This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2019 / Cataloged from student-submitted PDF version of thesis. "February 2019." / Includes bibliographical references. / The lysosome is the major catabolic organelle, is the site of activation of the master growth regulator mTORC1 (mechanistic target of rapamycin (mTOR) complex 1), and is often deregulated in common diseases, such as cancer. Given the critical role of lysosomes in maintaining cellular homeostasis, a better understanding of lysosomal function and metabolism and its relation to the mTOR pathway is necessary. Most components of the nutrient-sensing machinery upstream of mTORC1 localize to the lysosomal surface, and amino acids generated by lysosomes regulate mTORC1 by promoting its translocation there, a key step in its activation. Activation of mTORC1 by the amino acid arginine requires SLC38A9, a poorly understood lysosomal membrane protein with homology to amino acid transporters. To study SLC38A9 function at the lysosome, we developed a novel method for the rapid isolation of intact mammalian lysosomes suitable for metabolite profiling. / First, we validate that SLC38A9 is an arginine sensor for the mTORC1 pathway, and we uncover a central role for SLC38A9 in amino acid homeostasis. SLC38A9 mediates the transport, in an arginine-regulated fashion, of many essential amino acids out of lysosomes to be used in growth-promoting processes. Pancreatic cancer cells, which use lysosomal protein degradation as a nutrient source, require SLC38A9 to form tumors. Thus, through SLC38A9, arginine acts a lysosomal messenger to connect mTORC1 activation and the release of the essential amino acids to drive cell growth. Finally, by performing quantitative proteomic analyses of rapidly isolated lysosomes, we find that ribosome degradation provides the lysosomal arginine that promotes SLC38A9 activation. Lysosome degradation of ribosomes is mediated by NUFIP1 (nuclear fragile X mental retardation-interacting protein 1). / The starvation-induced degradation of ribosomes via autophagy (ribophagy) depends on the capacity of NUFIP1 to bind LC3B and promotes cell survival. Thus, the NUFIP1-mediated degradation of ribosomes provides both the necessary substrate to activate SLC38A9 and the nutrients needed to promote cell survival under starvation. Altogether, this work provides insight into the regulation of lysosomal nutrients and their role in cellular growth and survival. / by Gregory A. Wyant. / Ph. D. / Ph.D. Massachusetts Institute of Technology, Department of Biology

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2017 / Cataloged from PDF version of thesis. / Includes bibliographical references. / Populations are the central unit of evolution and ecology. In the context of evolution, populations are commonly defined as groups of organisms with a shared gene pool in which adaptive genes can spread freely through natural selection. Ecology takes a less abstract view of populations and conceives of them as members of a single species that occupy the same geographical area. Among sexual eukaryotes, gene pools are easily defined in terms of reproductive isolation and the geographical scales relevant for populations are well-matched to everyday human experience. Microbiologists, however, have faced a great challenge in applying these concepts to the microbial realm. Can closed gene pools form in the face of apparently rampant horizontal gene transfer? What exactly is a microbial species? And does the famous maxim that '"everything is everywhere" mean that the entire globe is to E. coli what Galapagos is to a finch? In this thesis, I hope to move closer to an answer to these large scale questions by asking two smaller ones. First, can ecologically cohesive microbial populations be identified using genomic information alone? Second, once such populations are identified, what are the relevant factors driving population-Ưlevel differentiation? Horizontal gene transfer plays a central role in answering both of these questions, acting both as a force that allows cohesive microbial populations to form and as a means by which new functions and capabilities are introduced into and spread within populations. / by Philip A. Arevalo. / Ph. D. / Ph.D. Massachusetts Institute of Technology, Department of Biology

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2017 / Cataloged from PDF version of thesis. "September 2017." / Includes bibliographical references. / Transcription is one of the most fundamental processes in cells, governing the conversion of genetic information to RNA. Numerous regulatory mechanisms function to ensure that desired transcripts are being expressed. Promoters transcribe divergently, producing low-abundant upstream antisense RNAs (uaRNAs) in addition to a stable downstream RNAs. Thus, a central question is what mechanisms are sense RNAs more stable compared to most transcription events. It is proposed that an asymmetric distribution of Ul snRNP binding sites and polyadenylation site (PAS) motifs known as the UI-PAS axis regulates early termination of RNA Polymerase II. Here, we generated a conditional knockout of the essential RNA exosome subunit, Exosc3, in mouse embryonic stem cells. Removal of Exosc3 resulted in stabilization of polyadenylated uaRNAs, enhancer RNAs and long noncoding RNAs. In addition, promoter proximal pausing increased modestly upon Exosc3 removal. / Interestingly, a large class of polyadenylated short transcripts in the sense direction terminate within the first intron, similar to premature termination observed upon Ul inhibition. Further investigation of these prematurely termination sites revealed they are found at the edges of stable nucleosome free regions demarcated by CpG islands and are