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Hyperspectral (HS) imaging combines spectral measurement of a pixel with 2D imaging technology. It is capable to provide a series of images containing both spectral and spatial information, and has been widely used in medical domain. However, most researches on medical HS imaging are regarding ex-vivo biopsy or skin and oral mucosa. The study on HS imaging regarding in-vivo disease lags far behind. In this thesis, we developed a novel flexible HS endoscope system. It is capable to obtain a series of HS images in vivo in a non-contact way among the wavelength range of 405 – 665 nm. After a lot of time-consuming modifying and debugging work, this new system has high stability and convenience to be applied in clinic now. We evaluated this system in clinic. First, we got ethics approval for clinical trials. Then, we obtained HS images regarding gastrointestinal (GI) diseases inside patients using this system. As far as we know, this type of in-vivo image data has not been reported in previous literatures. Thus using these HS images, we built a database for GI mucosa. Next, we analyzed some typical HS images tentatively. The method of Recursive Divergence is implemented to extract valuable and diagnostic information from these HS images. The results prove the effect and applicability of this new HS endoscope system, which has shown the great potential to be used as a platform and guidance for further medical studies. To further apply the analysis results in clinic, we propose a novel Adaptive Narrow-Band Imaging (ANBI) method based on band selection of HS images of a specific type of disease. It is expected that the new technique has higher accuracy, sensitivity, and specificity compared to conventional Narrow-Band Imaging (NBI) technique. In this thesis, we also discuss the future direction of the system improvement. Especially, to improve light intensity and signal-noise-ratio of HS images in wide-field view, we propose a new imaging method using broad- and overlapped-band filters. Although this method only performs greatly on the foundation of accurate image registration, we hope to apply it in our system in the future.

The determination of a symbiotic association as beneficial requires good assessment of the costs and benefits involved in the maintenance and transmission of these microbes across generations. In social insects, symbiotic associations are complex as they may involve a network of interactions between individual and colony that result in stable associations over evolutionary time. My goal was to investigate the roles of behavior and morphology as integrators that have enabled the benefits of harboring gut microbes to reach both adult and growing brood in a colony. To achieve this goal, I used turtle ants (Cephalotes), a group that has co-evolved with their gut microbes since the Eocene (Sanders et al. 2014) and that shows a variety of morphological and behavioral specializations likely connected to this symbiotic association. In my dissertation I present evidence that the specialized behavior and morphology of Cephalotes are indeed strongly associated with mechanisms that ensure stability of ant-gut microbe interactions over evolutionary time. In Appendix A, I show that a valve between the crop and midgut (proventriculus) of C. rohweri works as a filtration organ, capable of excluding possible pathogens from the mostly liquid diet consumed by turtle ants. In addition, the proventricular filter is also associated with the structuring of the gut microbiota, dividing it in at least two great groups: one upstream and another downstream of the proventriculus. Through behavioral observation and microscopy, we also suggest that the formation of the proventricular filter is only complete after young and sterile workers (callows) are inoculated with the core group of symbiotic bacteria. In Appendix B, I present results confirming that the compartmentalization of gut microbiota is also present in the congener C. varians. I compare these results with previously published data, defining the meta-communities of the gut microbiota, and demonstrate that the previously recognized core microbiota is composed of compartment-specific microbial communities and lineages. This compartmentalization of the gut microbiota is similar to the one found in highly specialized herbivores, both vertebrates and invertebrates. In addition, I also sampled the infrabuccal pocket, a characteristic oral cavity found in ants and that has largely been ignored in studies of gut symbiosis. Based on my results, I provide compelling evidence that hindgut microbes are inoculated into food particles trapped in the infrabuccal pocket, aiding in digestion of this substrate. Moreover, I suggest that trophallaxis olays a central role in inoculation of food and individuals, and might be responsible for the transmission of nutrients that are predicted to result from the gut bacteria metabolism. Finally, in Appendix C I characterize abdominal trophallaxis in C. rohweri to gain insight on its role in the context of symbiotic associations with gut microbes. I show that the hindgut contents, including bacteria, can be transmitted via abdominal trophallaxis. This interaction is found to occur between all combinations of major and minor workers, in addition to callows. The rate of solicitation of abdominal trophallaxis is higher when individuals are protein starved, indicating that hindgut content may also be nutritive. Using shotgun metagenomic data, we show that the microbiota present in the infrabuccal pocket (mostly hindgut bacteria) are indeed capable of re-utilizing nitrogen and synthesizing essential amino acids, in addition to breaking down plant material. We also report that oral trophallaxis is a possible route for transmission of crop-specific bacteria for callows, as this group has performed oral trophallaxis at a relatively higher rate than older workers. Put together, these results highlight the importance of nestmate interactions and gut morphology in the establishment and maintenance of symbiotic microbes in a social insect, introducing a new model for explaining the evolution and functioning of ant-gut microbe symbiosis.

