BIODIVERSITY, TAXONOMY AND SYSTEMATICS OF NEW WORLD FRESHWATER LEECHES (ANNELIDA: HIRUDINEA) WITH PARTICULAR EMPHASIS ON GLOSSIPHONIID LEECHES AND THEIR BACTERIAL ENDOSYMBIONTS
Author:
Alejandro Oceguera-Figueroa
Year of Dissertation:
2011
The phylum Annelida Lamarck, 1809 includes segmented worms such as leeches, earthworms, lugworms, sandworms and clamworms that inhabit almost all possible environments and places of the world. Leeches (Class Hirudinea) represents only one group of around 680 species out of the approximately 16,500 described species of Annelida. The class Hirudinea has been divided in two groups based on their mouthparts. The order Rhynchobdellida, a paraphyletic assemblage, includes species with a large and eversible proboscis and the order Arhynchobdellida that includes species with a muscular pharynx with or without jaws. Both orders include organisms specialized to feed on vertebrate blood. This study includes the description of eight species of leeches new to science that belong to three families (Glossiphoniidae, Macrobdellidae and Praobdellidae). The phylogenetic relationships of species of three families (Glossiphoniidae, Macrobdellidae and Praobdellidae) and one suborder (Erpobdelliformes) were investigated using molecular and morphological data and a suite of phylogenetic methods (Parsimony, Maximum Likelihood and Bayesain Inference). The description of the new species Tyrannobdella rex (Praobdellidae) and Oxyptychus bora (Macrobdellidae) are discussed in the context of their placement in phylogenies. The phylogenetic study of Erpobdelliformes includes the comparison of alternative classification schemes. Based on the results, the phylogenetic position of the terrestrial and macrophagous Orobdella octonaria (Gastrostomobdellidae) within the Erpobdelliformes is established for the first time. The phylogenetic relationships of the proboscis-bearing species of the genera Haementeria, Helobdella and Placobdella were investigated using a combination of nuclear and mitochondrial markers and Parsimony and Bayesian Inference methods. In addition to the monophyly of Haementeria, Helobdella and Placobdella, the 3 genera formed a monophyletic group notwithstanding their different feeding preferences. The correlation with phylogeny and some morphological traits is shown. These include, eyespot morphology, annulation patterns, shape of the ovisacs, sensory organs on the dorsal surface and presence of bacteriomes. Species of Haementeria and Placobdella have specialized organs called bacteriomes associated with their salivary complex that harbor symbiotic proteobacteria. Using DNA bacterial sequences (16S rRNA), the exclusive association of Haementeria spp. with gammaproteobacteria and Placobdella spp. with alphaproteobacteria is shown. Using pyrosequencing technology, the nucleotide sequences of a DNA sample extracted from the bacteriomes of Placobdella parasitica were analyzed. A total of 1,053,345 DNA fragments were obtained and assembled. Leech and symbiont DNA fragments were separated using Blast tools and 50 bacterial and Helobdella robusta genomes for reference. Finally, the so-called DNA barcoding protocol is discussed and some recommendations were given to increase the information content of the database (Bold system). In addition, DNA barcoding protocol was used to estimate the diversity of species of Helobdella from Mexico.
Genetic, Morphological, and Ecological Relationships Among Populations of the Clam Shrimp, Caenestheriella gynecia.
Year of Dissertation:
2011
Little is known about the ecology of the clam shrimp, Caenestheriella gynecia. Caenestheriella gynecia was first discovered in 1939 in a single pool in Oxford, Ohio. Schmidt and Kiviat (2007) reported four new localities of C. gynecia in New York and New Jersey, three within the Hudson Valley of New York and one in northeastern New Jersey. Caenestheriella gynecia may have originated from a very small founder population due possibly to unusual dispersal vectors from its natural range to the west, in Ohio. Egg samples and hatched individuals were obtained from all study sites and specimens were raised in the lab to estimate several growth and survivorship traits. In the field, puddle habitats were observed between the months of May and August where water quality parameters (i.e., dissolved oxygen, temperature, conductivity and pH, and nutrient composition) were recorded. Genetic comparisons across the study sites were made using nuclear DNA sequencing and random amplified polymorphic DNA (RAPD) analysis. The results of this study presented a wide range in the hydro-chemical and physical characteristics of the ephemeral pools in which C. gynecia seem to tolerate.
