Catechol 2,3-dioxygenase-assisted cleavage of aromatics by “anaerobic” termite gut spirochetes and genomic evidence of a complete meta-pathway

The termite hindgut microbial ecosystem functions like a miniature lignocellulose-metabolizing natural bioreactor, has significant implications to nutrient cycling in the terrestrial environment, and represents an array of microbial metabolic diversity. Deciphering the intricacies of this microbial community to obtain as complete a picture as possible of how it functions as a whole, requires a combination of various traditional and cutting-edge bioinformatic, molecular, physiological, and culturing approaches. Isolates from this ecosystem, including Treponema primitia str. ZAS-1 and ZAS-2 as well as T. azotonutricium str. ZAS-9, have been significant resources for better understanding the termite system. While not all functions predicted by the genomes of these three isolates are demonstrated in vitro, these isolates do have the capacity for several metabolisms unique to spirochetes and critical to the termite system’s reliance upon lignocellulose. In this thesis, work culturing, enriching for, and isolating diverse microorganisms from the termite hindgut is discussed. Additionally, strategies of members of the termite hindgut microbial community to defend against O₂-stress and to generate acetate, the “biofuel” of the termite system, are proposed. In particular, catechol 2,3-dioxygenase and other meta-cleavage catabolic pathway genes are described in the “anaerobic” termite hindgut spirochetes T. primitia str. ZAS-1 and ZAS-2, and the first evidence for aromatic ring cleavage in the phylum (division) Spirochetes is also presented. These results suggest that the potential for O₂-dependent, yet nonrespiratory, metabolisms of plant-derived aromatics should be re-evaluated in termite hindgut communities. Potential future work is also illustrated.

Flexible microimplants for in vivo sensing

The work in this thesis develops two types of microimplants for the application of cardiovascular in vivo biomedical sensing, one for short-term diagnosis and the other for long-term monitoring.

Despite advances in diagnosis and therapy, atherosclerotic cardiovascular disease remains the leading cause of morbidity and mortality in the Western world. Predicting metabolically active atherosclerotic plaques has remained an unmet clinical need. A stretchable impedance sensor manifested as a pair of quasi-concentric microelectrodes was developed to detect unstable intravascular. By integrating the impedance sensor with a cardiac catheter, high-resolution Electrochemical Impedance Spectroscopy (EIS) measurements can be conducted during cardiac catheterization. An inflatable silicone balloon is added to the sensor to secure a well-controlled contact with the plaque under test in vivo. By deploying the device to the explants of NZW rabbit aorta and live animals, distinct EIS measurements were observed for unstable atherosclerotic plaques that harbored active lipids and inflammatory cells.

On the other hand, zebrafish (Danio rerio) is an emerging genetic model for heart regenerative medicine. In humans, myocardial infarction results in the irreversible loss of cardiomyocytes. Zebrafish hearts can fully regenerate after two months with 20% ventricular resection. Long-term electrocardiogram (ECG) recording can characterize the heart regeneration in a functional dimension. A flexible microelectrode membrane was developed to be percutaneously implanted onto a zebrafish heart and record epicardial ECG signals from specific regions on it. Region-specific aberrant cardiac signals were obtained from injured and regenerated hearts. Following that, in order to achieve continuous and wireless recording from non-sedated and non-restricted small animal models, a wireless ECG recording system was designed for the microelectrode membrane, prototyped on a printed circuit board and demonstrated on a one-day-old neonatal mouse. Furthermore, a flexible and compact parylene C printed circuit membrane was used as the integration platform for the wireless ECG recording electronics. A substantially miniature wireless ECG recording system was achieved.

MEMS for Diabetic Retinopathy

As the worldwide prevalence of diabetes mellitus continues to increase, diabetic retinopathy remains the leading cause of visual impairment and blindness in many developed countries. Between 32 to 40 percent of about 246 million people with diabetes develop diabetic retinopathy. Approximately 4.1 million American adults 40 years and older are affected by diabetic retinopathy. This glucose-induced microvascular disease progressively damages the tiny blood vessels that nourish the retina, the light-sensitive tissue at the back of the eye, leading to retinal ischemia (i.e., inadequate blood flow), retinal hypoxia (i.e., oxygen deprivation), and retinal nerve cell degeneration or death. It is a most serious sight-threatening complication of diabetes, resulting in significant irreversible vision loss, and even total blindness.

