O entendimento dos mecanismos de representação e processamento de odores pelo sistema olfatório é uma das questões centrais da neurociência moderna. Os odores são codificados pela circuitaria interna do bulbo olfatório em padrões espaço-temporais refletidos pela atividade de suas células de saída, as células mitrais e tufosas, que transmitem os resultados das computações dessa estrutura inicial de processamento a regiões corticais superiores. A arquitetura das conexões existentes no bulbo olfatório apresenta inibição lateral em duas camadas diferentes de sua estrutura laminar, intermediadas por dois tipos distintos de interneurônios. Na camada glomerular, mais externa, a inibição lateral é mediada pelas células periglomerulares e na camada plexiforme externa, mais interna, a inibição lateral é mediada pelas células granulares. O papel desses dois níveis distintos de inibição lateral e os mecanismos segundo os quais eles atuam moldando os padrões espaço-temporais de resposta do bulbo olfatório a odores diferentes são ainda pouco conhecidos. O objetivo deste trabalho foi construir um modelo de rede neural biologicamente plausível do bulbo olfatório para investigar como dois tipos diferentes de interneurônios, atuando em estágios distintos de processamento, podem contribuir para a discriminação de odores e a coordenação dos padrões de disparo das células mitrais. O modelo de rede construído, com representação de odores pela atividade das células mitrais e baseado nas interações recíprocas entre essas células e os interneurônios inibitórios, mostrou que a inibição gerada pelas células periglomerulares pode melhorar o contraste entre odores similares, facilitando a discriminação de odores, enquanto que a inibição das células granulares atua no refinamento da resposta de saída da informação olfatória. / The understanding of odor representation and processing mechanisms by the olfactory system is one of the central questions of modern neuroscience. Odors are encoded by the olfactory bulb circuitry in terms of spatiotemporal spiking patterns. These are reflected in the activity of the mitral cells, which are the output cells of the olfactory bulb that transmit the information processed in this early structure to higher cortical regions. The architecture of the olfactory bulb connections presents lateral inhibition at two different layers of its laminar structure, mediated by two distinct types of interneurons. In the glomerular layer, lateral inhibition is mediated by periglomerular cells. In the external plexiform layer, lateral inhibition is mediated by granule cells. The role of these two different lateral inhibition levels and the mechanisms whereby they shape the spatial and temporal patterns of the olfactory bulb response to different odors is not well known. The aim of this work was to build a biologically plausible neural network model of the olfactory bulb to investigate how two different types of interneurons, acting at different processing stages, could contribute to odor discrimination and the coordination of the mitral cells spiking patterns. The results of simulations of the network model shown that the inhibition generated by periglomerular cells can provide contrast enhancement and odors discrimination, while the granule cell inhibition can refine the output response of the olfactory information.