A análise de sinais mioelétricos provenientes do tubo gastro-intestinal de animais de laboratório (ratos), conseguidos por meio de eletrodos cronicamente implantados, é peça-chave no entendimento das desordens associadas ao sistema digestivo. Esta análise enfrenta consideráveis dificuldades quando realizadas por métodos clássicos, em especial os baseados na transformada de Fourier. A interação de várias componentes mioelétricas torna muito complicado e trabalhoso o acompanhamento destes sinais ao longo do tubo digestivo e a obtenção de parâmetros típicos como a velocidade de propagação entre eletrodos. Estuda-se aqui uma alternativa mais nova e promissora: a transformada Wavelet. Utilizando esta ferramenta matemática, torna-se possível obter uma melhor resolução tempo-freqüencial dos sinais estudados, permitindo encontrar padrões referentes à propagação do sinal mesmo em leituras ruidosas e compostas de várias freqüências. Foram analisados 82 leituras de 9 animais normais do Laboratório de Investigação Médica da Faculdade de Medicina da USP, sendo possível determinar dois parâmetros: a velocidade de propagação média entre eletrodos (cerca de 1.2 cm/s) e as componentes principais da freqüência basal (0.63 e 0.65 Hz). / The analysis of myoelectric signals from the gastro-intestinal tube of laboratory animals (mice), recorded by chronically implanted electrodes, is a key stone in understanding the disorders associated to the digestive system. This analysis meets considerable difficulties when done by classical methods, specially those based in the Fourier transform. The many myoelectric components interactions makes the following of these signals along the digestive tract and the retrieval of typical parameters (such as the propagation velocity between electrodes) a very complicated and laborious task. Here is studied a newer and more promising alternative: the Wavelet transform. Using this mathematical tool, it becomes possible to obtain a better time-frequency resolution of the studied signals, allowing to find patterns related to the signal propagation even in noisy and multifrequencial readings. 82 readings from 9 normal animals belonging to the Medical Investigation Laboratory of the Medicine Faculty of University of São Paulo were analyzed, becoming feasible to determine two parameters: the mean propagation velocity between electrodes (about 1.2 cm/s) and the main components of the basal frequency (0.63 e 0.65 Hz).