suppressed by U1 snRNP. Interestingly, promoter-proximal Pol II pausing consists of two processes: TSS-proximal and +1 stable nucleosome pausing. Genes associated with premature termination have increased +1 stable nucleosome pausing, association of chromatin remodelers and are more sensitive to inhibition by flavopiridol or a Myc inhibitor. Additionally, the nuclear poly(A) binding protein, Pabpnl, promotes degradation of polyadenylated uaRNAs. Most Pabpnl sensitive uaRNAs are also Exosc3 substrates, and sensitivity to Pabpnl inhibition inversely correlates with the proximity of the termination site to the TSS. / Interestingly, at uaRNAs and sense RNAs, Pabpnl -sensitive PAS termination events also occur near the first stable nucleosome, similar to Exosc3-sensitive PAS termination events, suggesting that Pabpnl collaborates with Exosc3 to regulate stability of polyadenylated transcripts. Hence, this supports a model whereby Ul snRNP, +1 stable nucleosomes and the degradation machinery converge to create a transcription elongation checkpoint downstream of promoter-proximal pausing. / by Anthony Chun-yin Chiu. / Ph. D. / Ph.D. Massachusetts Institute of Technology, Department of Biology

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2017 / Cataloged from PDF version of thesis. / Includes bibliographical references. / Cells require their genetic information to be expressed appropriately; the ability to modulate gene expression in a proper spatiotemporal response to external and internal signals is central to survival. Transcription factors are a major class of regulatory proteins that specifically bind DNA to modulate the expression of targeted genes. While they have been extensively studied, major questions remain about the protein-DNA interaction underlying this hub of regulation. What binding site sequences functionally interact with a given regulator? How does the regulon sample from available functional sequences? How independent is each half of a two part binding site? How do mutations in the regulator impact the regulon? Using PhoP, the regulator from the E. coli magnesium-responsive two-component system PhoPQ, I sought to address these questions. I identified the genomic binding locations for PhoP, verifying and expanding our knowledge of the PhoP regulon. Using two randomized libraries of over 65,000 variants each, I interrogated how changes in DNA sequence impact functional binding of PhoP. Comparing this with genomic binding data showed PhoP regulon members may avoid some sequences based on the dysfunctionality of their neighboring sequences. The functional library sequences reveal context dependence for each half-site and interaction within and across binding site halves. Finally, using an orthogonal PhoP mutant, I found that although these two proteins interacted with very few overlapping promiscuous sequences, there were many single mutations that would switch a promoter from interacting specifically with one protein to the other. / by Katie Lynn Moravec. / Ph. D. / Ph.D. Massachusetts Institute of Technology, Department of Biology

Shell disease is a common affliction in marine crustaceans. It manifests as necrotic lesions on the exoskeleton that are caused by bacteria producing extracellular enzymes capable of degrading crustacean cuticle. Prior to 1998, shell disease was not reported in the Florida spiny lobster, Panulirus argus. Since that time it has been seen in P. argus in the Florida Keys. In 1999, an outbreak of severe shell disease occurred in the American lobster, Homarus americanus. Shell disease has been reported in this species for almost a century. To determine if shell disease etiology is the same between the species, a comparative study was undertaken. Healthy and shell-diseased cuticle was sampled in P. argus and H. americanus to determine if a consistent culturable bacterial flora exists on the exoskeleton, and if it the same flora found in lesions. Bacteria were identified by 16S ribosomal DNA sequencing. At least 600 bases of the ribosomal RNA gene were aligned with sequences of identified marine bacteria and phylogenetic relationships were determined. Seven groups of bacteria, six of which are in the gamma proteobacteria, emerged consistently on healthy and diseased cuticle. No primary pathogen was isolated from either species. Six of the groups were isolated from both lobster species and one group was isolated only from P. argus. The association of the bacterial groups with both healthy and shell-diseased cuticle suggests that the normal bacterial flora is in part responsible for shell disease lesions. For each lobster species, histological, scanning electron microscope, and transmission electron microscope observations were made of lesions. In both species, Gram-negative rods were the predominant bacterial morphology present, but cocci and pleomorphic bacteria were also seen. The pathology of the disease appeared to be very different between the lobster species. In P. argus, lesions appear to spread laterally via formation of an extracellular matrix that encapsulates the bacteria. The bacteria seem to secrete degradative enzymes into the matrix, which breaks down surrounding cuticle. Many lesions appeared to be initiated by trauma in P. argus. In H. americanus, the lesions appear to spread by direct bacterial contact with and degradation of the cuticle. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Summer Semester, 2004. / Date of Defense: July 15, 2004. / American Lobster, Spiny Lobster, Shell Disease, Panulirus, Homarus / Includes bibliographical references. / Robert H. Reeves, Professor Directing Dissertation; Joel Kostka, Outside Committee Member; William Herrnkind, Committee Member; Laura Keller, Committee Member; David Quadagno, Committee Member.