O gene, uma seqüência de nucleotídeos necessária para a síntese de moléculas funcionais, é transcrito e regulado por um conjunto de processos e fatores extremamente complexos. Entender o momento e o tecido em que os genes são expressos, as isoformas funcionais, as regiões controladoras e os fatores envolvidos na regulação da expressão de cada gene é um dos grandes desafios da biologia molecular moderna. Hoje, com a enorme quantidade de informações de seqüências genômicas e de transcriptomas, aliado ao desenvolvimento de métodos computacionais para agrupar e analisar estes dados em larga escala, o estudo dos fenômenos relacionados à transcrição e regulação gênica está passando por uma revolução. Por exemplo, é possível medir, concomitantemente, a expressão gênica de milhares de genes em diferentes tecidos, assim como identificar diversos fenômenos que atuam nestes genes. Neste trabalho nós desenvolvemos e aplicamos métodos computacionais no estudo de quatro temas envolvendo aspectos chave da transcrição e regulação gênica. No primeiro trabalho, nós abordamos a expressão gênica tecido-específica através do estudo dos genes expressos no cérebro e em dez regiões cerebrais de camundongo. No segundo trabalho, nós identificamos seqüências potencialmente envolvidas no controle da transcrição gênica através do estudo de motivos sobre representados na região promotora dos genes de receptores olfativos. No terceiro trabalho, analisamos o transcriptoma humano quanto a presença de eventos de retenção de intron, um tipo de splicing alternativo. No quarto trabalho, nós abordamos a complexidade do transcriptoma e a regulação da expressão gênica através do estudo de pares de genes senso-antisenso em humanos e camundongos. Em todos os trabalhos, obtivemos resultados que nos permitiram tirar conclusões específicas sobre cada fenômeno estudado e nos mostraram a importância de estudá-los através de uma abordagem em larga escala. Adicionalmente, verificamos que os nossos métodos computacionais foram eficientes e adequados para o estudo da transcrição e regulação gênica em Homo sapiens e Mus musculus. / Genes, nucleotide sequences necessary for the synthesis of functional molecules, are transcribed and regulated by extremely complex cellular and molecular processes. To understand when and in which tissues the genes are expressed, their functional isoforms, control regions and the factors involved in gene regulation is one of major challenges of modern molecular biology. Today, the availability of complete genome sequences and transcriptomes, together with the development of new computational methods allows the study of phenomena related to the transcription and gene regulation in a large scale. For example, it is possible to quantify, concomitantly, gene expression of thousands of genes in different tissues and analyze different aspects of their regulation. In this work we developed and applied computational methods to the study of four key aspects of gene transcription and regulation. In the first study, we addressed tissue specific gene expression through the study of genes that are preferentially expressed in the brain and ten different mouse brain regions. In the second study, we identified sequences that are potentially involved in the control of gene transcription through the study of motifs that are over represented in the promoter region of olfactory receptor genes. In the third study, we browsed the human for the presence of intron retention, a type of alternative splicing. In the fourth study, we addressed the transcriptoma complexity and gene expression regulation through the study of pair of sense-antisense genes in human and mouse. In all studies, our results allowed us to make specific conclusions about each phenomenon analyzed which showed us the importance of a large scale approach. In addition, we verified that our computational methods can be efficiently applied to the study of transcription and gene regulation in Homo sapiens and Mus musculus.

Isovaleric Acid (IVA) is a 5-carbon branched chain fatty acid present in fermented foods and produced by the fermentation of leucine by colonic bacteria. IVA activates G-protein coupled receptors such as FFAR2, FFAR3, and OR51E1 known to be expressed on enteric neurons and enteroendocrine cells. We previously reported that the shorter, straight chain fatty acids acetate, propionate and butyrate, differentially affect colonic propulsion; however, the effect of branched chain fatty acids on gastrointestinal motility is unknown. We hypothesize that IVA relaxes smooth muscle in a cAMP/PKA dependent manner by direct action on smooth muscle cells. IVA will also decrease peristalsis and encourage retention of luminal contents. This thesis investigates the effect of IVA on smooth muscle tension and peristaltic activity in isolated colon and individual smooth muscle cells. Colon segments from C57BL/6J mice were placed in a longitudinal orientation in organ baths in Krebs buffer and fastened to force transducers. Segments were contracted with 10 μM acetylcholine (ACh) and the effects of IVA at several concentrations were measured in the absence and presence of Nitric Oxide Synthase inhibitor L-N-nitroarginine (L-NNA), neuronal action potential inhibitor tetrodotoxin (TTX), and adenylate cyclase inhibitor SQ22536. To study individual live cells, mouse smooth muscle was isolated from colon, suspended in smooth muscle buffer, and after contraction with ACh were relaxed with micromolar concentrations of IVA. For peristalsis studies, whole colonic segments isolated from C57BL/6J were catheterized and placed horizontally in organ baths with circulating Krebs buffer. The colon was clamped on the anal end, and a solution (5 μL per mm of colon length) of either Krebs buffer or 50 mM IVA was delivered from the oral end to the lumen. Video of the peristalsis was then analyzed for diameter, changes in diameter, velocity of diameter changes along the length of the colon, normalized to the anatomical changes in the proximal region. IVA in concentrations of 10 mM to 50 mM relaxed the ACh-induced contraction in a sigmoidal fashion. In separate studies, L-NNA nor TTX affected the ability of IVA to inhibit relaxation. SQ22536 inhibited IVA induced relaxation in longitudinal colon compared to vehicle control. In isolated cells, SQ22536 and PKA inhibitor H-89 inhibited IVA-induced relaxation. In peristalsis studies, 50 mM IVA in Krebs buffer changed the character of the peristaltic action by increasing proximal diameter, inhibiting contractions in the proximal end of the colon, and decreasing overall velocity of peristaltic contractions in the proximal region. The data indicate that the branched chain fatty acid IVA causes a concentration-dependent relaxation of colonic smooth muscle that is direct to the smooth muscle and independent of neuronal activity. This relaxation is cAMP/PKA dependent. In addition to the direct relaxation of smooth muscle, intraluminal IVA decreased overall colonic propulsive activity and encouraged retention of the luminal contents. We conclude that the ingestion and production of branched chain fatty acids could affect overall GI motility and is an area for study in dietary and therapeutic control of bowel activity.

