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.

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

Abstract This thesis is a study of the odour responses of insect olfactory (or odorant) receptor neurons (ORN) of blowfly (Calliphora vicina), mosquito (Aedes communis), fruitflies (Drosophila melanogaster and D. virilis) and large pine weevil (Hylobius abietis). A power-law dependence (similar to Stevens' law in psychophysics) was obtained for the action potential rate of ORN responses vs. odour concentration in measurements with metal microelectrodes from blowfly ORNs and an analysis system was developed for the extracellularily recorded action potentials (or nerve pulses). Odour exposure sequences were used to study action potential rates quantitatively as a function of odour concentration in air exposure. For an odour exposure sequence, a known initial amount of the odour compound in a filter paper inside a Pasteur pipette at the beginning of repeated exposures caused a gradual dilution of the odour concentration in the exposure sequence. The concentration at each exposure was calculated according to the discrete multiple headspace extraction and dilution (DMHED) method. The estimated odour concentration was assumed to obey in the method an exponential law with respect to the exposure number in the sequence. Despite that many uncontrollable parameters remain for measuring quantitatively the characteristics of the ORNs, the results obtained, e.g., sensitivity, specificity, adaptability, and the power-law realation are both biologically and technically very interesting. A time-to-voltage converter (TVC) was utilized for the response analysis in determining action potential intervals originating from a single ORN. A precision analysis of TVC was also performed. With the mosquito (Aedes communis), fruitflies (Drosophila melanogaster and D. virilis) and large pine weevil (Hylobius abietis) antennae were tested for inhibitory and excitatory effects to find out repellents and attractants. Human sweat was found to cause strong stimulus exposure in the responses of the mosquito ORNs and Neutroil® caused inhibitory responses in pine weevil ORNs, respectively. The power-law exponents for blowfly ORNs were about 0.19 in the case of 1-hexanol (HX), 0.065 in the case of 1,4-diaminobutane (14DAB) and 0.32 in the case of butyric acid (BA). The corresponding Stevens' law exponent values 0.39 and 0.33 have been reported for HX and BA, respectively, by Patte et al. (1975).

Ce projet de recherche est focalisé sur le lien entre la structure des molécules odorantes et leurs interactions avec les récepteurs olfactifs exprimés dans les neurones olfactifs. Cette recherche fondamentale est d'une importance primordiale pour la construction d'un «nez virtuel », physiologiquement inspiré, qui reproduit la fonction des 400 types de récepteurs olfactifs impliqués dans la détection des odeurs. Ici, chaque récepteur olfactif est représenté par un système moléculaire qui est reproduit atome par atome dans un modèle informatique. Un protocole optimal a été conçu pour prédire les structures de ces récepteurs grâce à l’analyse bioinformatiques de leurs séquences sous contraintes de données expérimentales. Ensuite, les bases de la relation entre la séquence d’un récepteur et son mécanisme d’activation en fonction de la structure d’une molécule odorante liée à sa cavité ont été établies. Par ailleurs, l’analyse des structures de molécules d’une même famille olfactive peut conduire à l’identification des récepteurs impliqués dans leur perception. L’ensemble de ces résultats constitue les bases pour l’étude des relations structure-odeur à l’ère post-génomique. / This research project is focused on the link between chemical structures of odorant molecules and their interactions with odorant receptors expressed in olfactory neurons. This basic research is of primary importance for building a physiologically-inspired “computational nose” that reproduces the function of the 400 types of odorant receptors involved in the perception of smells. Here, each odorant receptor is represented as a molecular system, reproduced atom per atom in a computational model. An optimal protocol has been built to predict the structure of these receptors using bioinformatics analyses of their sequences under the constraints of experimental data. Then, the relationship between the sequence and the activation mechanism of a receptor as a function of the structure of a molecule bound to its cavity has been established. Furthermore, the structural analysis of molecules belonging to the same olfactory family was shown to lead to the prediction of some receptors involved in their perception. These results constitute a basis for structure-odor relationships studies in the postgenomic era.

