IMEG

Institute of Molecular
Evolutionary Genetics

 
 
 
          
 

IMEG SEMINARS
Spring 2005
 
Previous IMEG Seminars and Abstracts:
Fall 2009

Spring 2009

Fall 2008

Spring 2008

Fall 2007
Spring 2007
Fall 2006
Spring 2006
Fall 2005
Spring 2005

Fall 2004
Spring 2004

Fall 2003

Spring 2003
Fall 2002

Spring 2002

Fall 2001

Spring 2001

Fall 2000

Fall 1999
Spring 1998

Fall 1997

 Date Speaker and title of seminar

 01/12/05


Speaker: Dr. Stephen Schaeffer - Department of Biology


Title: "Comparative Genomics of Drosophila: Insights on chromosomal and repetitive DNA evolution."


Abstract: 
Lower levels of nucleotide diversity in a chromosomal region can be due to selective constraint, directional selection, or chromosomal context.  Breakpoints for chromosomal rearrangements will tend to
have low levels of variation due to reduced genetic flux that homogenizes variation among gene arrangements.
I will talk about recent advances in our knowledge of chromosomal evolution that has emerged from
comparative genomic sequencing in Drosophila and examine how chromosomal context influences levels of nucleotide sequence diversity.


References:
Navarro, A., E. Betrán, A. Barbadilla and A. Ruiz, 1997 Recombination and gene flux caused by gene
conversion and crossing over in inversion heterokaryotypes. Genetics 146: 695-709.

Schaeffer, S. W., P. Goetting-Minesky, M. Kovacevic, J. Peoples, J. L. Graybill, J. M. Miller, K. Kim, J. G. Nelson
and W. W. Anderson, 2003 Evolutionary genomics of inversions in Drosophila pseudoobscura: Evidence for epistasis. Proceedings of the National Academy of Sciences USA 100: 8319-8324.

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 Research 15: 1-18.


 01/19/05

Speaker: Dr. Cooduvalli Shashikant - Department of Molecular and Developmental Biology


Title:
"Cis-regulatory Analysis of a Mouse Homeobox Gene."


Abstract:
There is a considerable interest in understanding how cis-regulatory modifications drive
morphological changes across species.  Because developmental regulatory genes, including Hox genes, are remarkably conserved, their noncoding regulatory regions are likely sources for variations.  Modifications of Hox cis-regulatory elements have potential to alter Hox gene expression, and, hence axial morphologies.  In vertebrates, differences in the axial levels of Hox gene expression correlate with differences in the number and relative position of thoracic vertebrae.  Variation in cis-regulatory elements of Hox genes can be identified by comparative sequence and reporter gene analysis in transgenic mouse embryos.  Using these approaches,we show a remarkable divergence of the Hoxc8 early enhancers between mammals and fishes representing diverse axial morphologies.  Extensive restructuring of the Hoxc8 early enhancer including nucleotide substitutions, inversion and divergence result in distinct patterns of reporter gene expression along the embryonic axis.  Our results provide an evolutionary perspective on how the enhancer elements are engineered and support the hypothesis that remodeling Hox regulatory elements in different species has played a significant role in generating morphological diversity.


References:
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 analyses identify new elements of the mouse Hoxc8 early enhancer. J.Exp.Zool. Mol.Dev.Evol. 302, 436-445, 2004.

Anand, S., W.C.H. Wang, D.R Powell, S.A. Bolanowski, J. Zhang, C. Ledje, A.B. Pawashe, C.T. Amemiya, and C.S. Shashikant. Divergence of Hoxc8 early enhancer parallels diverged axial morphologies between mammals and fishes. Proc. Natl. Acad. Sci. (USA) 100, 15666-15669, 2003.


 01/26/05

Speaker: Dr. Reka Albert - Department of Physics


Title: "Lessons from modeling Drosophila segmentation: robustness of gene regulatory networks."


