Digital Commons Network^™

Evidence That Talin Alternative Splice Variants From Ciona Intestinalis Have Different Roles In Cell Adhesion, Richard H. Singiser, Richard O. Mccann

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Talins are large, modular cytoskeletal proteins found in animals and amoebozoans such as Dictyostelium discoideum. Since the identification of a second talin gene in vertebrates, it has become increasingly clear that vertebrate Talin1 and Talin2 have non-redundant roles as essential links between integrins and the actin cytoskeleton in distinct plasma membrane-associated adhesion complexes. The conserved C-terminal I/LWEQ module is important for talin function. This structural element mediates the interaction of talins with F-actin. The I/LWEQ module also targets mammalian Talin1 to focal adhesion complexes, which are dynamic multicomponent assemblies required for cell adhesion and cell motility. Although Talin1 is …

Homologous Neurons And Their Locomotor Functions In Nudibranch Molluscs, James M. Newcomb

Biology Dissertations

These studies compare neurotransmitter localization and the behavioral functions of homologous neurons in nudibranch molluscs to determine the types of changes that might underlie the evolution of species-specific behaviors. Serotonin (5-HT) immunohistochemistry in eleven nudibranch species indicated that certain groups of 5 HT-immunoreactive neurons, such as the Cerebral Serotonergic Posterior (CeSP) cluster, are present in all species. However, the locations and numbers of many other 5 HT-immunoreactive neurons were variable. Thus, particular parts of the serotonergic system have changed during the evolution of nudibranchs. To test whether the functions of homologous neurons are phylogenetically variable, comparisons were made in species …

Insights Into Transcription Enhancer Factor 1 (Tef-1) Activity From The Solution Structure Of The Tea Domain, Asokan Anbanandam, Diana C Albarado, Catherine T Nguyen, Georg Halder, Xiaolian Gao, Sudha Veeraraghavan

Journal Articles

Transcription enhancer factor 1 is essential for cardiac, skeletal, and smooth muscle development and uses its N-terminal TEA domain (TEAD) to bind M-CAT elements. Here, we present the first structure of TEAD and show that it is a three-helix bundle with a homeodomain fold. Structural data reveal how TEAD binds DNA. Using structure-function correlations, we find that the L1 loop is essential for cooperative loading of TEAD molecules on to tandemly duplicated M-CAT sites. Furthermore, using a microarray chip-based assay, we establish that known binding sites of the full-length protein are only a subset of DNA elements recognized by TEAD. …

Comparative Analysis Of Vertebrate Eif2ak2 (Pkr) Genes And Assignment Of The Equine Gene To Eca15q24-Q25 And The Bovine Gene To Bta11q12-Q15, Andrey A. Perelygin, Teri L. Lear, Andrey A. Zharkikh, Margo A Brinton

Veterinary Science Faculty Publications

The structures of the canine, rabbit, bovine and equine EIF2AK2 genes were determined. Each of these genes has a 5' non-coding exon as well as 15 coding exons. All of the canine, bovine and equine EIF2AK2 introns have consensus donor and acceptor splice sites. In the equine EIF2AK2 gene, a unique single nucleotide polymorphism that encoded a Tyr329Cys substitution was detected. Regulatory elements predicted in the promoter region were conserved in ungulates, primates, rodents, Afrotheria (elephant) and Insectifora (shrew). Western clawed frog and fugu EIF2AK2 gene sequences were detected in the USCS Genome Browser and compared to those of other …

Gene Order Data From A Model Amphibian (Ambystoma): New Perspectives On Vertebrate Genome Structure And Evolution, Jeramiah J. Smith, S. Randal Voss

Biology Faculty Publications

BACKGROUND: Because amphibians arise from a branch of the vertebrate evolutionary tree that is juxtaposed between fishes and amniotes, they provide important comparative perspective for reconstructing character changes that have occurred during vertebrate evolution. Here, we report the first comparative study of vertebrate genome structure that includes a representative amphibian. We used 491 transcribed sequences from a salamander (Ambystoma) genetic map and whole genome assemblies for human, mouse, rat, dog, chicken, zebrafish, and the freshwater pufferfish Tetraodon nigroviridis to compare gene orders and rearrangement rates.

