. (2000) The ABCs of floral evolution. Cell.
Mar 31;101:5-8.
Soltis, D. E.,
Soltis, P. S., Albert, V. A., Oppenheimer, D. G., dePamphilis, C. W., Ma, H., Frohlich,
M. W., and Theissen, G. Floral Genome Project Research Group.
(2002) Missing links: the genetic architecture of flowers
[correction of flower] and floral diversification.
Trends in Plant Sciences. Jan;7:22-31.
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09/17/03 |
Speaker:
Barbara Bliss,
Dept. of Biology, Penn State Univ.
Title:
Revealing multiple transfers among
plant organelle genomes
Abstract:
Phylogenetic analysis of vertically
transferred (parent to offspring) sequence information illustrates
accepted species relationships. Greater similarity of sequence is
presumed to reflects conserved function or a more recent common
ancestor. Horizontal gene transfer (HGT) is also revealed with
phylogenetic analysis, in which case the resulting topology differs
from the accepted organismal topology. Historically, putative HGTs
have been uncovered one at a time, using careful hybridization
experiments to probe unlikely genomes. Functional information about
a candidate sequence may suggest that it did not arise there
independently or be conserved to perform an essential function. I
used a bioinformatics approach to develop a whole genome view of
multiple organelles, revealing numerous putative horizontal
transfers, large and small. Experimental evidence from PCR and
sequencing reactions confirmed the existence of these sequences, and
phylogenetic analyses support the hypothesis that organelle genomes
have been extensively invaded by horizontal gene transfer.
Present-day availability of whole, well-annotated genomes and the
tools to manipulate them allows rapid identification and analysis of
evolutionary events involving multiple genomes.
References:
Lawrence, J. G., and Ochman, H. (1997)
Amelioration of bacterial genomes: Rates of change and exchange.
Journal of Molecular Evolution 44:383-397.
Woese, C.
(1998) The universal ancestor. Proceedings of the National Academy
of Sciences of the United States of America 95:6854-6859.
Cummings, M.
P., Nugent, J. M., Olmstead, R. G., and Palmer, J. D. (2003)
Phylogenetic analysis reveals five independent transfers of the
chloroplast gene rbcL to the mitochondrial genome in angiosperms.
Current Genetics 43:131-138.
Schwartz, S.,
Zhang, A., Frazer, K. A., Smit, A., Riemer, C., Bouck, J., Gibbs,
R., Hardison, R., and Miller, W.
(2000) PipMaker - A web server for
aligning two genomic DNA sequences. Genome Research 10:577-586.
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09/24/03 |
Speaker:
Dr. Ning Zhang,
Dept. of
Plant Pathology, Penn State Univ.
Title:
Discula destructiva,
the causal agent of dogwood anthracnose is thought to have been
introduced to North America in late 1970s. Two distinct groups of
D. destructiva isolates, one from the western U. S. and the
other from the eastern U. S., were identified with amplified
fragment length polymorphism (AFLP) markers and sequences of several
genes. The remarkably low genetic diversity indicated that it is
still under intense selection pressure. In another important group
of fungi, Fusarium solani species complex, a number of new
lineages were identified based on phylogeny of the Elongation Factor
1-alpha gene, suggesting that there are more species in the F.
solani complex than previously recognized. In order to apply
phylogenetic species concept to the F. solani complex,
multiple loci were analyzed for a subset of isolates. The results
show support for clades corresponding to known mating populations,
in addition to a number of new lineages. Overall, the F. solani
complex was found to contain a tremendous amount of phylogenetic
diversity.
References:
Zhang, N., and Blackwell, M. (2002)
Population structure of dogwood anthracnose fungus. Phytopathology
92: 1276-1283.
O’Donnell, K. (2000) Molecular phylogeny of the Nectria haematococca-Fusarium solani species complex. Mycologia 92:
919-938.
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10/01/03 |
Dr. Wojciech
Makalowski, Dept. of
Biology, Penn State Univ.