Orientador: Fabio Papes / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T05:41:39Z (GMT). No. of bitstreams: 1 Souza_MateusAugustodeAndrade_M.pdf: 6121419 bytes, checksum: a603ea19d560e8cfebddccca9b7d824a (MD5) Previous issue date: 2015 / Resumo: Em mamíferos, os neurônios sensoriais do Sistema Olfatório (OSNs) se encontram no interior da cavidade nasal, mas estão diretamente expostos ao ambiente externo. Por um lado, tal localização permite a esses neurônios o acesso imediato aos estímulos químicos ambientais, tomando vantagem do fluxo respiratório. Por outro lado, esses neurônios estão constantemente sujeitos a injúrias por agentes nocivos, como toxinas e patógenos, capazes de destruir essas células sensoriais. Sua perda constante, contudo, é contrabalanceada pela geração de novos OSNs durante toda a vida do indivíduo, fato que torna o Sistema Olfatório um dos poucos locais do organismo com neurogênese contínua na idade adulta. A regeneração dos OSNs tem atraído a atenção da comunidade científica tanto pelo seu potencial uso como modelo de estudo do Sistema Nervoso quanto pela sua potencial aplicação para o tratamento de doenças neurodegenerativas. Nesse sentido, muito conhecimento já foi produzido sobre a dinâmica de fatores de transcrição que acompanha a diferenciação dos progenitores neuronais olfatórios em OSNs. Porém, uma grande lacuna no conhecimento diz respeito a outros elementos capazes de coordenar esse processo, como os fatores moduladores da cromatina. Diante desse cenário, escolhemos como objeto de estudo as proteínas do Grupo Polycomb (PcG), que constituem uma maquinaria de controle transcricional relacionada a modificações na organização da cromatina. Neste trabalho, genes PcG selecionados foram caracterizados molecular e funcionalmente no epitélio olfatório principal de camundongos (MOE). Através de ensaios de hibridação in situ, cinco dos seis genes avaliados apresentaram expressão ubíqua por todo o epitélio (Cbx2, Cbx4, Phc2, Ezh1, Bcl6), enquanto um (Ezh2) mostrou-se expresso somente nos estratos basais do MOE. Em ensaios de colocalização, provamos que Ezh2 é expresso exclusivamente nos progenitores olfatórios, onde o processo de diferenciação se inicia, e em parte dos OSNs recém-diferenciados, ainda não funcionais. Esta foi a primeira vez que a expressão de um gene PcG foi analisada detalhadamente no Sistema Olfatório. O interessante perfil de expressão de Ezh2 foi sugestivo de um possível papel funcional relacionado à diferenciação dos progenitores olfatórios. Para investigar essa hipótese, utilizamos como ferramenta experimental a habilidade do MOE em se regenerar após a indução de injúrias específicas. Para isso, o MOE de camundongos foi lesionado quimicamente com o composto diclobenil, que leva à perda abrupta de OSNs, estimulando a proliferação e a diferenciação dos progenitores olfatórios para repovoar as regiões lesionadas. Os animais assim tratados receberam, por via intranasal, o fármaco GSK126, uma molécula inibidora específica da atividade da proteína EZH2. Acompanhando a regeneração subsequente do MOE, observamos que a inibição da atividade de EZH2 levou ao incremento de OSNs no epitélio, favorecendo a sua regeneração. Interessantemente, esse incremento também foi observado em MOEs não lesionados, mostrando que o efeito de GSK126 não é dependente da indução de injúrias prévias. Através dessa investigação molecular e funcional, buscamos contribuir para o melhor entendimento da diferenciação neuronal do MOE, e apontamos as proteína PcG como elementos importantes para esse processo / Abstract: In mammals, the olfactory sensory neurons (OSNs) are located inside the nasal cavity, but they are directly exposed to the external environment. Taking advantage of the respiratory flux, this location favors the access to the chemical stimuli presented by the environment. On the other hand, it leads OSNs to be continually damaged by pathogens and toxic substances carried by the inhaled air. However, the persistence of neuronal progenitors in the olfactory epithelium makes the constant reposition of the OSNs possible. This unique ability of regeneration makes the Olfactory System one of the few sites of neurogenesis throughout the adult life. Olfactory regeneration has attracted the attention scientific community because of its potential as a model of study of the Nervous System and application in the treatment of neurodegenerative diseases. A great amount of knowledge has been accumulated about the transcription factor dynamics that follows the differentiation of neuronal progenitors into OSNs. However, there is a great gap about other elements that could coordinate this process, such as chromatin modulator factors. In this scenario, we decided to study the Polycomb Group (PcG) proteins, a transcription control machinery involved in chromatin structure organization. In the present study, selected PcG genes were molecular and functionally analyzed in the mouse main olfactory epithelium (MOE). Using in situ hybridization assays, we characterized the expression of six PcG genes. Five of them were shown to be expressed throughout the MOE (Cbx2, Cbx4, Phc2, Ezh1, Bcl6), while one (Ezh2) was