RESULTS: Ambystoma has experienced a rate of genome rearrangement that is substantially lower than mammalian …

Phylogeny Of The Parasitic Plant Family Orobanchaceae Inferred From Phytochrome A, Jonathan R. Bennett, Sarah Mathews

Faculty Publications

Partial sequences of the nuclear gene encoding the photoreceptor phytochrome A (PHYA) are used to reconstruct relationships within Orobanchaceae, the largest of the parasitic angiosperm families. The monophyly of Orobanchaceae, including nonphotosynthetic holoparasites, hemiparasites, and nonparasitic Lindenbergia is strongly supported. Phytochrome A data resolve six well-supported lineages that contain all of the sampled genera except Brandisia, which is sister to the major radiation of hemiparasites. In contrast to previous plastid and ITS trees, relationships among these major clades also are generally well supported. Thus, the robust phylogenetic hypothesis inferred from the PHYA data provides a much better context in which …

Evolutionary Genetics Of The Family Placobranchidae (Mollusca: Gastropoda: Opisthobranchia: Sacoglossa), Anna Lee Bass

USF Tampa Graduate Theses and Dissertations

Members of the family Placobranchidae have been the focus of numerous studies because of their interesting physiological adaptations (kleptochemistry and kleptoplasty) and ecological associations with marine algae. More than 100 species have been described since the 1800's, but no determination of phylogenetic relationships in the family has occurred. DNA sequences from two mitochondrial genes (large subunit ribosomal and cytochrome c oxidase subunit I) and one nuclear gene (Histone 3) were used to reconstruct relationships among 34 nominal species within the Placobranchidae. Strong support for terminal nodes was found using Bayesian phylogenetic methods; however, a "soft" polytomy was detected at internal …

Post-Miocene Expansion, Colonization, And Host Switching Drove Speciation Among Extant Nematodes Of The Archaic Genus Trichinella, D. S. Zarlenga, B. M. Rosenthal, G. Larosa, E. Pozio, Eric P. Hoberg

Harold W. Manter Laboratory of Parasitology: Faculty and Staff Publications

Parasitic nematodes of the genus Trichinella cause significant food-borne illness and occupy a unique evolutionary position at the base of the phylum Nematoda, unlike the free-living nematode Caenorhabditis elegans. Although the forthcoming genome sequence of Trichinella spiralis can provide invaluable comparative information about nematode biology, a basic framework for understanding the history of the genus Trichinella is needed to maximize its utility. We therefore developed the first robust and comprehensive analysis of the phylogeny and biogeographic history of Trichinella using the variation in three genes (nuclear small-subunit rDNA, and second internal transcribed spacer, mitochondrial large-subunit rDNA, and cytochrome oxidase …

Phylogeny And Androecial Evolution In Schisandraceae, Inferred From Sequences Of Nuclear Ribosomal Dna Its And Chloroplast Dna TrnL-F Regions, Zhong Liu, Gang Hao, Yi-Bo Luo, Leonard B. Thien, Samuel W. Rosso, An-Ming Lu, Zhi-Duan Chen

Faculty Publications

Sequences of nuclear ribosomal DNA ITS and chloroplast trnL‐F regions were used to construct a phylogeny of Schisandraceae. The results show that there are two major clades in Schisandraceae. One is composed entirely of Schisandra species; the other contains a mixture of Schisandra and Kadsura species. Molecular data place Smith’s sect. Sphaerostema of Schisandra prominently within Kadsura, and thus neither Schisandra nor Kadsura is monophyletic, refuting the traditional division of the family into two genera based on morphological characters of mature fruits. The sister relationship between S. glabra (North America) and S. bicolor (China) and the monophyly of …

Phylogenetic Approach To The Study Of Triatomines (Triatominae, Heteroptera) = Abordagem Filogenética Em Triatomíneos (Triatominae, Heteroptera), Ester Tartarotti, Maria Tercília Vilela De Azeredo-Oliveira, Carlos Roberto Ceron