O período embrionário se estende do 15º ao 45º dia de gestação na vaca, onde ocorre um rápido crescimento e diferenciação, durante o qual os principais órgãos, tecidos e sistemas são estabelecidos e as principais características são reconhecidas. Nos bovinos, a maioria dos órgãos e partes do corpo é formada entre a 2ª e a 6ª semana de gestação. Durante este período, o trato digestivo, os pulmões, o fígado e o pâncreas se desenvolvem do intestino primitivo, sendo estabelecidos os primórdios do sistema muscular, esquelético, nervoso e urogenital. Aproximadamente 25 a 45% dos embriões bovinos são perdidos até o processo final de implantação, no entanto, a literatura relacionada a sua organogênese é escassa, uma vez que crescem as inovações tecnológicas ligadas a reprodução bovina. Assim, julgamos oportuno e necessário um estudo sobre a biologia do desenvolvimento do aparelho digestório de embriões bovinos oriundos de monta natural, utilizando microscopia de luz e microscopia eletrônica de transmissão. Nossos resultados revelam que em embriões com idade gestacional estimada de 20 dias (CR 9,0 mm) ocorreu a formação do septo traqueoesofágico dividindo o intestino anterior no tubo laringotraqueal e esôfago, separando-se totalmente aos 28/29 dias de gestação. Ao redor do 60º de gestação (CR 70,0 mm) um estômago pluricavitário característico dos ruminantes é evidente e apresentam epitélio endodérmico em diferenciação, tecido conjuntivo mesodérmico e tecido muscular liso. Os núcleos das células epiteliais acompanham o formato da célula e a lâmina basal delimita área de epitélio e mesênquima, estando as células unidas umas às outras através dos desmossomos, que promovem sustentação celular. / The embryonary period extends itself from 15th to 45th day of gestation in cows, when a fast growing and differentiation occurs, during which the main organs, tissues and systems are established and the main characteristics are recognized. In bovines, most of the organs and parts of body are formed between 2th and 6th week of gestation. During this period, the digestive tract, the lungs, the liver and the pancreas are developed from the primitive intestine; being established the origins of the muscle, skeletal, nervous and urogenital systems. Approximately 25 to 45% of bovine embryos are lost until the final process of implantation; however, the literature related to their organogenesis is scant, since the technologic innovations related to bovine reproduction are growing. Thus, we think it is opportune and necessary a study about the biology of development of digestive tract of bovine embryos derived from natural coition, using optic microscopy and transmission electronic microscopy. Our results disclose that in embryos having a estimated gestational age of 20 days (CR 9,0 mm), it occurred a formation of tracheoesophagic septum, dividing the anterior intestine in laringotracheal tube and esophagus, separating itself totally on 28/29 days of gestation. At about 60th day of gestation (CR 70,0 mm), a multicavity stomach, characteristic of ruminants, is evident and presents endodermic epithelium on differentiation, mesodermic connective tissue and smooth muscle tissue. The epithelial cells nuclei go along the cell shape and the basal lamina delimits the area of epithelium and mesenchyme, being the cells bound each other through desmosoms, which promote the cellular sustentation.

Calf diarrhea or scours is one of the most significant and costly problems dairy producers face on a daily basis. A study was designed and conducted to evaluate the effects of direct-fed microbials on the performance and digestive tract morphology of neo-natal/transition Holstein bull calves. Treatments consisted of a control (n = 21) and a treatment (n = 22) of direct-fed microbial (5 x 108 cfu) supplemented daily. Samples of the rumen, duodenum, and ileum were harvested at the time of slaughter and examined for differences in morphology. Although the direct-fed microbial did not effect performance, it positively effected the ruminal papillae as well as the ileal villi. These data indicate that direct-fed microbials may increase the nutrient absorptive surface area of the rumen and ileum, resulting in a healthier digestive tract.

A análise de sinais mioelétricos provenientes do tubo gastro-intestinal de animais de laboratório (ratos), conseguidos por meio de eletrodos cronicamente implantados, é peça-chave no entendimento das desordens associadas ao sistema digestivo. Esta análise enfrenta consideráveis dificuldades quando realizadas por métodos clássicos, em especial os baseados na transformada de Fourier. A interação de várias componentes mioelétricas torna muito complicado e trabalhoso o acompanhamento destes sinais ao longo do tubo digestivo e a obtenção de parâmetros típicos como a velocidade de propagação entre eletrodos. Estuda-se aqui uma alternativa mais nova e promissora: a transformada Wavelet. Utilizando esta ferramenta matemática, torna-se possível obter uma melhor resolução tempo-freqüencial dos sinais estudados, permitindo encontrar padrões referentes à propagação do sinal mesmo em leituras ruidosas e compostas de várias freqüências. Foram analisados 82 leituras de 9 animais normais do Laboratório de Investigação Médica da Faculdade de Medicina da USP, sendo possível determinar dois parâmetros: a velocidade de propagação média entre eletrodos (cerca de 1.2 cm/s) e as componentes principais da freqüência basal (0.63 e 0.65 Hz). / The analysis of myoelectric signals from the gastro-intestinal tube of laboratory animals (mice), recorded by chronically implanted electrodes, is a key stone in understanding the disorders associated to the digestive system. This analysis meets considerable difficulties when done by classical methods, specially those based in the Fourier transform. The many myoelectric components interactions makes the following of these signals along the digestive tract and the retrieval of typical parameters (such as the propagation velocity between electrodes) a very complicated and laborious task. Here is studied a newer and more promising alternative: the Wavelet transform. Using this mathematical tool, it becomes possible to obtain a better time-frequency resolution of the studied signals, allowing to find patterns related to the signal propagation even in noisy and multifrequencial readings. 82 readings from 9 normal animals belonging to the Medical Investigation Laboratory of the Medicine Faculty of University of São Paulo were analyzed, becoming feasible to determine two parameters: the mean propagation velocity between electrodes (about 1.2 cm/s) and the main components of the basal frequency (0.63 e 0.65 Hz).

