Bariatric surgery is currently the only treatment for obesity that is effective in both the short and long term. Despite this, little is known about the mechanisms through which these surgeries act. While no single critical system has yet been identified, a number of major hypotheses have been proposed. One hypothesis is that adaptive hyperplasia of the intestines following Roux-en-Y gastric bypass (RYGB) surgery is required in order to receive the beneficial effects of the surgery. In this thesis I characterized the adaptive response of the intestines following RYGB and showed that significant hyperplasia occurs in the intestinal mucosa. In addition, I characterized the proliferation of enteroendocrine cells. I found that there is an increase in the number, but not density, of glucagon-like-peptide 1, neurotensin, and serotonin releasing cells, as well as an increase in both number and density of cholecystokinin releasing cells, in the Roux and common limbs following RYGB. This could link adaptive hyperplasia to increased circulating levels of these hormones, which has been implicated in a reduction of food intake and an improvement in glucose homeostasis. A second hypothesis that has been proposed states that RYGB and vertical sleeve gastrectomy (VSG), two similar but ultimately different surgeries, work through a common mechanism of action. In contrast to our observations in rats following RYGB, we found that adaptive hyperplasia is absent following VSG. This leads to the conclusion that either RYGB and VSG share a common mechanism that does not involve adaptive hyperplasia of the intestines, or they do not share a common mechanism.

No description available.

Evaluating the conservation status of threatened species requires a sequential process of 1) taxonomic classification, 2) distributional mapping, and 3) evaluation of species according to criteria established by the IUCN Red List. Knowledge gaps in the first two phases of this process have been termed the Linnaean and Wallacean Shortfalls, respectively. The Indonesian archipelago is one of the most biologically diverse areas of the planet, as well as one of the most threatened and poorly studied, and the Linnaean and Wallacean Shortfalls pose substantial challenges for conservation in the region. Here I address each of the three stages of categorizing threatened species through a series of case studies on birds in two regions of Indonesia: Java and the Northern Moluccas. The first chapter addresses an example of the Linnaean Shortfall; using behavioural and vocal data, I provide insight on the taxonomic status of woodcock (genus: Scolopax) on Java. The display and vocalizations of these birds confirm that they are a distinct biological species and should be evaluated separately from woodcock in New Guinea. The second chapter focuses on the Wallacean Shortfall, and clarifies avian distributions in three Javan montane areas and on the North Moluccan island of Obi. On Obi, in particular, previous knowledge of bird distribution is woefully incomplete; I report nine species of resident birds previously unknown on the island. In the third and final section, I incorporate criteria from the IUCN Red List to re-evaluate the conservation status of two species on Obi, Chattering Lory Lorius garrulus and Moluccan Woodcock Scolopax rochussenii. One case results in good news for conservation; the Moluccan Woodcock is more common than previously believed, tolerates human habitat modification, and should be down-listed from Endangered to Vulnerable. The other is not; Chattering Lory is heavily trapped for the parrot trade and without conservation action, may likely become locally extinct. As such, it is more endangered than currently appreciated and should be considered Endangered rather than Vulnerable.