Unfortunately, although current treatments of diabetic retinopathy (i.e., laser therapy, vitrectomy surgery and anti-VEGF therapy) can reduce vision loss, they only slow down but cannot stop the degradation of the retina. Patients require repeated treatment to protect their sight. The current treatments also have significant drawbacks. Laser therapy is focused on preserving the macula, the area of the retina that is responsible for sharp, clear, central vision, by sacrificing the peripheral retina since there is only limited oxygen supply. Therefore, laser therapy results in a constricted peripheral visual field, reduced color vision, delayed dark adaptation, and weakened night vision. Vitrectomy surgery increases the risk of neovascular glaucoma, another devastating ocular disease, characterized by the proliferation of fibrovascular tissue in the anterior chamber angle. Anti-VEGF agents have potential adverse effects, and currently there is insufficient evidence to recommend their routine use.

In this work, for the first time, a paradigm shift in the treatment of diabetic retinopathy is proposed: providing localized, supplemental oxygen to the ischemic tissue via an implantable MEMS device. The retinal architecture (e.g., thickness, cell densities, layered structure, etc.) of the rabbit eye exposed to ischemic hypoxic injuries was well preserved after targeted oxygen delivery to the hypoxic tissue, showing that the use of an external source of oxygen could improve the retinal oxygenation and prevent the progression of the ischemic cascade.

The proposed MEMS device transports oxygen from an oxygen-rich space to the oxygen-deficient vitreous, the gel-like fluid that fills the inside of the eye, and then to the ischemic retina. This oxygen transport process is purely passive and completely driven by the gradient of oxygen partial pressure (pO₂). Two types of devices were designed. For the first type, the oxygen-rich space is underneath the conjunctiva, a membrane covering the sclera (white part of the eye), beneath the eyelids and highly permeable to oxygen in the atmosphere when the eye is open. Therefore, sub-conjunctival pO₂ is very high during the daytime. For the second type, the oxygen-rich space is inside the device since pure oxygen is needle-injected into the device on a regular basis.

To prevent too fast or too slow permeation of oxygen through the device that is made of parylene and silicone (two widely used biocompatible polymers in medical devices), the material properties of the hybrid parylene/silicone were investigated, including mechanical behaviors, permeation rates, and adhesive forces. Then the thicknesses of parylene and silicone became important design parameters that were fine-tuned to reach the optimal oxygen permeation rate.

The passive MEMS oxygen transporter devices were designed, built, and tested in both bench-top artificial eye models and in-vitro porcine cadaver eyes. The 3D unsteady saccade-induced laminar flow of water inside the eye model was modeled by computational fluid dynamics to study the convective transport of oxygen inside the eye induced by saccade (rapid eye movement). The saccade-enhanced transport effect was also demonstrated experimentally. Acute in-vivo animal experiments were performed in rabbits and dogs to verify the surgical procedure and the device functionality. Various hypotheses were confirmed both experimentally and computationally, suggesting that both the two types of devices are very promising to cure diabetic retinopathy. The chronic implantation of devices in ischemic dog eyes is still underway.

The proposed MEMS oxygen transporter devices can be also applied to treat other ocular and systemic diseases accompanied by retinal ischemia, such as central retinal artery occlusion, carotid artery disease, and some form of glaucoma.

Analisis de las entidades no lucrativas del Pais Vasco dedicadas a la protección animal

This Final Project Grade, whose title is “Analysis of the non-lucrative entities of the Basque Country dedicated to animal protection”, has as main purpose the study of the historical, theoretical and legal context in which these institutions develop their activity, focusing in those which occur in the Basque Country.