Title: Genomic scrap yard: how genomes utilize all that junk
Abstract: Interspersed repetitive sequences are major components of eukaryotic
genomes. Repetitive elements comprise over 50% of the mammalian
genome. Because the specific function of these elements remains to
be defined and because of their unusual behavior in the genome,
they are often quoted as a selfish or junk DNA. Our view of the
entire phenomenon of repetitive elements has to now be revised in
light of data on their biology and evolution, especially in the
light of what we know about the retroposons. I would like to argue
that even if we cannot define the specific functions of these
elements, we still can show that they are not useless pieces of the
genomes. The repetitive elements interact with the whole genome and
influence its evolution. Repetitive elements interact with the
surrounding sequences and nearby genes. They may serve as
recombination hot spots or acquire specific cellular functions such
as RNA transcription control or even become part of protein coding
regions. Finally, they provide very eYcient mechanism for genomic
shuZing. As such, repetitive elements should be called genomic scrap
yard rather than junk DNA.
References:
Makalowski, W. (2000) Genomic scrap yard: how genomes utilize all
that junk. Gene 259:61-67.
Brosius, J. (2003) The contribution of RNAs and
retroposition to evolutionary novelties. Genetica. 118:99-116.
Makalowski, W. (2003) Not Junk After All.
Science 300:1246-1247.
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10/08/03 |
Speaker:
Dr. Kazuhiko
Kawasaki, Dept. of Anthropology, Penn State Univ.
Title:
Paralogue after
paralogue in teeth and bones
Abstract:
Mineralized tissue
is a critical innovation in vertebrate evolution. The mammalian
tooth forms in three layers, enamel, dentin, and bone, each of which
crystallizes on specific extracellular matrix (ECM) proteins. We
have characterized the secretory calcium-binding phosphoprotein (SCPP)
gene family, which arose from a common ancestor by gene
duplications, and specialized into enamel or dentin/bone ECM protein
genes early in vertebrate evolution. Later in mammals, an enamel
ECM protein gene eventually created milk casein and salivary protein
gene clusters by recurrent duplications. These proteins help grow
or maintain teeth and bones. The SCPP gene sequences are poorly
conserved during evolution; hence efforts to identify fish SCPP
genes have been largely unsuccessful. However, by searching the
Fugu genome syntenic to the human SCPP gene locus, we found an SCPP
gene cluster. Surprisingly, none of these genes show sequence
homology to mammalian genes. Thus, apparently a different SCPP
family developed in Teleosts, suggesting that different sets of
paralogous genes organize mammalian and fish mineralized tissues.
References:
Toyosawa, S.,
O’hUigin, C., Figueroa, F., Tichy, H., and Klein, J. (1998)
Identification and characterization of amelogenin genes in
nomotremes, reptiles, and amphibians. Proc. Natl. Acad. Sci. USA.
95:13056-13061.
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.
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10/15/03 |
Speaker:
Li Hao, Dept. of
Biology, Penn State Univ.
Title: Sequence and Phylogenetic Analysis of the Ly49 Gene Cluster in Rats:
A Very Rapidly Evolving Gene Family in Rodent Lineage
Abstract: The natural killer cell receptors play a significant role in innate
immunity as the first line of defense against pathogens.
Interestingly, primates and rodents use different gene families to
perform the equivalent function: killer cell immunoglobulin-like
receptors (KIRs) in primates and Ly49s in rodents.
However both of these two gene families duplicate at an unexpectedly
high rate in either primates or rodents. Here we examined the rapid
evolution of Ly49 genes in rats and compare them with mouse Ly49
homologues. More than 20 new Ly49 loci have been characterized in
rat chromosome 4. Excluding short gene fragments, a total of 31 Ly49
genes are clustered in a 1.8 Mb genomic region. Compared to the
mouse Ly49 cluster, the rat Ly49 cluster is more complicated in
terms of gene number and gene arrangement. Sequence analysis also
shows the extreme difference between mouse and rat Ly49 genes. Most
of the Ly49 genes in these two species form highly divergent and
species-specific groups, suggesting that multiple duplications and
diversification have been occurring after the mice-rats divergence.