ABSTRACT Synapse formation is driven by precisely orchestrated intercellular communication between presynaptic and postsynaptic cells. Signals traverse a complex extracellular environment, where glycans attached to glycoproteins and proteoglycans modulate trans-synaptic signaling driving synapse formation, function and plasticity. To interrogate glycan effects on synapse structure and function, I performed a Drosophila transgenic RNAi screen targeting the glycan genome, including N/O/GAG-glycan biosynthesis/modifying enzymes and glycan-binding lectins. From the screen hits, I characterized two functionally paired genes to show unique synaptic effects. The first pair comprises the heparan sulfate (HS) 6-O-sulfotransferase (hs6st) and sulfatase (sulf1), which bidirectionally control HS proteoglycan (HSPG) sulfation. RNAi knockdown of hs6st and sulf1 causes opposite effects on functional synapse development, with neurotransmission strength and postsynaptic glutamate receptor machinery decreased in hs6st but elevated in sulf1 null mutants. Consistently, hs6st and sulf1 nulls differentially misregulate WNT (Wingless) and BMP (Glass Bottom Boat) ligands, their HSPG co-receptors Dally-like Protein and Syndecan, and downstream signaling. Genetic correction of altered WNT/BMP signaling restores normal synaptic development in both mutant conditions, proving that the altered trans-synaptic signaling causes the functional differentiation defects. The second screen-derived functional pair is two protein α-N-acetylgalactosaminyltransferases (pgant3 and pgant35A) that regulate synaptic O-linked glycosylation (GalNAcα1-O-S/T). Loss of either pgant alone elevates presynaptic/postsynaptic molecular assembly and evoked neurotransmission strength, but synapses appear restored to normal in double mutants. Likewise, activity-dependent facilitation, augmentation and post-tetanic potentiation are all suppressively impaired in pgant mutants. I show that Position Specific 2 (αPS2) integrin receptor and transmembrane tenascin ligand are both suppressively downregulated in pgant mutant synapses. Channelrhodopsin-driven electrical activity rapidly (<1 min) drives integrin signaling in wildtype synapses, but is suppressively abolished in pgant mutants. Optogenetic stimulation alters presynaptic vesicle trafficking and postsynaptic pocket size during perturbed integrin signaling underlying synaptic plasticity defects in pgant mutants. Critically, acute blockade of integrin signaling acts synergistically with pgant mutants to eliminate all activity-dependent synaptic plasticity. Thus, I identify two O- glycosylation synaptomatrix mechanisms that regulate trans-synaptic signaling underlying synaptic transmission and activity-dependent plasticity.

Zebrafish spontaneously regenerate their retinas after a variety of retinal insults. Key to regeneration are resident support cells called Müller glia (MG), which respond to injury by reverting to a stem cell-like state and generating progenitor cells that can proliferate, migrate and differentiate into any of the lost retinal cell types. Although studies have identified and characterized a number of genes and signaling pathways that control distinct steps of the regeneration process, very little is known about how expression of these genes is regulated. Small non-coding RNAs called microRNAs (miRNAs) regulate regeneration of various tissues in lower vertebrates. However, the functions and overall requirement of miRNAs for zebrafish retina regeneration are poorly understood. Using in vivo loss-of-function studies, we demonstrate that miRNAs are required for normal initiation and progression of retina regeneration. Small RNA high throughput sequencing revealed that miRNAs expression is dynamic during regeneration, but returned to its basal expression levels once regeneration was completed. We characterize the functions of two miRNAs that were downregulated during regeneration, miR-203 and miR-216, and discover that they regulate progenitor cell proliferation and MG dedifferentiation, respectively, during adult zebrafish retina regeneration.

Oyster reefs in the Gulf of Mexico provide water quality enhancement, shoreline stabilization, carbon sequestration, and facilitate spat recruitment. They are also essential refuges for numerous resident fish and invertebrates, in turn supporting commercial fisheries. Oyster reefs are however in danger worldwide as oyster fisheries increase and pollution from oil spills, such as the Deepwater Horizon spill further degrade reefs. The development of artificial reefs has therefore become a necessity. This study assesses both the long-term and acute response of oyster reef commensal communities to hydrocarbon contamination, as well as comparing the efficacy of artificial reef substrates for restoring these faunal assemblages. Long-term effects were analyzed by quantifying commensal abundance, taxa richness, and diversity from cultch-filled bags deployed at two sites in Barataria Bay, Louisiana, that experienced oiling from Deepwater Horizon, and two control sites. Bags were deployed seasonally in both 2012 and 2013, and the results indicated that while commensal abundance was generally greater at oiled sites, the effects of hydrocarbon contamination several years post spill were neither large nor consistent. To observe the acute colonization response, oil-soaked and control bags were retrieved 1, 2, 4, and 8 weeks after deployment at Grand Isle, LA, an area in Barataria Bay where no oil contamination was documented, in both June and September 2013. Oil effects on commensal communities were inconsistent and minimal by week 8, perhaps due to biodegradation of the hydrocarbons. Commensal communities were also sampled from bags containing either disarticulated oyster shell, limestone rubble or a composite material known as OysterCrete. While OysterCrete had the greatest abundance of commensal organisms, the experiments indicated that seasonal variation was more influential for commensal community dynamics, as well as new spat recruitment and growth, than the presence of hydrocarbons or various substrates. In areas in close proximity to major oil operations, such as the northern Gulf of Mexico, any restoration efforts that provide a hard substrate will be beneficial for the recruitment of commensal organisms if natural oyster reefs are impacted by anthropogenic disturbances.