found only in the basal layers of this epithelium. Using colocalization strategies, we proved that Ezh2 gene is expressed exclusively in the olfactory progenitor cells, where the differentiation process begins, and in part of the newly differentiated OSNs that are still not functional. It was the first time that a PcG gene expression profile was finely analyzed in the Olfactory System. This interesting expression profile presented by Ezh2 suggested a possible involvement with the MOE neuronal progenitor differentiation. For this functional investigation, we used MOE¿s neuronal regeneration after specific injuries as an experimental tool. For this purpose, the MOE was chemically damaged by the compound dichlobenil, which causes a great loss of OSNs, stimulating proliferation and differentiation of neuronal progenitor cells, leading to the repopulation of the damaged tissue. Next, mice received by intranasal route the pharmacological inhibitor GSK126, which blocks EZH2 protein activity. The observation of the MOE regeneration that followed showed us that GSK126 application resulted in an increased number of OSNs, improving MOE regeneration. Interestingly, this increase was also found in intact MOEs, pointing that GSK126¿s effects do not depend on previous olfactory injuries. By this molecular and functional investigation, we aimed at a better understanding of olfactory neuronal differentiation, and we targeted the PcG proteins as relevant elements to this process / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

A functional sense of smell is mediated by Olfactory Receptor proteins (ORs), which reside in olfactory sensory neurons (OSNs) in the epithelium of our nose. Only a singular OR allele out of roughly 2,400 other OR alleles is expressed in every OSN⁽¹˒ ²⁾. Singular expression of the active OR gene occurs in a unique transcriptional hub⁽³⁻⁵⁾. This hub contains one OR promoter and many interchromosomal enhancers that converge upon the hub from far nuclear distances⁽⁵˒ ⁶⁾. Once in the hub, the enhancers work in tandem with each other and with the transcription factors (TFs) Lhx2, EBF, and their cofactor, Ldb1⁽⁵˒ ⁷˒ ⁸⁾ The Greek islands contain a novel “composite” motif containing an Lhx2 and EBF binding site directly next to each other⁽⁸⁾. My work aims to understand how these proteins interact with each other and the composite motif to contribute to the accumulation of many enhancers around only a single promoter in the hub. Our findings illuminate how transcription factor interactions contribute to the hub's unique DNA architecture. To investigate the biochemical foundation of OR hubs, we used 𝑒. 𝑐𝑜𝑙𝑖 to grow and purify full-length and truncated forms of Lhx2, Ebf1, and Ldb1. We used the recombinant proteins with other biochemical methods to characterize the interactions between Lhx2, Ebf1, Ldb1, and different types of DNA found in the OR hub. We used EMSAs to quantify the binding affinity that Lhx2 and Ebf1 have for promoter versus enhancer DNA. Finally, we mixed the purified full-length proteins and used fluorescence microscopy to visualize their behavior in solution. This research combined with in vivo imaging in the Lomvardas lab provides a better understanding as to how molecular interactions 𝑖𝑛 𝑣𝑖𝑡𝑟𝑜 contribute to the hub’s architecture 𝑖𝑛 𝑣𝑖𝑣𝑜, and ultimately, stable OR expression. Our biochemical studies suggest that Lhx2 and Ebf1 can bind at the same time to a single composite motif yet they seem to bind independently of one another. We have used EMSAs to determine that Lhx2 binds much better to OR enhancer DNA compared to Ebf1 and that it might stabilize enhancer contacts. We have also found that Lhx2 and Ebf1 do not cooperatively bind to enhancers- indicating that affinity alone does not explain the accumulation of TFs to the OR hub. Our 𝑖𝑛 𝑣𝑖𝑡𝑟𝑜 imaging shows that Lhx2, Ebf1, and Ldb1 self-assemble into rigid nucleoprotein condensates driven by the composite motif of enhancer DNA. This imaging work also reveals that Lhx2 and Ldb1 are scaffolding proteins with low mobility which drive rigid condensate formation over enhancers. Ebf1 displays more plasticity and turnover into condensates indicating that it plays a more complex role as a recruited factor to these assemblies. We have coupled this data with 𝑖𝑛 𝑣𝑖𝑣𝑜 imaging of endogenous Lhx2, Ebf1, and Ldb1 to find that these factors display similar binding and dynamics 𝑖𝑛 𝑣𝑖𝑣𝑜. This data helps to provide a biophysical model of how OR hubs support multi-enhancer and protein-rich environments that are succinct from their surrounding environment. Our studies suggest that the OR hub forms a rigid phase separated compartment in the nucleus- driven by Lhx2 and Ldb1. This solid-like phase separation may contribute to how singular OR expression is achieved. Such long-range enhancer contacts must stay assembled long-term for continuous OR transcription. Therefore, traditional TF DNA binding dynamics would not explain the longevity of these contacts in the OR hub. This work challenges the traditional model of liquid phase separated nuclear compartments and may provide a broader understanding to how long range and inter-chromosomal compartments are maintained.

