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IMEG SEMINARS
Spring 2007
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| Previous IMEG
Seminars and Abstracts: |
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Date |
Speaker |
| 01/17/07 |
Speaker:
Dr.
Eddie
Holmes- Department of Biology
Title:
"The Evolutionary Genomics
of Influenza Virus."
Abstract: The
current interest in H5N1 avian influenza virus, and its potential
threat to human health, has generated a renewed interest in studies of
influenza virus evolution. Here I will show how the study of large
amounts of complete genome sequence data has shed light on the key
patterns and processes of influenza virus evolution. In particular, I
will show that reassortment among human influenza viruses is a far
more important process than generally envisaged and may have been
important for a number of “antigenic cluster jumps” in H3N2 influenza
virus. I will also reveal the evolutionary processes response for the
dramatic and global rise in resistance to adamantane drugs that
occurred in recent months. Through the intensive study of influenza
virus in a single population – New York state from 1995 to 2005 – I
will show that rather than being characterized by a single dominant
lineage, the viruses present during any season represent a small
sample of global genetic diversity, with little antigenic drift
occurring over a season. The evolution of influenza A vírus is
therefore an episodic process, characterized by occasional selective
sweeps.
References:
Holmes
EC,
Ghedin E, Miller N, Taylor J, Bao Y, St. George K, Grenfell BT,
Salzberg SL, Fraser CM, Lipman DJ & Taubenberger JK. (2005). Whole
genome analysis of human influenza A virus reveals multiple
persistent lineages and reassortment among recent H3N2 viruses.
PLoS.Biol. 3(9), e300.
Nelson
MI, Simonsen L, Viboud C, Miller MA, Taylor J, St. George K,
Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell
BT, Lipman DJ, Taubenberger JK & Holmes EC. (2006). Stochastic
processes are key determinants of the short-term evolution of
influenza A virus. PLoS Path. 2, e125.
|
| 01/24/07 |
Speaker:
Dr. Izabela
Makalowska- Department of Life Sciences
Title:
"Birth And Death of Gene
Overlaps in Vertebrates."
Abstract: Several
mechanisms have been proposed to explain gene overlap origination. For
instance, Keese and Gibbs suggested that overlapping genes arise as a
result of overprinting - a process of generating new genes from
preexisting nucleotide sequences. This process supposedly took place
after divergence of mammals from birds and overlapping genes represent
young, phylogeneticaly restricted genes encoding proteins with diverse
functions, and are therefore specialized to the present life-style of
the organism in which they are found. Shintani et al. suggested that
the overlap between genes ACAT2 (acetyl-Coenzyme A
acetyltransferase 2) and TCP1 (t-complex 1) arose during the
transition from therapsid reptiles to mammals as a result of
translocation accompanied (or followed) by loss of part of 3' URT
including polyadenylation signal and adoption of signals from the
neighboring gene locus. The ACAT2-TCP1 overlap evolution was
placed, similarly as in Keese anf Gibbs hypothesis, after the
divergence of mammals from birds. Dahary et al. places the origin of
most vertebrate overlaps much earlier. He found that human antisense
genes have largely conserved linkage in Fugu which may imply that big
fraction of human overlapping genes represents vertebrates' ancestral
overlaps. However, our previous study of human and mouse overlapping
genes showed that even between much closer related species overlaps
are not that well conserved. Here we present results of the
comparative analysis of seven vertebrate genomes: human, chimpanzee,
mouse, rat, chicken, fugu, and zebrafish. This comparative studies
shows that many of the vertebrate gene overlaps are not conserved and
are lineage specific. On the other hand, this work reveals new, not
published before, cases of genes overlap conservation in vertebrates.
We also show new mechanisms of overlapping genes evolution and
demonstrate, for the first time, that evolutionary events could not
only lead to the new gene overlaps origin but also to the loss of an
ancient overlap. Therefore luck of strong overlaps conservation
between even closely related species may result not only from the
origin of new, lineage specific overlap but also be resulting from the
loss of many overlaps in some lineages.
Examples from our studies show that one of the major forces leading to
overlaps origin is a development of new splice variant, which could
either replace the ancient one or be just an addition to already
present variants. In addition, our study emphasizes that in order to
fully understand the evolution of overlapping genes one has to work in
details on many lineages.