Harold W. Manter Laboratory: Library Materials

Triatomines are insects belonging to the Hemiptera order, Heteroptera suborder, Reduviidae family and Triatominae subfamily. All members of this subfamily are hematophagous. Triatomines evolved from Reduviidae predators and they are probably polyphyletic in origin. The combination of anatomical, physiological and ethological factors observed in this group, as well as the plesiomorphic and apomorphic characters that differentiate the five tribes and fourteen triatomine genera reinforce the polyphiletic hypotesis. However if we consider the five groups of triatomines, the Rhodniini, Cavernicolini, Bolboderini, Linshcosteini and Alberproseniini tribes constitute monophyletic groups, while the Triatomini tribe is considered polyphyletic. The New World is the center …

Functional Analysis Of The Amine Substrate Specificity Domain Of Pepper Tyramine And Serotonin N-Hydroxycinnamoyltransferases, Sei Kang, Kiyoon Kang, Gap Chae Chung, Doil Choi, Atsushi Ishihara, Dong-Sun Lee, Kyoungwhan Back

Journal Articles

Pepper (Capsicum annuum) serotonin N-hydroxycinnamoyltransferase (SHT) catalyzes the synthesis of N-hydroxycinnamic acid amides of serotonin, including feruloylserotonin and p-coumaroylserotonin. To elucidate the domain or the key amino acid that determines the amine substrate specificity, we isolated a tyramine N-hydroxycinnamoyltransferase (THT) gene from pepper. Purified recombinant THT protein catalyzed the synthesis of N-hydroxycinnamic acid amides of tyramine, including feruloyltyramine and p-coumaroyltyramine, but did not accept serotonin as a substrate. Both the SHT and THT mRNAs were found to be expressed constitutively in all pepper organs. Pepper SHT and THT, which have primary sequences that are 78% identical, were used as models …

A Comparison And Combination Of Plastid Atpb And Rbcl Gene Sequences For Inferring Phylogenetic Relationships Within Orchidaceae, Kenneth M. Cameron

Aliso: A Journal of Systematic and Floristic Botany

Parsimony analyses of DNA sequences from the plastid genes atpB and rbcL were completed for 173 species of Orchidaceae (representing 150 different genera) and nine genera from outgroup families in Asparagales. The atpB tree topology is similar to the rbcL tree, although the atpB data contain less homoplasy and provide greater jackknife support than rbcL alone. In combination, the two-gene tree recovers five monophyletic clades corresponding to subfamilies within Orchidaceae, and fully resolves them with moderate to high jackknife support as follows: Epidendroideae are sister to Orchidoideae, followed by Cypripedioideae, then Vanilloideae, and with …

Phylogenetic Analyses And Biogeography Of Trilliaceae, Susan B. Farmer

Aliso: A Journal of Systematic and Floristic Botany

Trilliaceae are plants of North Temperate forests with a holarctic distribution and a high degree of endemism. Molecular phylogenetic analyses are presented in order to examine the tribal, generic, and species-level classification of the family. These molecular studies, and earlier morphological studies, support the placement of the genus Pseudotrillium as basal in the family and sister to the tribes Trillieae and Parideae, which are monophyletic sister groups. Trillidium (Trillium) govanianum provides an unresolved problem: morphologically it is included within Parideae, but molecular data place it within Trillium as sister to T. undulatum. Within tribe Trillieae, clades are …

Mitochondrial Data In Monocot Phylologenetics, Gitte Peterson, Ole Seberg, Jerrold I. Davis, Douglas H. Goldman, Dennis W. Stevenson, Lisa M. Campbell, Fabian A. Michaelangeli, Chelsea D. Specht, Mark W. Chase, Michael E. Fay, J. Chris Pires, John V. Freudenstein, Christopher R. Hardy, Mark P. Simmons

Aliso: A Journal of Systematic and Floristic Botany

Mitochondrial sequences are an important source of data in animal phylogenetics, equivalent in importance to plastid sequences in plants. However, in recent years plant systematists have begun exploring the mitochondrial genome as a source of phylogenetically useful characters. The plant mitochondrial genome is renowned for its variability in size, structure, and gene organization, but this need not be of concern for the application of sequence data in phylogenetics. However, the incorporation of reverse transcribed mitochondrial genes ("processed paralogs") and the recurring transfer of genes from the mitochondrion to the nucleus are evolutionary events that must be taken into account. RNA …