No genoma de camundongo existem por volta de 1000 genes que codificam para receptores olfatórios (ORs) e 150 genes que codificam para receptores de feromônios do tipo 1 (V1Rs) distribuídos em vários cromossomos. Cada neurônio olfatório e vomeronasal seleciona um único alelo de um único gene de receptor OR ou de V1R, respectivamente, para expressar enquanto que o restante do repertório é mantido silenciado. Os mecanismos que regulam esse padrão de expressão não são conhecidos. As similaridades no padrão de expressão dos genes de ORs e de V1Rs sugerem que o mecanismo de regulação possa ser comum. Até então poucas regiões promotoras de genes de ORs e de genes de V1Rs haviam sido experimentalmente determinadas e pesquisadas. Realizamos uma análise na qual regiões a montante de um grande número de diferentes genes de ORs e de genes de V1Rs foram comparadas. Primeiro, utilizando a técnica de RLMRACE, combinada com o uso de oligonucleotídeos capazes de reconhecer regiões conservadas entre diversos membros das famílias de genes de ORs e de V1Rs, geramos centenas de cDNAs contendo a região 5UTR completa para um total de 198 genes de ORs e 39 genes de V1Rs diferentes. Então, alinhamos as sequências desses cDNAs contra o genoma de camundongo e localizamos a posição exata dos sítios de início da transcrição (TSSs) de cada gene. Extraímos seqüências a 5 dos TSSs dos 198 genes de ORs e dos 39 genes de V1Rs e buscamos por motivos de DNA comuns, presentes em várias dessas regiões promotoras, que pudessem ser 6 candidatos a elementos cis-atuantes envolvidos na regulação geral desses genes de receptores sensoriais. Identificamos, na grande maioria das regiões promotoras dos genes de ORs e dos genes de V1Rs analisadas, a presença de motivos semelhantes a sítios de ligação para os fatores de transcrição O/E que são fatores de transcrição já caracterizados e envolvidos com a expressão de genes específicos do sistema olfatório. Ensaios de EMSA mostraram que os motivos semelhantes aos sítios de ligação de O/E identificados interagem com proteínas nucleares de epitélio olfatório, mas não interagem com proteínas nucleares de cérebro e fígado. Identificamos também nas regiões promotoras de genes de V1Rs a presença de um sítio de ligação que não se assemelha a nenhum sítio de ligação de fatores de transcrição conhecido. Esse motivo de DNA, além de estar presente na maioria dos promotores de genes de V1Rs analisados (77% do total de 39 genes pesquisados), também aparece, com alta frequência, em promotores de genes de ORs (52% do total de 198 genes analisados), preferencialmente próximo aos TSSs. Ensaios de interação in vitro indicam que este novo motivo de DNA interage com proteínas nucleares extraídas de órgão vomeronasal e também de epitélio olfatório, mas não interage com proteínas nucleares de cérebro, fígado e pulmão. Nosso trabalho mostra que genes de ORs e de V1Rs compartilham elementos comuns em suas regiões promotoras os quais podem ser sítios de ligação de fatores de transcrição específicos do sistema olfatório envolvidos no mecanismo de regulação da expressão desses genes. / In the mouse genome there are approximately 1000 genes that encode olfactory receptors (ORs) and 150 genes that encode type 1 vomeronasal receptors (V1Rs) dispersed in various chromosomes. Each olfactory or vomeronasal neuron selects one single allele from one single receptor gene (OR or V1R) for expression while the rest of the repertoire remains silenced. The mechanisms underlying OR and V1R gene expression are still unknown. The similarities of the pattern of expression in both types of olfactory sensory neurons suggest that the regulation of OR and V1R gene expression may be under the control of a common mechanism. Until now, promoter regions of different OR and V1R genes had not been extensively analyzed. We carried out a comprehensive analysis in which the upstream regions of a large number of different OR and V1R genes were compared. First, using the RLM-RACE strategy, combined with degenerate PCR we generated hundreds of complete 5UTR cDNAs for a total of 198 OR genes and 39 V1R genes. Then, these cDNAs were aligned against the mouse genome sequence and the transcription start sites (TSSs) were precisely determined. Sequences upstream of the TSSs were retrieved and searched for common DNA motifs that may play a role as cis-acting elements involved in the general regulation of OR and V1R gene expression. The analysis revealed the presence of motifs that resemble O/E-like sites overrepresented in the OR and V1R promoter regions. These O/E-like motifs specifically interact with nuclear protein prepared from olfactory epithelium, but not from brain and liver. 