The similarity of the evolutionary pattern between KIR genes in
primates and Ly49 genes in rodents will be also discussed.
References:
Makrigiannis, A. P., Pau, A. T., Schwartzberg, P. L., McVicar, D.
W., Beck, T. W., and Anderson, S. K. (2002) A BAC contig map of the Ly49
gene cluster in 129 mice reveals extensive differences in gene
content relative to C57BL/6 mice. Genomics 79:437-444.
Naper, C., Hayashi,
S., Kveberg, L., Niemi, E. C., Lanier, L. L., Vaage, J. T., and Ryan,
J. C.. (2002a) Ly49-s3 is a promiscuous activating rat NK cell
receptor for nonclassical MHC class I-encoded target ligands. J.
Immunol. 169:22-30.
Naper, C., Hayashi,
S. Joly, E., Butcher, G. W., Rolstad, B., Vaage, J. T., and Ryan, J.
C. (2002b) Ly49i2 is an inhibitory rat natural killer cell
receptor for an MHC class Ia molecule (RT1-A1c). Eur. J. Immunol.
32:2031-2036.
Wilhelm, B. T., Gagnier,
L., and Mager, D. L. (2002) Sequence analysis of the Ly49
cluster in C57BL/6 mice: A rapidly evolving multigene family in the
immune system. Genomics 80:646-661.
Smith, H. R. C., Heusel,
J. W., Mehta, I. K., Kim, S. Dorner, B. G., Naidenko, O. V., Lizuka,
K., Furukawa, H., Beckman, D. L., Pingel, J. T., Scalzo, A. A., Fremont,
D. H., and Yokoyama, W. M. (2002) Recognition of a virus-encoded ligand by a natural killer cell activation receptor. Proc. Natl.
Acad. Sci. U S A 99:8826-31.
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10/22/03 |
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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10/29/03 |
Speaker:
Dr. Yoshihito Niimura,
Dept. of Biology, Penn State Univ.
Title:
Comparative
Evolutionary Analysis of Olfactory Receptor Genes: Humans Lost, Mice
Gained
Abstract: Olfactory receptor (OR) genes are the largest known multigene family
in mammalian genomes. Previously we reported that the complete human
genome contains ~800 OR functional genes and pseudogenes, and 52% of
them are pseudogenes. To see the difference in the evolution of OR
genes, we detected the entire OR gene family from mouse whole genome
sequences. We identified 1,037 potentially functional genes and 354
apparent pseudogenes, and they are distributed in 69 chromosomal
locations. The largest genomic cluster contains 267 OR genes, and it
occupies a 5-Mb region. By conducting extensive phylogenetic
analysis, we showed that the organization of genomic clusters in
mice are highly conserved with those in humans, though the number of
genes are much larger in mice than humans. We also found that each
of >150 human pseudogenes form a phylogenetic clade with mouse
functional gene(s), indicating that the human lineage lost many OR
genes after the separation of human and mouse lineages. In contrast,
most of the mouse OR pseudogenes seem to have generated after the
human-mouse divergence. Estimation of the divergence time at each
branching point suggests that the mouse lineage gained >300 OR genes
by gene duplications after the human-mouse divergence, while the
number is ~50 for the human lineage. These observations imply that
the difference in OR gene family between humans and mice has been
formed by two major processes: the human lineage lost many OR genes
by pseudogenizations, and the mouse lineage gained hundreds of OR
genes by tandem gene duplications.
References:
Niimura, Y., and Nei, M. (2003) Evolution of olfactory receptor genes in
the human genome. Proc. Natl. Acad. Sci. USA 14:12235-12240.
Young, J. M. et al. (2002) Different evolutionary processes shaped
the mouse and human olfactory receptor gene families. Hum. Mol.
Genet. 11:535-546.