Neuronal differentiation encompasses an elaborate developmental program which until recently was difficult to study in vitro. The advent of several cell lines able to differentiate in culture proved to be the turning point for gaining an understanding of molecular neuroscience. In particular the olfactory epithelium provides an attractive tool with which to investigate fundamental questions relating to neuronal differentiation, as it displays a unique capacity to regenerate and to retain a neurogenetic potential from its genesis and throughout adult life. The coordinated regulation of gene expression is fundamental to the control of neuronal differentiation. In order to reveal active processes at the molecular level and to dissect key components of molecular pathways, differential gene expression studies provide a foundation for the elucidation of dynamic molecular mechanisms. This thesis identified genes involved in neuronal differentiation by utilising a clonal olfactory receptor neuronal cell line (OLF442). Gene expression levels were identified using differential display and oligonucleotide array technology before and after serum deprivation. Differential display revealed two kinases whose expression levels were elevated during the differentiation of OLF442, identified as focal adhesion kinase (FAK) related non-kinase (FRNK) and mammalian ste20 like (MST)2 kinase. Furthermore, analysis of the oligonucleotide array data confirmed the expression of genes involved in altering presentation of extracellular matrix molecules, in mediating cytoskeletal rearrangements, and in ceasing the cell cycle, supporting the use of OLF442 as a model for studying differentiation. The differentiation of OLF442 results from the synchronisation of multiple transduction cascades and cellular responses as evidenced by the microarray data. A protein that can synchronise such signalling is the non-receptor protein tyrosine kinase, FAK. Thus the finding of the endogenous FAK inhibitor FRNK by differential display was intriguing as there was no difference in the expression level of FAK induced by differentiation, contrasting that of FRNK. This induced FRNK expression was derived autonomously as it was not responsive to the caspase-3 inhibitor, DEVD-CHO. This is particularly pertinent since the primary role of FRNK is to act as an inhibitor of FAK by competing with its substrates and reducing the phosphorylation of both FAK and its associated proteins. Differential display also revealed the upregulation of another kinase, which had 90% homology with rat MST2 kinase within the 3' UTR. Both mouse MST2 kinase (sequence submitted to GenBank, accession number AY058922) and the closely related family member MST1 kinase were sequenced and cloned. Moreover, evidence to support an autonomously expressed carboxyl-terminal domain of MST2 kinase is presented in Chapter 3 and provides a unique way in which MST2 may regulate its own activity. To further understand the role of MST in neuronal differentiation, a series of stable OLF442 transfections (with mutant and wild-type MST constructs) were carried out. MST was localised with cytoplasmic structures that may represent actin stress fibres, indicating a potential cytoskeletal role during neuronal differentiation. This indicated that MST1 may play a role in the morphological processes involved in neuronal differentiation. The identification of two kinases by differential display provided the motivation to understand the cellular context of OLF442 and to determine the phosphorylation status of the mitogen-activated protein kinase (MAPK) signalling cascades. Differentiation of OLF442 induced high-level phosphorylation of a putative B-Raf isoform, MEK2 and ERK1/2. Interestingly, there was a switch between preferential phosphorylation of MEK1 in undifferentiated OLF442 to preferential phosphorylation of MEK2 following differentiation. SAPK/JNK was also phosphorylated, as was the transcription factor c-Jun, which is a common substrate of both the ERK and SAPK/JNK signalling modules. The mapping of the cellular context of differentiating OLF442 has identified a promising model of a novel MAPK module. This consists of FAK signalling through Rap1 to ERK providing sustained activation, which is buffered or terminated by the expression of the endogenous FAK inhibitor FRNK. Furthermore, MST kinase could potentially play a role in regulating the cytoskeletal re-arrangements that are necessary for neuronal differentiation. MST kinase may signal transiently via the SAPK pathway to provide concomitant activation of c-Jun that is required for neuronal differentiation. An understanding of the gene expression pattern of the normal neuronal differentiation program allows a greater understanding of potential developmental aberrations. This could provide an opportunity for therapies to be conceived, while understanding the complexity of neuronal determination could also provide opportunities for stem cell transplantation.