References:Keese
PK, Gibbs A: Origins of genes: "big bang" or continuous creation?
Proc Natl Acad Sci U S A 1992, 89(20):9489-9493.
Shintani S, O'HUigin C, Toyosawa S, Michalova V, Klein J: Origin of
gene overlap: the case of TCP1 and ACAT2. Genetics 1999,
152(2):743-754.
Dahary D, Elroy-Stein O, Sorek R: Naturally occurring antisense:
transcriptional leakage or real overlap? Genome Res 2005,
15(3):364-368.
Veeramachaneni V, Makalowski W, Galdzicki M, Sood R, Makalowska I:
Mammalian overlapping genes: the comparative perspective.
Genome Res 2004, 14(2):280-286.
Zhang Y, Liu XS, Liu QR, Wei L: Genome-wide in silico
identification and analysis of cis natural antisense transcripts (cis-NATs)
in ten species. Nucleic Acids Res 2006, 34(12):3465-3475.
|
| 01/31/07 |
Speaker:
Dr.
Wen-Ya Ko-
Department of Biology
Title:
"Within- and between-species
sequence variation in the Drosophila yakuba species complex:
adaptive protein evolution on A/T to G/C mutations."
Abstract: Fine-scale
investigation of nucleotide changes is critical for studying molecular
evolution when the underlying evolutionary parameter(s) fluctuates
frequently on a gene tree and/or when patterns and rates of nucleotide
changes differ between polymorphism and divergence at terminal
lineages. Here, we studied within- and between-species nucleotide
variation from 19 loci (4530 codons) in D. yakuba and D.
santomea and from 6 loci (1414 codons) in D. teissieri.
Analysis of average number of polymorphic mutations per allele showed
that each terminal lineage contains a large proportion of polymorphic
mutations (0.69, 0.72, and 0.56 for D. teissieri, D. yakuba,
and D. santomea, respectively). The results suggest that
polymorphic mutations can have pronounced effects on inferring
patterns of nucleotide changes in a single-allele analysis where an
excess of G/C à A/T polymorphic mutations is observed in each
species. Differences in ratios of polymorphism to divergence between
protein and different fitness classes of synonymous mutations reveal
evidence of adaptive protein evolution for mutations from A/T à G/C,
but not for mutations in the reverse direction. Adaptive protein
evolution on A/T à G/C mutations possibly relates to selection
discriminating a subset of amino acids or codons during the processes
of protein synthesis.
References:
AKASHI, H., 1999 Within- and
between-species DNA sequence variation and the 'footprint' of natural
selection. Gene 238: 39-51.
AKASHI, H., W. Y. KO, S. PIAO, A. JOHN, P. GOEL et al., 2006
Molecular evolution in the Drosophila melanogaster species
subgroup: frequent parameter fluctuations on the timescale of
molecular divergence. Genetics 172: 1711-1726.
FAY, J. C., G. J. WYCKOFF and C. I. WU, 2002 Testing the neutral
theory of molecular evolution with genomic data from Drosophila.
Nature 415: 1024-1026.
SMITH, N. G., and A. EYRE-WALKER, 2002 Adaptive protein evolution in
Drosophila. Nature 415: 1022-1024.
|
| 02/07/07 |
Speaker:
Dr. Nikolas Nikolaidis-
Department of Biology
Title: "The
Land of DANGER: an Ancient Developmental Superfamily."
Abstract: Developmental
proteins in general and molecules involved in cell differentiation in
particular, play a pivotal role in the origin of animal complexity and
diversity. Therefore identifying and characterizing the evolutionary
history of such molecules is fundamentally important towards
understanding the origin of animal complexity and diversity. We have
recently identified a highly divergent developmental protein
superfamily (DANGER), which originated before the emergence of animals
(~850 million years ago) and experienced major expansion-contraction
events during metazoan evolution. Sequence analysis suggests that
DANGER proteins diverged via multiple mechanisms, including amino acid
substitution, intron gain and/or loss, and recombination. Divergence
for DANGER proteins is substantially greater than for the prototypic
member of the superfamily (Mab-21 family) and other developmental
protein families (e.g., WNT proteins). DANGER proteins are widely
expressed and display species-dependent tissue expression patterns,
with many members having roles in development. A member of this
superfamily, DANGER1A, promotes the differentiation and outgrowth of
neuronal processes. Regulation of development may be a universal
function of DANGER family members. This family provides a model system
to investigate how rapid protein divergence contributes to
morphological complexity.