Zhang, X.,
and Firestein, S. (2002) The olfactory receptor gene superfamily of the
mouse. Nat. Neurosci. 5:124-133.
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11/05/03 |
Speaker:
Dr. Hiroshi
Akashi, Dept. of Biology, Penn State Univ.
Title:
Metabolic economics and the Yeast proteome
Abstract:
The notion of "functional constraint" in
protein evolution considers mainly the relationship between the
primary structure of a protein and its function. Here, I test
whether selection for efficient synthesis acts as a global pressure
on the amino acid composition and sizes of proteins. The
Saccharomyces cerevisiae genome sequence, DNA microarray
expression data, tRNA gene numbers, and functional categorizations
of proteins are employed to determine whether the amino acid
composition of peptides reflects natural selection to optimize the
speed and accuracy of translation. Strong relationships between
synonymous codon usage bias and estimates of transcript abundance
suggest that DNA array data serve as adequate predictors of
translation rates. Amino acid usage also shows striking
relationships with expression levels. Stronger correlations between
tRNA concentrations and amino acid abundances among highly expressed
than among less abundant proteins supports adaptation of both tRNA
abundances and amino acid usage to enhance the speed and accuracy of
protein synthesis. Natural selection for efficient synthesis
appears to also favor shorter proteins as a function of their
expression levels. Comparisons restricted to proteins within
functional classes are employed to control for differences in amino
acid composition and protein size that reflect differences in the
functional requirements of proteins expressed at different levels.
References:
Akashi, H. (2001) Gene expression and
molecular evolution. Curr. Opin. Genet. Dev. 11:660-666.
Akashi, H. (2003) Translational selection and
yeast proteome evolution. Genetics 164:1291-1303.
Baudouin-Cornu, P., Surdin-Kerjan, Y., Marliere,
P., and Thomas, D. (2001) Molecular evolution of protein atomic
composition. Science 293:297-300.
Ikemura, T. (1985) Codon usage and tRNA
content in unicellular and multicellular organisms. Mol. Biol. Evol.
2:13-34.
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11/12/03 |
Speaker:
Dimitra Chalkia,
Dept. of Biology, Penn State Univ.
Title:
Phylogenetic analysis of formin
homology proteins in Arabidopsis thaliana and Oryza sativa
Abstract:
The plant cell
cytoskeleton plays an important role in many cellular processes,
including cell polarity establishment and cytokinesis. Proteins that
regulate cytoskeletal assembly are likely to be a part of the
signaling cascade that governs plant cell morphogenesis. Formins are
members of a large protein family that is defined by the presence of
the highly conserved Formin Homology II (FH2) domain. In a wide
range of organisms, including vertebrates, arthropods, nematodes and
fungi, formins have been implicated in the regulation of
cytoskeletal assembly and in the control of cytokinesis and cell
polarity establishment and maintenance. The genomes of
Arabidopsis thaliana and Oryza sativa contain putative
formin-like proteins based on the presence of an FH2 domain.
Arabidopsis thaliana formins have been tentatively sub-divided
into two clades: Type I and Type II, based on the FH2 domain
alignment. We have extended this analysis to cover both
Arabidopsis and rice and have provided an evolutionary context
for these plant formin families. Our phylogenetic analysis shows
that formins are divided in two distinct clades in plants. This
phylogenetic clustering is also supported by the structural features
of these proteins. This division of plant formins in two distinctive
groups seems to predate the split of monocots/eudicots. The detailed
evolutionary relationships of plant formins remain unclear. The
placement of fungi formins at the basal position of the tree is in
accordance with the most recent proposed phylogenetic scheme for
eukaryotes. Animal and plant formins cluster together, and split
into two major groups. This clustering may suggest that their last
common ancestor had already at least two different types of formins.
References:
Cvrckova, F.
(2000) Are plant formins integral membrane proteins? Genome
Biology; 1(1) research 001.1-001.7.