FUNCTIONAL EVOLUTION OF THE APETALA1/FRUITFULL GENE LINEAGE
Author:
Natalia Pabon Mora
Year of Dissertation:
2012
Several MADS-box gene lineages involved in flower development have undergone duplications that correlate with the diversification of large groups of flowering plants. In the APETALA1 gene lineage, a major duplication coincides with the origin of the core eudicots, resulting in the euFUL and the euAP1 clades. Arabidopsis FRUITFULL (FUL) and APETALA1 (AP1) function redundantly in specifying floral meristem identity, but function independently in sepal and petal identity (AP1) and in proper fruit development and determinacy (FUL). Many of these functions are largely conserved in other core-eudicot euAP1 and euFUL genes, but notably the role of APETALA1 as an "A-function" (sepal and petal identity) gene is thought to be Brassicaceae-specific. Understanding how functional divergence of the core-eudicot duplicates occurred requires a careful examination of the function of pre-duplication (FUL-like) genes. Using Virus Induced Gene Silencing (VIGS), it is shown that FUL-like genes in Papaver somniferum (opium poppy) and Eschscholzia californica (California poppy) function in axillary meristem growth and in floral meristem and sepal identity, and play a key role in fruit development. Interestingly, in opium poppy, these genes also control flowering time and petal identity, suggesting that AP1/FUL homologs might have been independently recruited in petal organ identity. In contrast, it is shown that the Aquilegia coerulea FUL-like homolog does not appear to play a role in flower or fruit development and instead has been recruited in leaf morphogenesis. In general the FUL-like gene functional repertoire encompasses all roles previously described for the core-eudicot euAP1 and euFUL genes, and subfunctionalization can be postulated as the functional outcome after the major AP1/FUL gene lineage duplication event. However, these results also point to significant functional variability of FUL-like genes within Ranunculales, most likely due to gene duplication and loss, as well as changes of FUL-like protein partners in different taxa.
Role of Toll-NF-kB Signaling in Inflammation and Immune Homeostasis in Drosophila melanogaster
Author:
Indira Paddibhatla
Year of Dissertation:
2011
Inflammation is defined as a localized reaction in response to injury or tissue destruction. It serves to contain or sequester the causative agent. Fundamentally important to human health, inflammation and its aberrant regulation underlie many diseases including cancer, diabetes and heart disease. Like humans, fruit flies respond to infection by coordinating complex defense responses. Parasitic wasps are natural enemies of Drosophila and attack larvae or pupae. They inject one or more eggs, each approximately 100 mm in size, into the hemocoel of the fly larva. Oviposition results either in the development of the wasp larva that gradually eats the Drosophila host tissue, or the host's blood cells encapsulate the wasp egg. In the latter scenario, circulating host blood cells surround the wasp egg and inhibit its development.
AUDITORY PROCESSING OF COMPLEX TONES IN NEWBORN INFANTS
Year of Dissertation:
2010
Pitch extraction from complex acoustic stimuli during neonatal period in infants was examined in this study. It is one of the most fundamental auditory processes. Pitch processing is crucial for speech intonation and musical melody perception. Preferences of newborns for "motherese" (or infant directed speech), which has different pitch characteristics compared to adult directed speech, suggest an early pitch information processing capability in newborns. Although auditory functional development in the auditory system at early ages draws much attention of researchers from different disciplines, the number of studies during the neonatal period is limited. We first asked how pitch information processing develops. It was hypothesized that newborns already possess ability to process pitch information early during perinatal period. Second, we hypothesized that the extraction of pitch information in acoustic stimuli depended on the integrity of the auditory pathway. Brain insult in the perinatal period has been shown highly likely to affect subcortical structures, including the auditory brainstem and midbrain, through different mechanisms. We reasoned that if there were delays in or problems with pitch processing in brain-injured or premature neonates when compared to healthy or premature infants of equal gestation, then, in the absence of peripheral disturbances, evidence for CNS mediation of the development of pitch processing could be argued.
A Phylogenetic Revision of the Medicinal Leeches of the World (Hirudinidae, Macrobdellidae, Praobdellidae)
Year of Dissertation:
2011
The term "medicinal leech" refers to more species than just Hirudo medicinalis, the preferred species for bloodletting in 19th century Europe. In the past, freshwater, leeches with similar morphological characterstics to H. medicinalis have been divided into two families: the bloodfeeding Hirudinidae and the non-bloodfeeding Haemopidae. With a broader taxon sampling than in previous analyses, an analysis of multiple nuclear (18S rDNA and 28S rDNA) and mitochondrial (12S rDNA and cytochrome c oxidase I) gene fragments found Hirudinidae not to be monophyletic, instead placing in two independently originated lineages separated by the two families of terrestrial leeches, Haemadipsidae and Xerobdellidae. Members of Haemopidae were scattered among members of Hirudinidae of both lineages, thus rendering Haemopidae polyphyletic. The lineage containing H. medicinalis retained the name Hirudinidae, while the other lineage was shown to consist of three families: Macrobdellidae (North and South American bloodfeeders), Semiscolecidae (South American non-bloodfeeders), and Praobdellidae (a biogeographically diverse clade of species that feed primarily from mammalian mucous membranes). With the familial relationships within these two lineages established, attention was given to revising the intra-familial and generic relationships. Two new genera and two new species resulted from these investigations: Tyrannobdella rex n. gen. n. sp., a leech found feeding inside the nasal passages of humans placed within Praobdellidae, Mesobdella lineata was re-described as Parapraobdella lineata n. gen. within Praobdellidae, and Hirudinaria bpling n. sp. placed within the Hirudinidae. Endosymbiotic bacteria from the digestive tracts of members of the Hirudinidae, Macrobdellidae, and Praobdellidae were detected and determined to be Aeromonas species as well as an unculturable Bacteroidetes. The Aeromonas isolates did not show a predictable association based on the phylogeny of the leech hosts or geography, while the Bacteroidetes isolates did show a correlation with leech taxonomy. An analysis with the most thorough taxon sampling to date of the families of Hirudiniformes and Erpobdelliformes was performed. Gastrostomobdellidae, a group of macrophagous leeches hypothesized to be similar to Erpobdelliformes or Hirudiniformes, was strongly supported within Erpobdelliformes. The establishment of the relationships provides a basis for further systematic study, as well as a investigations into the evolution of these charismatic worms.