<p>In the present thesis, three empirical studies investigate autobiographical odor memory with regard to: (a) whole life-span age distributions, (b) phenomenological experience, (c) semantic processing, and (d) odor imagery. Study I explored potential influences of cue type (words, pictures, odors) on the retrieval of autobiographical memories. The results indicated that odor-evoked events were older than memories evoked by words and pictures. The bump for olfactory evoked information peaked in the first decade of life (<10 years of age), whereas the bump of the word- and picture-evoked age distributions peaked in the second decade (i.e., 11-20 years of age). Also, olfactory evoked events were associated with stronger feelings of being brought back in time. Study II investigated the influence of verbal processing on the retrieval of autobiographical olfactory information. The results revealed that semantic knowledge (i.e., the odor name) affected both the age distribution and phenomenological experience. Also, olfactory memories were associated with a higher emotional arousal. Study III addressed the influences of olfactory imagery on the age distribution and phenomenological experiences. The results showed that events evoked by odor imagery were older than memories evoked by words. No differences in phenomenological experiences were found between the two cue conditions. Based on these findings, it is suggested that (a) memories evoked by olfactory information are older than memories evoked by verbal and visual information, (b) odor memories are more emotional and associated with stronger feelings of being brought back in time, (c) knowledge of an odor’s name produces a shift from a more perceptually to a more conceptually driven retrieval, and that (d) imagined odor cues mimic the age distribution of events evoked by real odors. Overall, the results suggest that memories triggered by the olfactory sensory system are different from memories evoked by verbal or visual information.</p>

In the present thesis, three empirical studies investigate autobiographical odor memory with regard to: (a) whole life-span age distributions, (b) phenomenological experience, (c) semantic processing, and (d) odor imagery. Study I explored potential influences of cue type (words, pictures, odors) on the retrieval of autobiographical memories. The results indicated that odor-evoked events were older than memories evoked by words and pictures. The bump for olfactory evoked information peaked in the first decade of life (&lt;10 years of age), whereas the bump of the word- and picture-evoked age distributions peaked in the second decade (i.e., 11-20 years of age). Also, olfactory evoked events were associated with stronger feelings of being brought back in time. Study II investigated the influence of verbal processing on the retrieval of autobiographical olfactory information. The results revealed that semantic knowledge (i.e., the odor name) affected both the age distribution and phenomenological experience. Also, olfactory memories were associated with a higher emotional arousal. Study III addressed the influences of olfactory imagery on the age distribution and phenomenological experiences. The results showed that events evoked by odor imagery were older than memories evoked by words. No differences in phenomenological experiences were found between the two cue conditions. Based on these findings, it is suggested that (a) memories evoked by olfactory information are older than memories evoked by verbal and visual information, (b) odor memories are more emotional and associated with stronger feelings of being brought back in time, (c) knowledge of an odor’s name produces a shift from a more perceptually to a more conceptually driven retrieval, and that (d) imagined odor cues mimic the age distribution of events evoked by real odors. Overall, the results suggest that memories triggered by the olfactory sensory system are different from memories evoked by verbal or visual information.