Abstract
: The segmentation of the fruit fly Drosophila melanogaster is controlled by about 40 genes organized in a hierarchical cascade of gene families. These genes are expressed in consecutive stages of embryonic development in a spatial pattern that is successively more precisely-defined, the genes at one step initiating or modulating the expression of those involved in the next step of the cascade. While most of these genes act only transiently, the segment polarity genes have a stable expression pattern that defines and maintains the borders between different parasegments and contributes to subsequent developmental processes.
The segment polarity genes refine and maintain their expression through a network of intra- and intercellular regulatory interactions between gene products. This seminar will present a model of these interactions and of how they lead to stable gene expression patterns. The model is deeply rooted in the topology of the segment polarity gene network, while it disregards the biochemical details of the interactions. This simple model is able to reproduce the wild type expression pattern of the segment polarity genes, as well as the ectopic expressions obtained for gene mutation experiments, and suggests a remarkable robustness in the function of the gene network. We will discuss how interaction patterns such as feedback loops and switches contribute to this robustness. The strong evolutionary conservation of the segment polarity genes suggests that these interaction patterns should be relevant to a host of other organisms as well.


References:
Reka Albert and Hans G. Othmer. The topology of the regulatory interactions predicts the expression pattern of the Drosophila segment polarity genes. Journal of Theoretical Biology 223, 1-18 (2003).

Reka Albert. Boolean modeling of genetic regulatory networks. In: Complex Networks editors: E. Ben-Naim, H. Frauenfelder and Z. Toroczkai), (Springer Verlag 2004).


 02/02/05

Speaker:  Dr. Ross Hardison - Department of Biochemistry and Molecular Biology


Title: "Gene regulatory elements discovered by vertebrate genome comparisons."


Abstract:
Four way comparisons of the human, rat, mouse and chicken genomes present an unprecedented opportunity to explore critical issues in genome evolution, structure and function. We find that about 1000Mb of DNA align in all three mammals. This conserved mammalian core contains not only about 95% of known functional sequences (coding exons and gene regulatory elements), but also a considerable amount of apparently neutral DNA. In contrast, only about 70Mb align reliably between human and chicken. Almost all of this is under purifying selection, but it does not include some functional mammalian sequences. Thus comparison of human to chicken will find functional elements with high specificity but at a considerable cost in sensitivity. To find candidates for cis-regulatory modules (CRMs) within these human-mouse-rat alignments, we compute (i) likelihood that a DNA sequence is subject to purifying selection (and hence is likely to be functional), (ii) the extent to which patterns in the alignments match those that are distinctive for known regulatory regions, and (iii) conserved matches to transcription factor binding sites. The scores are recorded in a public database of Genome ALignments and Annotation (GALA, http://www.bx.psu.edu/) and the UCSC Genome Browser (http://genome.ucsc.edu/), and we are developing a new metaserver, Galaxy, to integrate data from multiple sources and analyze it more completely. We applied these predictions to erythroid genes, in particular those revealed by microarray expression analysis to be co-expressed in two different mouse cell culture models of late erythroid differentiation (MEL cells and the Gata1-null G1E cells). Predicted CRMs around the co-expressed genes are tested for the ability to affect expression of the reporter after transient transfection of unintegrated plasmids into erythroid cells and after site-directed integration of the reporter cassettes into a chromosome, as well as by chromatin immunoprecipitations. Current results show that about 70% of the predicted CRMs have significant effects in these assays. The combination of bioinformatic predictions and experimental tests in somatic cell developmental models serves as a paradigm for global analysis of regulation in any tissue. 

 

References:
Waterston et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:
520-562.
Elnitski et al. 2003. Distinguishing regulatory DNA from neutral sites. Genome Res. 13: 64-72.
Hardison et al. 2003. Global Predictions and Tests of Erythroid Regulatory Regions. In The Genome of Homo
sapiens, pp. 335-344. Cold Spring Harbor Press, Cold Spring Harbor, NY.
Gibbs, et al. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature 428: 493-521.
Hillier et al. 2004. Sequence and comparative analysis of the chicken genome provide unique 
perspectives on vertebrate evolution. Nature 432: 695-716.
Miller et al. 2004. Comparative genomics. Annu Rev Genomics Hum Genet 5: 15-56.
Elnitski et al. 2005. Improvements to GALA and dbERGEII: Databases featuring genomic sequence 
alignment, annotation and experimental results. Nucl. Acids Res. 33 Database Issue: D466-D447.