8 We also identified a new motif that does not resemble any known transcription factor binding site. Besides, this new motif is present in 77% of the 39 V1R promoter regions and in 52% of the 198 OR promoter regions analyzed, preferentially concentrated near the TSSs. Interestingly, binding assays indicate that this new motif interacts with nuclear proteins prepared from the vomeronasal and the olfactory epithelia, but not from brain, liver and lung. Our results indicate that OR and V1R genes share common promoter elements that may be binding sites for specific olfactory transcription factors and may play a role in a common mechanism of olfactory and vomeronasal gene regulation

No genoma de camundongo existem por volta de 1000 genes que codificam para receptores olfatórios (ORs) e 150 genes que codificam para receptores de feromônios do tipo 1 (V1Rs) distribuídos em vários cromossomos. Cada neurônio olfatório e vomeronasal seleciona um único alelo de um único gene de receptor OR ou de V1R, respectivamente, para expressar enquanto que o restante do repertório é mantido silenciado. Os mecanismos que regulam esse padrão de expressão não são conhecidos. As similaridades no padrão de expressão dos genes de ORs e de V1Rs sugerem que o mecanismo de regulação possa ser comum. Até então poucas regiões promotoras de genes de ORs e de genes de V1Rs haviam sido experimentalmente determinadas e pesquisadas. Realizamos uma análise na qual regiões a montante de um grande número de diferentes genes de ORs e de genes de V1Rs foram comparadas. Primeiro, utilizando a técnica de RLMRACE, combinada com o uso de oligonucleotídeos capazes de reconhecer regiões conservadas entre diversos membros das famílias de genes de ORs e de V1Rs, geramos centenas de cDNAs contendo a região 5UTR completa para um total de 198 genes de ORs e 39 genes de V1Rs diferentes. Então, alinhamos as sequências desses cDNAs contra o genoma de camundongo e localizamos a posição exata dos sítios de início da transcrição (TSSs) de cada gene. Extraímos seqüências a 5 dos TSSs dos 198 genes de ORs e dos 39 genes de V1Rs e buscamos por motivos de DNA comuns, presentes em várias dessas regiões promotoras, que pudessem ser 6 candidatos a elementos cis-atuantes envolvidos na regulação geral desses genes de receptores sensoriais. Identificamos, na grande maioria das regiões promotoras dos genes de ORs e dos genes de V1Rs analisadas, a presença de motivos semelhantes a sítios de ligação para os fatores de transcrição O/E que são fatores de transcrição já caracterizados e envolvidos com a expressão de genes específicos do sistema olfatório. Ensaios de EMSA mostraram que os motivos semelhantes aos sítios de ligação de O/E identificados interagem com proteínas nucleares de epitélio olfatório, mas não interagem com proteínas nucleares de cérebro e fígado. Identificamos também nas regiões promotoras de genes de V1Rs a presença de um sítio de ligação que não se assemelha a nenhum sítio de ligação de fatores de transcrição conhecido. Esse motivo de DNA, além de estar presente na maioria dos promotores de genes de V1Rs analisados (77% do total de 39 genes pesquisados), também aparece, com alta frequência, em promotores de genes de ORs (52% do total de 198 genes analisados), preferencialmente próximo aos TSSs. Ensaios de interação in vitro indicam que este novo motivo de DNA interage com proteínas nucleares extraídas de órgão vomeronasal e também de epitélio olfatório, mas não interage com proteínas nucleares de cérebro, fígado e pulmão. Nosso trabalho mostra que genes de ORs e de V1Rs compartilham elementos comuns em suas regiões promotoras os quais podem ser sítios de ligação de fatores de transcrição específicos do sistema olfatório envolvidos no mecanismo de regulação da expressão desses genes. / In the mouse genome there are approximately 1000 genes that encode olfactory receptors (ORs) and 150 genes that encode type 1 vomeronasal receptors (V1Rs) dispersed in various chromosomes. Each olfactory or vomeronasal neuron