Behavior ecology of the Humboldt squid, Dosidicus gigas: insights from an animal-borne video and data logging system

Dosidicus gigas is a large pelagic cephalopod of the eastern Pacific that has recently undergone an unexpected, significant range expansion up the coast of North America. The impact that such a range expansion is expected to have on local fisheries and marine ecosystems has motivated a thorough study of this top predator, a squid whose lifestyle has been quite mysterious until recently. Unfortunately, Dosidicus spends daylight hours at depths prohibitive to making observations without significant artificial interference. Observations of this squid‟s natural behaviors have thus far been considerably limited by the bright illumination and loud noises of remotely-operated-vehicles, or else the presence of humans from boats or with SCUBA. However, recent technological innovations have allowed for observations to take place in the absence of humans, or significant human intrusion, through the use of animal-borne devices such as National Geographic‟s CRITTERCAM. Utilizing the advanced video recording and data logging technology of this device, this study seeks to characterize unknown components of Dosidicus gigas behavior at depth. Data from two successful CRITTERCAM deployments reveal an assortment of new observations concerning Dosidicus lifestyle. Tri-axial accelerometers enable a confident description of Dosidicus orientation during ascents, descents, and depth maintenance behavior - previously not possible with simple depth tags. Video documentation of intraspecific interactions between Dosidicus permits the identification of ten chromatic components, a previously undescribed basal chromatic behavior, and multiple distinct body postures. And finally, based on visualizations of spermatophore release by D. gigas and repetitive behavior patterns between squid pairs, this thesis proposes the existence of a new mating behavior in Dosidicus. This study intends to provide the first glimpse into the natural behavior of Dosidicus, establishing the groundwork for a comprehensive ethogram to be supported with data from future CRITTERCAM deployments. Cataloguing these behaviors will be useful in accounting for Dosidicus‟ current range expansion in the northeast Pacific, as well as to inform public interest in the impacts this expansion will have on local fisheries and marine ecosystems.

Diagnóstico de um grupo de familiares em risco para o câncer de mama: contribuição para a assistência de enfermagem

Devido a sua alta incidência, mortalidade e custos elevados, o câncer de mama feminino é considerado um problema de saúde pública no Brasil. Sua etiologia envolve uma interação de diversos fatores denominados de risco os quais podem ser ambientais e genéticos. A história familiar positiva para câncer de mama é um importante fator de risco para o desenvolvimento dessa patologia. Conhecer esses fatores e as medidas de proteção permite que mulheres com risco elevado possam criar estratégias pessoais que venham minimizar os danos causados pela doença. Diante do exposto, o presente estudo tem como objetivos avaliar o nível de conhecimento de mulheres acerca do risco de desenvolverem câncer de mama em decorrência do vínculo familiar com a população portadora desta neoplasia matriculada no Hospital do Câncer III, unidade do Instituto Nacional de Câncer (INCA) especializada no tratamento e controle do câncer de mama, localizada no município do Rio de Janeiro, Brasil; descrever as características sociodemográficas das mulheres familiares de pacientes portadoras de câncer de mama e descrever a história reprodutiva e hormonal, bem como seus hábitos de cuidado com a saúde. Metodologia: trata-se de um estudo exploratório sob a perspectiva quantitativa, transversal e descritiva com 52 mulheres que acompanhavam suas familiares internadas em unidade clínica e cirúrgica do Hospital do Câncer III. A coleta de dados ocorreu no período entre julho e agosto de 2011. A técnica de amostragem adotada foi a não probabilística, intencional Para o cálculo amostral aplicou-se a fórmula de população infinita. Foram selecionadas as seguintes variáveis para compor o estudo: aspectos sociodemográficos, aspectos da vida reprodutiva e hormonal, aspectos de cuidados com a saúde e aspectos de esclarecimento relacionados à patologia/doença. Realizou-se entrevista estruturada com utilização de um formulário composto por 63 questões. A descrição das variáveis foi feita através de frequência simples e porcentagem. Resultados: 61,5% eram filhas, 34,6% eram irmãs e 3,8% eram mães, 40,4% moram no município do Rio de Janeiro, 86,4% encontram-se na faixa etária entre 29 e acima de 51 anos de idade, 32% são pardas, 46,1% apresentavam 2 grau completo, 46,2% são do lar, 15,4% tiveram menarca precoce, 7,7 % tiveram na menopausa tardia, 7,7% fizeram Terapia de Reposição Hormonal, 38,5% nunca engravidaram, 3,8% engravidaram após 30 anos, 3,8% não amamentaram, 42,4% usam anticoncepcional hormonal por mais de 5 anos e 40,4% nunca fizeram descanso ou faz por tempo inferior a 6 meses, 7,7% e 7,6% nunca fizeram e apresenta mais de 24 meses que fizeram exame ginecológico. Quanto ao grau de esclarecimento 34% concordaram com as afirmativas sobre fatores de risco, 65% concordaram com medidas preventivas e os profissionais de saúde foram os que mais transmitiram informação sobre o câncer de mama. Conclusão: ser familiar de primeiro grau associado à falta de esclarecimento sobre a doença torna essas mulheres mais vulneráveis em relação à população geral feminina. Torna-se oportuno para a enfermagem estratégias educativas que visem à promoção da saúde e que contribuam para a modificação do panorama da doença, em razão da detecção mais precoce.