O período embrionário se estende do 15º ao 45º dia de gestação na vaca, onde ocorre um rápido crescimento e diferenciação, durante o qual os principais órgãos, tecidos e sistemas são estabelecidos e as principais características são reconhecidas. Nos bovinos, a maioria dos órgãos e partes do corpo é formada entre a 2ª e a 6ª semana de gestação. Durante este período, o trato digestivo, os pulmões, o fígado e o pâncreas se desenvolvem do intestino primitivo, sendo estabelecidos os primórdios do sistema muscular, esquelético, nervoso e urogenital. Aproximadamente 25 a 45% dos embriões bovinos são perdidos até o processo final de implantação, no entanto, a literatura relacionada a sua organogênese é escassa, uma vez que crescem as inovações tecnológicas ligadas a reprodução bovina. Assim, julgamos oportuno e necessário um estudo sobre a biologia do desenvolvimento do aparelho digestório de embriões bovinos oriundos de monta natural, utilizando microscopia de luz e microscopia eletrônica de transmissão. Nossos resultados revelam que em embriões com idade gestacional estimada de 20 dias (CR 9,0 mm) ocorreu a formação do septo traqueoesofágico dividindo o intestino anterior no tubo laringotraqueal e esôfago, separando-se totalmente aos 28/29 dias de gestação. Ao redor do 60º de gestação (CR 70,0 mm) um estômago pluricavitário característico dos ruminantes é evidente e apresentam epitélio endodérmico em diferenciação, tecido conjuntivo mesodérmico e tecido muscular liso. Os núcleos das células epiteliais acompanham o formato da célula e a lâmina basal delimita área de epitélio e mesênquima, estando as células unidas umas às outras através dos desmossomos, que promovem sustentação celular. / The embryonary period extends itself from 15th to 45th day of gestation in cows, when a fast growing and differentiation occurs, during which the main organs, tissues and systems are established and the main characteristics are recognized. In bovines, most of the organs and parts of body are formed between 2th and 6th week of gestation. During this period, the digestive tract, the lungs, the liver and the pancreas are developed from the primitive intestine; being established the origins of the muscle, skeletal, nervous and urogenital systems. Approximately 25 to 45% of bovine embryos are lost until the final process of implantation; however, the literature related to their organogenesis is scant, since the technologic innovations related to bovine reproduction are growing. Thus, we think it is opportune and necessary a study about the biology of development of digestive tract of bovine embryos derived from natural coition, using optic microscopy and transmission electronic microscopy. Our results disclose that in embryos having a estimated gestational age of 20 days (CR 9,0 mm), it occurred a formation of tracheoesophagic septum, dividing the anterior intestine in laringotracheal tube and esophagus, separating itself totally on 28/29 days of gestation. At about 60th day of gestation (CR 70,0 mm), a multicavity stomach, characteristic of ruminants, is evident and presents endodermic epithelium on differentiation, mesodermic connective tissue and smooth muscle tissue. The epithelial cells nuclei go along the cell shape and the basal lamina delimits the area of epithelium and mesenchyme, being the cells bound each other through desmosoms, which promote the cellular sustentation.