References:
Chow KL, Hall DH, Emmons SW (1995) The mab-21 gene of Caenorhabditis
elegans encodes a novel protein required for choice of alternate cell
fates. Development 121: 3615-3626.
Davidson EH, Erwin DH (2006) Gene regulatory networks and the
evolution of animal body plans. Science 311: 796-800.
Kusserow A,
Pang K, Sturm C, Hrouda M, Lentfer J et al.
(2005) Unexpected
complexity of the Wnt gene family in a sea anemone. Nature 433:
156-160.
Nikolaidis N, D Chalkia, DN Watkins, RK Barrow, SH Snyder, van Rossum
DB, RL Patterson. Ancient origin of a new developmental superfamily
DANGER. Plos ONE in press.
Technau U, Rudd S, Maxwell P, Gordon PM, Saina M et al. (2005)
Maintenance of ancestral complexity and non-metazoan genes in two
basal cnidarians.
Trends Genet
21: 633-639.
van
Rossum DB, Patterson RL, Cheung KH, Barrow RK, Syrovatkina V et al.
(2006) DANGER, a novel regulatory protein of inositol
1,4,5-trisphosphate-receptor activity. J Biol Chem 281: 37111-37116. |
|
02/14/07 |
Speaker:
Fabia Battistuzzi-
Department of Biology-CANCELLED
Title:
"Expanding the phylogeny and
timing of prokaryotes."
Abstract:
Genome sequences of
Eubacteria and Archaebacteria have proven informative for the
higher-level phylogeny and timing of these organisms that dominated
the biology of the early Earth. As this tree of prokaryotes continues
to grow with additional sequences, it is possible to better understand
how life coevolved with the planetary environment. However, the
chronological patterns and metabolic innovations of prokaryote
evolution ultimately rely on the phylogeny of these groups, phylogeny
that has proved challenging to define. Results from the comparison of
multiple phylogenetic trees (ML and distance methods for amino acids
and nucleotides data sets) suggest the presence of super-class
prokaryote groups, sub-class clusters, and classes that show a
problematic phylogenetic placement, leading to a partially resolved
consensus tree. They also show a consistent pattern of short internal
branches that might have consequences not only for the branching order
but also the time estimation of the major classes.
References:
Ciccarelli, F.D. et al.
Toward automatic reconstruction of a highly resolved tree of life.
Science 311, 1283-1287 (2006). |
| 02/21/07 |
Speaker:
Dr. Hong Ma-
Department of Biology
Title: "Highly
variable patterns of gene duplications in eukaryotic gene family
evolution: possible mechanisms and functional implications."
Abstract: Gene
duplication is an important means of gene family evolution,
particularly in the birth-and-death model of gene family evolution. We
have examined the evolution of multiple gene families in eukaryotes
and uncovered a wide range of patterns of gene duplications. Some
gene families have very stable gene numbers over most, if not all, of
the eukarytic history; many gene families have experienced moderate
gene duplication rates. In addition, some gene families have had very
high rates of gene births in land plants, particularly flowering
plants. It has been proposed that both animals and plants, as well as
some fungi, have had large-scale genome duplication(s) during their
evolutionary history. If we accept this theory, then the families that
maintain stable gene number must eliminate duplicates shortly after
their birth. Conversely, the births in some gene families can be
explained by large-scale genone duplications. The gene families with
very rapid birth rates can be explained by additional mechanisms such
as tanden duplications and retro-transpositions. It is possible that
the functions of different genes can affect the fate of duplicated
genes, and the differential survival of the duplicates in turn
facilitate the evolution of specific characteristics. The effects of
other factors on gene family evolution is also discussed.
References:
Hongzhi K, Leebens-Mack J,
Weimin N, dePamphilis C W and Ma H. (2004) Highly Heterogeneous Rates
of Evolution in the SKP1 Gene Family in Plants and Animals: Functional
and Evolutionary Implications. Mol Biol Evol 21(1):117–128.