selects one single allele from one single receptor gene (OR or V1R) for expression while the rest of the repertoire remains silenced. The mechanisms underlying OR and V1R gene expression are still unknown. The similarities of the pattern of expression in both types of olfactory sensory neurons suggest that the regulation of OR and V1R gene expression may be under the control of a common mechanism. Until now, promoter regions of different OR and V1R genes had not been extensively analyzed. We carried out a comprehensive analysis in which the upstream regions of a large number of different OR and V1R genes were compared. First, using the RLM-RACE strategy, combined with degenerate PCR we generated hundreds of complete 5UTR cDNAs for a total of 198 OR genes and 39 V1R genes. Then, these cDNAs were aligned against the mouse genome sequence and the transcription start sites (TSSs) were precisely determined. Sequences upstream of the TSSs were retrieved and searched for common DNA motifs that may play a role as cis-acting elements involved in the general regulation of OR and V1R gene expression. The analysis revealed the presence of motifs that resemble O/E-like sites overrepresented in the OR and V1R promoter regions. These O/E-like motifs specifically interact with nuclear protein prepared from olfactory epithelium, but not from brain and liver. 8 We also identified a new motif that does not resemble any known transcription factor binding site. Besides, this new motif is present in 77% of the 39 V1R promoter regions and in 52% of the 198 OR promoter regions analyzed, preferentially concentrated near the TSSs. Interestingly, binding assays indicate that this new motif interacts with nuclear proteins prepared from the vomeronasal and the olfactory epithelia, but not from brain, liver and lung. Our results indicate that OR and V1R genes share common promoter elements that may be binding sites for specific olfactory transcription factors and may play a role in a common mechanism of olfactory and vomeronasal gene regulation

Chemical sensing is believed to be the oldest sensory ability. The chemical senses, olfaction and gustation, developed to detect and analyze information in the form of air- or waterborne chemicals, to find food and mates, and to avoid danger. The organization of the olfactory system follows the same principles in almost all living animals, insects as well as mammals. Likely, the similarities are due to parallel evolution – the same type of organisation seems to have arisen more than once. Therefore, the olfactory system is often assumed to be close to optimally designed for its tasks.Paradoxically, the workings of the olfactory system are not yet well known,although several milestone discoveries have been made during the last decades. The most well-known is probably the disovery of the olfactory receptor gene family,announced in 1991 by Linda Buck and Richard Axel. For this and subsequent work, they were awarded a Nobel Prize Award in 2004. This achievement has been of immense value for both experimentalists and theorists, and forms the basis of the current understanding of olfaction. The olfactory system has long been a focus for scientific interest within several fields, both experimental and theoretical, and it has often been used asa model system. And ever since the field of computational neuroscience was founded, the functions of the olfactory system have been investigated through computational modelling. In this thesis, I present several approaches to biologically realistic computational models of parts of the olfactory system, with an emphasis on the earlier stages of the vertebrate olfactory system – olfactory receptor neurons (ORNs) and the olfactory bulb (OB). I have investigated the behaviour of the enzyme CaMKII, which is known to be critical for olfactory adaptation (suppression of constant odour stimuli) in the ORN, using a biochemical model. By constructing several OB models of different size, I have shown that the size of the OB network has an impact on its ability to process noisy information. Taking into account the reported variability of geometrical, electrical and receptor-dependent neuronal characteristics, I have been able to model the frequency response of a population of ORNs. I have used this model to find the key properties that govern most of the