Os microrganismos presentes no intestino de insetos podem desempenhar importantes funções na biologia de seus hospedeiros, como na nutrição, detoxificação de compostos de defesas das plantas, prevenção da infecção por patógenos e produção de semioquímicos importantes nas interações de insetos. O primeiro passo para entender as funções da microbiota do intestino na biologia de insetos consiste na identificação dessas comunidades. Neste trabalho, a diversidade de bactérias do intestino de larvas e adultos da mosca-das-frutas sul-americana, Anastrepha fraterculus (Wiedemann, 1830) (Diptera: Tephritidae), foi determinada por métodos baseados ou não no cultivo. O método baseado no cultivo foi utilizado no estudo da diversidade da microbiota de população de laboratório mantida em frutos de mamão, avaliando-se a diversidade presente no intestino de larvas e em duas regiões distintas do intestino de adultos, o papo e o intestino médio+posterior. A análise metagenômica pela avaliação de bibliotecas de 16S rDNA foi aplicada ao estudo da diversidade da microbiota associada a moscas oriundas de diferentes frutos hospedeiros (guabiroba, nêspera, maçã, mamão e pitanga). As análises por cultivo permitiram a identificação de 25 filotipos associados ao intestino de larvas e adultos, sendo a diversidade em larvas bem distinta daquela de adultos. Os Filos Actinobacteria, Bacteroidetes, Firmicutes e Proteobacteria foram representados por 10 famílias, sendo Enterobacteriaceae a mais abundante. Filotipo próximo à enterobacteriacea Cedecea davisae foi o único a ocorrer no intestino de larvas e papo e intestino de adultos. A análise metagenômica dos insetos obtidos em diferentes frutos hospedeiros estendeu a diversidade anteriormente identificada aos Filos Cyanobacteria, Deinococcus, Elusimicrobia, Planctomycetes e Verrucomicrobia. Novamente, Proteobacteria se destacou como o mais diverso. Esse estudo demonstrou que a comunidade microbiana associada ao intestino de A. fraterculus é inteiramente influenciado pelo fruto hospedeiro utilizado, sendo raros os filotipos compartilhados por insetos em diferentes frutos. A composição da microbiota do intestino do adulto é muito menos diversa do que a da larva, independentemente do fruto utilizado. Mas vários filotipos, como aqueles próximos a Acinetobacter bereziniae, Cedecea davisae, Comamonas koreensis, Enterobacter asburiae, Empedobacter brevis e Hydrogenophilus hirschii, além do parasita intracelular Wolbachia pipientis, mantiveram-se associadas ao intestino de larvas e adultos de A. fraterculus, mesmo após a metamorfose. A análise das comunidades bacterianas de A. fraterculus sugere que as variações em suas estruturas estão relacionadas ao substrato alimentar utilizado pelo inseto. / The microorganisms present in the insect gut can play important roles in the biology of their hosts such as nutrition, detoxification of compounds defenses of plants, preventing infection by pathogens and production of important semiochemicals in insect interactions. The first step to understanding the functions of the gut microbiota in insect biology is the identification of these communities. In this work, the diversity of gut bacteria in larvae and adult South American fruit fly, Anastrepha fraterculus (Wiedemann, 1830) (Diptera: Tephritidae) , were determined by methods based on the cultivation or not . The method based on the cultivation was used to study the microbial diversity of laboratory population maintained in papaya fruits, evaluating the diversity present in the gut of larvae and in two distinct regions of the intestine of adults, the crop and midgut + hindgut. The analysis of metagenomic libraries for evaluation of 16S rDNA was applied to the study of the diversity of the microbiota associated with fruit flies from different hosts (guabiroba , medlar , apple, papaya and pitanga). The analysis by cultivation allowed the identification of 25 phylotypes associated with the gut of larvae and adults, larvae diversity being quite different from that of adults. The phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria were represented by 10 families, Enterobacteriaceae being the most abundant. Filotipo near Enterobacteriacea Cedecea davisae strains was the only one to occur in the gut of larvae and adult chat and intestine. The metagenomic analysis of insects obtained in different fruit hosts extended to the diversity previously identified phyla Cyanobacteria, Deinococcus, Elusimicrobia, Planctomycetes and Verrucomicrobia. Again, Proteobacteria stood out as the most diverse. This study showed that the microbial community associated with the intestine of A. fraterculus is entirely influenced by host fruit used are rare phylotypes shared by insects in different fruits. The composition of the gut microbiota in adults is far less diverse than the larvae, irrespective of the fruit used. But several phylotypes, such as those near Acinetobacter bereziniae, Cedecea davisae strains, Comamonas koreensis, Enterobacter asburiae, Empedobacter brevis and Hydrogenophilus hirschii, besides the intracellular parasite Wolbachia pipientis, remained attached to the gut of larvae and adults of A. fraterculus, even after metamorphosis. The analysis of bacterial communities of A. fraterculus suggests that variations in their structures are related to the food substrate used by the insect.