 02/09/05

Speaker: Dr. Chris House - Department of Geosciences


Title: "Linking Molecular Taxonomy with Environmental Geochemsitry: the Anaerobic Oxidation of Methane in Cold Seeps & deeply Buried Sediments."


Abstract:
The linking of molecular taxonomy (including 16s rRNA) to environmental geochemistry is a powerful way to work out the interactions, metabolic activities, and food webs of microorganisms in their natural setting, whether it is sediment, soil, or a water column.  To this end, we developed a method for coupling an extant microorganism’s genetic information with geochemical data derived from the direct analysis of its cell. FISH–SIMS combines fluorescent in-situ hybridization (FISH) with secondary ion mass spectrometry (SIMS).  FISH is a culture-independent technique used to visually identify naturally occurring microorganisms by staining their ribosomal RNA.  Secondary ion mass spectrometry (SIMS) is a method by which geochemical information can be obtained from microsamples.  Using FISH-SIMS, a researcher can measure a target cell’s isotopic or elemental composition in a mixed environment.
The identification and study of methane-consuming microorganisms is an important step toward understanding the methane cycle and microbial response to methane release. The recent identification of two distinct Archaea capable of anaerobic methane oxidation was in part accomplished using FISH-SIMS.  Because natural methane is highly depleted in 13C, FISH-SIMS is particularly powerful at determining if a particular cell, collected from the environment, consumed methane as a substrate for its cell carbon. This research demonstrated that both the ANME-1 and ANME–2 Archaea from the Eel River Methane Seep are highly depleted in 13C due to growth on methane.
The deep marine biosphere is thought to contain abundant microbial inhabitants, estimated to be a tenth of the Earth’s total biomass. Sediments from this environment were recovered during Ocean Drilling Program (ODP) Leg 201, and were analyzed by both molecular biological and organic geochemical techniques. Of particular interest in these sediments were four sulfate/methane transition zones (SMTZ) seen at ODP Sites 1227, 1229 and 1230, two of which coincided with strongly elevated cell counts. Archaeal cells in these zones were analyzed for abundance and d13C composition by whole cell analysis (FISH-SIMS) and intact membrane lipids (HPLC-ESI-MSn). Fluorescent in-situ hybridization cell counts showed greater archaeal abundance than bacterial, which was reflected by intact membrane lipid abundance. Isotopic compositions by both techniques (often around -20?) suggest that methane is not an important carbon source for these cells. Autotrophic carbon fixation appears to be an unlikely metabolism given the relationship between the isotopic composition of DIC and archaeal biomass. The isotopic evidence suggests that the bulk archaeal community is heterotrophic, possibly mediating the oxidation of methane without consuming it as a carbon source. This novel information about the metabolism of uncultivated deeply buried Archaea raises interesting new questions regarding the significance of the elevated cell counts and archaeal activity at SMTZs in deep marine sediments.


References:
Orphan, V. J., Ussler III, W., Naehr, T., House,  C.H., Hinrichs, K. U. and Paull,  C. K., 2004.  Geological, Geochemical, and Microbiological Heterogeneity of the Seafloor Around Methane Vents in the Eel River Basin, offshore California.  Chemical Geology, 205:  265-289.  

D’Hondt, S., and 34 others., 2004.  Distributions of Microbial Activities in Deep Subseafloor Sediments.  Science, 306: 2216-2221.


 02/16/05

Speaker: Dr. Valeria Souza - National Autonomous University of Mexico


Title: "Which is the unit of selection in E. coli?"