Fleshy Fruits In Liliflorous Monocots, Finn N. Rasmussen, Signe Frederikson, Bo Johansen, Lise Bolt Jørgenson, Gitte Peterson

Aliso: A Journal of Systematic and Floristic Botany

Fleshy fruits occur in several monocot orders and families, and it is generally assumed that they have been derived from capsular fruits many times during the evolution of monocot lineages. Huber hypothesized in 1969 that most capsules in Asparagales are derived secondarily from berries and that this transformation was correlated with the evolution of phytomelan-coated seeds, a pivotal character in his circumscription of Asparagales as part of reclassifying Liliaceae s.l. Dahlgren and co-workers suggested several parallel derivations and "reversals" in this character, e.g., the transformation sequence trifollicular fruits → capsules → berries→ capsules→ berries. Mapping of fleshy fruits on a …

Speciation In Duckweeds (Lemnaceae): Phylogenetic And Ecological Inferences, Daniel J. Crawford, Elias Landolt, Donald H. Les, Rebecca T. Kimball

Aliso: A Journal of Systematic and Floristic Botany

Species of duckweeds (Letnnaceae) that were resolved as sister taxa in a phylogeny based on combined molecular and non-molecular data were compared for morphological, physiological, and ecological attributes to infer factors important in the initial divergence leading to speciation. The ability to survive extreme conditions such as desiccation and cold temperatures is the most common difference identified between species. Two morphological characters facilitating survival in extreme environments are production of special resting buds called turions and increased seed production. The prevalent geographic pattern for species pairs consists of one restricted species occurring on the periphery of a more widespread taxon; …

A Phylogenetic Study Of Arecaceae Based On Seedling Morphological And Anatomical Data, Flor M. Henderson, Dennis W. Stevenson

Aliso: A Journal of Systematic and Floristic Botany

A morphological and anatomical survey was carried out of seedlings of 62 taxa of palms representing all major groups. The data were analyzed using cladistic parsimony analysis. Seedling data were analyzed independently and combined with adult morphological data. Outgroup selection was made within the family using the calamoids and Nypa fruticans; outside the family, the monocot family Dasypogonaceae were used. The analysis with the calamoids and Nypa fruticans as outgroups resolved some of the major groups. The combined analysis, using both seedling and adult data and Dasypogonaceae as the outgroup, provided better resolution. Most of the major groups were …

Phylogeny Of Agavaceae Based On Ndhf, Rbcl, And Its Sequences, David J. Bogler, J. Chris Pires, Javier Francisco-Ortega

Aliso: A Journal of Systematic and Floristic Botany

Great advances have been made in our understanding of the phylogeny and classification of Agavaceae in the last 20 years. In older systems Agavaceae were paraphyletic due to overemphasis of ovary position or habit. Discovery of a unique bimodal karyotype in Agave and Yucca eventually led to a reexamination of concepts and relationships in all the lilioid monocots, which continues to the present day. Developments in cytogenetics, microscopy, phylogenetic systematics, and most recently DNA technology have led to remarkable new insights. Large-scale rbcL sequence studies placed Agavaceae with the core Asparagales and identified closely related taxa. Analysis of cpDNA …

The Never-Ending Story: Multigene Approaches To The Phylogeny Of Amaryllidaceae, Alan W. Meerow, Deirdre A. Snuman

Aliso: A Journal of Systematic and Floristic Botany

a whole, strongly supported the mostly African tribe Amaryllideae as sister to the rest of the family, and resolved geographically-based monophyletic groups, but failed to resolve the relationships among several basal lineages in the family (the African Haemantheae and Cyrtantheae, the Australasian Calostemmateae, and the American and Eurasian sister clades). We present analysis of plastid ndhF sequences that fully resolved the major clades of the family. The baccate-fruited Haemantheae and Calostemmateae are sister tribes, and the African endemic Cyrtantheae is sister to them both. This clade is sister to an American/Eurasian clade. We also present preliminary nuclear ribosomal ITS …

Phylogeny Of Iridaceae Subfamily Crocoideae Based On A Combined Multigene Plastid Dna Analysis, Peter Goldblatt, T. Jonathan Davies, John C. Manning, Michelle Van Der Bank, Vincent Savolainen