O pintado (Pseudoplatystoma coruscans), também comumente chamado de surubim é um dos peixes mais apreciados pelo mercado consumidor brasileiro, devido à excelente qualidade do filé. No entanto, trabalhos sobre a morfologia do seu trato digestório são escassos. No presente trabalho, a descrição histológica do esôfago, estômago e intestino do pintado, visa contribuir e fornecer subsídios científicos para compreensão dos processos digestivos dessa espécie. Foram obtidas amostras do esôfago, estômago e de todas as regiões intestinais e posteriormente analisadas à microscopia óptica. No esôfago, observou-se epitélio de revestimento do tipo pavimentoso estratificado não-queratinizado, apresentando células epiteliais, mucosas e grande quantidade de células claviformes. A presença de células claviformes são indicadores de que este órgão está sujeito a lesão e lacerações, participando no sistema de defesa do organismo. O estômago do pintado constitui-se de um órgão em forma de J, distinguindo-se três regiões: cárdica, fúndica e pilórica. O epitélio de revestimento encontrado é do tipo colunar simples. A superfície epitelial é interrompida pelas criptas gástricas, no fundo das quais se abrem as glândulas gástricas, sendo estas criptas mais profundas na região cárdica ou proximal do estômago. As glândulas gástricas apresentam-se maiores e mais numerosas no segmento proximal, diminuindo em quantidade e tamanho no sentido caudal, o que está relacionado a uma maior demanda na secreção de muco para proteção e digestão de proteínas. O intestino do pintado constitui-se de três regiões distintas e denominadas: intestino proximal, intestino médio e intestino distal ou reto. No epitélio intestinal foram encontrados macrófagos e linfócitos indicando uma barreira celular de defesa no organismo. No intestino distal, observou-se epitélio com cutícula estriada mais baixa do que nos segmentos anteriores. Podemos concluir que o pintado apresenta características particulares quanto à estrutura microscópica do seu trato digestório, em alguns aspectos, se comparado a outros teleósteos. / Pintado (Pseudoplatystoma coruscans), also commonly called surubim, is one of the most appreciated fish by the Brazilian consumer market, due to the excellent filet quality. However, works on the morphology of their digestive tract are scarce. In this work, the histological description of the esophagus, stomach and intestine of pintado, seeks to contribute and to supply scientific information for the better understanding of the digestive process of these species. Samples were obtained from esophagus, stomach and from all the intestinal areas and later analyzed with light microscope. In the esophagus, epithelium is stratified pavimentous type and was observed no queratinization, presenting epithelial cells, mucous membranes and great amount of club cells. The presence of club cells indicates that this organ is subjected to lesion and lacerations, participating in the organism defense system. The stomach of pintado is constituted of an organ in J form, being there distinguished three areas: cardic, fundic and piloric. The epithelium of the stomach is simple colunar type. The epithelial surface is interrupted by the gastric crypts, in the bottom of which opens up the gastric glands, being these deeper crypts in the cardic area or proximal of the stomach. The gastric glands come larger and more numerous in the proximal segment, decreasing in amount and size in the caudal way, what is related to a larger demand in the mucus secretion for protection and digestion of proteins. The pintado`s intestine is constituted of three different areas and denominated: proximal intestine, medium intestine and distal intestine or rectum. In the intestinal epithelium there were found macrophages and lymphocytes indicating a cellular barrier for the organism defense. In the distal intestine, epithelium was observed with cuticle grooved lower than in the previous segments. We can conclude that pintado presents private characteristics in relation to the microscopic structure of its digestive tract, in some aspects, if compared to other teleosts.