Abstract: 
Comparative genomic analysis is a powerful tool for understanding the history and organization of complete genomes.  The mathematical tools of population genetics combined with genomic analysis provide a powerful approach to dissect heterogeneities in genome evolution. This study presents a hierarchical analysis of the island LEE (35kb), which is found in the pathogenic E. coli strains EPEC and EHEC and in Citrobacter rodentium. The LEE locus in E.coli is considered to be a clonal unit inside a clonal organism and is expected to evolve as a single unit. This analysis examines the clonal assumption by determining genetic diversity, GC content and the substitution rates at the different functional levels of (1) the complete pathogenic island, (2) the five operons in which the island is organized, and (3) for each of the individual 41 genes that comprise the locus. We find that there is a conserved region that is composed of genes that belong to the Type III Secretion System (TTSS) and that may be products of horizontal transfer. A more diverse region is composed of genes for secreted proteins and genes that we infer to be original components of the E.coli genome. This genetic mosaic seems to be differentially affected by selection and mutation. Our results suggest that recombination and selection may be breaking this structure so that different elements are at best weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather much smaller units within the island.


References:
Castillo, A., L.E. Eguiarte, and V. Souza.  2005.  A genomic population genetics analysis of the pathogenic locus of the enterocyte effacement island in Escherichia coli: The search for the unit of selection.  Proc. Natl. Acad. Sci. USA in press.

Bjedov, I.,  O. Tenaillon, B. Gerard, V. Souza, E. Denamur, M. Radman,F. Taddei, and I. Matic1.  2003.  Stress-Induced Mutagenesis in Bacteria.  Science 300:1404-1409
 
Peek, A.S., V. Souza,  L.E. Eguiarte, and B.S. Gaut. 2001. The Interaction of Protein Structure, Selection, and Recombination on the Evolution of the Type-1 Fimbrial Major Subunit (fimA) from Escherichia coli. J Mol Evol 52:193–204


 02/23/05

Speaker: Dr. Alexander Bolshoy - Institute of Evolution, University of Haifa and School of Informatics, Indiana University


Title: "Overlapping messages as a strategy for vulnerability reduction."


Abstract:
The phenomenon of overlapping of various sequence messages in genomes is a puzzle for evolutionary theoreticians, geneticists, and sequence researchers. The overlapping is possible due to degeneracy of the messages, in particular, degeneracy of codons. It is often observed in organisms with a limited size of genome, possessing polymerases of low fidelity. The most accepted view considers the overlapping as a mechanism to increase the amount of information per unit length. Here we present a model that suggests direct evolutionary advantage of the message overlapping. Two opposing drives are considered: (a) reduction in the amount of vulnerable points when the overlapping of two messages involves common critical points and (b) cumulative compromising cost of coexistence of messages at the same site. Over a broad range of conditions the reduction of the target size prevails, thus making the overlapping of messages advantageous.


References:
Peleg O, Kirzhner V, Trifonov E, Bolshoy A. Overlapping messages and survivability. J Mol. Evol. 2004 Oct;59(4):520-7.


 03/02/05

Speaker: Dr. Eric Harvill - Department of Veterinary Science


Title: "Effects of host population dynamics on evolution of the bordetellae."


Abstract: Infectious diseases with high transmission rates and long lasting immunity result in disease primarily in children and immune adults.  Under these conditions there is strong selection for the ability to reinfect immune hosts.  Although whooping cough is considered a childhood disease, there is substantial evidence that children are infected by asymptomatic adult carriers, and there are increasing numbers of adult cases of Bordetella pertussis disease.  In order to improve the control of this and other such diseases it is critical to understand how B. pertussis is able to remain endemic even in highly vaccinated or immune populations.  Acute, highly contagious, immunizing pathogens face the significant epidemiological challenge of long-term persistence within the host population.  Immunity results in depletion of susceptible hosts through the course of each epidemic, thereafter host replenishment requires births or loss of immunity -- which is why pathogens that convey perfect immunity result in ‘childhood diseases’ (22).  Rapid contagion, in turn, results in fast transmission among hosts, which is a short-term evolutionary benefit to the pathogen (11, 5).  However, it also results in large-amplitude epidemics with intervening deep epidemic troughs; In small and medium host populations the chain of transmission will be broken in the troughs so that the pathogen will go extinct.  The most relevant theoretical models for childhood infections, the so-called realistic age-structured (RAS) models (4, 18), predict an endemic threshold of around 1/2 million hosts for transmission to be sustained through the epidemic troughs of acute, immunizing infections.  This prediction is closely matched by epidemiological surveillance data (3, 10).  Previous theoretical studies have highlighted two key adaptations that increase the height of the epidemic troughs to allow long-term endemism within smaller host communities.  These are: (1) reinfection of previously immunized hosts and adult carriers and (2) prolongation of the infectious period (5).  Our study is of wide epidemiological significance in showing that B. pertussis, through expression of PTX, slows migration of neutrophils and thereby extends the infection period (relative to B. pertussisDptx strains) and allow for transient reinfection of previously immunized hosts.  PTX expression may, therefore, be a key adaptation by B. pertussis for interacting with the unique population dynamics of its human host.