The development of multicellular animals involves a diverse array of cellular processes, including cell differentiation, proliferation, and polarization. The control of these processes is largely governed by communication between different cells. This intercellular communication, known as cell signaling, is therefore a fundamental aspect of developmental and cellular biology. Despite a wealth of knowledge regarding the canonical cell signaling pathways, many questions remain regarding the mechanistic nature of the communication taking place during specific developmental events, as well as questions regarding the control of activation of cell signaling. In this dissertation I will use the egg chamber of Drosophila melanogaster as a model system to investigate the genetics and cellular biology surrounding two important developmental events involving cell signaling. In the first part I describe a role for an adhesion molecule, Dystroglycan (DG), in the communication between two important cell types present in the egg chamber (the follicle cells and the oocyte). This communication is of great developmental significance because it creates the foundation for the polarization of the oocyte. The finding that DG is involved in this process suggests that changes in cell adhesion are important in the communication that establishes oocyte polarity. In the second part of the dissertation I identify a novel role for the gene, Belle (Bel), in controlling the activation of a key cell signaling pathway known as Notch. Notch activation in the follicle cells is essential for many aspects of egg chamber development. I also demonstrate that the regulation of Notch by Bel occurs through Bel's role in the microRNA pathway, possibly through regulation of levels of another protein, Delta. Together my research sheds new light on two key facets of egg chamber development that will potentially elucidate similar mechanisms present in other aspects of development in Drosophila, as well as other organisms. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Summer Semester, 2009. / Date of Defense: June 4, 2009. / Oocyte Polarity, MicroRNA, Dystroglycan, Follicle Cell, Belle / Includes bibliographical references. / Wu-Min Deng, Professor Directing Dissertation; Jamila I. Horabin, Outside Committee Member; Lloyd Epstein, Committee Member; Thomas Keller III, Committee Member; Hengli Tang, Committee Member.

Hadrosaurids were the most diverse and abundant dinosaurs at the end of the Cretaceous. However, their phylogeny is incompletely known and the relationships of many taxa, particularly European and South American, remains unresolved. Questions remain regarding the timing of their origin and which attributes might have allowed these animals to diversify and colonize nearly all continents by the late Campanian. Likewise, the center of origin and subsequent biogeographical history of hadrosaurids has remained contentious. With the goal of elucidating the evolutionary history of hadrosaurids, I present the most comprehensive and resolved phylogeny of these animals ever estimated, using a complete taxonomic sampling at specific level. I also report the results of a biogeographic analysis seeking to establish the ancestral area of Hadrosauridae, testing whether they originated in Asia, North or South America. In addition I used the same method to track their diversification in relation to intercontinental connections throughout their tenure. Parsimony and Bayesian methods were implemented to elucidate the phylogenetic relationships of all hadrosaurid species. These included specimens of 41 hadrosaurids from Europe, Asia and North and South America. Outgroup taxa included twelve iguanodontoidean species from Europe, North America and Asia. New characters were defined and old ones revised on the basis of new data collected from first hand examination of specimens. Traditional and geometric morphometrics were applied to discover patterns of variation containing phylogenetic information. Continuous geometries were studied using the Analysis of Planar Shapes Using Geodesic Paths, a novel landmark-free method that considers the continuous non-linear geometry of the bones. In this way, a total of 299 phylogenetically informative characters (205 cranial and 94 postcranial) were defined and documented, the most extensive character data set ever constructed for hadrosaurid dinosaurs. In general, parsimony and Bayesian analyses confirmed the dichotomic evolution of hadrosaurids into Saurolophinae and the hollow-crested Lambeosaurinae. Saurolophines consisted of "saurolophs" and "kritosaurs". Lambeosaurines consisted of a succession of Eurasian outgroups to two major clades, "parasaurolophs" and "amurosaurs" ("hypacrosaurs" and "corythosaurs"). Hadrosauridae was redefined as the clade stemming from the most recent common ancestor of Hadrosaurus foulkii and Parasaurolophus walkeri. Its monophyly was unambiguously supported by an iliac supraacetabular process that projects lateroventrally between half and three quarters of the dorsoventral depth of the central plate of the ilium and a craniocaudally short supraacetabular process that is less than 55% the length of the central plate of the ilium. The closest outgroup taxa to Hadrosauridae lived in eastern North