ORN population’s response, and investigated some of the possible implications of these key properties in subsequent studies of the ORN population and the OB – what we call the fuzzy concentration coding hypothesis. / Detektion av kemiska ämnen anses allmänt vara den äldsta sensoriska förmågan. De kemiska sinnena, lukt och smak, utvecklades för att upptäcka och analysera kemisk information i form av luft- eller vattenburna ämnen, för att hitta mat och partners, och för att undvika fara. Luktsystemet är organiserat efter samma principer hos nästan alla djurarter, insekter såväl som däggdjur. Troligen beror likheterna på parallell evolution – samma organisation verkar ha uppstått mer än en gång. Därför antas det ofta att luktsystemet är nära optimalt anpassat för sina arbetsuppgifter.Paradoxalt nog är luktsystemets arbetsprinciper ännu inte väl kända, även om flera banbrytande framsteg gjorts de senaste decennierna. Det mest välkända är nog upptäckten av genfamiljen av luktreceptorer, som tillkännagavs 1991 av Linda Buck och Rikard Axel. För detta och efterföljande arbete belönades de med Nobelpriset år 2004. Upptäckten har varit mycket värdefull för både experimentalister och teoretiker, och är grunden för vår nuvarande förståelse av luktsystemet. Luktsystemet har länge varit ett fokus för vetenskapligt intresse inom flera fält, experimentella såväl som teoretiska, och har ofta använts som ett modellsystem. Och ända sedan fältet beräkningsneurobiologi grundades har luktsystemet undersökts genom datormodellering. I denna avhandling presenterar jag flera ansatser till biologiskt realistiskaberäkningsmodeller av luktsystemet, med tonvikt på de tidigare delarna av ryggradsdjurens luktsystem – luktreceptorceller och luktbulben. Jag har undersökt beteendet hos enzymet CaMKII, som anses vara kritiskt viktigt för adaptation (undertryckning av ständigt närvarande luktstimuli) i luktsystemet, i en biokemisk modell. Genom att konstruera flera olika stora modeller av luktbulben har jag visat att storleken på luktbulbens cellnätverk påverkar dess förmåga att behandla brusig information. Genom att ta hänsyn till nervcellernas rapporterade variationer i geometriska, elektriska och receptor-beroende karaktärsdrag har jag lyckats modellera svarsfrekvenserna från en population av luktreceptorceller. Jag har använt denna modell för att hitta de nyckelprinciper som styr huvuddelen av luktreceptorneuron-populationens svar, ochundersökt några av de tänkbara konsekvenserna av dessa nyckelprinciper i efterföljande studier av luktreceptorneuron-populationen och luktbulben – det vi kallar ”fuzzy concentration coding”-hypotesen. / QC20100723

Objective: Decrease of olfactory function in Parkinson's disease (PD) is a well-investigated fact. Studies indicate that pharmacological treatment of PD fails to restore olfactory function in PD patients. The aim of this investigation was whether patients with PD would benefit from “training” with odors in terms of an improvement of their general olfactory function. It has been hypothesized that olfactory training should produce both an improved sensitivity towards the odors used in the training process and an overall increase of olfactory function. Methods: We recruited 70 subjects with PD and olfactory loss into this single-center, prospective, controlled non-blinded study. Thirty-five patients were assigned to the olfactory training group and 35 subjects to the control group (no training). Olfactory training was performed over a period of 12 weeks while patients exposed themselves twice daily to four odors (phenyl ethyl alcohol: rose, eucalyptol: eucalyptus, citronellal: lemon, and eugenol: cloves). Olfactory testing was performed before and after training using the “Sniffin' Sticks” (thresholds for phenyl ethyl alcohol, tests for odor discrimination, and odor identification) in addition to threshold tests for the odors used in the training process. Results: Compared to baseline, trained PD patients experienced a significant increase in their olfactory function, which was observed for the Sniffin' Sticks test score and for thresholds for the odors used in the training process. Olfactory function was unchanged in PD patients who did not perform olfactory training. Conclusion: The present results indicate that olfactory training may increase olfactory sensitivity in PD patients.