Rho GTPases are molecular switches that mediate the formation of dendritic spines actin-enriched protrusions that make excitatory synapses with nearby neurons. Once activated by guanine nucleotide exchange factors (GEFs), GTPases regulate actin dynamics within spines. The roles of several Rho GTPases are known in spines; the functions of many GEFs, however, are unclear. Here, we show that the Rac GEF Asef2 is important for the development of dendritic spines. Endogenous Asef2 localizes to spines, and spine and synapse density can be increased or decreased by expression or knockdown of Asef2, respectively. This effect is GEF activity-dependent, since mutation of Asef2s GEF domain blocks spine formation. Also, knockdown of Rac blocks Asef2-mediated spine formation, suggesting that Asef2 activates Rac to promote spine development. Finally, the actin-binding protein spinophilin also regulates Asef2 function by targeting Asef2 to spines. In a related project, we investigated the regulation of Asef2 activity by identifying putative phosphorylation sites. Six phosphorylation sites were identified by mass spectrometry. Most of these sites cluster around the autoinhibitory region of Asef2, suggesting that they may regulate Asef2 activity. To test this, one of the residues serine 106 was mutated to alanine (S106A, non-phosphorylatable analogue) or to aspartic acid (S106E, phosphomimetic analogue), and the effect of these mutations on cell migration (another actin-dependent process) was assessed. The S106A mutant inhibited Asef2-mediated Rac activation, cell migration, and adhesion turnover (a component of cell migration), while the S106E mutant promoted Rac activation but did not influence cell migration compared to wild-type Asef2. These results suggest that phosphorylation is an important mechanism for regulating Asef2 activity and function.

Since Darwin, biologists wonder how organisms cope with environmental variation, why there are so many species, and how species form. In my dissertation, I explore how species of long-lived, clonal reef organisms originate across depth gradients. In Chapter 2, I evaluate the strength of depth to isolate populations by comparing the genes and morphologies of pairs of depth-segregated populations of the candelabrum coral Eunicea flexuosa across the Caribbean. Eunicea flexuosa is a long-lived clonal cnidarian that associates with an alga of the genus Symbiodinium. Genetic analysis revealed two depth-segregated lineages, each genetically well-mixed across the Caribbean. Survivorship data, combined with estimates of selection coefficients based on transplant experiments, suggest that selection is strong enough to segregate these two lineages. Limited recruitment to reproductive age, even under weak annual selection advantage, is sufficient to generate habitat segregation because of the cumulative selection accrued during prolonged pre-reproductive growth. I then studied in detail the genetic diversity of Symbiodinium in each Shallow and Deep E. flexuosa lineage (Chapter 3). I sampled colonies of the two ecotypes across depths at three Caribbean locations. I find that each host lineage is associated with a unique Symbiodinium variant. This relationship between host and alga is maintained when host colonies are reciprocally transplanted. Even when the clades of both partners are present at intermediate depths, the specificity between host and algal lineages remained. I then test whether the Shallow/Deep adaptive divergence occurs in natural populations, by examining the frequencies of juvenile and adults. The habitat distributions of the two lineages are more distinct when inferred from adults than from juveniles. Selection coefficients from cohort data correlates with that from transplant experiments (Chapter 4). The two lineages form a narrow hybrid zone (100 m), with coincident clines of both the host coral and its algal symbiont. Effective dispersal estimates derived from the hybrid zone are small (20 m) for a broadcast spawner with a large dispersing potential (50 km). Ecological factors associated with depth act as filters generating strong barriers to gene flow despite extensive dispersal, altering morphologies, and contributing to the potential for speciation in the sea.