Zahn L M, Leebens-Mack J,
DePamphilis C W, Ma H, and Theissen G. (2005) To B or Not to B a
Flower: The Role of DEFICIENS and GLOBOSA Orthologs in the Evolution
of the Angiosperms. J Here 96(3):225–240. Lin Z, Kong H, Nei M, Ma H.
(2006). Origin and evolution of the recA/RAD51 gene family:
Evidence for ancient gene duplication and endosymbiotic gene transfer.
Proc Natl Acad Sci USA, 103:10328-10333. |
| 02/28/07 |
Speaker:
Richard Meisel-
Department of Biology
Title: "On
the Origin and Evolution of Segmentally Duplicated Genes in the
Drosophila pseudoobscura Genome."
Abstract:
Gene duplication has been
recognized as an important evolutionary force for over three decades.
The 12 sequenced Drosophila genomes offer an excellent
opportunity to study genome evolution, including gene duplication. We
identified recently duplicated genes in the Drosophila
pseudoobscura genome that arose via segmental duplication after
the divergence of D. pseudoobscura and D. melanogaster.
The relative orientations of paralogs, lengths of duplicated regions,
and sequences flanking duplicated regions provide insights into the
molecular mechanisms underlying segmental duplication in Drosophila
genomes. To gain a better understanding of the early evolution of
duplicated genes, we analyzed nucleotide and protein coding sequence
divergence between paralogs. I will present the results of these
analyses of recently segmentally duplicated genes in the D.
pseudoobscura genome.
References:
Moore and
Purugganan. 2003. The early stages
of duplicate gene evolution. PNAS 100:15682-25687.Richards,
et al. 2005. Comparative genome sequencing of
Drosophila
pseudoobscura: chromosomal, gene, and cis-element
evolution. Genome Res. 15:1-18.
|
| 03/07/07 |
Speaker:
Erika Kvikstad -Department of Biology
Title: "A
macaque’s-eye view of human insertions and deletions: regional rate
variation and mechanisms of mutagenesis."
Abstract: Insertions
and deletions (indels) cause numerous genetic diseases and lead to
pronounced evolutionary differences among genomes. The macaque
sequences provide an opportunity to gain insights into the mechanism
of these mutations on a genome-wide scale by establishing the
polarity of indels occurring in the human lineage since its
divergence from the chimpanzee. Here we apply multiple regression
analyses to demonstrate an extensive regional indel rate variation
stemming from local fluctuations in male and female recombination
rates, divergence, proximity to telomere, and other genomic factors.
We find that both replication and, surprisingly, recombination
contribute significantly to small indel formation. As the relative
input of these factors differs between insertions and deletions, the
two types of mutations are likely guided in part by distinct
mechanisms. These results bring us closer to unraveling the
processes of indel mutagenesis.
References:
Hellmann I, Prufer K, Ji H, Zody MC,
Paabo S, Ptak SE.
Why do human diversity
levels vary at a megabase scale?
Genome Res. 2005
Sep;15(9):1222-31.
|
| 03/14/07 |
Speaker:
SPRING
BREAK - NO SEMINAR |
|
03/21/07 |
Speaker:
Samir Wadhawan -Department of Biology
Title:
"Dual Coding,
Duplication, Imprinting, and Exon Shuffling Unite to Shape the
Evolution of GNAS/GNAL Complex."
Abstract:Gnas
and its paralog Gnal constitute the Gs family of G-proteins that
encodes the G-protein alpha subunit. The two loci are imprinted and
share significant structural resemblance. But a unique feature
distinguishing them is the presence of functional protein-coding
regions in Gnas that overlap for over 1,000 nucleotides. The two
reading frames are embedded in a large paternally transcribed (~2kb in
size) upstream exon known as the XL. Shifted one nucleotide relative
to each other, the two frames when translated code for XLαs and ALEX
proteins. XLαs represents the extra large form of the stimulatory
G-protein alpha subunit. ALEX appears to regulate signal transduction
properties of XLαs by binding to XLαs and preventing its association
with receptors. The XL exon, which encodes both proteins, evolves so
rapidly that it is virtually unalignable between primates and rodents.
Even within the rodents it is highly divergent. Despite showing so
much divergence, the +1 reading frame encoding ALEX is still preserved
in these species. Here we characterize the evolution of this exon by
sequencing it in several rodents, and analyzing the sequences together
with those available for other mammals from various genome assemblies.