References:
15.  Burns, V.C., Pishko, E.J., Preston, A., Maskell, D.J. and Harvill, E.T., The Role of Bordetella O-antigen in Respiratory Tract Infection (2003), Infection and Immunity,71(1):86-94.

16.  Kirimanjeswara, G.S., Mann, P.B., Harvill, E.T., (2003) The Role of Antibodies in Immunity to Bordetella Infections, Infection and Immunity, 71(4):1719-1724.

17.  Preston, A., Maxim, E., Toland, E., Pishko, E.J., Harvill, E.T., Caroff, M., and Maskell, D.J. (2003) Bordetella bronchiseptica PagP is a Bvg-regulated lipid A palmitoyl transferase that is required for persistent colonisation of the mouse respiratory tract.  Molecular Microbiology, 48(3):725-736.

18.  Pishko, E.J., Betting, D.J., Hutter, C.S. and Harvill, E.T., (2003) Bordetella pertussis Acquires Resistance to Complement Mediated Killing in vivo. Infection and Immunity,
71(9):4936-42.

19.  Mann, P.B., Kennett, M.J., Harvill, E.T., (2004),
Toll-Like Receptor 4 Is Critical to Innate Host Defense in a Murine Model of Bordetellosis.  J Infect Dis. 2004 Mar 1;189(5):833-836.

20.  Pishko, E.J., Kirimanjeswara, G.S, Gopinathan, L., Pilione, M.R., Kennett, M.J. and Harvill, E.T., (2004) Antibody-mediated Bacterial Clearance from the Lower Respiratory Tract of Mice Requires Complement Component C3.
Eur J Immunol.
34(1):184-93.

21.
 Liu, M., Liu, Y., Doulatov, S.R., Gingery, M., Eiserling, F.A., Baker, S., Davis, P., Preston, A., Maskell, D.J., Harvill, E.T., Parkhill, J. and Miller, J.F. (2004) Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes.
J Bacteriol. 186(5):1503-17.

22.  Pilione MR, Pishko EJ, Preston A, Maskell DJ, Harvill ET. (2004) pagP is required for resistance to antibody-mediated complement lysis during Bordetella bronchiseptica respiratory infection. Infection and Immunity. 72(5):2837-42.

23.  Mann, P.B., Elder, K.D., Kennett, M.J., and Harvill, E.T. (2004), TLR4 Dependent Early Elicited TNFa Expression is Critical for Innate Host Defense Against Bordetella bronchiseptica. Infection and Immunity. 72(11):6650-8.

24.  Elder, K.D. and Harvill, E.T. (2004).  Strain-Dependent Role of BrkA during Bordetella pertussis Infection of the Murine Respiratory Tract.  Infection and Immunity, 72(10):5919-24.


 03/09/05

No Classes - SPRING BREAK


 03/16/05

Speaker: Dr. Webb Miller - Department of Biology


Title: "Reconstructing the Genome Sequences of Ancient Mammals."


Abstract: To optimally organize genome sequence data from placental mammals, the genome browser at Santa Cruz is adopting an evolutionary perspective. The basic mammalian genome sequence, to which sequenced genomes are related by identified evolutionary operations, will be a computational reconstruction of the genome of a mammalian ancestor, as perhaps existed 100 million years ago. Moreover, we intend to provide reconstructions of genomes that existed at time points intermediate between that ancestor and modern mammals, together with an accounting of the evolutionary operations that occurred on each branch of the phylogenetic tree.  We outline the reconstruction procedure, describe approaches for validating its results, and present some of what it has taught us about the evolution of mammalian genomes.