America. The hadrosaurid radiation and the divergence of saurolophines from lambeosaurines occurred no later than the Santonian and was coincident with the evolution of a suite of mandibular characters (i.e., increased number of tooth families, presence of three teeth forming the dentary occlusal plane, ventral offset of the oral predentary-premaxilla contact). These characters may have been key innovations. These results suggest that feeding adaptations might have played a central role in the diversification of hadrosaurids. Circumnarial fossae and cranial crests evolved prior to the hadrosaurid radiation. Both of these characters were reconstructed to have evolved at the same time. Ancestral areas were reconstructed on the phylogeny derived from the weighted parsimony analysis of Hadrosauridae. Fitch parsimony and the Dispersal-Vicariance (DIVA) method were implemented to reconstruct ancestral areas for all clades of Hadrosauria. The results show that the genesis of Hadrosauridae occurred in eastern North America during the late Santonian. Soon after their origin, hadrosaurids dispersed to Asia, the ancestral area for the major Saurolophinae-Lambeosaurinae divergence. Lambeosaurines and saurolophines dispersed to North America and underwent major cladogenesis during the late Campanian. Within Saurolophinae, "maiasaurs" and "saurolophs" returned to Asia, while "kritosaurs" colonized South America by the late Campanian. Within Lambeosaurinae, "tsintaosaurs" dispersed to Europe no later than the late Campanian. The North American radiations of "hypacrosaurs", "parasaurolophs" and "corythosaurs" may have represented independent dispersal events from the Asian continent or, alternatively, were part of a single dispersal in the late Campanian with posterior occupations of Asia by a few species from those clades. Vicariant events may have occurred following several of the inferred hadrosaurid dispersals. Thus, both vicariance and dispersal may have been instrumental in shaping the recorded distribution of hadrosaurids. Two additional studies were conducted on European and South American hadrosaurids. Although well represented in Asia and North America, the presence of this animals in Europe and South America is known only from rare and fragmentary remains that are poorly documented and mostly unstudied. As a result, the impact of these animals on the phylogenetics and biogeography of hadrosaurids as a whole are not known. Here, I provide a revised and complete osteology of the type specimens and hypodigms for the only two taxa known from South America, Secernosaurus koerneri and Kritosaurus australis. K. australis is regarded as a junior synonym of S. koerneri, based on a combination of iliac and pubic characters unique to these two taxa. Inclusion of S. koerneri within the genus Kritosaurus is not supported by the phylogenetic analysis. S. koerneri is inferred to be a member of the "kritosaur" clade within Saurolophinae, as the sister taxon to the Argentinean OTU from Salitral Moreno. Another unnamed hadrosaurid, an OTU from Big Bend National Park, Texas, is positioned as the closest outgroup to the South American clade. The results of this biogeographical analysis indicates that the Secernosaurus clade originated in South America during the late Campanian after a dispersal event (probably followed by vicariance) from southern North America before the end of that geologic stage. Finally, and regarding European hadrosaurids, the observation of previously unrecognized characters in the maxilla and dentary of Tsintaosaurus spinorhinus (Campanian of China) and Pararhabdodon isonensis (Maastrichtian of Spain) led to a revision of the taxonomy and phylogenetic relationships of the latter. In particular, the extreme elongation of the symphyseal region of the type and only material of Koutalisaurus kohlerorum (a dentary from the Maastrichtian of Spain) was also observed in T. spinorhinus. This implied that K. kohlerorum is indistinct from T. spinorhinus. This, in combination with the fact that P. isonensis and T. spinorhinus share a maxilla with elevated jugal joint continuous with the ectopterygoid ridge (a character not seen among Iguanodontoidea), led me to the conclusion that K. kohlerorum as a junior synonym of P. isonensis. The incorporation of those new characters in Bayesian and parsimony phylogenetic analyses of Hadrosauridae resulted in the inference that Pararhabdodon isonensis and Tsintaosaurus spinorhinus form a clade of basal lambeosaurines—the "tsintaosaurs". Fitch parsimony and Dispersal-Vicariance reconstruction of ancestral areas on the resulting phylogeny indicated that "tsintaosaurs" originated in eastern Asia during the middle or late Campanian and that P. isonensis represents a dispersal event (followed by vicariance) to Europe that occurred before the end of that geologic stage. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Summer Semester, 2008. / Date of Defense: June 30, 2008. / Dinosauria, Lambeosaurinae, Hadrosauridae, Phylogeny, Cretaceous / Includes bibliographical references. / Gregory M. Erickson, Professor Directing Dissertation; William C. Parker, Outside Committee Member; Scott J. Steppan, Committee Member; David L. Swofford, Committee Member; Fredrik Ronquist, Committee Member.