Usage of substances and their dosage regimes in pharmacological animal models of schizophrenia

Background: Contrary to what is generally thought schizophrenia is a very common mental health issue. For this, several animal models are used to assess the illness in order to develop a definitive. The most widely spread paradigm is the use of pharmacological models. Aim: The aim of this review is to display which are the most used insults for the assessment of social behaviour related negative symptoms in animal models as well as to ascertain which is the most adequate regime. Design: Literature review. Methods: PubMed database was used for this article by the search of the indexed “schizophrenia”, “animal models”, “social behaviour” and “negative symptoms” descriptors. With the exception of a single article due to it value this review is based on articles from 10 years onwards. Besides, only clinical trials and reviews written in English or Spanish and that had laboratory rodents as target population were accepted. Results: The studies assessed agree that pharmacological models (specially those regarding the NMDA receptor antagonists) are a valuable means for the experimental investigation of negative symptoms in schizophrenia with the necessity to emphasise that only some negative symptoms (anhedonia and social interaction, mainly) can be experimentally assessed. Conclusions: There is not enough evidence regarding the fours aspects of this review. PCP, Ketamine or MK-801 in sub-acute dosage regimes are currently the most indicated insults to mimic schizophrenic symptoms in rodents, although further research in needed, albeit other substances are valuable as well. (In English language exclusively)

Contributions to learning Bayesian network models from weakly supervised data: Application to Assisted Reproductive Technologies and Software Defect Classification

162 p.

Direct detection of Yersinia pestis from the infected animal specimens by a fiber optic biosensor

The FOB-3, anew type fiber optic biosensor, is designed to rapidly detect a variety of biological agents or analytes with better stability, sensitivity and specificity. In order to detect Y. Pestis, a sandwich immunoassay was developed by using the purified antibody against antigen FI immobilized on polystyrene probes as the capture antibody and the monoclonal antibody-Cy5 conjugate as the detector. After a series of optimization for the stability, sensitivity and specificity of the FOB-3, 50-1000 ng/ml of antigen FI and 6 x 10(1)-6 x 10(7) CFU/ml Y. pestis could be detected constantly in about 20 min, and Y pestis could be detected specifically from Y. pseudotuberculosis, Y. enterocolitica, B. anthracis and E. coli. Then, 39 blind samples, including 27 tissues of mice infected with Y pestis and 12 tissues of healthy mice as negative control, were detected with the FOB-3. 92.6% infected tissues were identified from the tissues of healthy mice and the tissues containing more than 100 CFU/ml bacteria could be detected by the biosensor. The results demonstrated the feasibility of the FOB-3 as an effective method to detect Y. pestis rapidly and directly from the infected animal specimens with the advantage of portability, simple-operation as well as high sensitivity and specificity. (c) 2006 Elsevier B.V. All rights reserved.

Sobrevida e fatores prognósticos para o câncer de mama em Juiz de Fora, Minas Gerais, na coorte diagnosticada entre 1998 e 2000