The tree that held up the forest: Shihuahuaco (Dipteryx spp.) and the Chinese timber trade
Year of Dissertation:
2010
ABSTRACT
Systematics and Historical Biogeography of the Lampropeltinine Snakes
Year of Dissertation:
2009
Comparative studies in biology require phylogenetic hypotheses to make inferences about the processes which have shaped the evolutionary history of organisms. Thus, a complete phylogenetic estimate of a diverse group offers an excellent opportunity for examining the factors which have promoted the diversification of ecomorphological assemblages. Here, I detail such a study of the New World snake tribe Lampropeltini. The lampropeltinines comprise 31 currently recognized species, occurring from Canada to northern South America, inhabiting most major North American biomes, and exhibiting an unusual temperate peak in species richness. The Lampropeltini also exhibit an array of ecomorphological diversity, with adult sizes differing by an order of magnitude, specialization for both endothermic and ectothermic diets, and the evolution of putative Batesian mimicry of venomous coral and rattle snakes in several species. A new phylogeny inferred using multiple nuclear and mitochondrial genes allows for the stabilization of the taxonomy of the Lampropeltini. Subsequent analyses reveal that the extratropical increase in species richness is attributable to a combination of historical biogeographic factors related to the Tropical Conservatism Hypothesis (Wiens & Donoghue 2004), which are proposed as a general explanation for the in-situ evolution of biodiversity, dubbed the `Biogeographical Conservatism Hypothesis.' The ecomorphological diversification of the Lampropeltini occurred primarily along an axis of adult body size, with which is observed the correlated evolution of diet and color pattern. This pattern of correlated evolution of putatively unrelated characters suggests that body size may be a primary determinant of morphological diversification when multiple traits are linked to variables such as body size. Finally, examining the factors which drove lineage formation at the species level through a phylogeographic assessment of the transcontinentally distributed Common Kingsnake (Lampropeltis getula) reveals patterns of allopatric speciation due to both phylogenetic niche conservatism and niche divergence. This suggests that niche preferences are labile on short evolutionary timescales, and that speciation can occur simultaneously in both geographic and ecological dimensions. This phylogeographic estimate also allows for a systematic assessment of the taxonomy of the Common Kingsnake group, which is revised to include five species corresponding to the major phylogeographic lineages.
Characterization of the CYP97 and HYD carotene hydroxylase enzymes
Year of Dissertation:
2012
Vitamin A deficiency is a serious and widespread public health issue in developing countries. Provitamin A carotenoids such as β-carotene have therefore recently attracted interest as important neutraceuticals. Due to the nutritional value of carotenoids there is currently considerable interest in developing rational strategies for metabolic engineering of crops for enhanced carotenoid content. Efforts to improve the provitamin A content of cereal endosperm in staple crops such as maize will require characterization of the carotene ring hydroxylases involved in controlling the conversion of provitamin A carotenes to non-provitamin A xanthophylls.
Neural Targets of Electric Field Stimulation
Year of Dissertation:
2009
Clinical application of electric fields to the brain are promising non-invasive approaches for the treatment of psychiatric, neurological, and pain disorders. Low-magnitude electric fields, which do not cause neuronal firing but only create changes to the voltage necessary for inducing neuronal firing by approximately 1%, are known to have substantial behavioral effects and therapeutic outcomes. Transcranial direct current stimulation is one electric stimulation modality that induces such low-magnitude electric fields. Electric fields of magnitude sufficient to directly trigger neuronal firing may be induced by transcranial electric stimulation and transcranial magnetic stimulation. Many therapeutic advances have been made using these techniques, and they create new experimental approaches to increase our knowledge of how the brain works. Still, the fundamental mechanisms as to how these electric fields may affect neuronal elements of the brain are not fully understood. Chapter 1 of this thesis creates a mechanistic model describing how an electric field of any small magnitude may still have an effect on neuronal processing by changes in spike timing. This mechanistic framework has implications for the effects of endogenous, brain-generated electric fields as well as electric stimulation modalities. The second chapter of this thesis develops a model of how cortical neuronal morphology and cell type may be used to predict changes in polarization and firing caused by electric fields. Both of these studies employed techniques to record from single cells in the brain, and all models described have been experimentally verified through these techniques.