Reversible phosphorylation plays an integral role in the regulation of eukaryotic cellular proteins, especially transcription factors. YY1 is a multifunctional transcription factor involved in the regulation of a wide spectrum of essential cellular processes. YY1 has been proposed to be a phosphoprotein and several studies have reported that phosphorylation affects its DNA binding activity. However, these results were indirect and contradictory. In this study, we provide direct evidence that YY1 is a phosphoprotein in normally cycling HeLa cells. Using purified YY1, we present direct evidence that phosphorylation has a negative effect on its DNA binding activity, using several binding sites. We have mapped three phosphorylated sites on YY1 in vivo. The phosphorylated serine residue 247 was detected in asynchronously growing HeLa cells. A phosphomimetic substitution at this site had no effect on the sub-cellular localization of YY1 and only a moderate negative effect on the DNA binding activity of YY1. The other two phosphorylated sites, at threonines 348 and 378, were detected in nocodazole–arrested HeLa cells. Threonines 348 and 378 are located in the linker peptides between the zinc finger motifs of the DNA binding domain of YY1. Phosphorylation at these two residues was correlated with cytoplasmic distribution of YY1 away from the condensed DNA. Moreover, diminished DNA binding activity was observed for YY1 in whole cell extracts from nocodazole-arrested HeLa cells, in in vitro electrophoretic mobility shift assays (EMSA). This diminished binding activity was reversed by dephosphorylation of YY1 with phosphatases. Consistent with these results, phosphomimetic substitutions at threonines 348 and 378 resulted in the loss of YY1 DNA binding activity. However, these mutations caused no observable effect on the subcellular localization of YY1 in interphase HeLa cells. We also show that YY1 is excluded from the condensing chromosomes at prophase in normally growing cells and it remains dispersed away from DNA until telophase. At this stage of mitosis, YY1 is recruited back to DNA in the nucleus at the same time of chromosome decondensation. These observations propose a mechanism for the inactivation of YY1 DNA binding activity in mitosis, through phosphorylation of its DNA binding domain. To identify kinases that phosphorylate YY1, we have tested bacterially expressed and purified YY1 against one hundred kinases in vitro. Several kinases were shown to highly phosphorylate YY1. Polo-like kinase 1 (Plk1) and Casein Kinase 2á1 (CK2á1) showed the highest activity in phosphorylating YY1 of the kinases examined. Using deletion and point-substitution mutants of YY1, we have shown that Plk1 specifically phosphorylates threonine 39 in the acidic trans-activation motif in the N-terminal domain of YY1. Phosphorylation at this site could play a role in the regulation of the transcriptional activity of YY1. In addition, CK2á1 was shown to phosphorylate YY1 at serine 118, located in the caspase consensus cleavage site. Phosphorylation at serine 118 may play an important role in regulating the cleavage of YY1 during apoptosis. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2008. / October 21, 2008. / YY1, Yin-Yang 1, Phosphorylation, Cell Cycle, Mitosis, G2/M / Includes bibliographical references. / Myra M. Hurt, Professor Directing Dissertation; Cathy Levenson, Outside Committee Member; Lloyd Epstein, Committee Member; Thomas C. S. Keller, III, Committee Member; Hank Bass, Committee Member.