Este estudo teve como objetivo analisar a sobrevida e fatores prognósticos para o câncer de mama feminino, com ênfase no papel de variáveis relacionadas aos serviços de saúde. Foram analisadas 782 mulheres com câncer invasivo da mama e submetidas à cirurgia curativa, que realizaram tratamento cirúrgico e/ou terapia complementar no município de Juiz de Fora, Minas Gerais, com diagnóstico da doença entre 1998 e 2000. O recrutamento dos casos foi efetuado a partir de busca ativa nos registros médicos de todos os serviços de saúde que prestam atendimento em oncologia na cidade. O seguimento foi realizado mediante retorno aos prontuários e complementado por busca no banco do Sistema de Informação sobre Mortalidade (SIM), contato telefônico e consulta de situação cadastral no Cadastro de Pessoas Físicas (CPF). As principais variáveis analisadas foram: cor da pele, idade ao diagnóstico, tamanho do tumor, comprometimento de linfonodos, estadiamento, cidade de residência e variáveis relativas aos serviços de saúde, entre outras. As funções de sobrevida foram calculadas por meio do método de Kaplan-Meier. Foi utilizado o modelo de riscos proporcionais de Cox para avaliação dos fatores prognósticos. No primeiro artigo, foi observada taxa de sobrevida específica em cinco anos de 80,9%, sendo identificados tamanho tumoral e comprometimento de linfonodos axilares como importantes fatores prognósticos associados de forma independente à sobrevida pela doença na população de estudo (HR=1,99, IC95%: 1,27-3,10 e HR=3,92, IC95%: 2,49-6,16, respectivamente). No segundo artigo, quando consideradas as variáveis relativas aos serviços de saúde, foi verificada pior sobrevida para as mulheres assistidas no serviço público, embora com significância limítrofe (p=0,05), e para aquelas que não tinham plano privado de saúde, apesar de não significativa (p=0,1). As funções de sobrevida não ajustadas e estratificadas por natureza do serviço de saúde exibiram sobrevida mais desfavorável para as mulheres não brancas e para os casos com nenhum ou menos de 10 linfonodos isolados somente no serviço público, embora com significâncias estatísticas apenas marginais (p=0,09 e p=0,07, respectivamente). Na análise multivariada, foi observado maior risco de óbito nas mulheres que não fizeram uso de hormonioterapia apenas para os casos assistidos no serviço público (HR=1,56; IC95%: 1,01-2,41), independentemente do tamanho tumoral e do status ganglionar axilar. Tais achados sugerem desigualdades sociais e disparidades na prevenção primária e secundária da doença na região estudada, com desvantagem para o serviço público de saúde, enfatizando a maior necessidade de esclarecimento sobre a doença, assim como de diagnóstico e tratamento dos casos em estádios mais precoces. Destacou-se, ainda, o valor de se trabalhar com informações produzidas pelos serviços de saúde responsáveis pela assistência oncológica no país, possibilitando a caracterização do perfil e da sobrevida das pacientes assistidas e fornecendo subsídios aos órgãos competentes do setor saúde local para nortear a adoção de estratégias de prevenção direcionadas ao controle da doença na população avaliada.

Altered expression of Alzheimer's disease-related genes in the cerebellum of autistic patients: a model for disrupted brain connectome and therapy

Autism and Alzheimer's disease (AD) are, respectively, neurodevelopmental and degenerative diseases with an increasing epidemiological burden. The AD-associated amyloid-beta precursor protein-alpha has been shown to be elevated in severe autism, leading to the 'anabolic hypothesis' of its etiology. Here we performed a focused microarray analysis of genes belonging to NOTCH and WNT signaling cascades, as well as genes related to AD and apoptosis pathways in cerebellar samples from autistic individuals, to provide further evidence for pathological relevance of these cascades for autism. By using the limma package from R and false discovery rate, we demonstrated that 31% (116 out of 374) of the genes belonging to these pathways displayed significant changes in expression (corrected P-values <0.05), with mitochondria- related genes being the most downregulated. We also found upregulation of GRIN1, the channel-forming subunit of NMDA glutamate receptors, and MAP3K1, known activator of the JNK and ERK pathways with anti-apoptotic effect. Expression of PSEN2 (presinilin 2) and APBB1 (or F65) were significantly lower when compared with control samples. Based on these results, we propose a model of NMDA glutamate receptor-mediated ERK activation of alpha-secretase activity and mitochondrial adaptation to apoptosis that may explain the early brain overgrowth and disruption of synaptic plasticity and connectome in autism. Finally, systems pharmacology analyses of the model that integrates all these genes together (NOWADA) highlighted magnesium (Mg2+) and rapamycin as most efficient drugs to target this network model in silico. Their potential therapeutic application, in the context of autism, is therefore discussed.