Aliso: A Journal of Systematic and Floristic Botany

The phylogeny of Crocoideae, the largest of four subfamilies currently recognized in Tridaceae, has eluded resolution until sequences of two more plastid DNA regions were added here to a previously published matrix containing sequences from four DNA plastid regions. Sister to the core Nivenioideae, the woody Klattia, Nivenia, and Witsenia, Crocoideae are a climax group in lridaceae, comprising some 995 species, slightly more than half of the total in the family. Synapomorphies of Crocoideae include pollen exine perforate, pollen aperture operculate, ovule campylotropous (or hypotropous), root xylem vessels with simple perforations, cormous rootstock, inflorescence a spike, and plants deciduous. The …

Patterns In Evolution In Characters That Define Iris Subgenera And Sections, Carol A. Wilson

Aliso: A Journal of Systematic and Floristic Botany

Subgeneric groups have been circumscribed in Iris based on a small number of morphological characters. Recent DNA sequence data has indicated that several of the subgenera, sections, and series that have previously been delineated are paraphyletic or polyphyletic. The evolution of characters that have traditionally been used to distinguish sub generic and sectional groups within Iris was investigated by mapping these characters on a phylogenetic tree based on matK sequence data. Results indicate that rhizomes are pleisomorphic for the genus and that three bulb types have arisen independently. My analysis shows that sepal beards, sepal crests, and seed arils …

The Role Of Phylogenetic Constraints In The Evolution Of Pollination Mechanisms In Iridaceae Of Sub-Saharan Africa, Peter Bernhardt, Peter Goldblatt

Aliso: A Journal of Systematic and Floristic Botany

Novel, specialized systems exploiting bibionid flies, oil-collecting bees, wasps, or crepuscular settling moths as pollen vectors are added to the range of recorded pollination mechanisms in sub-Saharan Africa Iridaceae, while knowledge of the pollination of previously understudied genera such as Aristea, Bahiana, Ferraria, Hesperantha, and Tritoniopsis is expanded. The pollination of 357 species of the sub-Saharan African Iridaceae now includes 17 discrete systems. Based on repetitive interlinked suites of floral attractants and rewards we now infer pollination mechanisms for an additional 883 species. Many pollination systems recur in genera containing > 10 species. The ancestral pollination in African Iridaceae, and …

Phlogeny And Biogeography Of The Prayer Plant Family, Linda M. Prince, W. John Kress

Aliso: A Journal of Systematic and Floristic Botany

Marantaceae are the second largest family in the order Zingiberales, with approximately 31 genera and 535 species. Earlier studies based on morphological and molecular characters could not confidently determine the relationships among major lineages of the family, nor could they identify the basal branch of the family tree. Phylogenetic analyses of DNA sequence data from all three genomic compartments (chloroplast: matK, ndhF, rbcL, rps16 intron, and trnL-trnF intergenic spacer; mitochondrion: cox1; nucleus: ITS region and the 5'-end of 26S) for a restricted set of taxa were conducted under parsimony criteria to define …

Systematic Floral Anatomy Of Pontederiaceae, Michael G. Simpson, Darren H. Burton

Aliso: A Journal of Systematic and Floristic Botany

Twenty species of Pontederiaceae and six species of the outgroup families Haemodoraceae and Philydraceae were investigated with regard to floral anatomy, using standard histological methods and graphic reconstructions. Variation is described in several features, including functional carpel number, the distribution of floral aerenchyma, the presence of unusual floral epithelial cells, the presence, type, and distribution of tannin cells, crystal type and distribution, aspects of placentation, ovule number, number of ovule rows per carpel, and septal nectary presence. In order to better assess character homology, one of these features, placentation, was divided into three discrete characters: septal fusion, placenta position, and …

A Novel Approach To Phylogenetic Tree Construction Using Stochastic Optimization And Clustering, Ling Qin, Yixin Chen, Yi Pan, Ling Chen

Computer Science Faculty Publications

Background: The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology.

Results: A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects.