References:
M. Blanchette, E. Green, W. Miller, and D. Haussler (2004) Reconstructing large regions of an ancestral mammalian genome in silico. Genome Research 14, 2412-2423.


 03/23/05

Speaker: Dr. Kateryna Makova - Department of Biology


Title:  "Strong and weak male mutation bias at different sites in the primate genomes: Insights from the human-chimpanzee comparison."


Abstract:
While several studies indicated male bias for nucleotide substitutions in primates, they disagreed about the magnitude of this bias. Furthermore, it is presently unknown whether all types of nucleotide substitutions exhibit male bias and thus result from errors in DNA replication. Here we investigate male mutation bias using human-chimpanzee whole-genome alignments. When all nucleotide substitutions are considered together, male mutation bias is strong: the male-to-female mutation rate ratio (alpha) is ~4-6, similar to the male-to-female ratio in the number of germline cell divisions. This suggests that most substitution mutations that occurred in the human and chimpanzee lineages since their common ancestor were caused by errors in DNA replication. The observed bias is not explained by regional variation in substitution rate. Remarkably, while male mutation bias is strong at non-CpG sites (alpha is around 4-6), it is weak at CpG dinucleotides (alpha is around 2), which are usually methylated. This is consistent with the methylation-induced and replication-independent origin of transitions leading to loss of CpG sites. In contrast, unmethylated CpG sites located in CpG islands exhibit strong male mutation bias, suggesting that mutations at these sites are replication-dependent. Thus, the strength of male mutation bias appears to be non-uniform in the primate genomes.


 03/30/05

Speaker: Dr. Anton Nekrutenko - Department of Biochemistry and Molecular Biology


Title: "Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: an XLas/ALEXrelay."


Abstract:
XLas and ALEX are structurally unrelated mammalian proteins translated from alternative overlapping reading frames of a single transcript. Not only are they encoded by the same locus, but a specific XLas/ALEX interaction is essential for G-protein signaling in neuroendocrine cells. A disruption of this interaction leads to abnormal human phenotypes including mental retardation and growth deficiency. The region of overlap between the two reading frames evolves at a remarkable speed: the divergence between human and mouse ALEX polypeptides makes them virtually unalignable! To trace the evolution of this puzzling locus, we sequenced it in apes, Old World monkeys, and a New World monkey. We show that the overlap between the two reading frames and the physical interaction between the two proteins forces the locus to evolve in an unprecedented way. Namely, to maintain two overlapping protein-coding regions the locus is forced to have high GC content, which significantly elevates its intrinsic evolutionary rate. However, the two encoded proteins cannot afford to change too quickly relative to each other as this may impair their interaction and lead to severe physiological consequences. As a result XLas and ALEX evolve in an oscillating fashion constantly balancing the rates of amino acid replacements. This is the first example of a rapidly evolving locus encoding interacting proteins via overlapping reading frames with a possible link to the origin of species-specific neurological differences.


 04/06/05

Speaker: Valer Gotea - Department of Biology


Title: "Transposable elements contributed to proteomes: support from molecular evolution and phylogenetics."


Abstract:
With an initial dataset restricted to proteins likely to be functional, we showed that about 2% of human proteins contain fragments encoded by TE-like sequences. As most of the TE-cassettes found have low alignment scores, we attempted to reconstruct the phylogeny of every protein, to demonstrate when and how the exaptation of TE cassettes occurred. As the presence of most protein TE cassettes found can be reasonably explained in a phylogenetic context, TEs should be regarded as an important factor that contributed to the evolution of genomes.


References:
Lorenc A. and Makalowski W. (2003) Transposable Elements and Vertebrate Protein Diversity. Genetica, 118: 183-191.


 04/13/05

Speaker: Dr. Laura Zahn - Department of Biology


Title: "Evolution of the SEPALLATA subfamily: A Pre-Angiosperm Origin of a Potentially Floral Specific MADS-box gene."