In addition we decipher the selection constraints acting on other
coding regions at both loci and also analyze the evolution of the Gs
family.
References:
1.
Nekrutenko, A., S.
Wadhawan, et al. (2005). "Oscillating evolution of a mammalian locus
with overlapping reading frames: an XLalphas/ALEX relay." PLoS
Genet 1(2): e18.
2.
Klemke, M., R. H.
Kehlenbach, et al. (2001). "Two overlapping reading frames in a single
exon encode interacting proteins--a novel way of gene usage." Embo
J 20(14): 3849-60.
3.
Freson, K., J. Jaeken,
et al. (2003). "Functional polymorphisms in the paternally expressed
XLalphas and its cofactor ALEX decrease their mutual interaction and
enhance receptor-mediated cAMP formation." Hum Mol Genet 12(10):
1121-30.
4.
Corradi, J. P., V.
Ravyn, et al. (2005). "Alternative transcripts and evidence of
imprinting of GNAL on 18p11.2." Mol Psychiatry 10(11):
1017-25. |
| 03/28/07 |
Speaker:
Dr. Hiroshi
Akashi-
Department of Biology
Title: "Genome
evolution in the Drosophila melanogaster subgroup: Lineage effects and
the time-scale of parameter fluctuations."
Abstract: Recently
sequenced genomes of close relatives of Drosophila melanogaster allow
investigation of the frequency, magnitude, and genomic breadth of
parameter fluctutations in molecular evolution. In this study, we
compare patterns of codon usage and protein evolution among five
species in the D. melanogaster subgroup (D. melanogaster, simulans,
sechellia, yakuba, and erecta) for close to 10,000 genes. We employ a
maximum likelihood approach to infer ancestral states and assign
substitutions to five lineages. The magnitude of parameters governing
“silent” DNA evolution appears to have varied frequently among
lineages, genomic regions, and synonymous families. At least some of
this heterogeneity is consistent with lineage-specific selection
intensity. Large-scale changes in expression patterns may underly
strong regional heterogeneity in codon bias evolution.
References:
(1)
Akashi, H., W.Y. Ko, S. Piao, A. John,
P. Goel, C. F. Lin, and A. Vitins, 2006 Molecular evolution in the
Drosophila melanogaster species subgroup: Frequent parameter
fluctuations on the time-scale of molecular divergence. Genetics 172:
1711-1726. (2) Ko, W. Y.,
S. Piao, and H. Akashi, 2006 Strong regional heterogeneity in base
composition evolution on the Drosophila X chromosome. Genetics 174:
349-362.
|
| 04/04/07 |
Speaker:
Dr. Saby Das-
Department of Biology
Title: "Signatures
of Dynamic Evolution on Immunoglobulin Variable Gene Families."
Abstract: The
distinction of light chain variable genes (VL) as kappa (V
) and lambda (V ) are often confusing and their evolutionary history
is unclear. Different methods for tree building can be used but none
of them so far resolved the confusion. On the other hand, the
frequency of expansion and contraction of various heavy chain variable
(VH) gene families and their importance for the evolution
of immunoglobulin heavy chain repertoire in vertebrates is an open
question. To understand the evolutionary dynamics of VL
and VH genes we identified VL and VH
sequences from several completely sequenced vertebrate genomes. We
clearly defined and distinguished the kappa and lambda variable genes
on the basis of three distinct but conserved features. We proposed
the kappa ancient hypothesis and a model for the evolution of light
chain variable genes. The ratio of the total number of kappa and
lambda chain genes varied in different lineage. It is probably due to
the differences in lineage specific expansion and/or contraction of V
or V genes. The all vertebrate VH genes can be
phylogenetically separated into eight major groups (Group A – H), in
which tetrapods are represented by three groups (groups F, G and H).
There is a biased expansion of group H genes and/or group G genes. We
hypothesized that this biased expansion can be correlated with the
biased usage of group H genes and/or group G genes and this
relationship is well conserved during evolution. There are enormous
diversities in VH gene numbers and gene orders in eutherian
mammals, but the VH locus is conserved in the subtelomeric
region of the chromosome. This diversity in number and organization of
VH genes partly can be explained by differences in
evolutionary turnover of subtelomeric regions in different species.