Deeks, M. J.,
Hussey, P. J., and Davies, B. (2002) Formins: intermediates in
signal-transduction cascades that affect cytoskeletal
reorganization. Trends Plant Sci 7 13:492-498.
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11/19/03 |
Speaker:
Norman Barr,
Dept. of Entomology, Penn State Univ.
Title: Phylogenetics of the genus Ceratitis (Tephritidae) based on
mtDNA and the nuclear gene period
Abstract:
The genus
Ceratitis, native to the Afrotropics, consists of 88 described
species in six recognized subgenera. Like other tephritids,
Ceratitis species feed on and damage the fruit of host plants.
Several species within the genus are polyphagous and pose a threat
to agriculture. For example, the Medfly (C. capitata), which
attacks over 300 species in almost 70 plant families, is considered
one of the world’s worst insect pests. Despite its importance to
agriculture, the systematic positions of Ceratitis relative
to closely related genera, subgenera within Ceratitis, and
species within the Ceratitis subgenera are yet uncertain. I
have produced Ceratitis phylogenies using mitochondrial (cytochrome
oxidase 1 and NADH dehydrogenase 6) and nuclear (period)
genes, to help understand the systematics of this important group.
References:
De Meyer, M. (1999) Phylogeny of the genus Ceratitis (Dacinae
Ceratitidini). In Fruit Flies (Tephritidae) Phylogeny and Evolution
of Behavior, M. Aluja and A. Norrbom (eds), CRC Press, Boca Raton,
FLorida.
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11/26/03 |
Thanksgiving Holiday |
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12/03/03 |
Speaker:
Dr. Kateryna
Makova, Dept. of Biology, Penn State Univ.
Title: Divergence in the spatial pattern of gene expression between human
duplicate genes
Abstract: Microarray gene expression data provide a wealth of information for
elucidating the mode and tempo of molecular evolution. In the
present study, we analyze the spatial expression pattern of human
duplicate gene pairs by using oligonucleotide microarray data, and
study the relationship between coding sequence divergence and
expression divergence. First, we find a strong positive correlation
between the proportion of duplicate gene pairs with divergent
expression (as presence or absence of expression in a tissue) and
both synonymous (K(S)) and nonsynonymous divergence (K(A)). The
divergence of gene expression between human duplicate genes is
rapid, probably faster than that between yeast duplicates in terms
of generations. Second, we compute the correlation coefficient (R)
between the expression levels of duplicate genes in different
tissues and find a significant negative correlation between R and
K(S). There is also a negative correlation between R and K(A), when
K(A) <or=0.2. These results indicate that protein sequence
divergence and divergence of spatial expression pattern are
initially coupled. Finally, we compare the functions of those
duplicate genes that show rapid divergence in spatial expression
pattern with the functions of those duplicate genes that show no or
little divergence in spatial expression.
References:
Makova, K. D., and Li, W. H. Divergence in the spatial pattern of
gene expression between human duplicate genes. Genome Res. 2003
Jul;13(7):1638-45.
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12/10/03 |
Speaker:
Dr. Vamshi
Veeramachaneni, Dept. of Biology, Penn State Univ.
Title: Database of Evolutionary Distances
Abstract: A large database of homologous sequence alignments with good
estimates of evolutionary distances can be a valuable resource for
molecular evolutionary studies and phylogenetic research in
particular. We recently created a prototype database containing
69,000 genes from human, mouse and rat species. Approximately 17,000
homology groups were identified with the help of Ensembl homology
evidence. At the macro-level the database allows us to answer
questions of the form:
1. "What is the average k-distance between 5'UTRs of human and
mouse?"
2. "List the 10 groups with the highest Ka/Ks ratio between mouse
and rat"
3. "List all identical proteins between human and rat"
Researchers interested in specific proteins can use a simple
web-interface to retrieve the homology groups of interest, examine
all pair-wise distances between members of the group, and study the
exon-intron gene structures using graphical interface.
Current data, access to the database, and proposed extensions will
be discussed.
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