The main olfactory bulb (OB) receives odorant information from the nasal epithelium, interprets much of that information, and transmits the results to higher cortical regions. The predominant excitatory neurotransmitter in the OB and throughout the brain is glutamate. Modulators of glutamatergic activity influence synaptic transmission of intrabulbar circuits profoundly; therefore, the effects of neuromodulators must be thoroughly characterized in order to understand fully how OB circuits function. Investigations performed here address the capacity of dopamine receptor (DAR) and kainate receptor (KAR) activation to modulate glutamate transmission from principal cells to interneurons in OB primary cultures. Initially, I obtained immunocytochemical evidence for DARs expressed in principal cells. Subsequent electrophysiological analyses revealed that the D2-like receptor subtype (D2Rs) attenuated both spontaneous and evoked glutamatergic transmission. Information gleaned from studies of input resistances and calcium currents allowed me to determine that the site of modulation is located on the presynaptic cell. My research into KARs demonstrated the existence of functional KARs in OB neurons and began to elucidate their physiological roles in OB neurotransmission. First, I gathered immunocytochemical evidence to visualize KARs expressed both at and near synapses. In situ hybridization (ISH) was employed to map which OB neurons express mRNA for each KAR subunit. Expression levels for each subunit were quantified in parallel studies using the reverse transcriptase-polymerase chain reaction (RT-PCR). Electrophysiological approaches were used to determine whether or not KARs participate in synaptic transmission between OB neurons in primary cultures. I provide evidence for KAR-mediated modulation of both spontaneous and evoked glutamatergic transmission between OB neurons. Taken together, this work supports the notion that synaptic transmission of OB neurons can be modulated by either metabotropic or ionotropic ligand-gated ion channels. In addition, this is the first thorough characterization of KAR expression and physiology in OB neurons. / A Dissertation submitted to the Program in Neuroscience in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Fall Semester, 2003. / Date of Defense: November 5, 2003. / Electrophysiology / Includes bibliographical references. / Paul Trombley, Professor Directing Dissertation; Charles Ouimet, Outside Committee Member; Marc Freeman, Committee Member; Betty Gaffney, Committee Member; Michael Meredith, Committee Member.

Conditioned taste aversion (CTA) is a form of associative learning in which an animal avoids and reacts aversively to a taste (conditioned stimulus, CS) that has been previously paired with a toxin or other malaise-inducing stimulus (unconditioned stimulus, US). CTA is unique among Pavlovian learning paradigms because conditioning is supported across long delays (minutes to hours) between taste and toxin [Garcia et al., 1966; Kalat & Rozin, 1973; Smith & Roll, 1967] and is robust in that an animal can form a strong aversion that can last for months [Houpt et al., 1996; Martin & Timmins, 1980; Steinert et al., 1980] after only a single trial of a taste-toxin pairing [Garcia & Koelling, 1967]. CTA learning is easily manipulated, as the strength or magnitude of the aversion is dependent on the concentration, saliency, and duration of the CS, as well as the amount or strength of the US [Barker, 1976; Dragoin, 1971; Nachman & Ashe, 1973]. The anatomical pathway involved in CTA is well characterized and includes the nucleus of the solitary tract, parabrachial nucleus, amygdala, and gustatory cortex [for a review, see Yamamoto, 2006]. The two forebrain regions, the amygdala and gustatory cortex, are particularly important as lesions of these areas cause deficits in CTA learning [Josselyn et al., 2004; Nerad et al., 1996], and both structures exhibit cellular changes during and after CTA acquisition, such as induction of long-term potentiation [Escobar & Bermudez-Ratoni, 2000], activation of immediate early genes such as c-fos [Lamprecht and Dudai, 1995], phosphorylation of markers such as MAPK [Berman et al., 1998], phosphorylation of NMDAR subunits such as NR2B [Rosenblum et al., 1997], and changes in the activation and expression of genes such as CREB, fra-2, and fen-1 [Desmedt et al., 2003; Kwon et al., 2008; Saavedra-Rodríguez et al., 2009]. As with other forms of associative learning, CTA is N-methyl-D-aspartate receptor (NMDAR)-dependent [Jimenez & Tapia, 2004]. Pharmacological inactivation of NMDARs attenuates or blocks CTA [e.g. Gutierrez et al., 1999] while activation by NMDAR agonists enhances CTA learning [Land & Riccio, 1997]. Data from our lab show that the NMDAR agonist, D-cycloserine (DCS), dose-dependently enhances taste learning, but only under certain parameters [Nunnink et al., 2007]. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Spring Semester, 2011. / Date of Defense: March 31, 2011. / Taste aversion, D-cycloserine, NMDA receptor, D-serine, Lesion, MAP kinase, Learning, c-Fos, Conditioned taste aversion / Includes bibliographical references. / Thomas A. Houpt, Professor Directing Dissertation; Colleen M. Kelley, University Representative; Thomas C. S. Keller III, Committee Member; Charles C. Ouimet, Committee Member; Paul Q. Trombley, Committee Member.