Both VH and VL genes evolution can be
characterized by birth-and-death model. There is a significant
positive correlation between total numbers of VH and VL
families as well as between the numbers of functional genes for the
same. It supports the coevolution of VH and VL
gene families in the peculiarities of the immune systems in various
organisms.
References:
(1) Hsu E, Pulham N
et al (2006). “The plasticity of immunoglobulin gene systems in
evolution.” Immunol Rev 210: 8-26.
(2) Zahorsky-Reeves JL, Gregory C (2006). “Similarities in the
immunoglobulin response and VH gene usage in rhesus monkeys and humans
exposed to porcine hepatocytes.” BMC Immunol. 7: 3. (3)
Pilstrom L (2002). “ The mysterious immunoglobulin light chain.” Dev
Comp Immunol 26: 207-215. (4) Sitnikova T, Su C (1998).
“Coevolution of immunoglobulin heavy- and light chain variable region
gene families” Mol Biol Evol 15: 617-625. (5) Ota T, Nei
M (1994). “ Divergent evolution and evolution by the birth-and-death
process in the immunoglobulin VH gene family” Mol Biol Evol
11: 469-482.
|
|
04/11/07 |
Speaker:
Valer Gotea-
Department of Biology
Title:
"The protein coding
potential of Alu elements."
Abstract:
Transposable elements
represent a significant portion of mammalian genomes, and have been
shown to impact their functionality in several ways (Makalowski,
2000). Of particular interest to us is their contribution to
proteomes, and we recently described cases of functional proteins that
contain TE-encoded fragments (Gotea and Makalowski, 2006). Alu
elements are particularly important to primate evolution, as they are
very abundant (~1.2 million copies in the human genome, ~10% of the
genome size) and contribute with alternatively spliced exons to many
genes (Sorek et al, 2002). Here we investigate the potential of Alu
elements to encode functional protein fragments. We also take
advantage of the recently sequenced macaque genome to infer the
selection acting on Aluternative exons, and we discuss controversial
functional evidence supporting the existence of Aluternative gene
variants (Shi et al., 1999).
References:
(1) Gotea, V., W.
Makalowski (2006) Do transposable elements really contribute to
proteomes? Trends in Genetics 22(5): 260-267
(2)
Makalowski, W. (2000) Genomic scrap yard: how genomes utilize all that
junk. Gene 259(1-2): 61-67 (3) Shi, B. et al. (1999)
Identification and characterization of Baxe, a novel Bax variant
missing the BH2 and the transmembrane domains. Biochemical and
Biophysical Research Communications 254: 779-785 (4) Sorek, R.,
G. Ast, D. Graur (2002) Alu-containing exons are alternatively
spliced. Genoem Research 12: 1060-1067
|
| 04/18/07 |
Speaker:
Song Li-
Department of Biology
Title: "Global
Regulation of Gene Expression in Guard Cells."
Abstract: Guard
cells (GC) have been long studied for elucidation of ABA signal
transduction using electrophysiological, biochemical and molecular
genetic methods. Here we take a genomics approach to study the
transcriptome of GC. We have established methods to obtain pure GC RNA
with or without ABA treatment and have used these samples to hybridize
whole genome Affymetrix chips (ATH1). Leaf (LF) RNA samples with or
without ABA were also used to hybridize to ATH1 chips in parallel.
Gene expression in higher
eukaryotes is a complex process and is under integrated control of
both developmental and environmental cues. We study developmental
control by looking at tissue specific gene expression profiles of
Arabidopsis guard cells (GC) versus leaves (LF), and we study
environmental control by comparing gene expression in the two tissues
in response to the stress hormone, abscisic acid (ABA).
We use the gene
expression profiles generated from our lab, and integrate other
publicly available computational and experimental resources, to study
four putative regulatory mechanisms that are likely to be involved in
transcriptional regulation in GC and LF. The four mechanisms we look
at are cis-regulatory element regulated gene expression, co-expression
clusters on chromosomes, microRNA regulated gene expression and cis-antisense
regulated gene expression. We finally evaluate the relative importance
of four regulatory mechanisms using a log likelihood score (LLS).
References:
Sona
Pandey*, Song Li*, Zhixin Zhao*, Laetitia Perfus*, Liza
Wilson*, Timothy Gookin*, and Sarah M. Assmann*
*Biology Department, Penn State University.