Coral reefs are the most productive and species rich ecosystems in the ocean yet we lack knowledge about the distribution of genetic variation the within and among reef species, particularly for the sponges (Porifera). My dissertation describes how genetic variation at mitochondrial and nuclear genes is partitioned among and within species in the sponge genus Callyspongia. I compared patterns of genetic diversity and population subdivision in the mitochondrial and nuclear genomes of one species, C. vaginalis, in Florida (Chapter 2). Previous work revealed three divergent mitochondrial lineages, but nuclear alleles did not correspond to either mitochondrial clade or geography. Coalescent simulations showed mito-nuclear discordance was not the result of incomplete lineage sorting. Instead, patterns in mitochondrial and nuclear DNA were consistent with changes in population size and sperm-mediated gene flow. Across the Caribbean, I found subdivision in C. vaginalis for mitochondrial and nuclear DNA was concordant, suggesting geographic features and habitat discontinuity are important for structuring populations at large spatial scales (Chapter 3). Clustering analyses found C. vaginalis populations were divided west-east and model-based tests of species boundaries supported a cryptic lineage in Central America. Phylogeographic patterns for three invertebrate sponge commensals also showed a west-east split between Florida and the Bahamas. I tested for mismatches between morphological and molecular species boundaries for seven Caribbean Callyspongia species (Chapter 4). Genetic distances calculated within and among species support C. fallax, C. tenerrima, and C. plicifera as distinct species. However, C. armigera, C. longissima, C. ?eschrichtii and C. vaginalis shared alleles across loci and genetic distances among these taxa overlapped distances within them. Model-based species delimitation supported the hypothesis that these latter four taxa represent one evolutionarily significant unit. This dissertation demonstrates that in the common reef sponge Callyspongia vaginalis, demographic processes and geography influence population structure at small and large spatial scales, respectively, and genetic markers from different genomes can show contrasting patterns. My work also shows the relationship between morphology and evolutionary history is not straightforward in sponges and points to the importance of inter- and intraspecific genetic data for a thorough documentation of biodiversity in marine invertebrates.

Barataria Bay, in southeast Louisiana is home to productive oyster reefs that are both ecologically and economically important, but was threatened by the Deepwater Horizon oil spill in April 2010. This study was designed to determine how the oil spill affected long- and short-term oyster recruitment, and spat (juvenile oysters) cellular health. I also investigated how predators in the bay affect spat survival. Four study sites were selected in Barataria Bay: two control and two oiled, each with a low and high salinity location. To determine whether there were long-term effects of the oil spill on oyster recruitment, tiles were placed at each site in 2012 and 2013 and spat recruitment quantified monthly. Results indicate that in 2012, recruitment varied more with salinity, but in 2013 when early summer salinity was lower, recruitment only occurred at the control sites. Tiles with 5 mL of light crude oil absorbed were used to study the short-term effects of oil on oyster and barnacle recruitment in 2013. Spat recruitment was lower on oiled tiles but there was no difference in spat size between treatments; alternately, there was a slight tendency for oil to increase barnacle recruitment. The effect of No (0 ppm), Low (500 ppm) or High (25,000 ppm) oil concentrations in 10 and 20 PSU seawater on spat cellular function was determined. Lysosomal stability was lower in low and high oil treatments suggesting oiling can affect spat health after just 10 days of exposure. The effect of predators on spat survival at each site was determined by quantifying predation on spat with no cage or in predator exclusion cages with 0.5, 1.0, or 3.0 cm mesh openings. The presence of a cage reduced predation of oyster spat. Predation rates were greatest on spat without cages suggesting larger predators such as blue crabs and oyster drills, with access to exposed spat, may play greater roles in post-settlement spat mortality than other predators such as mud crabs. Oyster recruitment and spat survival seems to depend more on salinity and predation than long-term hydrocarbon contamination. However, the short-term effect of hydrocarbon contamination can detrimentally impact spat recruitment and health; thus, clean-up efforts immediately following an oil spill and continuous monitoring efforts are necessary to maintain healthy oyster populations.