Abstract: 
Members of the SEPALLATA (SEP) MADS-box subfamily are required for specifying the “floral state” by contributing to floral organ and meristem identity. SEP genes have not been detected in gymnosperms and have previously been hypothesized to have originated since the lineage leading to extant angiosperms diverged from extant gymnosperms. Therefore, both functional and evolutionary studies suggest they may have been critical for the origin of the flower. To gain insights into the evolution of SEP genes, we isolated nine genes from plants that occupy phylogenetically important positions. Phylogenetic analyses of SEP sequences show that several gene duplications occurred during the evolution of this subfamily providing potential opportunities for functional divergence. The timing of the first SEP duplication approximately coincides with duplications in the DEFICIENS/GLOBOSA and AGAMOUS MADS-box subfamilies, which may have resulted from either a proposed genome-wide duplication in the ancestor of extant angiosperms or multiple independent duplication events. Regardless of the mechanism of gene duplication, these pairs of duplicate transcription factors provided new possibilities of genetic interactions that may have been important in the origin of the flower.


References:
DITTA, G., A. PINYOPICH, P. ROBLES, S. PELAZ and M. F. YANOFSKY, 2004 The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Curr Biol 14: 1935-1940.

PELAZ, S., G. S. DITTA, E. BAUMANN, E. WISMAN and M. F. YANOFSKY, 2000 B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature 405: 200-203.

ZAHN, L. M.,  H. KONG, J. H. LEEBENS-MACK, S. KIM, P. S. SOLTIS, L. L. LANDHERR, D. E. SOLTIS, C. W. dePAMPHILIS, and H. MA, 2005. The Evolution of the SEPALLATA subfamily of MADS-box genes:  A pre-angiosperm origin with multiple duplications throughout angiosperm history.  Genetics.  In press.


 04/20/05

Speaker: Jaime Blair - Department of Biology


Title: "Evolutionary Sequence Analysis of Complete Eukaryote Genomes."


Abstract: 
Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation. Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies. Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes.


References:
JE Blair & SB Hedges (2005) BMC Bioinformatics 6:53.


 04/27/05

Speaker: Wei Hu - Department of Biology


Title: "Evolutionary and functional study of zinc finger homeodomain protein family."


Abstract: 
Zinc finger homeodomain protein (ZF-HD) family was recently recognized in plants. These proteins have a putative novel zinc finger domain at N terminus that functions for homo- and hetero-dimer formation. The C-terminal homeodomain is distantly related to the classic homeodomains and was demonstrated to be able to bind to DNA. However, the evolutionary history and in vivo function of these ZF-HD proteins are largely unknown. Our studies show that the origin of this family can be traced back to the earliest land plant Physcomitrella, but not unicellular green algae Chlamydomonas.  The complete genome of Arabidopsis, rice and poplar indicates the size of ZF-HD family is quite stable. Gene duplication is studies in particular in Arabidopsis, along with examination of gene expression pattern. The challenge of functional study of this family using reversed genetics approach is evaluated with our current experimental results and understanding of their evolutionary aspect. We further identified a group of small genes with only the N-terminal zinc finger domain, which we named them as MINI ZINC FINGER (MIF). These MIF proteins are highly conserved at least among seed plants, as indicated by analysis of available sequences. The possibility that MIF proteins evolved from the loss of HD domain of ZF-HD proteins, or ZF-HD proteins evolved from the gain of HD domain of MIF proteins is addressed from sequence analysis and phylogenetic perspective. Overexpression of one of Arabidopsis MIF genes resulted in pleiotropic growth defects. Phenotypic, physiological, and whole-genome expression profiling analyses all suggest that multiple hormonal signaling pathways were interfered in the transgenic plants. Our long-term goal is to elucidate ZF-HD family, plus its MIF subfamily, as important plant regulatory genes throughout evolution. 


Reference: Windhovel A, Hein I, Dabrowa R, Stockhaus J (2001) Characterization of a novel class of plant homeodomain proteins that bind to the C4 phosphoenolpyruvate carboxylase gene of Flaveria trinervia. Plant Mol Biol 45: 201-214