This reference not yet published.
|
| 04/25/07 |
Speaker: Jill
Duarte- Department of Biology
Title: "Identification
of conserved single copy nuclear genes in Arabidopsis, Populus, and
rice and their phylogenetic utility."
Authors: Duarte, J. M.,
Wall, P. K., Beckmann, K., Landherr, L. L., Leebens-Mack, J. H.,
dePamphilis, C. W.
Abstract:
Although the overwhelming majority of genes found in angiosperms are
members of gene families, we have identified a series of genes that
are conserved as single copy genes in the Arabidopsis, Populus, and
rice genomes. To characterize these genes, we have performed a number
of analyses examining GO annotations, cDNA length, number of exons,
expression patterns, and presence in the Selaginella and
Physcomitrella genomes. There are 1574 single copy nuclear genes
conserved in Arabidopsis and rice; 727 single copy genes conserved in
Arabidopsis, Populus, and rice; and the majority of these genes are
also present in the Selaginella and Physcomitrella draft genomes. The
selective forces leading to continuous loss of duplicated genes for
some kinds of genes and not others are still unknown, but the
collection of genes is biased toward organellar genes and genes of
unknown biological function. Public EST sets for 41 species suggest
that most of these genes are conserved as single or very low copy
genes, though exceptions are seen especially in very recent polyploidy
taxa. In order to explore the phylogenetic utility of a number of
these genes we have performed a series of phylogenetic analyses using
publicly available ESTs. Conserved single copy nuclear genes provide a
vast source of new evidence for plant phylogeny, genome mapping, and
other applications.
References:
Mort, M.-E., and D. J.
Crawford. 2004. The continuing search: low-copy nuclear sequences for
lower-level plant molecular phylogenetic studies. Taxon 53:257-261.
Sang, T. 2002. Utility of
low-copy nuclear gene sequences in plant phylogenetics. Critical
Reviews in Biochemistry and Molecular Biology 37:121-147.
Small, R. L., R. C. Cronn, and
J. F. Wendel. 2004. Use of nuclear genes for phylogeny reconstruction
in plants. Australian Systematic Botany 17:145-170. |
| 05/02/07 |
Speaker:
Dimitra Chalkia-
Department of Biology
Title: “Phylogenetic
Analysis of Formin Genes in Eukaryotes and Inference of their
Functional Divergence.”
Abstract:
One of the most interesting
properties of the eukaryotic cell is the ability to change its shape
and activity rapidly in response to internal and external signals.
This property comes from the cell’s ability to remodel the actin and
microtubule cytoskeletons with appropriate timing and precision.
Recently, formin has emerged as a key molecular regulator of the
eukaryotic cytoskeletal assembly and organization. Formin is a large
multidomain protein that is expressed widely in mammalian cells. This
dynamic molecule associates with a variety of other cellular factors
and assembles actin filaments through a novel migratory mechanism. In
this study we have shown that formin genes exist in all eukaryotic
genomes while bacterial and archaeal genomes are devoid of formin or
formin-like genes. Our phylogenetic analysis, based on formin’s most
conserved module (FH2 module), suggests that multiple events of
expansion and contraction of copy number have occurred in this gene
family. Of special interest is the birth of all metazoan formin gene
groups before the emergence of multicellular organisms. Unicellular
organisms that form colonies under certain conditions (e.g.,
Monosiga brevicollis and Dictyostellium discoideum) have
multiple copies of formin genes, which are orthologous to most animal
formin genes. The pattern of modular architecture of eukaryotic formin
proteins can be classified according to the phylogenetic clustering.
The conservation of the functionally important residues in all formins
implies that the core function of the FH2 domain, i.e. polymerization
and assembly of actin filaments is conserved. Our data suggest that
the high degree of divergence of different groups of formin molecules
is a product of mutations that evolved in a more or less neutral
fashion. We speculate that neutral mutations coupled with the
insertion/deletion of specific modules provided the means for temporal
and/or spatial differentiation of gene function and thus led to the
evolution of a highly coordinated cytoskeletal regulatory system.
References:
Higgs HN (2005) Formin
proteins: a domain based approach. Trends Biochem. Sci.
30(6):342-353.Goode BL and Eck MJ (2007) Mechanism and function of
formins in the control of actin assembly. Ann. Rev. Biochem
76:32.1-32.35.
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