The olfactory system is important for social behaviors, feeding and avoiding predators. Detection of odorous molecules is made by odorant receptors on specialized sensory neurons in the olfactory epithelial sheet. The olfactory sensory neurons are organized into a few regions or “zones” based on the spatially limited expression of odorant receptors. In this thesis the zonal division and functional specificity of olfactory sensory neurons have been studied in the mouse. We find that zones 2-4 show overlapping expression of odorant receptors while the border between the regions that express a zone 1 and a zone 2 odorant receptor, respectively, is sharp. This result indicates that zone 1 and zones 2-4 are inherently different from each other. In cDNA screens, aimed at finding genes whose expression correlate to the zonal expression pattern of odorant receptors, we have identified a number of signaling proteins implicated in neural-tissue organogenesis in other systems. The differential expression pattern of identified genes suggests that regional organization is maintained during the continuous neurogenesis in the olfactory epithelium as a result of counter gradients of positional information. We show that the gene c-fos is induced in olfactory sensory neurons as a result of cell activation by odorant exposure. A zonal and scattered distribution of c-Fos-positive neurons resembled the pattern of odorant receptor expression and a change of odorant results in a switch in which zone that is activated. Whereas earlier studies suggest that the odorant receptors are relatively broadly tuned with regard to ligand specificity, the restricted patterns of c-Fos induction suggests that low concentrations of odorous molecules activate only one or a few ORs. Studies on olfactory detection abilities of mice with zonal-restricted lesions in the olfactory epithelium show that loss of a zone has severe effects on the detection of some odorants but not others. These findings lend support to a hypothesis that odorant receptors are tuned to more limited numbers of odorants. Regional differences in gene expression and differences in response to toxic compounds between the zones indicate that there may be differences in tissue homeostasis within the epithelium. We have found that there are differences in proliferation and survival of olfactory sensory neurons in regions correlating to receptor expression zones. Identified differences with regard to gene expression, tissue homeostasis and odorant detection show that the olfactory epithelium is divided into regions that transduce different stimulus features.

Primates have traditionally been viewed as having a poorly developed sense of smell. However, in recent years, studies have shown that at least some primate species use olfaction in a number of behaviors, and that they have a high olfactory sensitivity for various chemical classes of odorants. Using a two-choice instrumental conditioning paradigm, the present study assessed olfactor ydetection thresholds of three spider monkeys (Ateles geoffroyi) for eight aliphatic alcohols and aldehydes, known as "green odors". With all odorants, the animals detected concentrations below 1 parts per million, with single individuals performing even better. The type of functional group present systematically affected olfactory detection thresholds, whereas the presence, position and configuration of a double bond did not. Compared to previously tested classes of odorants, thespider monkeys were not particularly sensitive to "green odors". Furthermore, they are lesssensitive for "green odors" compared to humans and mice. The present results suggest that neuroanatomical and genetic comparisons across species are poor predictors of olfactory sensitivity.

The effect of environmental modification of predator sensory abilities remains largely unknown, despite the importance of predators to ecosystem function. I conducted a series of experiments to investigate effects of hydrodynamics on the chemosensory search behavior and foraging success of two species of marine gastropods, knobbed whelks (

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 87-99).