Conclusion: Our phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that …

Myxozoan Genera: Definition And Notes On Taxonomy, Life-Cycle Terminology And Pathogenic Species, Jiří Lom, Iva Dyková

Harold W. Manter Laboratory: Library Materials

A list of myxozoan genera is presented in the current taxonomical scheme. These genera are defined; their type species and most important pathogens along with their hosts are listed. Simultaneously, definitions of actinospore stages representing sexual stages of the myxosporean life cycle are given; altogether, 17 actinospore collective groups with 180 types have been described. Life cycles of the two classes of the phylum Myxozoa, Malacosporea and Myxosporea, are briefly outlined with specification of the appropriate terms. Up to now, 4 malacosporean and 2,180 myxosporean species assigned to a total of 62 genera, have been established. The surviving classification of …

Phylogeny Of Hinterhubera, Novenia And Related Genera Based On The Nuclear Ribosomal (Nr) Dna Sequence Data (Asteraceae: Astereae), Vesna Karaman

LSU Doctoral Dissertations

Analyses of ITS, ETS and matK sequences for genera of the subtribe Hinterhuberinae, including representatives of 17 subtribes from the tribe Astereae, rooted on Anthemideae, Calenduleae and Inuleae, provide no support for the monophyly of the Hinterhuberinae. Chiliotrichum and Celmisia groups, Olearia in part, Novenia, Oritrophium and Pteronia are in the basal group that also includes subtribe Felicinae. Madagaster, Remya, Olearia in part, Achnophora and Hinterhubera group lie in the Southern Hemisphere grade, with Asterinae, Bellidinae, Brachycominae, Grangeinae, Podocominae, Lagenophorinae and Baccharidinae. Monophyly of Asterinae, Grangeinae, Podocominae and Lagenophorinae is not supported. Instead South American representatives of Lagenophorinae, Grangeinae and …

Evolutionary Patterns In Snake Mitochondrial Genomes, Zhijie Jiang

LSU Doctoral Dissertations

In this dissertation I describe a number of patterns and interesting aspects associated with the evolution of snake mitochondrial genomes (mtDNA). I also attempt to resolve the phylogeny of squamates, focusing on the relationship between the snakes and lizards. The results of this study indicate that snakes and worm lizards (amphisbaenians) appear to share an exclusive common ancestor, and snakes appear to have undergone strong selective pressure that shaped snake mtDNAs. Snake mtDNAs have several unique features, including a compact size, duplicated control regions, and an elevated evolutionary rate. Based on the correlation resulting from the asymmetric replication of mtDNA, …

Characterization Of Hard2, A Processed Hard1 Gene Duplicate, Encoding A Human Protein N-Alpha-Acetyltransferase., Thomas Arnesen, Matthew J Betts, Frédéric Pendino, David A Liberles, Dave Anderson, Jaime Caro, Xianguo Kong, Jan E Varhaug, Johan R Lillehaug

Department of Medicine Faculty Papers

BACKGROUND: Protein acetylation is increasingly recognized as an important mechanism regulating a variety of cellular functions. Several human protein acetyltransferases have been characterized, most of them catalyzing epsilon-acetylation of histones and transcription factors. We recently described the human protein acetyltransferase hARD1 (human Arrest Defective 1). hARD1 interacts with NATH (N-Acetyl Transferase Human) forming a complex expressing protein N-terminal alpha-acetylation activity. RESULTS: We here describe a human protein, hARD2, with 81 % sequence identity to hARD1. The gene encoding hARD2 most likely originates from a eutherian mammal specific retrotransposition event. hARD2 mRNA and protein are expressed in several human cell lines. …

Assembly Of The Eastern North American Herpetofauna: New Evidence From Lizards And Frogs, J. Robert Macy, James A. Schulte Ii, Jared L. Strasburg, Jennifer A. Brisson, Allan Larson, Natalia B. Ananjeva, Yuezhao Wang, James F. Parham, Theodore J. Papenfuss

School of Biological Sciences: Faculty Publications

Darwin first recognized the importance of episodic intercontinental dispersal in the establishment of worldwide biotic diversity. Faunal exchange across the Bering Land Bridge is a major example of such dispersal. Here, we demonstrate with mitochondrial DNA evidence that three independent dispersal events from Asia to North America are the source for almost all lizard taxa found in continental eastern North America. Two other dispersal events across Beringia account for observed diversity among North American ranid frogs, one of the most species-rich groups of frogs in eastern North America. The contribution of faunal elements from Asia via dispersal across Beringia is …